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Expansion of cultured bacterial diversity by large-scale dilution-to-extinction culturing from a single seawater sample
Yang SJ et al . Microb Ecol. 2016 Jan;71(1):29-43. doi: 10.1007/s00248-015-0695-3. Epub 2015 Nov 14.
Abstract -
High-throughput cultivation (HTC) based on a dilution-to-extinction method has been applied broadly to the cultivation of marine bacterial groups, which has often led to the repeated isolation of abundant lineages such as SAR11 and oligotrophic marine gammaproteobacteria (OMG). In this study, to expand the phylogenetic diversity of HTC isolates, we performed a large-scale HTC with a single surface seawater sample collected from the East Sea, the Western Pacific Ocean. Phylogenetic analyses of the 16S rRNA genes from 847 putative pure cultures demonstrated that some isolates were affiliated with not-yet-cultured clades, including the OPB35 and Puniceicoccaceae marine group of Verrucomicrobia and PS1 of Alphaproteobacteria. In addition, numerous strains were obtained from abundant clades, such as SAR11, marine Roseobacter clade, OMG (e.g., SAR92 and OM60), OM43, and SAR116, thereby increasing the size of available culture resources for representative marine bacterial groups. Comparison between the composition of HTC isolates and the bacterial community structure of the seawater sample used for HTC showed that diverse marine bacterial groups exhibited various growth capabilities under our HTC conditions. The growth response of many bacterial groups, however, was clearly different from that observed with conventional plating methods, as exemplified by numerous isolates of the SAR11 clade and Verrucomicrobia. This study showed that a large number of novel bacterial strains could be obtained by an extensive HTC from even a small number of samples.

Characterization of the mechanism of prolonged adaptation to osmotic stress of Jeotgalibacillus malaysiensis via genome and transcriptome sequencing analyses
Yaakop AS et al . Sci Rep. 2016 Sep 19;6:33660. doi: 10.1038/srep33660.
Abstract -
Jeotgalibacillus malaysiensis, a moderate halophilic bacterium isolated from a pelagic area, can endure higher concentrations of sodium chloride (NaCl) than other Jeotgalibacillus type strains. In this study, we therefore chose to sequence and assemble the entire J. malaysiensis genome. This is the first report to provide a detailed analysis of the genomic features of J. malaysiensis, and to perform genetic comparisons between this microorganism and other halophiles. J. malaysiensis encodes a native megaplasmid (pJeoMA), which is greater than 600 kilobases in size, that is absent from other sequenced species of Jeotgalibacillus. Subsequently, RNA-Seq-based transcriptome analysis was utilised to examine adaptations of J. malaysiensis to osmotic stress. Specifically, the eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) and KEGG (Kyoto Encyclopaedia of Genes and Genomes) databases were used to elucidate the overall effects of osmotic stress on the organism. Generally, saline stress significantly affected carbohydrate, energy, and amino acid metabolism, as well as fatty acid biosynthesis. Our findings also indicate that J. malaysiensis adopted a combination of approaches, including the uptake or synthesis of osmoprotectants, for surviving salt stress. Among these, proline synthesis appeared to be the preferred method for withstanding prolonged osmotic stress in J. malaysiensis.

Ecophysiology and Comparative Genomics of Nitrosomonas mobilis Ms1 Isolated from Autotrophic Nitrifying Granules of Wastewater Treatment Bioreactor
Thandar SM et al . Front Microbiol. 2016 Nov 22;7:1869. eCollection 2016.
Abstract -
Ammonia-oxidizing bacteria (AOB), which oxidize ammonia to nitrite in the first step of nitrification, play an important role in biological wastewater treatment systems. Nitrosomonas mobilis is an important and dominant AOB in various wastewater treatment systems. However, the detailed physiological and genomic properties of N. mobilis have not been thoroughly investigated because of limited success isolating pure cultures. This study investigated the key physiological characteristics of N. mobilis Ms1, which was previously isolated into pure culture from the nitrifying granules of wastewater treatment bioreactor. The pure culture of N. mobilis Ms1 was cultivated in liquid mineral medium with 30 mg-N L-1 (2.14 mM) of ammonium at room temperature under dark conditions. The optimum growth of N. mobilis Ms1 occurred at 27°C and pH 8, with a maximum growth rate of 0.05-0.07 h-1, which corresponded to a generation time of 10-14 h. The half saturation constant for ammonium uptake rate and the maximum ammonium uptake rate of N. mobilis Ms1 were 30.70 ± 0.51 μM NH4+ and 0.01 ± 0.002 pmol NH4+ cells-1 h-1, respectively. N. mobilis Ms1 had higher ammonia oxidation activity than N. europaea in this study. The oxygen uptake activity kinetics of N. mobilis Ms1 were Km(O2) = 21.74 ± 4.01 μM O2 and V max(O2) = 0.06 ± 0.02 pmol O2cells-1 h-1Ms1 grew well at ammonium and NaCl concentrations of up to 100 and 500 mM, respectively. The nitrite tolerance of N. mobilis Ms1 was extremely high (up to 300 mM) compared to AOB previously isolated from activated sludge and wastewater treatment plants. The average nucleotide identity between the genomes of N. mobilis Ms1 and other Nitrosomonas species indicated that N. mobilis Ms1 was distantly related to other Nitrosomonas species. The organization of the genes encoding protein inventory involved in ammonia oxidation and nitrifier denitrification processes were different from other Nitrosomonas species. The current study provides a needed physiological and genomic characterization of N. mobilis-like bacteria and a better understanding of their ecophysiological properties, enabling comparison of these bacteria with other AOB in wastewater treatment systems and natural ecosystems.

Analysis of Antimicrobial Activity of Titaniumdioxide Nanoparticles on Aerobic and Anaerobic Dental Isolates
Rimjhim et al . 2016 IJSRSET | Volume 2 | Issue 4 | Print ISSN: 2395-1990 | Online ISSN : 2394-4099
Abstract -
Dental plaque is a biofilm or mass of bacteria that grows on surface within the mouth. It is a sticky colorless deposit at first, but when it forms tartar it is brown or pale yellow that is commonly found between the teeth, front of teeth, behind teeth, on chewing surface, along the gumline,. A study was carried out to isolate microorganisms from patients with dental problems. Total 8 dental plaque samples were collected from Savitha dental clinic, Hyderabad, which showed the presence of both aerobic and anaerobic bacteria. Titanium dioxide nanoparticle was synthesized and checked for its antimicrobial activity against dental plaque samples. TiO2 nanoparticles were then incorporated into some commercial toothpastes and checked against dental plaque causing organisms using commercial toothpaste as control. The activity was also checked using bulk TiO2. TiO2 nanoparticles incorporated into tooth paste showed enhanced activity compared to toothpaste alone. Antimicrobial activity of TiO2 synthesized by wet chemical method was compared against commercial TiO2 P23.It was observed that TiO2 nanoparticles synthesized by wet chemical method showed greater antimicrobial activity than commercial TiO2 nanoparticles and bulk oxide. Astringent mouthwash was prepared and TiO2 nanoaprticles were incorporated into it and the activity was compared.
The growth kinetics and metabolic and antioxidant activities of the functional synbiotic combination of Lactobacillus gasseri 505 and Cudrania tricuspidata leaf extract
Oh NS et al . Appl Microbiol Biotechnol. 2016 Dec;100(23):10095-10106. Epub 2016 Oct 28.
Abstract -
In a previous study, the synbiotic combination of selected Lactobacillus gasseri strains and Cudraniatricuspidata leaf extract (CT) was shown to significantly improve the functionality of fermented milk, and the greatest synbiotic effect was exhibited with L. gasseri 505. The aim of the present study was to investigate the growth kinetics and fermentation metabolism of this specific synbiotic combination. Fermentation was carried out in synthetic media and milk with or without CT supplementation using L. gasseri 505. Whole genome sequencing and comparative genomics analyses were conducted to verify the novelty of strain. Titratable acidity, pH, microbial population, and organic acid production were measured during the fermentation period. The addition of CT accelerated the acidification rate, supporting the growth of L. gasseri 505, and the production of fermentation metabolites such as lactic acid and pyruvic acid also significantly increased during fermentation of both of CT-supplemented synthetic media and milk. In particular, the formic acid and propionic acid in CT were significantly utilized during fermentation of milk by L. gasseri 505. Moreover, the antioxidant capacity of CT-supplemented fermented milk increased due to the release of bioactive compounds until the exponential growth phase, after which the antioxidant activity declined due to degradation and loss of potency. Therefore, this study established that L. gasseri 505 efficiently utilized the CT-related nutrients during fermentation producing resulting metabolites with health-promoting effects, although it is necessary to control the fermentation time to obtain dairy products with optimum functionality.

Genomic Analysis of the Extremely Halophilic Archaeon Halobacterium noricense CBA1132 Isolated from Solar Salt That Is an Essential Material for Fermented Foods
Lim et al . J Microbiol Biotechnol. 2016 Aug 28;26(8):1375-82. doi: 10.4014/jmb.1603.03010.
Abstract -
The extremely halophilic archaeon Halobacterium noricense is a member of the genus Halobacterium. Strain CBA1132 (= KCCM 43183, JCM 31150) was isolated from solar salt. The genome of strain CBA1132 assembled with 4 contigs, including three rRNA genes, 44 tRNA genes, and 3,208 open reading frames. Strain CBA1132 had nine putative CRISPRs and the genome contained genes encoding metal resistance determinants: copper-translocating P-type ATPase (CtpA), arsenical pump-driving ATPase (ArsA), arsenate reductase (ArsC), and arsenical resistance operon repressor (ArsR). Strain CBA1132 was related to Halobacterium noricense, with 99.2% 16S rRNA gene sequence similarity. Based on the comparative genomic analysis, strain CBA1132 has distinctly evolved; moreover, essential genes related to nitrogen metabolism were only detected in the genome of strain CBA1132 among the reported genomes in the genus Halobacterium. This genome sequence of Halobacterium noricense CBA1132 may be of use in future molecular biological studies.

Global transcriptomic response of Anoxybacillus sp. SK 3‐4 to aluminum exposure
Lim JC et al . J Basic Microbiol. 2017 Feb;57(2):151-161. doi: 10.1002/jobm.201600494. Epub 2016 Nov 17
Abstract -
Anoxybacillus sp. SK 3-4 is a Gram-positive, rod-shaped bacterium and a member of family Bacillaceae. We had previously reported that the strain is an aluminum resistant thermophilic bacterium. This is the first report to provide a detailed analysis of the global transcriptional response of Anoxybacillus when the cells were exposed to 600 mg L-1 of aluminum. The transcriptome was sequenced using Illumina MiSeq sequencer. Total of 708 genes were differentially expressed (fold change >2.00) with 316 genes were up-regulated while 347 genes were down-regulated, in comparing to control with no aluminum added in the culture. Based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, the majority of genes encoding for cell metabolism such as glycolysis, sulfur metabolism, cysteine and methionine metabolism were up-regulated; while most of the gene associated with tricarboxylic acid cycle (TCA cycle) and valine, leucine and isoleucine metabolism were down-regulated. In addition, a significant number of the genes encoding ABC transporters, metal ions transporters, and some stress response proteins were also differentially expressed following aluminum exposure. The findings provide further insight and help us to understand on the resistance of Anoxybacillus sp. SK 3-4 toward aluminium.

Characterization of microbiome in bronchoalveolar lavage fluid of patients with lung cancer comparing with benign mass like lesions.
Lee et al . Lung Cancer. 2016 Dec;102:89-95. doi: 10.1016/j.lungcan.2016.10.016. Epub 2016 Oct 31.
Abstract -

OBJECTIVES:

Disruption in the stability of respiratory microbiota is known to be associated with many chronic respiratory diseases. However, only few studies have examined microbiomes in lung cancer. Therefore, we characterized and compared the microbiomes of patients with lung cancer and those with benign mass-like lesions.

MATERIALS AND METHODS:

Bronchoalveolar fluid was collected prospectively to evaluate lung masses in patients who had undergone bronchoscopies from May to September 2015. Twenty-eight patients (20 male, 8 female) were enrolled: 20 diagnosed with lung cancer and 8 diagnosed with benign diseases. Samples were analysed by 16S rRNA-based next-generation sequencing.

RESULTS:

The participants' mean age was 64±11years. Bacterial operational taxonomic units were classified into 26 phyla, 44 classes, 81 orders, 153 families, 288 genera, and 797 species. The relative abundance of two phyla (Firmicutes and TM7) was significantly increased in patients with lung cancer (p=0.037 and 0.035, respectively). Furthermore, two genera (Veillonella and Megasphaera) were relatively more abundant in lung cancer patients (p=0.003 and 0.022, respectively). The area under the curve of a combination of these two genera used to predict lung cancer was 0.888 (sensitivity=95.0%, specificity=75.0% and sensitivity=70.0%, specificity=100.0%; p=0.002).

CONCLUSION:

The results indicate that differences exist in the bacterial communities of patients with lung cancer and those with benign mass-like lesions. The genera Veillonella and Megasphaera showed the potential to serve as biomarkers to predict lung cancer. Thus, the lung microbiota may change the environment in patients with lung cancer.


Microbial Community Evolution Is Significantly Impacted by the Use of Calcium Isosaccharinic Acid as an Analogue for the Products of Alkaline Cellulose Degradation
Isaac A. Kyeremeh et al . PLoS One. 2016 Nov 2;11(11):e0165832. doi: 10.1371/journal.pone.0165832. eCollection 2016.
Abstract -
Diasteriomeric isosaccharinic acid (ISA) is an important consideration within safety assessments for the disposal of the United Kingdoms' nuclear waste legacy, where it may potentially influence radionuclide migration. Since the intrusion of micro-organisms may occur within a disposal concept, the impact of ISA may be impacted by microbial metabolism. Within the present study we have established two polymicrobial consortia derived from a hyperalkaline soil. Here, α-ISA and a diatereomeric mix of ISAs' were used as a sole carbon source, reflecting two common substrates appearing within the literature. The metabolism of ISA within these two consortia was similar, where ISA degradation resulted in the acetogenesis and hydrogenotrophic methanogenesis. The chemical data obtained confirm that the diastereomeric nature of ISA is likely to have no impact on its metabolism within alkaline environments. High throughput sequencing of the original soil showed a diverse community which, in the presence of ISA allowed for the dominance the Clostridiales associated taxa with Clostridium clariflavum prevalent. Further taxonomic investigation at the genus level showed that there was in fact a significant difference (p = 0.004) between the two community profiles. Our study demonstrates that the selection of carbon substrate is likely to have a significant impact on microbial community composition estimations, which may have implications with respect to a safety assessment of an ILW-GDF.

Genome sequence of a commensal bacterium, Enterococcus faecalis CBA7120, isolated from a Korean fecal sample.
Kim JY et al . Gut Pathog. 2016 Nov 25;8:62. eCollection 2016.
Abstract -

BACKGROUND:

Enterococcus faecalis, the type strain of the genus Enterococcus, is not only a commensal bacterium in the gastrointestinal tract in vertebrates and invertebrates, but also causes serious disease as an opportunistic pathogen. To date, genome sequences have been published for over four hundred E. faecalis strains; however, pathogenicity of these microbes remains complicated. To increase our knowledge of E. faecalis virulence factors, we isolated strain CBA7120 from the feces of an 81-year-old female from the Republic of Korea and performed a comparative genomic analysis.

RESULTS:

The genome sequence of E. faecalis CBA7120 is 3,134,087 bp in length, with a G + C content of 37.35 mol%, and is comprised of four contigs with an N50 value of 2,922,046 bp. The genome showed high similarity with other strains of E. faecalis, including OG1RF, T13, 12107 and T20, based on OrthoANI values. Strain CBA7120 contains 374 pan-genome orthologous groups (POGs) as singletons, including "Phages, Prophages, Transposable elements, Plasmids," "Carbohydrates," "DNA metabolism," and "Virulence, Disease and Defense" subsystems. Genes related to multidrug resistance efflux pumps were annotated in the genome.

CONCLUSIONS:

The comparative genomic analysis of E. faecalis strains presented in this study was performed using a variety of analysis methods and will facilitate future identification of hypothetical proteins.


Vertical distribution of bacterial community is associated with the degree of soil organic matter decomposition in the active layer of moist acidic tundra.
Kim HM et al . J Microbiol. 2016 Nov;54(11):713-723. Epub 2016 Oct 29.
Abstract -
The increasing temperature in Arctic tundra deepens the active layer, which is the upper layer of permafrost soil that experiences repeated thawing and freezing. The increasing of soil temperature and the deepening of active layer seem to affect soil microbial communities. Therefore, information on soil microbial communities at various soil depths is essential to understand their potential responses to climate change in the active layer soil. We investigated the community structure of soil bacteria in the active layer from moist acidic tundra in Council, Alaska. We also interpreted their relationship with some relevant soil physicochemical characteristics along soil depth with a fine scale (5 cm depth interval). The bacterial community structure was found to change along soil depth. The relative abundances of Acidobacteria, Gammaproteobacteria, Planctomycetes, and candidate phylum WPS-2 rapidly decreased with soil depth, while those of Bacteroidetes, Chloroflexi, Gemmatimonadetes, and candidate AD3 rapidly increased. A structural shift was also found in the soil bacterial communities around 20 cm depth, where two organic (upper Oi and lower Oa) horizons are subdivided. The quality and the decomposition degree of organic matter might have influenced the bacterial community structure. Besides the organic matter quality, the vertical distribution of bacterial communities was also found to be related to soil pH and total phosphorus content. This study showed the vertical change of bacterial community in the active layer with a fine scale resolution and the possible influence of the quality of soil organic matter on shaping bacterial community structure.

Effect of Storage Period on the Changes of Odorous Compound Concentrations and Bacterial Ecology for Identifying the Cause of Odor Production from Pig Slurry.
Hwang OH et al . PLoS One. 2016 Sep 19;11(9):e0162714. doi: 10.1371/journal.pone.0162714. eCollection 2016.
Abstract -
Odor from buildings where pigs are housed is generated by anaerobic fermentation of undigested materials in pig slurry stored for several weeks in pit. The objective of this study was to investigate the effect of storage period on the level of odorous compounds in pig slurry and on its bacterial community. A slurry sample (15 L) was taken from the pit of a finisher pig building and incubated in acryl chambers for six- weeks. Slurry for analysis was sampled every two-week. Levels of odorous compounds in the slurry sample were drastically changed after two weeks of storage period; levels of phenols and short chain fatty acids (SCFAs) were decreased (P<0.05), whereas indoles and branched-chain fatty acids (BCFAs) were increased (P<0.05). Among dominant bacteria, Bacteroides and Porphyromonadacese_uc_g revealed a strong positive correlation with the levels of phenols and SCFAs. Populations of AC160630_g, Acholeplasmatales_uc_g, Mollicutes_uc_g and Cloacamonas_f_uc_g positively correlated with indole and BCFAs content. Taken together, levels of odorous compounds were increased after two weeks of storage, possibly because of changes in the predominant bacterial groups to those that use protein as a carbon source in the hypo-carbohydrate conditions.
Comparative study of rhizobacterial communities in pepper greenhouses and examination of the effects of salt accumulation under different cropping systems.
Hahm MS et al . Arch Microbiol. 2017 Mar;199(2):303-315. doi: 10.1007/s00203-016-1304-7. Epub 2016 Nov 9.
Abstract -
This study compared rhizobacterial communities in pepper greenhouses under a paddy-upland (rice-pepper) rotational system (PURS) and a monoculture repeated cropping system (RCS) and examined adverse effects of high salinity on soil properties. The following soil properties were analyzed: electrical conductivity (EC), pH, concentration of four cations (Na, Ca, Mg, and K), total nitrogen, and organic matter content. Rhizobacterial communities were analyzed using culture-based and culture-independent (pyrosequencing) methods. In addition, all culturable bacteria isolated from each soil sample were tested for traits related to plant growth promotion. The EC of rhizospheric soils was 5.32-5.54 dS/m for the RCS and 2.05-2.19 dS/m for the PURS. The culture-based method indicated that the bacterial communities and bacterial characteristics were significantly more diverse in the PURS soil than in the RCS soil. The pyrosequencing data also indicated that the richness and diversity of bacterial communities were greater in the PURS soil. Proteobacteria was the most abundant phylum in soil samples under both cropping systems. However, Firmicutes and Gemmatimonadetes were more prevalent in the RCS soil, while the PURS soil contained a greater number of Chloroflexi. Spearman's correlation coefficients showed that soil EC was significantly positively correlated with the abundance of Firmicutes and Gemmatimonadetes and negatively correlated with the abundance of Acidobacteria, Chloroflexi, and Deltaproteobacteria. This is the first study on the rhizobacterial communities in peppergreenhouses under two different cropping systems using both culture- and pyrosequencing-based methods.

Bio-Prospecting Laccases in the Bacterial Diversity of Activated Sludge From Pulp and Paper Industry
Gupta V et al . Indian J Microbiol. 2017 Mar;57(1):75-82. doi: 10.1007/s12088-016-0624-2. Epub 2016 Sep 26.
Abstract -
Activated sludge is an artificial ecosystem known to harbor complex microbial communities. Bacterial diversity in activated sludge from pulp and paper industry was studied to bioprospect for laccase, the multicopper oxidase applicable in a large number of industries due to its ability to utilize a wide range of substrates. Bacterial diversity using 454 pyrosequencing and laccase diversity using degenerate primers specific to conserved copper binding domain of laccase like multicopper oxidase (LMCO) genes were investigated. 1231 OTUs out of 11,425 sequence reads for bacterial diversity and 11 OTUs out of 15 reads for LMCO diversity were formed. Phylum Proteobacteria (64.95 %) with genus Thauera (13.65 %) was most abundant followed by phylum Bacteriodetes (11.46 %) that included the dominant genera Paludibacter (1.93 %) and Lacibacter (1.32 %). In case of LMCOs, 40 % sequences showed affiliation with Proteobacteria and 46.6 % with unculturable bacteria, indicating considerable novelty, and 13.3 % with Bacteroidetes. LMCOs belonged to H and J families.

Genome Sequence of Bacillus cereus FORC_021, a Food-Borne Pathogen Isolated from a Knife at a Sashimi Restaurant.
Chung HY et al . J Microbiol Biotechnol. 2016 Dec 28;26(12):2030-2035. doi: 10.4014/jmb.1604.04094.
Abstract -
Bacillus cereus causes food-borne illness through contaminated foods; therefore, its pathogenicity and genome sequences have been analyzed in several studies. We sequenced and analyzed B. cereus strain FORC_021 isolated from a sashimi restaurant. The genome sequence consists of 5,373,294 bp with 35.36% GC contents, 5,350 predicted CDSs, 42 rRNA genes, and 107 tRNA genes. Based on in silico DNA-DNA hybridization values, B. cereus ATCC 14579T was closest to FORC_021 among the complete genome-sequenced strains. Three major enterotoxins were detected in FORC_021. Comparative genomic analysis of FORC_021 with ATCC 14579T revealed that FORC_021 harbored an additional genomic region encoding virulence factors, such as putative ADP-ribosylating toxin, spore germination protein, internalin, and sortase. Furthermore, in vitro cytotoxicity testing showed that FORC_021 exhibited a high level of cytotoxicity toward INT-407 human epithelial cells. This genomic information of FORC_021 will help us to understand its pathogenesis and assist in managing food contamination.
Spatial distribution of cold-adapted Synechococcus during spring in seas adjacent to Korea
Dong Han Choi et al . Algae 2016; 31(3): 231-241.
Abstract -
We examined the genetic diversity and abundance of picocyanobacteria using barcoded amplicon sequencing approaches and flow cytometry in the East Sea and the East China Sea to determine the distribution patterns of diversity during spring in seas adjacent to the Korean Peninsula. Synechococcus clades I and IV, which have been known as cold-adapted ecotypes, dominated at most stations. However, the relative abundances of the two dominant clades differed in their spatial patterns. Clade I was exclusively dominant in the shelf area of the East China Sea and the north East Sea. However, the dominant genotypes belonging to clade I had different spatial distributions in the two areas and responded oppositely to seawater temperature. The dominance of distinct genotypes under the different ecological conditions suggests the presence of ecologically different ecotypes within the clade. Abundances of clade IV were greater than those of clade I at most stations in the southwest East Sea, showing an apparently different pattern from that of the other areas. A warm-water adapted clade II was observed at significant levels only at stations located in the eastern East China Sea affected by a branch of the warm Kuroshio Current. These results suggest that the physicochemical properties of influencing water masses play an important role in determining the distribution of Synechococcus genotypes

Modulation of gut microbiota and delayed immunosenescence as a result of syringaresinol consumption in middle-aged mice
Cho SY et al . Sci Rep. 2016 Dec 15;6:39026. doi: 10.1038/srep39026.
Abstract -
Age-associated immunological dysfunction (immunosenescence) is closely linked to perturbation of the gut microbiota. Here, we investigated whether syringaresinol (SYR), a polyphenolic lignan, modulates immune aging and the gut microbiota associated with this effect in middle-aged mice. Compared with age-matched control mice, SYR treatment delayed immunosenescence by enhancing the numbers of total CD3+ T cells and naïve T cells. SYR treatment induced the expression of Bim as well as activation of FOXO3 in Foxp3+regulatory T cells (Tregs). Furthermore, SYR treatment significantly enhanced the Firmicutes/Bacteroidetes ratio compared with that in age-matched controls by increasing beneficial bacteria, Lactobacillus and Bifidobacterium, while reducing the opportunistic pathogenic genus, Akkermansia. In addition, SYR treatment reduced the serum level of lipopolysaccharide-binding protein, an inflammatory marker, and enhanced humoral immunity against influenza vaccination to the level of young control mice. Taken together, these findings suggest that SYR may rejuvenate the immune system through modulation of gut integrity and microbiota diversity as well as composition in middle-aged mice, which may delay the immunosenescence associated with aging.

Bacterial Communities and Antibiotic Resistance Communities in a Full-Scale Hospital Wastewater Treatment Plant by High-Throughput Pyrosequencing
Ahn YH et al . Water 8.12 (2016): 580.
Abstract -
The community of whole microbes and antibiotic resistance bacteria (ARB) in hospital wastewater treatment plants (WWTP) receiving domestic wastewater (DWW) and hospital wastewater (HWW) was investigated. Samples from an influent of a secondary clarifier, at each treatment train, were characterized for the whole microbial community and ARB on the antibiotic resistance database, based on high-throughput pyrosequencing. The pyrosequencing analysis revealed that the abundance of Bacteroidetes in the DWW sample was higher (~1.6 times) than in the HWW sample, whereas the abundance of Proteobacteria in the HWW sample was greater than in the DWW sample. At the top twenty of the genus level, distinct genera were observed—Saprospiraceae in the DWW and Zoogloea in the HWW. Apart from the top twenty genera, minor genera showed various antibiotic resistance types based on the antibiotic resistance gene database.

Dynamics of bacterial communities in rice field soils as affected by different long-term fertilization practices
Ahn JH et al . J Microbiol. 2016 Nov;54(11):724-731. Epub 2016 Oct 29.
Abstract -
Fertilization and the response of the soil microbial community to the process significantly affect crop yield and the environment. In this study, the seasonal variation in the bacterial communities in rice field soil subjected to different fertilization treatments for more than 50 years was investigated using 16S rRNA sequencing. The simultaneous application of inorganic fertilizers and rice straw compost (CAPK) maintained the species richness of the bacterial communities at levels higher than that in the case of non-fertilization (NF) and application of inorganic fertilizers only (APK) in the initial period of rice growth. The seasonal variation in the bacterial community structure in the NF and APK plots showed cyclic behavior, suggesting that the effect of season was important; however, no such trend was observed in the CAPK plot. In the CAPK plot, the relative abundances of putative copiotrophs such as Bacteroidetes, Firmicutes, and Proteobacteria were higher and those of putative oligotrophs such as Acidobacteria and Plactomycetes were lower than those in the other plots. The relative abundances of organotrophs with respiratory metabolism, such as Actinobacteria, were lower and those of chemoautotrophs that oxidize reduced iron and sulfur compounds were higher in the CAPK plot, suggesting greater carbon storage in this plot. Increased methane emission and nitrogen deficiency, which were inferred from the higher abundances of Methylocystis and Bradyrhizobium in the CAPK plot, may be a negative effect of rice straw application; thus, a solution for these should be considered to increase the use of renewable resources in agricultural lands.

Effect of Basic Oxygen Furnace Slag used as Structural Filling Materials on the Subsurface Environment
Hosub Lee et al . Journal of Soil and Groundwater Environment, Volume 21, Issue 3, 2016, pp.6-13, Publisher : Korean Society of Soil and Groundwater Environment, DOI : 10.7857/JSGE.2016.21.3.006
Abstract -
The effect of blast oxygen furnace (BOF) slag used as filling materials on the soil environment was studied using column tests that simulated the flow of the BOF slag leachate through the soil layer. The Cu, Mn, Zn, Ni, and F contents of the leachate affected soil were similar to that of the controls (i.e., soils that were not affected by the leachate). The As, Cd, and Pb contents were lower in the leachate affected soils than the controls. The changes in these contaminants contents can be attributed to the interactions between anions such as alkalinity generating anions (e.g., CO32−, HCO3, OH) or calcium ions with heavy metals or F, which consequently affected the fate of heavy metals and F in the leachate affected soils. The germination and growth of Spinapis alba in the soils affected by the leachate and the controls were also similar. However, the proportion of alkalophilic bacteria in the soils affected by the leachate significantly increased, and this can be explained by the increased soil pH due to the alkaline leachate. Overall, this study shows that the alkalinity of the BOF slag leachate, rather than the presence of heavy metals and F in the leachate, needs to be considered when the BOF slag is to be reused as structural filling materials.
Characterization of microbial communities and soil organic carbon degradation associated with the depth and thawing effects on tundra soil in Alaska
Ha Ju Park* et al . Korean Journal of Microbiology (2016) Vol. 52, No. 3, pp. 365-374
Abstract -
In high-latitude regions, temperature has risen (0.6°C per decade) and this leads to the increase in microbial degradability against soil organic carbon (SOC). Furthermore, the decomposed SOC is converted into green-house gases (CO2 and CH4) and their release could further increase the rate of climate change. Thus, understanding the microbial diversity and their functions linked with SOC degradation in soil-thawing model is necessary. In this study, we divided tundra soil from Council, Alaska into two depth regions (30-40 cm and 50-60 cm of depth, designated as SPF and PF, respectively) and incubated that for 108 days at 0°C. A total of 111,804 reads were obtained through a pyrosequencing-based metagenomic study during the microcosm experiments, and 574-1,128 of bacterial operational taxonomic units (OTUs) and 30-57 of archaeal OTUs were observed. Taxonomic analysis showed that the distribution of bacterial taxa was significantly different between two samples. In detail, the relative abundance of phyla Actinobacteria and Firmicutes largely increased in SPF and PF soil, respectively, while phyla Crenarchaeota was increased in both soil samples. Weight measurement and gel permeation chromatography of the SOC extracts demonstrated that polymerization of humic acids, main component of SOC, occurred during the microcosm experiments. Taken together our results indicate that these bacterial and archaeal phyla could play a key function in SOC degradation and utilization in cold tundra soil.

Proteomic and transcriptomic investigations on cold-responsive properties of the psychrophilic Antarctic bacterium Psychrobacter sp. PAMC 21119 at subzero temperatures.
Koh HY et al . Environ Microbiol. 2017 Feb;19(2):628-644. doi: 10.1111/1462-2920.13578. Epub 2016 Dec 8.
Abstract -
Psychrobacter spPAMC 21119, isolated from Antarctic permafrost soil, grows and proliferates at subzerotemperatures. However, its major mechanism of cold adaptation regulation remains poorly understood. We investigated the transcriptomic and proteomic responses of this species to cold temperatures by comparing profiles at -5°C and 20°C to understand how extreme microorganisms survive under subzero conditions. We found a total of 2,906 transcripts and 584 differentially expressed genes (≥ twofold, P <0.005) by RNA-seq. Genes for translation, ribosomal structure and biogenesis were upregulated, and lipid transport and metabolism was downregulated at low temperatures. A total of 60 protein spots (≥ 1.8 fold, P < 0.005) showed differential expression on two-dimensional gel electrophoresis and the proteins were identified by mass spectrometry. The most prominent upregulated proteins in response to cold were involved in metabolite transport, protein folding and membrane fluidity. Proteins involved in energy production and conversion, and heme protein synthesis were downregulated. Moreover, isoform exchange of cold-shock proteins was detected at both temperatures. Interestingly, pathways for acetyl-CoA metabolism, putrescine synthesis and amino acid metabolism were upregulated. This study highlights some of the strategies and different physiological states that Psychrobacter spPAMC 21119 has developed to adapt to the cold environment in Antarctica.

Characterization of the Microbial Diversity and Chemical Composition of Gouda Cheese made by Potential Probiotic Strains as an Adjunct Starter Culture
Oh NS et al . J Agric Food Chem. 2016 Oct 5;64(39):7357-7366. Epub 2016 Sep 26.
Abstract -
This study characterized the microbial diversity and chemical properties of Gouda cheese made by probiotics during ripening periods. Lactobacillus plantarum H4 (H4) and Lactobacillus fermentum H9 (H9), which demonstrate probiotic properties and bioactivity, were used as adjunct starter cultures. Gouda cheese made with H4 (GCP1) and H9 (GCP2) demonstrated the highest production of formic acid and propionic acid, respectively. Moreover, the bacterial diversity, including richness and evenness of nonstarter lactic acid bacteria (NSLAB), increased in probiotic cheeses. Specifically, Lactobacillus, Leuconostoc, and Streptococcaceae were present at higher concentrations in probiotic cheeses than in control Gouda cheese (GCC). The proportion of H4 in GCP1 increased and culminated at 1.76%, whereas H9 in GCP2 decreased during ripening. Peptide profiles were altered by the addition of probiotics and included various bioactive peptides. In particular, three peptide fragments are newly detected. Therefore, Gouda cheese could be used as an effective probiotic carrier for H4 and H9.

Genomic Analysis of Vulcanisaeta thermophila Type Strain CBA1501T Isolated from Solfataric Soil
Kim JY et al . Front Microbiol. 2016 Oct 19;7:1639. eCollection 2016.
Abstract -
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Periodic change in coastal microbial community structure associated with submarine groundwater discharge and tidal fluctuation
Eunhee Lee et al . Limnology and Oceanography 62.2 (2017): 437-451.
Abstract -
Coastal areas where submarine groundwater discharge (SGD) occurs are active mixing zones with characteristic biogeochemical and ecological functions. In this study, we investigated the microbial community associated with the changes in groundwater discharge flux at a coastal beach site on Jeju Island, South Korea. We performed water chemistry analyses, 16S rRNA gene-based pyrosequencing, and microbial community statistical analyses on coastal water samples systematically collected as functions of tidal stage and distance from the groundwater discharge point. We also carried out groundwater level monitoring and numerical simulation of the coastal aquifer to reproduce tidally induced variations in the SGD rates of the study site. Pyrosequencing and statistical analyses revealed a periodic shift in the microbial communities in the coastal waters as functions of tidal stage and SGD rates. Interestingly, the community structures in the samples collected at flood and ebb tide were markedly different, despite the similarities in their water chemistry. Groundwater simulation and canonical correspondence analyses suggest that groundwater discharging at higher velocities at ebb tide can detach and transport subsurface bacteria from the aquifer to the coastal water body, resulting in an increase in facultative anaerobes in the ebb tide samples. In addition, release of the sand-attached bacteria as a result of particle resuspension and flushing of shallow subsurface bacteria in the intertidal zone could contribute to shaping the relative abundance of the coastal microbial community. We conclude that SGD rate is an important factor influencing the dynamics of the bacterial community structure at the coastal zone of the study site.

Effect of substrate feeding frequencies on the methane production and microbial communities of laboratory-scale anaerobic digestion reactors
ZH Piao et al . Journal of Material Cycles and Waste Management: 1-8.
Abstract -
Even though full-scale digesters have been designed based on laboratory-scale tests, the substrate feeding modes of laboratory-scale tests might be different from those of full-scale digesters. The effect of substrate feeding frequencies on the performance and microbial community of laboratory-scale anaerobic digestion reactors was investigated. Feeding frequencies of twice a day, once a day, and every two days were tested in three 2-L reactors with an organic loading rate of 0.5 g-glucose/L/day under mesophilic condition. According to the results of this study, all the reactors showed similar methane production rates and SCOD removal efficiencies after sufficient time of acclimation, but frequently feeding promoted more stable digestion. Although there was no significant difference in microbial diversities from pyrosequencing analyses, the changes of archaeal community composition were observed. The decrease in feeding frequency appeared to cause shifts from acetoclastic methanogens affiliated with Methanosaeta to H2-utilizing methanogens. The increase of Methanosaeta at a frequently feeding might contribute to the stability of reactor operation. Since this study uses glucose as the substrate, there is still possibility of different results for more complex substrates, such as sludge, food waste, etc.

Long-term performance of anaerobic digestion for crop residues containing heavy metals and response of microbial communities
Lee J et al . Waste Manag. 2017 Jan;59:498-507. doi: 10.1016/j.wasman.2016.10.005. Epub 2016 Oct 17.
Abstract -
In order to investigate the long-term stability on the performance of the anaerobic digestion process, a laboratory-scale continuous stirred-tank reactor (CSTR) was operated for 1100 days with sunflower harvested in a heavy metal contaminated site. Changes of microbial communities during digestion were identified using pyrosequencing. According to the results, soluble heavy metal concentrations were lower than the reported inhibitory level and the reactor performance remained stable up to OLR of 2.0g-VS/L/day at HRT of 20days. Microbial communities commonly found in anaerobic digestion for cellulosic biomass were observed and stably established with respect to the substrate. Thus, the balance of microbial metabolism was maintained appropriately and anaerobic digestion seems to be feasible for disposal of heavy metal-containing crop residues from phytoremediation sites.
Influence of applied voltage on the performance of bioelectrochemical anaerobic digestion of sewage sludge and planktonic microbial communities at ambient temperature.
Feng Q et al . Bioresour Technol. 2016 Nov;220:500-8. doi: 10.1016/j.biortech.2016.08.085. Epub 2016 Aug 24.
Abstract -
The influence of applied voltage on the bioelectrochemical anaerobic digestion of sewage sludge was studied at ambient temperature (25±2°C). The stability of the bioelectrochemical anaerobic digestion was considerably good in terms of pH, alkalinity and VFAs at 0.3V and 0.5V, but VFA accumulation occurred at 0.7V. The specific methane production rate (370mLCH4/L.d) was the highest at 0.3V, but the methane content (80.6%) in biogas and the methane yield (350mLCH4/gCODr) were higher at 0.5V, significantly better than those of 0.7V. The VS removal efficiency was 64-66% at 0.3V and 0.5V, but only 31% at 0.7V. The dominant species of planktonic microbial communities was Cloacamonas at 0.3V and 0.5V, but the percentage of hydrolytic bacteria species such as Saprospiraceae, Fimbriimonas, and Ottowia pentelensis was much higher at 0.7V. The optimal applied voltage for bioelectrochemicalanaerobic digestion was 0.3-0.5V according to digestion performance and planktonic microbialcommunities.

Forensic analysis using microbial community between skin bacteria and fabrics
Noah Fierer et al . Proc Natl Acad Sci U S A. 2010 Apr 6; 107(14): 6477–6481. Published online 2010 Mar 15. doi: 10.1073/pnas.1000162107
Abstract -
Recent work has demonstrated that the diversity of skin-associated bacterial communities is far higher than previously recognized, with a high degree of interindividual variability in the composition of bacterial communities. Given that skin bacterial communities are personalized, we hypothesized that we could use the residual skin bacteria left on objects for forensic identification, matching the bacteria on the object to the skin-associated bacteria of the individual who touched the object. Here we describe a series of studies de-monstrating the validity of this approach. We show that skin-associated bacteria can be readily recovered from surfaces (including single computer keys and computer mice) and that the structure of these communities can be used to differentiate objects handled by different individuals, even if those objects have been left untouched for up to 2 weeks at room temperature. Furthermore, we demonstrate that we can use a high-throughput pyrosequencing-based ap-proach to quantitatively compare the bacterial communities on objects and skin to match the object to the individual with a high degree of certainty. Although additional work is needed to further establish the utility of this approach, this series of studies introduces a forensics approach that could eventually be used to independently evaluate results obtained using more traditional forensic practices.
Pyrosequencing analysis of bacterial community diversity in long-term fertilized paddy field soil
Aileen Rose Daquiado et al . Applied Soil Ecology Volume 108, December 2016, Pages 84–91
Abstract -
Analysis of soil bacterial community and its diversity in conditions of intensive fertilization using high-throughput sequencing in paddy field soil has to date, not been extensive. Using 454 pyrosequencing of 16S rRNA genes, the current study investigated how bacterial succession changed under seven different fertilizer regimes (NP, NK, PK, NPK, compost, NPK + compost and unfertilized) in a 45-year old paddy field trial. Of the selected treatment variables the application of compost best enhanced soil fertility. Unexpectedly, long-term fertilization had no significant effects on soil microbial structure in paddy soils. The bacterial communities were dominated by Proteobacteria and Chloroflexi. Actinobacteria and Firmicutes were substantially abundant in the compost and NPK + compost treatments. Our findings highlight the fact that organic fertilizer amendment activates diverse groups of Gram-positive microorganisms when compared to conventionally used chemical fertilizers. Abundance of Rhizobiales that directly influences rice growth through symbiosis or indirectly through nutrient cycling, and Methylococcales that combat greenhouse gas (methane) emissions, were high in treatments that received compost, in comparison to inorganic fertilizer amended and unfertilized treatments. Consequently, the application of long-term organic fertilizer has a reasonable and beneficial impact on the bacterial community inhabiting the soil, and can lead to a good crop yield.

Characterisation of microbial diversity and chemical properties of Cheddar cheese prepared from heat-treated milk
Lee JY et al . International Dairy Journal Volume 63, December 2016, Pages 92–98
Abstract -
Cheese made with low temperature/long time-treated milk and thermised milk (LC and TC, respectively) showed diverse bacterial community patterns, while cheese made with high temperature/short time-treated milk (HC) showed the lowest microbial diversity. Although the proportion of subdominant species was <1%, significant differences in community patterns were observed. In particular, the proportions of Lactobacillus casei and Lactobacillus delbrueckii in LC and TC were significantly greater than those in HC. Moreover, chemical analysis revealed the highest proteolytic and lipolytic activities in TC. Based on these results, the characteristics of Cheddar cheese were influenced by bacterial communities in low abundance, which were affected by the type of heating applied to the cheese milks. Furthermore, the diversity of these bacterial communities is highly correlated with the heat treatment of milk, and different treatment methods can be used to alter the chemical metabolism of lactose, fat, and protein during ripening.

Comparison of microbial communities during the anaerobic digestion of Gracilaria under mesophilic and thermophilic conditions
Azizi A et al . World J Microbiol Biotechnol. 2016 Oct;32(10):158. doi: 10.1007/s11274-016-2112-6. Epub 2016 Aug 25.
Abstract -
Mesophilic and thermophilic anaerobic digesters (MD and TD, respectively) utilizing Gracilaria and marine sediment as the substrate and inoculum, respectively, were compared by analyzing their performances and microbial community changes. During three successive transfers, the average cumulative methane yields in the MD and TD were 222.6 ± 17.3 mL CH4/g volatile solids (VS) and 246.1 ± 11 mL CH4/g VS, respectively. The higher hydrolysis rate and acidogenesis in the TD resulted in a several fold greater accumulation of volatile fatty acids (acetate, propionate, and butyrate) followed by a larger pH drop with a prolonged recovery than in the MD. However, the operational stability between both digesters remained comparable. Pyrosequencing analyses revealed that the MD had more complex microbial diversity indices and microbial community changes than the TD. Interestingly, Methanomassiliicoccales, the seventh methanogen order was the predominant archaeal order in the MD along with bacterial orders of Clostridiales, Bacteriodales, and Synergistales. Meanwhile, Coprothermobacter and Methanobacteriales dominated the bacterial and archaeal community in the TD, respectively. Although the methane yield is comparable, both MD and TD show a different profile of pH, VFA and the microbial communities.

Impact of Long-Term Proton Pump Inhibitor Therapy on Gut Microbiota in F344 Rats: Pilot Study.
Shin CM et al . Gut Liver. 2016 Nov 15;10(6):896-901. doi: 10.5009/gnl15529.
Abstract -

BACKGROUND/AIMS:

To evaluate changes in gut microbiota composition following long-term proton pumpinhibitor (PPI) treatment.

METHODS:

Twenty-four-week-old F344 rats were fed diets with (n=6) or without (n=5) lansoprazole for 50 weeks. Profiles of luminal microbiota in the terminal ileum were then analyzed. Pyrosequencing of the 16S rRNA gene was performed using an FLX genome sequencer (454 Life Sciences/Roche).

RESULTS:

Rats treated with lansoprazole showed significantly reduced body weights compared to controls (lansoprazole-treated rats and controls, 322.3±15.3 g vs 403.2±5.2 g, respectively, p<0.001). However, stool frequencies and consistencies did not differ between the two groups. The composition of the gut microbiota in lansoprazole-treated rats was quite different from that of the controls. In the controls, the microbiota profiles obtained from the terminal ileum showed a predominance of Proteobacteria (93.9%) due to the abundance of Escherichia and Pasteurella genera. Conversely, lansoprazole-treated rats showed an elevated population of Firmicutes (66.9%), which was attributed to an increased ratio of Clostridium g4 to Lactobacillus genera.

CONCLUSIONS:

This preliminary study suggests that long-term administration of PPI may cause weight loss and changes to the microbiota in the terminal ileum.


Changes of Mouse Gut Microbiota Diversity and Composition by Modulating Dietary Protein and Carbohydrate Contents: A Pilot Study
Eunjung Kim et al . Prev Nutr Food Sci. 2016 Mar; 21(1): 57–61.
Abstract -
Dietary proteins influence colorectal cancer (CRC) risk, depending on their quantity and quality. Here, using pyrosequencing, we compared the fecal microbiota composition in Balb/c mice fed either a normal protein/carbohydrate diet (ND, 20% casein and 68% carbohydrate) or a high-protein/low-carbohydrate diet (HPLCD, 30% casein and 57% carbohydrate). The results showed that HPLCD feeding for 2 weeks reduced the diversity and altered the composition of the microbiota compared with the ND mice, which included a decrease in the proportion of the family Lachnospiraceae and Ruminococcaceae and increases in the proportions of the genus Bacteroides and Parabacteroides, especially the species EF09600_s and EF604598_s. Similar changes were reported in patients with inflammatory bowel disease, and in mouse models of CRC and colitis, respectively. This suggests that HPLCD may lead to a deleterious luminal environment and may have adverse effects on the intestinal health of individuals consuming such a diet.

Bacterial Diversity and Community Structure in Korean Ginseng Field Soil Are Shifted by Cultivation Time
Nguyen NL et al . PLoS One. 2016 May 17;11(5):e0155055. doi: 10.1371/journal.pone.0155055. eCollection 2016.
Abstract -
Traditional molecular methods have been used to examine bacterial communities in ginseng-cultivated soil samples in a time-dependent manner. Despite these efforts, our understanding of the bacterial community is still inadequate. Therefore, in this study, a high-throughput sequencing approach was employed to investigate bacterial diversity in various ginseng field soil samples over cultivation times of 2, 4, and 6 years in the first and second rounds of cultivation. We used non-cultivated soil samples to perform a comparative study. Moreover, this study assessed changes in the bacterial community associated with soil depth and the health state of the ginsengBacterial richness decreased through years of cultivation. This study detected differences in relative abundance of bacterial populations between the first and second rounds of cultivation, years of cultivation, and health states of ginseng. These bacterial populations were mainly distributed in the classes Acidobacteria, Alphaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Sphingobacteria. In addition, we found that pH, available phosphorus, and exchangeable Ca+ seemed to have high correlations with bacterial class in ginseng cultivated soil.

Molecular investigation of bacterial communities: Data from two frequently used surfaces in the São Paulo Institute of Tropical Medicine.
Pereira da Fonseca TA et al . Data Brief. 2016 Jun 2;8:399-403. doi: 10.1016/j.dib.2016.05.064. eCollection 2016.
Abstract -
This article contains data on the bacterial population of two frequently used surfaces in the São PauloInstitute of Tropical Medicine (ITM) using the Illumina sequencing for massive parallel investigation of the bacterial 16S ribosomal RNA gene. Surface samples were obtained from restroom surfaces and the fingerprint door clock system. Mothur package and Shannon-ace-table.pl software programs (Chunlab Inc.: Seoul, Korea) were used to compute the diversity indices of bacterial community. The sequencing data from both surfaces have been uploaded to Zenodo: http://dx.doi.org/10.5281/zenodo.47709.

Heterofermentative lactic acid bacteria dominate in Korean commercial kimchi
Hee-Young KimYeon-Ju BongJi-Kang JeongSungbum LeeByung-Yong KimKun-Young Park et al . Food Sci Biotechnol (2016) 25: 541. doi:10.1007/s10068-016-0075-x
Abstract -
Lactic acid bacterial communities in kimchi prepared by representative Korean kimchi companies were investigated using a pyrosequencing method. The pH values of 9 kimchi varieties (K1-K9) ranged from 4.3 to 4.7, and total lactic acid bacterial (LAB) counts ranged from 1.3x107 to 1.6x109 CFU/g. WeissellaLactobacillus, and Leuconostoc were the dominant genera accounting for 52, 28, and 20%, respectively, of identified genera. At the species level, Weissella koreensis (35%) dominated, followed by Lactobacillus graminis (13%), and Weissella cibaria (11%). Dominant LAB were all heterofermentative LAB. K1 had the most diverse operational taxonomic units (OTUs), and clustering analysis showed that distributions of microorganisms in K2, K6, K5, and K4 were similar each other. LAB communities in kimchi are diverse and heterofermentative LAB dominate in Korean commercial kimchi.

Comparative analysis of prokaryotic diversity in solar salterns in eastern Anatolia (Turkey).
Çınar S et al . Extremophiles. 2016 Sep;20(5):589-601. doi: 10.1007/s00792-016-0845-7. Epub 2016 Jun 15.
Abstract -
The prokaryotic communities of four salterns (Bingöl, Fadlum, Kemah, and Tuzlagözü) in Turkey were examined and compared using the cultivation and cultivation-independent methods [fluorescence in situ hybridization (FISH) and 454 pyrosequencing]. FISH analysis with universal probes revealed that feeding waters carried 1.6 × 10(2)-1.7 × 10(3) cells mL(-1), while crystallization ponds carried 3.8 × 10(6)-2.0 × 10(7) cells mL(-1) that were mostly haloarchaea, including square cells (except for Kemah). High-throughput 16S rRNA-based gene sequencing showed that the most frequent archaeal OTUs in Bingöl, Fadlum, Tuzlagözü, and Kemah samples were affiliated with Haloquadratum (76.8 %), Haloarcula (27.8 %), Halorubrum (49.6 %), and Halonotius (59.8 %), respectively. Bacteroidetes was the dominant bacterial phylum in Bingöl and Fadlum, representing 71.5 and 79.5 % of the bacterial OTUs (respectively), while the most abundant bacterial phylum found in the Kemah saltern was Proteobacteria (79.6 %). The majority of the bacterial OTUs recovered from Tuzlagözü belonged to the Cyanobacteria (35.7 %), Bacteroidetes (35.0 %), and Proteobacteria (25.5 %) phyla. Cultivation studies revealed that the archaeal isolates were closely related to the genera Halobacterium, Haloarcula, and Halorubrum. Bacterial isolates were confined to two phyla, Proteobacteria (Alphaproteobacteria and Gammaproteobacteria classes) and Bacteroidetes. Comparative analysis showed that members of the Euryarchaeota, Bacteroidetes, Proteobacteria, and Cyanobacteria phyla were major inhabitants of the solar salterns.

The Fecal Microbial Communities of Dairy Cattle Shedding Shiga Toxin–Producing Escherichia coli or Campylobacter jejuni
Dong HJ et al . Foodborne Pathog Dis. 2016 Sep;13(9):502-8. doi: 10.1089/fpd.2016.2121. Epub 2016 Jul 6.
Abstract -
Cattle are a natural reservoir of Shiga toxin-producing Escherichia coli (STEC) and have recently been recognized as a major source of Campylobacter jejuni contamination. While several factors are known to be associated with bacterial colonization, the underlying microbial factors have not been clarified. In this study, we characterized the fecal microbiota of dairy cattle (n = 24) using next-generation sequencing to elucidate the intestinal bacterial communities and the microbial diversity in relation to the presence of the foodborne pathogens STEC and C. jejuni (STEC-positive samples, n = 9; STEC-negative samples, n = 15; C. jejuni-positive samples, n = 9; and C. jejuni-negative samples, n = 15). While no significant differences were observed in alpha diversity between STEC-positive and STEC-negative samples, a high diversity index was observed in C. jejuni-positive samples compared to C. jejuni-negative samples. Nine phyla, 13 classes, 18 orders, 47 families, 148 genera, and 261 species were found to be the core microbiota in dairy cattle, covering 80.0-100.0% of the fecal microbial community. Diverse microbial communities were observed between cattle shedding foodborne pathogens and nonshedding cattle. C. jejuni-positive cattle had a higher relative abundance of Bacteroidetes (p = 0.035) and a lower relative abundance of Firmicutes (p = 0.035) compared to C. jejuni-negative cattle. In addition, while the relative abundance of 2 and 6 genera was significantly higher in cattle-shedding STEC and C. jejuni, respectively, the relative abundance of 3 genera was lower in both STEC- and C. jejuni-negative cattle. Our findings provide fundamental information on the bacterial ecology in cattle feces and might be useful in developing strategies to reduce STEC or C. jejuni shedding in dairy cattle, thereby reducing the incidence of STEC infection and campylobacteriosis in humans.
The first case of disease of the sponge Lubomirskia baicalensis: Investigation of its microbiome
N. N. DenikinaE. V. DzyubaN. L. Bel’kovaI. V. KhanaevS. I. FeranchukM. M. MakarovN. G. GraninS. I. Belikov et al . Biology Bulletin May 2016, Volume 43, Issue 3, pp 263–270
Abstract -
The first metagenomic analysis of the microbiome of the first sample of diseased endemic sponge Lubomirskia baicalensis (Pallas, 1771) from Lake Baikal and the comparison of the results with data published earlier on the microbiome of healthy sponges were carried out. Essential changes in the composition and structure of the microbial community were detected in the diseased individual possessing an uncharacteristic pink coloring. Cyanobacteria were predominant in the community, the fraction of the representatives of Verrucomicrobia was increased. The diversity and number of eukaryotic algae, as well as of representatives of Bacteroidetes, Proteobacteria, Actinobacteria, and Planctomycetes, were decreased. A wide range of minor phyla were eliminated. The factors affecting the composition of symbiotic communities in sponges were considered. It was supposed that changes in the structure of symbiotic communities resulting in mass disease and death could be caused by an increase in the methane concentration in the water column of Lake Baikal.

Beneficial effects of voglibose administration on body weight and lipid metabolism via gastrointestinal bile acid modification.
Do HJ et al . Endocr J. 2016 Aug 31;63(8):691-702. doi: 10.1507/endocrj.EJ15-0747. Epub 2016 Jun 25.
Abstract -
This study was designed with the goal of examining the effects of voglibose administration on body weight and lipid metabolism and underlying mechanism high fat diet-induced obese mice. Male C57BL/6 mice were randomly assigned to one of four groups: a control diet (CTL), high-fat diet (HF), high-fat diet supplemented with voglibose (VO), and high fat diet pair-fed group (PF). After 12 weeks, the following characteristics were investigated: serum lipid and glucose levels, serum polar metabolite profiles, and expression levels of genes involved in lipid and bile acid metabolism. In addition, pyrosequencing was used to analyze the composition of gut microbiota found in feces. Total body weight gain was significantly lower in the VO group than in the CTL, HF, and PF groups. The VO group exhibited improved metabolic profiles including those of blood glucose, triglyceride, and total cholesterol levels. The 12-week vogliboseadministration decreased the ratio of Firmicutes to Bacteroidetes found in feces. Circulating levels of taurocholic and cholic acid were significantly higher in the VO group than in the HF and CTL groups. Deoxycholic acid levels tended to be higher in the VO group than in the HF group. Vogliboseadministration downregulated expression levels of CYP8B1 and HNF4α genes and upregulated those of PGC1α, whereas FXRα was not affected. Voglibose administration elicits changes in the composition of the intestinal microbiota and circulating metabolites, which ultimately has systemic effects on body weight and lipid metabolism in mice.

Complete genome sequence of Celeribacter marinus IMCC12053(T), the host strain of marine bacteriophage P12053L.
Yang JA et al . Mar Genomics. 2016 Apr;26:5-7. doi: 10.1016/j.margen.2015.11.012. Epub 2015 Dec 12.
Abstract -
Isolated from coastal seawater from Yellow Sea of Korea, Celeribacter marinus IMCC12053 was used as the host bacterium for bacteriophage P12053L. Here we report the complete genome sequence of strain IMCC12053 for further study of the marine bacteriophage P12053L functional genes. Single molecule real-time technology (PacBio RSII) was used for the single circular chromosome that is 3,096,705 base pairs in length and the GC content is 56.24%. It contains 3155 ORFs with 45 tRNAs and 6 rRNAs genes. N(6)-methyladenosine patterns were also investigated for 32 unmethylated genes and intergenic regions that covered many regulators and phage genes as well as ribosomal RNA genes and tRNA genes. Cryptic N(4)-methylcytosine pattern was investigated to speculate GpC methylase activity throughout the genome. Comparative genomics with other Celeribacter genomes were carried out for polyaromatic hydrocarbon degradation, but there were no aromatic ring oxygenases in IMCC12053 when compared to Celeribacter indicus P73.

Complete genome sequence of biofilm-forming strain Staphylococcus haemolyticus S167
Hong J et al . Genome Announc. 2016 Jun 16;4(3). pii: e00567-16. doi: 10.1128/genomeA.00567-16.
Abstract -
Staphylococcus haemolyticus S167 has the ability to produce biofilms in large quantities. Genomic analyses revealed information on the biofilm-related genes of S. haemolyticus S167. Detailed studies of biofilm formation at the molecular level could provide a foundation for biofilm control research.

Complete genome sequence of Vibrio parahaemolyticus strain FORC_008, a foodborne pathogen from a flounder fish in South Korea.
Suyeon Kim Han Young Chung Dong-Hoon Lee Jong Gyu Lim Se Keun Kim Hye-Jin Ku You-Tae Kim Heebal Kim Sangryeol Ryu Ju-Hoon Lee et al . Pathog Dis. 2016 Jul;74(5). pii: ftw044. doi: 10.1093/femspd/ftw044. Epub 2016 May 10.
Abstract -
Vibrio parahaemolyticus is a Gram-negative, motile, nonspore-forming pathogen that causes foodborne illness associated with the consumption of contaminated seafoods. Although many cases of foodborne outbreaks caused by V. parahaemolyticus have been reported, the genomes of only five strains have been completely sequenced and analyzed using bioinformatics. In order to characterize overall virulence factors and pathogenesis of V. parahaemolyticus associated with foodborne outbreak in South Korea, a new strain FORC_008 was isolated from flounder fish and its genome was completely sequenced. The genomic analysis revealed that the genome of FORC_008 consists of two circular DNA chromosomes of 3266 132 bp (chromosome I) and 1772 036 bp (chromosome II) with a GC content of 45.36% and 45.53%, respectively. The entire genome contains 4494 predicted open reading frames, 129 tRNAs and 31 rRNA genes. While the strain FORC_008 does not have genes encoding thermostable direct hemolysin (TDH) and TDH-related hemolysin (TRH), its genome encodes many other virulence factors including hemolysins, pathogenesis-associated secretion systems and iron acquisition systems, suggesting that it may be a potential pathogen. This report provides an extended understanding on V. parahaemolyticus in genomic level and would be helpful for rapid detection, epidemiological investigation and prevention of foodborne outbreak in South Korea.

Complete genome sequence of Vibrio parahaemolyticus FORC_023 isolated from raw fish storage water
Han Young Chung Eun Jung Na Kyu-Ho Lee Sangryeol Ryu Hyunjin Yoon Ju-Hoon Lee Hyeun Bum Kim Heebal Kim Sang Ho Choi Bong-Soo Kim et al . Pathog Dis. 2016 Jun;74(4):ftw032. doi: 10.1093/femspd/ftw032. Epub 2016 Apr 11.
Abstract -
Vibrio parahaemolyticusis a Gram-negative halophilic bacterium that causes food-borne gastroenteritis in humans who consumeV. parahaemolyticus-contaminated seafood.The FORC_023 strain was isolated from raw fish storage water, containing live fish at a sashimi restaurant. Here, we aimed to sequence and characterize the genome of the FORC_023 strain. The genome of the FORC_023 strain showed two circular chromosomes, which contained 4227 open reading frames (ORFs), 131 tRNA genes and 37 rRNA genes. Although the genome of FORC_023 did not include major virulence genes, such as genes encoding thermostable direct hemolysin (TDH) and TDH-related hemolysin (TRH), it contained genes encoding other hemolysins, secretion systems, iron uptake-related proteins and severalV. parahaemolyticusislands. The highest average nucleotide identity value was obtained between the FORC_023 strain and UCM-V493 (CP007004-6). Comparative genomic analysis of FORC_023 with UCM-V493 revealed that FORC_023 carried an additional genomic region encoding virulence factors, such as repeats-in-toxin and type II secretion factors. Furthermore,in vitrocytotoxicity testing showed that FORC_023 exhibited a high level of cytotoxicity toward INT-407 human epithelial cells. These results suggested that the FORC_023 strain may be a food-borne pathogen.

Effects of Undaria pinnatifida and Laminaria japonica on Rats Intestinal Microbiota and Metabolite
Kim JY et al . J Nutr Food Sci 6:502.
Abstract -
This study examined the effects on weight changes, intestinal microorganisms, and production of short chain fatty acids (SCFAs) in rats following the consumption of Undaria pinnatifida (U. pinnatifida) and Laminaria japonica (L. japonica) and in vitro fermentation by intestinal microbiota. Forty-eight Sprague-Dawley rats aged four weeks were divided in to a basal diet group (control), a basal diet+10% dried U. pinnatifida group (BDUP), and a basal diet+10% dried L. japonica group (BDLJ) and subjected to a four-week feeding trial. The rat weights showed smaller increases after four weeks for the BDUP and BDLJ groups when compared to the control. The intestinal microorganisms through 16S ribosomal RNA (rRNA) profiling revealed distributions of Firmicutes in the intestinal microorganisms of 92, 72, and 78% in the control, BDUP, and BDLJ groups, respectively, while the distribution of Bacteroidetes were 4, 24, and 20, respectively. All 36 species of microorganisms that fall under PrevotellaAlistipes, and Bacteroides genera increased in number by at least four fold, whereas RoseburiaMollicute, and Oscillibacter decreased more than half. Fifty-two species of microorganisms belonging to ClostridiumEscherichia, and Enterobacter genera classified as pathogenic microorganisms decreased in all the treatment groups when compared to the control groups. Implementation of in vitro intestinal fermentation gave larger butyric acid yields for the feeds containing U. pinnatifida and L. japonica when compared to the basal diet. These results indicate that the provision of U. pinnatifida and L. japonica changed the balance of the intestinal microbiota in rats, thereby suppressing weight gain while promoting butyric acid production in the large intestine.

Bacterial community analysis of Tatsoi cultivated by hydroponics
Koo OK et al . J Environ Sci Health B. 2016 Jul 2;51(7):490-6. doi: 10.1080/03601234.2016.1159462. Epub 2016 Apr 12.
Abstract -
Tatsoi (Brassica narinosa) is a popular Asian salad green that is mostly consumed as a source of fresh produce. The purpose of this study was to assess the microbial diversity of Tatsoi cultivated in a hydroponic system and of its ecosystem. Tatsoi leaves, nutrient solution, and perlite/earth samples from a trickle feed system (TFS) and an ebb-and-flow system (EFS) were collected and their microbial communities were analyzed by pyrosequencing analysis. The results showed that most bacteria in the leaves from the TFS contained genus Sporosarcina (99.6%), while Rhizobium (60.4%) was dominant in the leaves from the EFS. Genus Paucibacter (18.21%) and Pelomonas (12.37%) were the most abundant microbiota in the nutrient solution samples of the TFS. In the EFS, the nutrient solution samples contained mostly genus Rhodococcus and Acinetobacter. Potential microbial transfer between the leaves and the ecosystem was observed in the EFS, while samples in the TFS were found to share only one species between the leaves, nutrient solution, and earth. Together, these results show that the bacterial populations in Tatsoi and in its ecosystem are highly diverse based on the cultivation system.

Complete genome sequence of Vibrio vulnificus FORC_017 isolated from a patient with a hemorrhagic rash after consuming raw dotted gizzard shad.
Chung HY et al . Gut Pathog. 2016 Jun 20;8:22. doi: 10.1186/s13099-016-0104-6. eCollection 2016.
Abstract -

BACKGROUND:

Vibrio vulnificus, a resident in the human gut, is frequently found in seafood, causing food-borne illnesses including gastroenteritis and severe septicemia. While V. vulnificus has been known to be one of the major food-borne pathogens, pathogenicity and virulence factors are not fully understood yet. To extend our understanding of the pathogenesis of V. vulnificus at the genomic level, the genome of V. vulnificus FORC_017 isolated from a female patient experiencing a hemorrhagic rash was completely sequenced and analyzed.

RESULTS:

Three discontinuous contigs were generated from a hybrid assembly using Illumina MiSeq and PacBio platforms, revealing that the genome of the FORC_017 consists of two circular chromosomes and a plasmid. Chromosome I consists of 3,253,417-bp (GC content 46.49 %) containing 2943 predicted open reading frames (ORFs) and chromosome II of 1,905,745-bp (GC content 46.90 %) containing 1638 ORFs. The plasmid pFORC17 consists of 70,069-bp (GC content 43.77 %) containing 84 ORFs. The average nucleotide identity (ANI) value of the FORC_017 and CMCP6 strains was 98.53, suggesting that they are closely related.

CONCLUSIONS:

Pathogenesis-associated genes including vvhA, rtx gene cluster, and various hemolysin genes were present in FORC_017. In addition, three complete secretion systems (Type I, II and VI) as well as iron uptake-related genes for virulence of the FORC_017 were detected, suggesting that this strain is pathogenic. Further comparative genome analysis revealed that FORC_017 and CMCP6 share major toxin genes including vvhA and rtx for pathogenesis activities. The genome information of the FORC_017 provides novel insights into pathogenicity and virulence factors of V. vulnificus.

Reclassification of Halomonas caseinilytica Wu et al. 2008 as a later synonym of Halomonas sinaiensis Romano et al. 2007, and emendation of the species description.
Hwang CY et al . Antonie Van Leeuwenhoek. 2016 Oct;109(10):1345-52. doi: 10.1007/s10482-016-0733-2. Epub 2016 Jul 14.
Abstract -
The taxonomic relationship between Halomonas sinaiensis DSM 18067(T) and Halomonas caseinilytica JCM 14802(T) has not been established, despite the high similarity (99.6 %) of their 16S rRNA gene sequences. To clarify their taxonomic positions, a polyphasic approach was applied to both type strains. Genomic relatedness analyses between H. sinaiensis DSM 18067(T) and H. caseinilytica JCM 14802(T) resulted in an average nucleotide identity of 99.5 % and an estimated DNA-DNA hybridization of 96.1 % by the genome-to-genome distance calculator, indicating that they belong to a single species. Phenotypic and chemotaxonomic characteristics showed no pronounced differences between the two type strains. Based on the results of this polyphasic study, it is proposed that H. caseinilytica JCM 14802(T) is a later heterotypic synonym of H. sinaiensis DSM 18067(T). An emended description for the species H. sinaiensis is given.
Long-term effects of imbalanced fertilization on the composition and diversity of soil bacterial community
Jinu Eoa et al . Agriculture, Ecosystems & Environment Volume 231, 1 September 2016, Pages 176–182
Abstract -
Repeated fertilization in a monoculture system causes a nutrient imbalance, disturbing the soil bacterial community. To investigate the long-term effects of imbalanced fertilization, we analysed soils under pepper (Capsicum annum L.) cultivation for 18 years. The soil was treated with one of five regimens: untreated control, NPK, PK, NP, and NK. Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, and Firmicutes were the dominant phyla. Pyrosequencing revealed that diversity indices were not significantly influenced by different fertilization treatments. We found that the effect of fertilization varied at the genus level even within the same phylum, demonstrating divergent ecological responses of bacterial groups to disturbance at low taxonomic levels. The percentage abundances of Acidobacteria and Nitrospira were decreased in all fertilized plots. The percentages of genus Sphingomonas and JF421159 were increased only with NPK treatment, and our results suggested that bacterial community composition is altered by fertilization lacking one of three components. The percentages of Chloroflexi and Planctomycetes were decreased in the plots receiving N, while the percentage of candidate division TM7 showed an increase with N. The percentages of these genera were correlated with soil chemical parameters such as nitrate content and pH. Our study suggests that N promotes some bacterial groups, which are involved in the degradation of materials; however, it has an overall negative impact on the percentages of some other groups due to changes in the soil chemical properties. The percentages of Koribacter and Pseudolabrys were increased with NK treatment, likely due to a lack of P. Our results implied that N and P exert substantial effect on specific bacterial groups; in contrast, K has minimal effect. We suggested that an imbalanced N-P-K ratio caused by repeated fertilization could be a driving force altering the bacterial community composition not its diversity.

Organotrophic bacteria of the Baikal Rift Zone hot springs
A. A. Radnagurueva et al . Microbiology May 2016, Volume 85, Issue 3, pp 367–378
Abstract -
Pyrosequencing of the 16S rRNA gene fragments was used to investigate the bacterial community of an Alla hot spring microbial mat. The mat community was mainly represented by the members of five phyla: Deinococcus-ThermusNitrospiraeAtribacteria (OP9), ProteobacteriaChloroflexi, and Firmicutes, with other groups responsible for not more than 2% of the total number. From hot springs of the Baikal Rift Zone (Buryatia, Russia), 13 strains of aerobic alkaliphilic thermophilic organotrophic bacteria were isolated, and their morphology, ecology, physiology, and phylogenetic position were studied. Based on analysis of their 16S rRNA gene sequences, the isolates were identified as members of the family Bacillaceae. Strains Al-9-1, Se-1, Ga-1-1, Ga-9-2, and Se-1-10 were assigned to the genus Anoxybacillus; strains Ur-6, Br-2-2, А2, and Um-09m, to the genus Bacillus; strains Gor-10s and Gа-35, to the genus Paenabacillus. Secreted endopeptidases of the isolates were shown to have relatively narrow substrate specificity. The investigated enzymes were characterized by high pH (6.3–11.4) and temperature stability (23–70°C), which makes it possible to carry out organic matter degradation in the environment under variable ecological conditions.

Gut microbiota‐associated bile acid deconjugation accelerates hepatic steatosis in ob/ob mice
Park MY et al . J Appl Microbiol. 2016 Sep;121(3):800-10. doi: 10.1111/jam.13158. Epub 2016 Jul 29.
Abstract -

Nonalcoholic hepatic fat accumulation has been hypothesized to be associated with alterations in gut microbiota composition, although mechanistic explanations for this link are largely insufficient. The aim of this study was to elucidate the microbiota-driven mechanisms involved in the development of nonalcoholic hepatic steatosis.

METHODS AND RESULTS:

Ob/ob mice and their wild-type lean control mice were fed an AIN-93G diet for 12 weeks. Faecal microbiota composition, faecal bile acid (BA) profile and intestinal and hepatic markers of BA metabolism were analysed. Ob/ob mice had significantly less faecal taurine-conjugated BAs compared to their lean controls. The proportions of butyrate-producing bacteria were lower in ob/ob mice compared to those in lean mice. Intestinal expression of farnesoid X receptor (FXR) mRNA was significantly higher, whereas hepatic expression of cholesterol-7α-hydroxylase 1 (CYP7A1) and small heterodimer partner (SHP) were significantly lower in ob/ob mice compared to those in control mice.

CONCLUSION:

Microbiota-associated BAs deconjugation may induce nonalcoholic fatty liver disease (NAFLD) by activating intestinal FXR signalling and blocking hepatic FXR-SHP pathway, thereby accelerating fat synthesis.

SIGNIFICANCE AND IMPACT OF THE STUDY:

We provided evidences that changes in the gut microbiota and their metabolites can alter the profile of BAs, thereby providing a mechanism by which an altered microbiota profile contributes to the development of NAFLD.


The presence of bacteria within tissue provides insights into the pathogenesis of oral lichen planus
Yun Sik Choi et al . Sci Rep. 2016; 6: 29186. Published online 2016 Jul 7. doi: 10.1038/srep29186
Abstract -
Oral lichen planus (OLP) is a chronic T cell-mediated mucocutaneous disease of unknown etiopathogenesis. Although various antigens have been considered, what actually triggers the inflammatory response of T cells is unknown. In the present study, we propose that intracellular bacteria present within tissues trigger T cell infiltration and provide target antigens. Sections of OLP (n = 36) and normal (n = 10) oral mucosal tissues were subjected to in situ hybridization using a universal probe targeting the bacterial 16S rRNA gene and immunohistochemistry with anti-CD3, anti-CD4, anti-CD8, and anti-macrophage-specific antibodies. Bacteria were abundant throughout the epithelium and the lamina propria of OLP tissues, which exhibited positive correlations with the levels of infiltrated CD3+, CD4+, and CD8+ cells. Furthermore, bacteria were detected within the infiltrated T cells. Pyrosequencing analysis of the mucosal microbiota from OLP patients (n = 13) and control subjects (n = 11) revealed a decrease in Streptococcus and increases in gingivitis/periodontitis-associated bacteria in OLP lesions. Using the selected bacterial species, we demonstrated that certain oral bacteria damage the epithelial physical barrier, are internalized into epithelial cells or T cells, and induce production of T cell chemokines CXCL10 and CCL5. Our findings provide insights into the pathogenesis of OLP.
First Case of Human Brucellosis Caused by Brucella melitensis in Korea
Kim HN et al . Received 2015 Nov 17; Revised 2015 Dec 22; Accepted 2016 Feb 22.
Abstract -

Human brucellosis is the most common zoonosis worldwide and is caused by gram-negative bacteria, Brucella spp. [1]. Among the Brucella spp., B. abortus, B. canis, B. melitensis, and B. suis can cause human brucellosis. Human brucellosis involves various organs including bone marrow (BM), shows non-specific clinical manifestations including fever, fatigue, back pain, and arthralgia, and can progress to septicemia or multi-organ failure [1,2]. In Korea, since the first case of human brucellosis in 2002 [3], all reported 747 cases have been caused by B. abortus, and the majority were related to the out-break of bovine brucellosis in mid-2000 [4]. We report the first Korean case of human brucellosis caused by B. melitensis.

Six-week Diet Correction for Body Weight Reduction and Its Subsequent Changes of Gut Microbiota: A Case Report
Oh B et al . Clin Nutr Res. 2016 Apr;5(2):137-40. doi: 10.7762/cnr.2016.5.2.137. Epub 2016 Apr 30.
Abstract -
Impact of intestinal microbes on obesity and health is a new topic recently started to get attention. Comparing to the global concern and research trends, there are few research on the association between intestinal bacteria and life style disease in Korean. One voluntary case (female) was reported to show the change in gut microbiota and weight by diet intervention. She was overweight (BMI 23.2 kg/m(2)) and has abnormal liver function, and the causes of overweight were frequent drinking and meat consumption at the late evening hours. For 47 days, she was administered an improved diet on breakfast and dinner with reduction of meat consumption frequency by 50%. Alcohol consumption was reduced to once a week. As a result, she lost 3 kilograms of body weight. Her fecal sample was collected before and after the intervention, and gut microbiota change was compared using a high-throughput sequencing technique. After diet correction, the shift of gut microbiota was clearly observed with decreased proportion of Firmicutes (from 75.7% to 47.3% in total microbiota) but increased proportion of Bacteroidetes upto 47.7%. After incorporating the diet intervention, it is meaningful to confirm the changes in dominant gut microbiota and weight loss.

Towards high through-put biological treatment of municipal wastewater and enhanced phosphorus recovery using a hybrid microfiltration-forward osmosis membrane bioreactor with hydraulic retention time in sub-hour level
Qiu G et al . Bioresour Technol. 2016 Nov;219:298-310. doi: 10.1016/j.biortech.2016.07.126. Epub 2016 Jul 29.
Abstract -
This work uncovers an important feature of the forward osmosis membrane bioreactor (FOMBR) process: the decoupling of contaminants retention time (CRT) and hydraulic retention time (HRT). Based on this concept, the capability of the hybrid microfiltration-forward osmosis membrane bioreactor (MF-FOMBR) in achieving high through-put treatment of municipal wastewater with enhanced phosphorus recovery was explored. High removal of TOC and NH4(+)-N (90% and 99%, respectively) was achieved with HRTs down to 47min, with the treatment capacity increased by an order of magnitude. Reduced HRT did not affect phosphorus removal and recovery. As a result, the phosphorus recovery capacity was also increased by the same order. Reduced HRT resulted in increased system loading rates and thus elevated concentrations of mixed liquor suspended solids and increased membrane fouling. 454-pyrosequecing suggested the thriving of Bacteroidetes and Proteobacteria (especially Sphingobacteriales Flavobacteriales and Thiothrix members), as well as the community succession and dynamics of ammonium oxidizing and nitrite oxidizing bacteria.
Mucosal and salivary microbiota associated with recurrent aphthous stomatitis
Kim YJ et al . BMC Microbiol. 2016 Apr 1;16 Suppl 1:57. doi: 10.1186/s12866-016-0673-z.
Abstract -

BACKGROUND:

Recurrent aphthous stomatitis (RAS) is a common oral mucosal disorder of unclear etiopathogenesis. Although recent studies of the oral microbiota by high-throughput sequencing of 16S rRNA genes have suggested that imbalances in the oral microbiota may contribute to the etiopathogenesis of RAS, no specific bacterial species associated with RAS have been identified. The present study aimed to characterize the microbiota in the oral mucosa and saliva of RAS patients in comparison with control subjects at the species level.

RESULTS:

The bacterial communities of the oral mucosa and saliva from RAS patients with active lesions (RAS, n = 18 for mucosa and n = 8 for saliva) and control subjects (n = 18 for mucosa and n = 7 for saliva) were analyzed by pyrosequencing of the 16S rRNA genes. There were no significant differences in the alpha diversity between the controls and the RAS, but the mucosal microbiota of the RAS patients showed increased inter-subject variability. A comparison of the relative abundance of each taxon revealed decreases in the members of healthy core microbiota but increases of rare species in the mucosal and salivary microbiota of RAS patients. Particularly, decreased Streptococcus salivarius and increased Acinetobacter johnsonii in the mucosa were associated with RAS risk. A dysbiosis index, which was developed using the relative abundance of A. johnsonii and S. salivarius and the regression coefficients, correctly predicted 83 % of the total cases for the absence or presence of RAS. Interestingly, A. johnsonii substantially inhibited the proliferation of gingival epithelial cells and showed greater cytotoxicity against the gingival epithelial cells than S. salivarius.

CONCLUSION:

RAS is associated with dysbiosis of the mucosal and salivary microbiota, and two species associated with RAS have been identified. This knowledge may provide a diagnostic tool and new targets for therapeutics for RAS.

Influences of NOM composition and bacteriological characteristics on biological stability in a full-scale drinking water treatment plant
Park JW et al . Chemosphere. 2016 Oct;160:189-98. doi: 10.1016/j.chemosphere.2016.06.079. Epub 2016 Jul 6
Abstract -
The influences of natural organic matter (NOM) and bacteriological characteristics on the biologicalstability of water were investigated in a full-scale drinking water treatment plant. We found that prechlorination decreased the hydrophobicity of the organic matter and significantly increased the high-molecular-weight (MW) dissolved organic matter, such as biopolymers and humic substances. High-MW organic matter and structurally complex compounds are known to be relatively slowly biodegradable; however, because of the prechlorination step, the indigenous bacteria could readily utilise these fractions as assimilable organic carbon. Sequential coagulation and sedimentation resulted in the substantial removal of biopolymer (74%), humic substance (33%), bacterial cells (79%), and assimilable organic carbon (67%). Rapid sand and granular activated carbon filtration induced an increase in the low-nucleic-acid content bacteria; however, these bacteria were biologically less active in relation to enzymatic activity and ATP. The granular activated carbon step was essential to securing biologicalstability (the ability to prevent bacterial growth) by removing the residual assimilable organic carbon that had formed during the ozone treatment. The growth potential of Escherichia coli and indigenous bacteria were found to differ in respect to NOM characteristics. In comparison with E. coli, the indigenous bacteria utilised a broader range of NOM as a carbon source. Principal component analysis demonstrated that the measured biological stability of water could differ, depending on the NOMcharacteristics, as well as on the bacterial inoculum selected for the analysis.

Metagenomic insight of nitrogen metabolism in a tannery wastewater treatment plant bioaugmented with the microbial consortium BM-S-1
Sul WJ et al . J Environ Sci Health A Tox Hazard Subst Environ Eng. 2016 Nov 9;51(13):1164-72. doi: 10.1080/10934529.2016.1206387. Epub 2016 Jul 28.
Abstract -
Nitrogen (N) removal in a tannery wastewater treatment plant was significantly enhanced by the bioaugmentation of the novel consortium BM-S-1. In order to identify dominant taxa responsible for N metabolisms in the different stages of the treatment process, Illumina MiSeq Sequencer was used to conduct metagenome sequencing of the microbial communities in the different stages of treatment system, including influent (I), buffering (B), primary aeration (PA), secondary aeration (SA) and sludge digestion (SD). Based on MG-RAST analysis, the dominant phyla were Proteobacteria, Bacteroidetes and Firmicutes in B, PA, SA and SD, whereas Firmicutes was the most dominant in I before augmentation. The augmentation increased the abundance of the denitrification genes found in the genera such as Ralstonia (nirS, norB and nosZ), Pseudomonas (narG, nirS and norB) and Escherichia (narG) in B and PA. In addition, Bacteroides, Geobacter, Porphyromonasand Wolinella carrying nrfA gene encoding dissimilatory nitrate reduction to ammonium were abundantly present in B and PA. This was corroborated with the higher total N removal in these two stages. Thus, metagenomic analysis was able to identify the dominant taxa responsible for dissimilatory N metabolisms in the tannery wastewater treatment system undergoing bioaugmentation. This metagenomic insight into the nitrogen metabolism will contribute to a successful monitoring and operation of the eco-friendly tannery wastewater treatment system.

A single gene of a commensal microbe affects host susceptibility to enteric infection
Mi Young Yoon et al . Nat Commun. 2016 May 13;7:11606. doi: 10.1038/ncomms11606.
Abstract -
Indigenous microbes inside the host intestine maintain a complex self-regulating community. The mechanisms by which gut microbes interact with intestinal pathogens remain largely unknown. Here we identify a commensal Escherichia coli strain whose expansion predisposes mice to infection by Vibrio cholerae, a human pathogen. We refer to this strain as 'atypical' E. coli (atEc) because of its inability to ferment lactose. The atEc strain is resistant to reactive oxygen species (ROS) and proliferates extensively in antibiotic-treated adult mice. V. cholerae infection is more severe in neonatal mice transplanted with atEc compared with those transplanted with a typical E. coli strain. Intestinal ROS levels are decreased in atEc-transplanted mice, favouring proliferation of ROS-sensitive V. cholerae. An atEc mutant defective in ROS degradation fails to facilitate V. cholerae infection when transplanted, suggesting that host infection susceptibility can be regulated by a single gene product of one particular commensal species.

Analysis of Soil Bacterial Community in Ihwaryeong and Yuksimnyeong Restoration Project Sites Linking the Ridgeline of Baekdudaegan
Park YD et al . Journal of Agriculture & Life Science Vol.50 No.1 pp.117-124 DOI : https://doi.org/10.14397/jals.2016.50.1.117
Abstract -
Researches on soil microbial community are increasing to assess ecosystem responses to anthropogenic disturbances and to provide an indicator of ecosystem recovery. Microbial communities are able to respond more rapidly to environmental changes than plants and therefore they may provide an early indication of the ecosystem recovery trajectory. This study was conducted using 16S rRNA gene pyrosequencing of soil samples to compare soil bacterial community composition between artificially covered soils of the Baedudaegan ridgeline and their adjacent forest soils in two restoration project sites, Ihwaryeong and Yuksimnyeong, which were completed in 2012 and 2013, respectively. Richness of the Phylum level was 29.3 in Ihwaryeong and 32.3 in Yuksimnyeong. Significant difference in the richness between artificial restored soils and adjacent forest soils(p<0.01) was observed, however no significant difference was observed for site location and soil depth. Acidobacteria(37.3%) and Proteobacteria(31.1%) were more abundant than any other phylum in collected soil samples. Also, we found the significant difference in the relative abundance of the two abundant phyla between artificially restored soils and their adjacent forest soils (Proteobacteria, 38.1% in restored soils vs 24.2% in adjacent forest soils, p<0.01; Acidobacteria, 55.4% in restored soils vs 19.2% in adjacent forest soils, p<0.001). The results support the previous researches indicating that soil bacterial community composition is affected by nutritional status of soils and that Acidobacteria is also strongly influenced by pH, thus favoring soils with lower pH. This study could be utilized to monitor and evaluate restoration success of forest soil environment quantitatively.

Similarities and Contrasts in the Archaeal Community of Two Japanese Mountains: Mt. Norikura Compared to Mt. Fuji.
Singh D et al . Microb Ecol. 2016 Feb;71(2):428-41. doi: 10.1007/s00248-015-0681-9. Epub 2015 Sep 30.
Abstract -
The community ecology, abundance, and diversity patterns of soil archaea are poorly understood-despite the fact that they are a major branch of life that is ubiquitous and important in nitrogen cycling in terrestrial ecosystems. We set out to investigate the elevational patterns of archaeal ecology, and how these compare with other groups of organisms. Many studies of different groups of organisms (plants, birds, etc.) have shown a series of distinct communities with elevation, and often a diversity maximum in mid-elevations. We investigated the soil archaeal communities on MtNorikura, Japan, using 454 pyrosequencing of the 16S ribosomal RNA (rRNA) gene. There was a strong mid-elevation maximum in diversity, and a mid-elevation maximum in abundance of soil archaea 16S rRNA and amoA genes. These diversity and abundance maximums could not be correlated with any identifiable soil parameter, nor plant diversity. Discrete, predictable communities of archaea occurred at each elevational level, also not explicable in terms of pH or major nutrients. When we compared the archaeal community and diversity patterns with those found in an earlier study of MtFuji, both mountains showed mid-elevation maximums in diversity and abundance of archaea, possibly a result of some common environmental factor such as soil disturbance frequency. However, they showed distinct sets of archaeal communities at similar elevational sampling points. Presumably, the difference reflects their distinct geology (Norikura being andesitic, while Fuji is basaltic) and the resulting combinations of soil chemistry and environmental conditions, although no explanatory variable was found. Clearly, many soil archaea have strongly defined niches and will only occur in a narrow subset of the range of possible climate and soil conditions. The findings of a mid-elevation diversity maximum on Norikura provides a further instance of how widespread this unexplained pattern is in nature, in a wide variety of groups of organisms.
Applicability of Enhanced-phytoremediation for Arsenic-contaminated Soil
Jeong et al . J. Soil Groundw. Environ. Vol. 21(1), p. 40~48, 2016
Abstract -
A siderophore-producing bacterium (i.e., Pseudomonas aeruginosa) capable of chelating Fe3+ from its mineral form (i.e., iron oxides) was used to enhance As uptake by plants. Since As in soil is mainly associated with iron oxides, siderophore can play an important role in As mobilization through the dissolution of As-bearing iron oxides. A series of pot experiment using Pteris cretica showed that As removal by P. cretica with siderophore-producing bacteria addition increased more than three times compared to that without bacteria addition. Competition between indigenous bacteria and introduced bacteria (i.e., P. aeruginosa) was also observed, but such competition seemed not to be significant. This study suggests that enhanced-phytoremediation by siderophore-producing bacteria addition could be a visible option for longterm As removal in the forest area at the former Janghang smelter site.

Comparison of Gastric Microbiota Between Gastric Juice and Mucosa by Next Generation Sequencing Method
Sung JH et al . J Cancer Prev. 2016 Mar; 21(1): 60–65. Published online 2016 Mar 30. doi: 10.15430/JCP.2016.21.1.60
Abstract -

Background:

Not much is known about the role of gastric microbiota except for Helicobacter pylori in human health and disease. In this study, we aimed to detect human gastric microbiota in both gastric mucosa and gastric juice by barcoded 454-pyrosequencing of the 16S rRNA gene and to compare the results from mucosa and juice.

Methods:

Gastric biopsies and stomach juices were collected from 4 subjects who underwent standard endoscopy at Seoul National University Bundang Hospital. Gastric microbiota of antral mucosa, corpus mucosa samples, and gastric fluids were analyzed by barcoded 454-pyrosequencing of the 16S rRNA gene. The analysis focused on bacteria, such as H. pylori and nitrosating or nitrate-reducing bacteria.

Results:

Gastric fluid samples showed higher diversity compared to that of gastric mucosa samples. The mean of operational taxonomic units was higher in gastric fluid than in gastric mucosa. The samples of gastric fluid and gastric mucosa showed different composition of phyla. The composition of H. pylori and Proteobacteria was higher in mucosa samples compared to gastric fluid samples (H. pylori, 66.5% vs. 3.3%, P = 0.033; Proteobacteria, 75.4% vs. 26.3%, P = 0.041), while ActinobacteriaBacteroidetes, and Firmicutes were proportioned relatively less in mucosa samples than gastric fluid. However there was no significant difference. (Actinobacteria, 3.5% vs. 20.2%, P = 0.312; Bacteroidetes, 6.0% vs. 14.8%, P = 0.329; Firmicutes, 12.8% vs. 33.4%, P = 0.246).

Conclusions:

Even though these samples were small, gastric mucosa could be more effective than gastric fluid in the detection of meaningful gastric microbiota by pyrosequencing.


Dynamic changes in the composition of photosynthetic picoeukaryotes in the northwestern Pacific Ocean revealed by high-throughput tag sequencing of plastid 16S rRNA genes.
Choi DH et al . FEMS Microbiol Ecol. 2016 Feb;92(2). pii: fiv170. doi: 10.1093/femsec/fiv170. Epub 2015 Dec 27.
Abstract -
Photosynthetic picoeukaryotes (PPEs) are major oceanic primary producers. However, the diversity of such communities remains poorly understood, especially in the northwestern (NW) Pacific. We investigated the abundance and diversity of PPEs, and recorded environmental variables, along a transect from the coast to the open Pacific OceanHigh-throughput tag sequencing (using the MiSeq system) revealed the diversity of plastid 16S rRNA genes. The dominant PPEs changed at the class level along the transect. Prymnesiophyceae were the only dominant PPEs in the warm pool of the NW Pacific, but Mamiellophyceae dominated in coastal waters of the East China Sea. Phylogenetically, most Prymnesiophyceae sequences could not be resolved at lower taxonomic levels because no close relatives have been cultured. Within the Mamiellophyceae, the genera Micromonas and Ostreococcus dominated in marginal coastal areas affected by open water, whereas Bathycoccus dominated in the lower euphotic depths of oligotrophic open waters. Cryptophyceae and Phaeocystis (of the Prymnesiophyceae) dominated in areas affected principally by coastal water. We also defined the biogeographical distributions of Chrysophyceae, prasinophytes, Bacillariophyceaea and Pelagophyceae. These distributions were influenced by temperature, salinity and chlorophyll a and nutrient concentrations.

Development and Characterization of PCE-to-Ethene Dechlorinating Microcosms with Contaminated River Sediment.
Lee J et al . J Microbiol Biotechnol. 2016 Jan;26(1):120-9. doi: 10.4014/jmb.1510.10026.
Abstract -
An industrial complex in Wonju, contaminated with trichloroethene (TCE), was one of the most problematic sites in Korea. Despite repeated remedial trials for decades, chlorinated ethenes remained as sources of down-gradient groundwater contamination. Recent efforts were being made to remove the contaminants of the area, but knowledge of the indigenous microbial communities and their dechlorination abilities were unknown. Thus, the objectives of the present study were (i) to evaluate the dechlorination abilities of indigenous microbes at the contaminated site, (ii) to characterize which microbes and reductive dehalogenase genes were responsible for the dechlorination reactions, and (iii) to develop a PCE-to-ethene dechlorinating microbial consortium. An enrichment culture that dechlorinates PCE to ethene was obtained from Wonju stream, nearby a trichloroethene (TCE)-contaminated industrial complex. The community profiling revealed that known organohalide-respiring microbes, such as Geobacter, Desulfuromonas, and Dehalococcoides grew during the incubation with chlorinated ethenes. Although Chloroflexi populations (i.e., Longilinea and Bellilinea) were the most enriched in the sediment microcosms, those were not found in the transfer cultures. Based upon the results from pyrosequencing of 16S rRNA gene amplicons and qPCR using TaqMan chemistry, close relatives of Dehalococcoides mccartyi strains FL2 and GT seemed to be dominant and responsible for the complete detoxification of chlorinated ethenes in the transfer cultures. This study also demonstrated that the contaminated site harbors indigenous microbes that can convert PCE to ethene, and the developed consortium can be an important resource for future bioremediation efforts.
Functional characterization of a chemical defoliant that activates fruit cluster Leaf defoliation in 'Fuji'apple trees
Chang-Hee LeeSang-Hyun SeoO-Jun KwonMan ParkWon-Chan Kim et al . Applied Biological Chemistry October 2016, Volume 59, Issue 5, pp 711–720
Abstract -
The removal of fruit cluster leaves was shown to be a valuable method for controlling fruit quality and producing high-grade apples. A chemical defoliant that functions as an activation switch was shown to turn on the genes necessary for fruit cluster leaf defoliation. Elucidating the mechanism involved in leaf defoliation is crucial to our understanding of the use of chemical defoliants in fruit trees. To gain insight into chemical defoliant-mediated leaf defoliation, we first confirmed the occurrence of ethylene production by applying a chemical defoliant on fruit cluster leaves. Then, we used RNA-seq analysis to obtain a series of transcriptome profiles for genes and proteins involved in leaf senescence induction. Within 2 days of applying the chemical defoliant to apple trees, 1-aminocyclopropane carboxylic acid (ACC) oxidase, ACC synthase, a chlorophyll binding protein, and polygalacturonase-related genes were up-regulated at least sixfold. An in vitro enzyme assay showed that lanolin oil activates ACC synthase activity, a key regulatory enzyme in the ethylene pathway. We also showed that chemical defoliant decreased the light saturation point and total chlorophyll content. Then, we used a polygalacturonase activity assay to confirm the effects of chemical defoliant on leaf senescence in vivo. Furthermore, treatment with chemical defoliant resulted in a significant increase in the chromaticity value of a*, whereas L* and b* decreased in the apple fruit. Taken together, we conclude that chemical defoliant could selectively affect fruit cluster leaves, which suggested that it can be used as a selective defoliant.
Clinical Fusobacterium mortiferum Isolates Cluster with Undifferentiated Clostridium rectumSpecies Based on 16S rRNA Gene Phylogenetic Analysis
Lee Y et al . Ann Clin Lab Sci. 2016 May;46(3):279-81.
Abstract -
The most commonly encountered clinical Fusobacterium species are F. nucleatum and F. necrophorum; other Fusobacteria, such as F. mortiferum and F. varium, have occasionally been isolated from human specimens. Clostridium rectum is a gram-positive species characterized as a straight bacillus with oval sub-terminal spores. The close 16S rRNA gene sequence relationship of C. rectum with the genus Fusobacterium is unexpected given their very different phenotypic characteristics. Between 2014 and 2015, a total of 19 Fusobacterium isolates were recovered from the colonic tissue of 10 patients at a university hospital. All isolates were identified based on 16S rRNA gene sequencing. The phylogenetic relationship among these isolates was estimated using the neighbor-joining method and the Molecular Evolutionary Genetic Analysis (MEGA) version 6. Based on phylogenetic analysis, the F. mortiferum isolates clustered into two groups - F. mortiferum DSM 19809 (group I) and F. mortiferum ATCC 25557 (group II) - even though they are of the same species. Furthermore, the F. mortiferum DSM 19809 (group I) showed a close phylogenetic relationship with C. rectum, even though C. rectum is classified as a gram-positive spore-producing bacillus. C. rectum is clearly unrelated to the genus Clostridium as it shows highest 16S rRNA gene sequence similarity with species from the genus Fusobacterium Therefore, additional methods such as Gram staining and other biochemical methods should be performed for Fusobacterium identification.

Microbial Profiling of a Suppressiveness-Induced Agricultural Soil Amended with Composted Almond Shells.
Vida C et al . Front Microbiol. 2016 Jan 22;7:4. doi: 10.3389/fmicb.2016.00004. eCollection 2016.
Abstract -
This study focused on the microbial profile present in an agricultural soil that becomes suppressive after the application of composted almond shells (AS) as organic amendments. For this purpose, we analyzed the functions and composition of the complex communities present in an experimental orchard of 40-year-old avocado trees, many of them historically amended with composted almond shells. The role of microbes in the suppression of Rosellinia necatrix, the causative agent of avocado white root rot, was determined after heat-treatment and complementation experiments with different types of soil. Bacterial and fungal profiles obtained from natural soil samples based on the 16S rRNA gene and ITS sequencing revealed slight differences among the amended (AS) and unamended (CT) soils. When the soil was under the influence of composted almond shells as organic amendments, an increase in Proteobacteria and Ascomycota groups was observed, as well as a reduction in Acidobacteria and Mortierellales. Complementary to these findings, functional analysis by GeoChip 4.6 confirmed these subtle differences, mainly present in the relative abundance of genes involved in the carbon cycle. Interestingly, a group of specific probes included in the "soil benefit" category was present only in AS-amended soils, corresponding to specific microorganisms previously described as potential biocontrol agents, such as Pseudomonas spp., Burkholderia spp., or Actinobacteria. Considering the results of both analyses, we determined that AS-amendments to the soil led to an increase in some orders of Gammaproteobacteria, Betaproteobacteria, and Dothideomycetes, as well as a reduction in the abundance of Xylariales fungi (where R. necatrix is allocated). The combination of microbial action and substrate properties of suppressiveness are discussed.

Comparison of the oral microbiome of siblings using next‐generation sequencing: a pilot study
H-S Lee et al . Oral Dis. 2016 Sep;22(6):549-56. doi: 10.1111/odi.12491. Epub 2016 May 27.
Abstract -

The purpose of this study was to compare the oral microbiome of siblings with and without dental caries using next-generation sequencing.

MATERIALS AND METHODS:

To investigate the oral microbiome composition, 14 young siblings, seven with caries and seven without, were enrolled from seven sibling-pair families. Supragingival plaque samples were collected from the cervicobuccal area of posterior teeth. All samples were analyzed by pyrosequencing, based on the 16S rRNA gene hypervariable regions, V1-V4.

RESULTS:

The organisms identified belonged to 65 genera. Fifty-two genera were identified in the subjects with caries and 58 in those without; 45 genera were shared by both groups. In the Shannon index, the caries group showed lower bacterial diversity than the caries-free group and the difference was significant (Wilcoxon signed-rank test, P < 0.05). Additionally, similarities between siblings were evident in analyses based on weighted UniFrac distances (P < 0.05).

CONCLUSIONS:

In this study, the diversity of the microbiome was reduced in subjects with dental caries, while similarity between siblings seemed to be retained.


Gut commensal Bacteroides acidifaciensprevents obesity and improves insulin sensitivity in mice
J-Y Yang et al . Mucosal Immunol. 2017 Jan;10(1):104-116. doi: 10.1038/mi.2016.42. Epub 2016 Apr 27.
Abstract -
In humans, the composition of gut commensal bacteria is closely correlated with obesity. The bacteria modulate metabolites and influence host immunity. In this study, we attempted to determine whether there is a direct correlation between specific commensal bacteria and host metabolism. As mice aged, we found significantly reduced body weight and fat mass in Atg7ΔCD11c mice when compared with Atg7f/f mice. When mice shared commensal bacteria by co-housing or feces transfer experiments, body weight and fat mass were similar in both mouse groups. By pyrosequencing analysis, Bacteroides acidifaciens (BA) was significantly increased in feces of Atg7ΔCD11c mice compared with those of control Atg7f/f mice. Wild-type C57BL/6 (B6) mice fed with BA were significantly more likely to gain less weight and fat mass than mice fed with PBS. Of note, the expression level of peroxisome proliferator-activated receptor alpha (PPARα) was consistently increased in the adipose tissues of Atg7ΔCD11c mice, B6 mice transferred with fecal microbiota of Atg7ΔCD11cmice, and BA-fed B6 mice. Furthermore, B6 mice fed with BA showed elevated insulin levels in serum, accompanied by increased serum glucagon-like peptide-1 and decreased intestinal dipeptidyl peptidase-4. These finding suggest that BA may have potential for treatment of metabolic diseases such as diabetes and obesity.

Analysis of single nucleotide polymorphism among Varicella-Zoster Virus and identification of vaccine-specific sites
Jeon JS et al . Virology. 2016 Sep;496:277-86. doi: 10.1016/j.virol.2016.06.017. Epub 2016 Jul 1.
Abstract -
Varicella-zoster virus (VZV) is a causative agent for chickenpox and zoster. Live attenuated vaccines have been developed based on Oka and MAV/06 strains. In order to understand the molecular mechanisms of attenuation, complete genome sequences of vaccine and wild-type strains were compared and single nucleotide polymorphism (SNP) was analyzed. ORF22 and ORF62 contained the highest number of SNPs. The detailed analysis of the SNPs suggested 24 potential vaccine-specific sites. All the mutational events found in vaccine-specific sites were transitional, and most of them were substitution of AT to GC pair. Interestingly, 18 of the vaccine-specific sites of the vaccine strains appeared to be genetically heterogeneous. The probability of a single genome of vaccine strain to contain all 24 vaccine-type sequences was calculated to be less than 4%. The average codon adaptation index (CAI) value of the vaccine strains was significantly lower than the CAI value of the clinical strains.

Biostimulation of metal-resistant microbial consortium to remove zinc from contaminated environments.
Mejias Carpio IE et al . Sci Total Environ. 2016 Apr 15;550:670-5. doi: 10.1016/j.scitotenv.2016.01.149. Epub 2016 Feb 2.
Abstract -
Understanding the diversity and metal removal ability of microorganisms associated to contaminated aquatic environments is essential to develop metal remediation technologies in engineered environments. This study investigates through 16S rRNA deep sequencing the composition of a biostimulated microbial consortium obtained from the polluted Tietê River in São Paulo, Brazil. The bacterial diversity of the biostimulated consortium obtained from the contaminated water and sediment was compared to the original sample. The results of the comparative sequencing analyses showed that the biostimulated consortium and the natural environment had γ-Proteobacteria, Firmicutes, and uncultured bacteria as the major classes of microorganisms. The consortium optimum zinc removal capacity, evaluated in batch experiments, was achieved at pH=5 with equilibrium contact time of 120min, and a higher Zn-biomass affinity (KF=1.81) than most pure cultures previously investigated. Analysis of the functional groups found in the consortium demonstrated that amine, carboxyl, hydroxyl, and phosphate groups present in the consortium cells were responsible for zinc uptake.

Complete genome sequence of Halocynthiibacter arcticus PAMC 20958T from an Arctic marine sediment sample
Lee YM et al . J Biotechnol. 2016 Apr 20;224:12-3. doi: 10.1016/j.jbiotec.2016.03.005. Epub 2016 Mar 4.
Abstract -
Here, we present the first complete genome sequence of the strain PAMC 20958(T) from the genus Halocynthiibacter. Halocynthiibacter arcticus PAMC 20958(T), isolated from a marine sediment of the Arctic, is a gram-negative, aerobic, and rod-shaped bacterium. The complete genome contains 4,329,554 base pairs with 53.21% GC content and a 44,566 base pair plasmid with 48.72% GC content. This genome contained genes encoding alkaline phosphatase and lipase, and genes that confer resistance to arsenic, cadmium, tellurite, and acriflavin.

Repeated Batch-Fed Bioevaporation of Food Waste Using Biofilm-Developed Sponge
Benqin Yang and Deokjin Jahng et al . Drying Technology: An International Journal, Volume 34, Issue 1, 2016. DOI: 10.1080/07373937.2015.1009536
Abstract -
By aerobically cultivating the fragmented sponge in synthetic wastewater containing activated sludge obtained from a wastewater treatment plant (WWTP), biofilm was developed on its surface, and this biofilm-containing sponge was used as a bulking agent and microbial carrier for food waste (FW) bioevaporation. The water of the FW was evaporated by metabolic heat released from the aerobic microbial degradation of the volatile solids (VS) contained in FW. Repeated running of FW bioevaporation for 10 cycles was successful in that 85–96% of the H2O added as FW was removed by consuming 56–71% of the FW VS during the second to tenth cycles. For the first cycle, it was found by microbial community analysis using a pyrosequencing technique that heat production was less than subsequent cycles (second to tenth cycles) because thermophilic microorganisms were not fully developed yet. From the second to tenth cycles, thermophilic bacteria, mostly belonging to the genus Bacillus, accounted for 43–83% of the total population, whereas less than 1% was identified as Bacillusamong microorganisms contained in the FW, fresh biofilm, and the feed (mixture of FW and biofilm-developed sponge). B. thermolactics, B. coagulans, and Pseudoxanthomonas taiwanensis were the major species in the second to tenth cycles of the bioevaporation process. It was also found that the accumulated VS was further degraded by adding water into the bioevaporation reactor. From these results, it was concluded that repeated bioevaporation was possible by using biofilm-developed sponge.

Revealing the combined effects of lactulose and probiotic enterococci on the swine faecal microbiota using 454 pyrosequencing
Chae JP et al . Microb Cell Fact. 2016 Jan 22;15:20. doi: 10.1186/s12934-016-0420-z.
Abstract -

BACKGROUND:

An efficient microbial cell factory requires a microorganism that can utilize a broad range of substrates to economically produce value-added chemicals and fuels. The industrially important bacterium Corynebacteriumglutamicum has been studied to broaden substrate utilizations for lignocellulose-derived sugars. However, C. glutamicum ATCC 13032 is incapable of PTS-dependent utilization of cellobiose because it has missing genes annotated to β-glucosidases (bG) and cellobiose-specific PTS permease.

RESULTS:

We have engineered and evolved a cellobiose-negative and xylose-negative C. glutamicum that utilizescellobiose as sole carbon and co-ferments cellobiose and xylose. NGS-genomic and DNA microarray-transcriptomic analysis revealed the multiple genetic mutations for the evolved cellobiose-utilizing strains. As a result, a consortium of mutated transporters and metabolic and auxiliary proteins was responsible for the efficient cellobiose uptake. Evolved and engineered strains expressing an intracellular bG showed a better rate of growth rate on cellobiose as sole carbon source than did other bG-secreting or bG-displaying C. glutamicum strains under aerobic culture. Our strain was also capable of co-fermenting cellobiose and xylose without a biphasic growth, although additional pentose transporter expression did not enhance the xylose uptake rate. We subsequently assessed the strains for simultaneous saccharification and fermentation of cellulosic substrates derived from Canadian Ponderosa Pine.

CONCLUSIONS:

The combinatorial strategies of metabolic engineering and adaptive evolution enabled to construct C. glutamicum strains that were able to co-ferment cellobiose and xylose. This work could be useful in development of recombinant C. glutamicum strains for efficient lignocellulosic-biomass conversion to produce value-added chemicals and fuels.



Adaptive evolution and metabolic engineering of a cellobiose- and xylose- negative Corynebacterium glutamicum that co-utilizes cellobiose and xylose
Jungseok Lee et al . Microb Cell Fact. 2016 Jan 22;15:20. doi: 10.1186/s12934-016-0420-z.
Abstract -

Abstract

BACKGROUND:

An efficient microbial cell factory requires a microorganism that can utilize a broad range of substrates to economically produce value-added chemicals and fuels. The industrially important bacterium Corynebacteriumglutamicum has been studied to broaden substrate utilizations for lignocellulose-derived sugars. However, C. glutamicum ATCC 13032 is incapable of PTS-dependent utilization of cellobiose because it has missing genes annotated to β-glucosidases (bG) and cellobiose-specific PTS permease.

RESULTS:

We have engineered and evolved a cellobiose-negative and xylose-negative C. glutamicum that utilizescellobiose as sole carbon and co-ferments cellobiose and xylose. NGS-genomic and DNA microarray-transcriptomic analysis revealed the multiple genetic mutations for the evolved cellobiose-utilizing strains. As a result, a consortium of mutated transporters and metabolic and auxiliary proteins was responsible for the efficient cellobiose uptake. Evolved and engineered strains expressing an intracellular bG showed a better rate of growth rate on cellobiose as sole carbon source than did other bG-secreting or bG-displaying C. glutamicum strains under aerobic culture. Our strain was also capable of co-fermenting cellobiose and xylose without a biphasic growth, although additional pentose transporter expression did not enhance the xylose uptake rate. We subsequently assessed the strains for simultaneous saccharification and fermentation of cellulosic substrates derived from Canadian Ponderosa Pine.

CONCLUSIONS:

The combinatorial strategies of metabolic engineering and adaptive evolution enabled to construct C. glutamicum strains that were able to co-ferment cellobiose and xylose. This work could be useful in development of recombinant C. glutamicum strains for efficient lignocellulosic-biomass conversion to produce value-added chemicals and fuels.


Effect of biogeochemical interactions on bioaccessibility of arsenic in soils of a former smelter site in Republic of Korea.
Yang K et al . Environ Geochem Health. 2016 Dec;38(6):1347-1354. Epub 2016 Jan 14.
Abstract -
The total concentration-based regulations for soil remediation do not consider the possible changes in bioaccessibility of remaining arsenic (As) in soils due to biogeochemical interactions after remediation. This study used As-contaminated soil and pore water samples that were collected from the rice paddy and forest/farmland located in the vicinity of a former smelter site in Republic of Korea to elucidate the changes in As bioaccessibility due to biogeochemical interactionsBioaccessibility and chemical forms of As in soils were determined by using an in vitro method and sequential extraction, respectively, and soil microbial community was evaluated. Bioaccessibility of As in the rice paddy soil samples was higher than that in the forest/farmland soil samples. This could be attributed to relatively higher dependence of bioaccessible As in the rice paddy soils on the soil concentration of iron (Fe), aluminum, or manganese, which could lead to greater changes in bioaccessible As via reductive dissolution. The strong linear relationship (R 2 = 0.90, p value ≤0.001) between the pore water As and Fe concentrations, and the greater portion of bacterial species related to reductive dissolution of Fe oxides in the rice paddies can support the higher As bioaccessibility promoted by reductive dissolution. Therefore, it is necessary to consider the potential changes in the bioaccessible As due to biogeochemical interactions in remediation of As-contaminated soils, particularly when soils are likely to be reused under reductive dissolution-promoting conditions (e.g., flooded conditions).
Diversity and homogeneity of oral microbiota in healthy Korean pre-school children using pyrosequencing
Lee SE et al . Acta Odontol Scand. 2016 Jul;74(5):335-6. doi: 10.3109/00016357.2015.1132006. Epub 2016 Jan 12.
Abstract -

Objectives The purpose of this study was designed to identify the oral microbiota in healthy Korean pre-school children using pyrosequencing. Materials and methods Dental plaque samples were obtained form 10 caries-free pre-school children. The samples were analysed using pyrosequencing. Results The pyrosequencing analysis revealed that, at the phylum level, Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Fusobacteria showed high abundance. Also, predominant genera were identified as core microbiome, such as Streptococcus, Neisseria, Capnocytophaga, Haemophilus and Veilonella. Conclusions The diversity and homogeneity was shown in the dental plaque microbiota in healthy Korean pre-school children.


Comparison of bacterial diversity and species composition in three endemic Baikalian sponges
Seo EY et al . Ann. Limnol. - Int. J. Lim. 52 (2016) 27-32
Abstract -
Baikalian sponges are unique organisms with many species harboring symbiotic microbes that produce novel bioactive compounds. To investigate bacterial diversity of three species of Baikalian sponges, specimens of Lubomirskia baicalensisBaikalospongia intermedia and Swartschewskia papyracea collected from Lake Baikal were processed by pyrosequencing. We found differences in the species composition and diversity in bacteria among these sponges. Cyanobacteria accounted for the highest proportion and the second group was Proteobacteria in three sponges. The bacterial communities in B. intermedia and L. baicalensis were highly similar but less similar to the bacterial community associated with S. papyracea. Diversity of the bacterial community in S. papyracea was higher than in L. baicalensis and B. intermedia. In particular, the relative abundance of Actinobacteria was higher in S. papyracea. Bacterial species in phyla Acidobacteria and Gemmatimonadetes were only found in S. papyracea.

Complete genome sequence of Staphylococcus equorum KS1039 isolated from Saeu-jeotgal, Korean high-salt-fermented seafood
Jeong DW et al . J Biotechnol. 2016 Feb 10;219:88-9. doi: 10.1016/j.jbiotec.2015.12.025. Epub 2015 Dec 21.
Abstract -
Staphylococcus equorum KS1039 was isolated from a form of traditional Korean high-salt-fermented seafood called Saeu-jeotgal, and exhibited growth at a NaCl (w/v) concentration of 25%. Comparative genome analyses with two other strains revealed the presence of two potassium voltage-gated channel genes uniquely in KS1039, which might be involved in salt tolerance. This first complete genome sequence of the species will increase our understanding of the genetic factors allowing it to be safely consumed by humans and to inhabit high-salt environments.

Genome Sequence of a Unique t2247-ST692-III Livestock-Associated Methicillin-Resistant Staphylococcus aureus Strain from Chicken Carcass
Moon DC et al . Genome Announc. 2016 Feb 25;4(1). pii: e00026-16. doi: 10.1128/genomeA.00026-16.
Abstract -
We report the draft genome sequence of a novel livestock-associated t2247-ST692-III methicillin-resistant Staphylococcus aureus strain designated K12S0375, which was isolated from a chickencarcass in South Korea. The K12S0375 strain contains uncommon genes, including antimicrobial resistance genes (tetL and tetS) and leukotoxin (lukED), and the genomic distance indicates a single lineage in a genome-based phylogenetic tree compared with 459 S. aureus genome sequences. This genome sequence will contribute to understanding epidemiological and genomic features of the ST692 lineage, including antimicrobial resistance and virulence genes.
Gut microbiota lipopolysaccharide accelerates inflamm-aging in mice
Kim KA et al . BMC Microbiol. 2016 Jan 16;16:9. doi: 10.1186/s12866-016-0625-7.
Abstract -

BACKGROUND:

The constitutive inflammation that characterizes advanced age is termed inflamm-aging. This process is associated with age-related changes to immune homeostasis and gut microbiota. We investigated the relationship between aging and gut microbiota lipopolysaccharide (LPS)-inducible inflammation.

RESULTS:

A taxonomy-based analysis showed that aging resulted in increased prevalence of the phyla Firmicutes and Actinobacteria and a reduced prevalence of Bacteroidetes and Tenericutes, resulting in an increase in the Firmicutes to Bacteroidetes ratio. The levels of plasmatic and fecal lipopolysaccharides were higher in aged mice. Aging induced the expression of p16 and the activation of nuclear factor-kappa B (NF-κB) in the colon of aged mice. Interestingly, the expression level of sterile α-motif domain- and HD domain-containing protein 1 (SAMHD1) in the colon was higher in aged mice than in young mice, while cyclin-dependent kinase-2 and cyclin E levels were lower in aged mice than in young mice. The lipopolysaccharide fraction of fecal lysates (LFL) from young or aged mice increased p16 and SAMHD1 expression and NF-κB activation in peritoneal macrophages from wild-type mice, in a TLR4-dependent manner. However, LFLs did not induce NF-κB activation and SAMHD1 expression in peritoneal macrophages from TLR4-deificent mice, whereas they significantly induced p16 expression. Nevertheless, p16 expression was induced more potently in macrophages from WT mice than in macrophages from TLR4-deficient mice.

CONCLUSION:

Aging increased p16 and SAMHD1 expression, gut microbiota LPS production, and NF-κB activation; thereby, signifying that gut microbiota LPS may accelerate inflamm-aging and SAMHD1 may be an inflamm-aging marker.


Analysis of bacterial community profiles of endodontically infected primary teeth using pyrosequencing
Yun KH et al . Int J Paediatr Dent. 2017 Jan;27(1):56-65. doi: 10.1111/ipd.12226. Epub 2016 Feb 12.
Abstract -

OBJECTIVE:

The purpose of this study was to identify the endodontic microbiome in primary teeth with dental caries using high-throughput pyrosequencing and to establish data on the oral microbiome of primary teeth with endodontic infection.

METHODS:

Ten primary teeth with dental caries and endodontic infection were included. Samples were collected from root canals using sterilized paper points and analyzed by pyrosequencing, based on the V1-V3 hypervariable region of the 16S rRNA gene. The data were analyzed using the CLcommunity software.

RESULTS:

Analysis of the 10 samples yielded a total of 64,291 16S rRNA gene sequences. In total, 1586 OTUs (range, 91-235), six bacterial phyla, including unclassified, and 187 genera were assigned. At the genus level, Neisseria (group A), Acinetobacter (group B), and Fusobacterium (group C) were prominent. These predominant microorganisms were associated with the clinical condition and reflected the progression of endodontic infection in primary teeth.

CONCLUSIONS:

This study revealed a relationship between the oral microbiome and endodontic infection in primary teeth. Additionally, anaerobic bacteria such as Fusobacterium species were dominant in the teeth with apical abscesses.


Diversity of Bacterial Communities on Four Frequently Used Surfaces in a Large Brazilian Teaching Hospital
Tairacan Augusto Pereira da Fonseca et al . Int J Environ Res Public Health. 2016 Feb; 13(2): 152. Published online 2016 Jan 22. doi: 10.3390/ijerph13020152
Abstract -
Frequently used hand-touch surfaces in hospital settings have been implicated as a vehicle of microbial transmission. In this study, we aimed to investigate the overall bacterial population on four frequently used surfaces using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Surface samples were collected from four sites, namely elevator buttons (EB), bank machine keyboard buttons (BMKB), restroom surfaces, and the employee biometric time clock system (EBTCS), in a large public and teaching hospital in São Paulo. Taxonomical composition revealed the abundance of Firmicutes phyla, followed by Actinobacteria and Proteobacteria, with a total of 926 bacterial families and 2832 bacterial genera. Moreover, our analysis revealed the presence of some potential pathogenic bacterial genera, including Salmonella entericaKlebsiella pneumoniae, and Staphylococcus aureus. The presence of these pathogens in frequently used surfaces enhances the risk of exposure to any susceptible individuals. Some of the factors that may contribute to the richness of bacterial diversity on these surfaces are poor personal hygiene and ineffective routine schedules of cleaning, sanitizing, and disinfecting. Strict standards of infection control in hospitals and increased public education about hand hygiene are recommended to decrease the risk of transmission in hospitals among patients.

Analysis of Gastric Microbiota by Pyrosequencing: Minor Role of Bacteria Other Than Helicobacter pylori in the Gastric Carcinogenesis
Jo HJ et al . Helicobacter. 2016 Oct;21(5):364-74. doi: 10.1111/hel.12293. Epub 2016 Feb 24.
Abstract -

BACKGROUND:

Little is known about the role of gastric microbiota except for Helicobacter pylori (HP) in human health and disease. We compared the differences of human gastric microbiota according to gastric cancer or control and HP infection status and assessed the role of bacteria other than HP.

METHODS:

Gastric microbiota of 63 antral mucosal and 18 corpus mucosal samples were analyzed by bar-coded 454 pyrosequencing of the 16S rRNA gene. Antral samples were divided into four subgroups based on HP positivity in pyrosequencing and the presence of cancer. The analysis was focused on bacteria other than HP, especially nitrosating or nitrate-reducing bacteria (NB). The changes of NB in antral mucosa of 16 subjects were followed up.

RESULTS:

The number of NB other than HP (non-HP-NB) was two times higher in the cancer groups than in the control groups, but it did not reach statistical significance. The number of non-HP-NB tends to increase over time, but this phenomenon was prevented by HP eradication in the HP-positive control group, but not in the HP-positive cancer group.

CONCLUSION:

We could not find the significant role of bacteria other than HP in the gastriccarcinogenesis.


Evaluation of the fate and transport of chlorinated ethenes in a complex groundwater system discharging to a stream in Wonju, Korea
Lee SS et al . J Contam Hydrol. 2015 Nov;182:231-43. doi: 10.1016/j.jconhyd.2015.09.005. Epub 2015 Sep 13.
Abstract -
Chlorinated ethenes such as trichloroethylene (TCE) are common and persistent groundwater contaminants. If contaminated groundwater discharges to a stream, then stream water pollution near the contamination site also becomes a problem. In this respect, the fate and transport of chlorinated ethenes around a stream in an industrial complex were evaluated using the concentration of each component, and hydrogeochemical, microbial, and compound-specific carbon isotope data. Temporal and spatial monitoring reveal that a TCE plume originating from main and local source zones continues to be discharged to a stream. Groundwater geochemical data indicate that aerobic conditions prevail in the upgradient area of the studied aquifer, whereas conditions become anaerobic in the downgradient. The TCE molar fraction is high at the main and local source zones, ranging from 87.4 to 99.2% of the total volatile organic compounds (VOCs). An increasing trend in the molar fraction of cis-1, 2-Dichloroethene (cis-DCE) and vinyl chloride (VC) was observed in the downgradient zone of the study area. The enriched δ(13)C values of TCE and depleted values of cis-DCE in the stream zone, compared to those of the source zone, also suggest biodegradation of VOCs. Microbial community structures in monitoring wells adjacent to the stream zone in the downgradient area were analyzed using 16S rRNA gene-based pyrosequencing to identify the microorganisms responsible for biodegradation. This was attributed to the high relative abundance of dechlorinating bacteria in monitoring wells under anaerobic conditions farthest from the stream in the downgradient area. The multilateral approaches adopted in this study, combining hydrogeochemical and biomolecular methods with compound-specific analyses, indicate that contaminants around the stream were naturally attenuated by active anaerobic biotransformation processes.
Effect of Dietary Protein Levels on Composition of Odorous Compounds and Bacterial Ecology in Pig Manure
Cho S et al . Asian-Australas J Anim Sci. 2015 Sep;28(9):1362-70. doi: 10.5713/ajas.15.0078.
Abstract -
This study was performed to investigate the effect of different levels of dietary crude protein (CP) on composition of odorous compounds and bacterial communities in pig manure. A total of 48 male pigs (average initial body weight 45 kg) fed diets containing three levels of dietary CP (20%, 17.5%, and 15%) and their slurry samples were collected from the pits under the floor every week for one month. Changes in composition of odorous compounds and bacterial communities were analyzed by gas chromatography and 454 FLX titanium pyrosequencing systems, respectively. Levels of phenols, indoles, short chain fatty acid and branched chain fatty acid were lowest (p<0.05) in CP 15% group among three CP levels. Relative abundance of Bacteroidetes phylum and bacterial genera including Leuconostoc, Bacillus, Atopostipes, Peptonphilus, Ruminococcaceae_uc, Bacteroides, and Pseudomonas was lower (p<0.05) in CP 15% than in CP 20% group. There was a positive correlation (p<0.05) between odorous compounds and bacterial genera: phenol, indole, iso-butyric acid, and iso-valeric acid with Atopostipes, p-cresol and skatole with Bacteroides, acetic acid and butyric acid with AM982595_g of Porphyromonadaceae family, and propionic acid with Tissierella. Taken together, administration of 15% CP showed less production of odorous compounds than 20% CP group and this result might be associated with the changes in bacterial communities especially whose roles in protein metabolism.

(p)ppGpp, a Small Nucleotide Regulator, Directs the Metabolic Fate of Glucose in Vibrio cholerae
Oh YT et al . J Biol Chem. 2015 May 22;290(21):13178-90. doi: 10.1074/jbc.M115.640466. Epub 2015 Apr 16.
Abstract -
When V. cholerae encounters nutritional stress, it activates (p)ppGpp-mediated stringent response. The genes relA and relV are involved in the production of (p)ppGpp, whereas the spoT gene encodes an enzyme that hydrolyzes it. Herein, we show that the bacterial capability to produce (p)ppGpp plays an essential role in glucose metabolism. The V. cholerae mutants defective in (p)ppGpp production (i.e. ΔrelAΔrelV and ΔrelAΔrelVΔspoT mutants) lost their viability because of uncontrolled production of organic acids, when grown with extra glucose. In contrast, the ΔrelAΔspoT mutant, a (p)ppGpp overproducer strain, exhibited better growth in the presence of the same glucose concentration. An RNA sequencing analysis demonstrated that transcriptions of genes consisting of an operon for acetoin biosynthesis were markedly elevated in N16961, a seventh pandemic O1 strain, but not in its (p)ppGpp(0) mutant during glucose-stimulated growth. Transposon insertion in acetoin biosynthesis gene cluster resulted in glucose-induced loss of viability of the ΔrelAΔspoT mutant, further suggesting the crucial role of acetoin production in balanced growth under glucose-rich environments. Additional deletion of the aphA gene, encoding a negative regulator for acetoin production, failed to rescue the (p)ppGpp(0) mutant from the defective glucose-mediated growth, suggesting that (p)ppGpp-mediated acetoin production occurs independent of the presence of AphA. Overall, our results reveal that (p)ppGpp, in addition to its well known role as a stringent response mediator, positively regulates acetoin production that contributes to the successful glucose metabolism and consequently the proliferation of V. cholerae cells under a glucose-rich environment, a condition that may mimic the human intestine.
Biochemical and structural characterization of a keratin-degrading M32 carboxypeptidase from Fervidobacterium islandicumAW-1
Lee YJ et al . Biochem Biophys Res Commun. 2015 Dec 25;468(4):927-33. doi: 10.1016/j.bbrc.2015.11.058. Epub 2015 Nov 19.
Abstract -
Comparative genomics of the keratin-degrading extremophilic eubacterium Fervidobacterium islandicum AW-1 and the closely related Fervidobacterium nodosum with no keratinolytic activity suggested that the FIAW1_1600 gene encoding a carboxypeptidase (CP) plays an important role in keratin degradation. The presumptive 489 amino acid sequence of the gene showed a conserved HEXXH motif with low levels of sequence identity (<38%) to reported thermostable M32 CPs. To identify its functional role, the FIAW1_1600 gene was overexpressed in Escherichia coli, and the recombinant enzyme was purified and characterized in detail. F. islandicum AW-1 CP (FisCP) formed a homodimer with a molecular mass of 107 kDa, and its apoenzyme exhibited maximal activity at 80 °C and pH 7.0 in the presence of Co(2+). This metalloenzyme mainly cleaved the C-termini of peptides with a basic amino acid sequence. The crystal structure of FisCP at 2.2 Å resolution showed high levels of structural similarities (root-mean-square deviations of <1.7 Å) to those of other M32 CP homologs. Remarkably, the enzyme significantly enhanced the degradation of native chicken feathers. This study suggests that FisCP, a keratinolytic member of the thermostable M32 CP family, plays an important role in keratin degradation for cellular metabolism in F. islandicum AW-1.
Bacterial core community in soybean rhizosphere
Youngmi Lee et al . Korean Journal of Microbiology (2015) Vol. 51, No. 4, pp. 347-354.
Abstract -
Soybean is well known to be originated from Korea and far-east Asian countries, and studies of many root nodule bacteria associated with soybean have mainly-focused on nitrogen fixation, but much less study was carried out on bacterial community in the rhizosphere of soybean. In this study, we analyzed the bacterial community in rhizosphere of Korean soybean, Daepungkong using the pyrosequencing method based on the 16S rRNA gene to characterize the change of the rhizosphere community structure according to the growth stages of soybeans and to elucidate bacterial core community in rhizosphere of soybean. Our results revealed that bacterial community of rhizosphere soil differed from that of bulk soil and was composed of a total of 21 bacterial phyla. The predominant phylum in the rhizosphere of soybean was Proteobacteria (36.6–42.5%) and followed by Acidobacteria (8.6–9.4%), Bacteroidetes (6.1–10.9%), Actinobacteria (6.4–9.8%), and Firmicutes (5.7–6.3%). The bacterial core community in soybean rhizosphere was mainly composed of the operational taxonomic units (OTUs) belonging to the phylum Proteobacteria throughout all growth stages. The OTU00006 belonged to the genus Bradyrhizobium had the highest abundance and Steroidobacter, Streptomyces, Devosia were followed. These results show that bacterial core community in soybean rhizosphere was mainly composed of OTUs associated with plant growth promotion and nutrient cycles

RNA helicase HEL-1 promotes longevity by specifically activating DAF-16/FOXO transcription factor signaling in Caenorhabditis elegans
Seo M et al . Proc Natl Acad Sci U S A. 2015 Aug 4;112(31):E4246-55. doi: 10.1073/pnas.1505451112. Epub 2015 Jul 20.
Abstract -
The homeostatic maintenance of the genomic DNA is crucial for regulating aging processes. However, the role of RNA homeostasis in aging processes remains unknown. RNA helicases are a large family of enzymes that regulate the biogenesis and homeostasis of RNA. However, the functional significance of RNA helicases in aging has not been explored. Here, we report that a large fraction of RNA helicases regulate the lifespan of Caenorhabditis elegans. In particular, we show that a DEAD-box RNA helicase, helicase 1 (HEL-1), promotes longevity by specifically activating the DAF-16/forkhead box O (FOXO) transcription factor signaling pathway. We find that HEL-1 is required for the longevity conferred by reduced insulin/insulin-like growth factor 1 (IGF-1) signaling (IIS) and is sufficient for extending lifespan. We further show that the expression of HEL-1 in the intestine and neurons contributes to longevity. HEL-1 enhances the induction of a large fraction of DAF-16 target genes. Thus, the RNA helicase HEL-1 appears to promote longevity in response to decreased IIS as a transcription coregulator of DAF-16. Because HEL-1 and IIS are evolutionarily well conserved, a similar mechanism for longevity regulation via an RNA helicase-dependent regulation of FOXO signaling may operate in mammals, including humans.

Assessment of bacterial community structure in nitrifying biofilm under inorganic carbon-sufficient and -limited conditions
Bae H et al . Journal of Environmental Science and Health, Part A Toxic/Hazardous Substances and Environmental Engineering Volume 50, 2015 - Issue 2
Abstract -
In this work, nitrification and changes in the composition of the total bacterial community under inorganic carbon (IC)-limited conditions, in a nitrifying moving bed biofilm reactor, was investigated. A culture-independent analysis of cloning and sequencing based on the 16S rRNA gene was applied to quantify the bacterial diversity and to determine bacterial taxonomic assignment. IC concentrations had significant effects on the stability of ammonia-oxidation as indicated by the reduction of the nitrogen conversion rate with high NH4+-N loadings. The predominance of Nitrosomonas europaea was maintained in spite of changes in the IC concentration. In contrast, heterotrophic bacterial species contributed to a high bacterial diversity, and to a dynamic shift in the bacterial community structure, under IC-limited conditions. In this study, individual functions of heterotrophic bacteria were estimated based on taxonomic information. Possible key roles of coexisting heterotrophic bacteria are the assimilation of organic compounds of extracellular polymeric substances produced by nitrifiers, and biofilm formation by providing a filamentous structure and aggregation properties.

Optimization of biostimulant for bioremediation of contaminated coastal sediment by response surface methodology (RSM) and evaluation of microbial diversity by pyrosequencing
Subha B et al . Mar Pollut Bull. 2015 Sep 15;98(1-2):235-46. doi: 10.1016/j.marpolbul.2015.06.042. Epub 2015 Jun 29.
Abstract -
The present study aims to optimize the slow release biostimulant ball (BSB) for bioremediation of contaminated coastal sediment using response surface methodology (RSM). Different bacterial communities were evaluated using a pyrosequencing-based approach in contaminated coastal sediments. The effects of BSB size (1-5cm), distance (1-10cm) and time (1-4months) on changes in chemical oxygen demand (COD) and volatile solid (VS) reduction were determined. Maximum reductions of COD and VS, 89.7% and 78.8%, respectively, were observed at a 3cm ball size, 5.5cm distance and 4months; these values are the optimum conditions for effective treatment of contaminated coastal sediment. Most of the variance in COD and VS (0.9291 and 0.9369, respectively) was explained in our chosen models. BSB is a promising method for COD and VS reduction and enhancement of SRB diversity.
Eco-friendly remediation and reuse for coastal dredged materials using a bioaugmentation technology
Kim et al . Korean Journal of Microbiology (2015) Vol. 51, No. 4, pp. 374-381.
Abstract -
Occurrences of coastal dredged materials are ever increasing due to port construction, navigational course maintenance and dredging of polluted coastal sediments. Ocean dumping of the coastal dredged materials has become virtually prohibited as London Treaty will be enacted as of the year 2012. It will be necessary to treat and recycle the dredged materials that may carry organic pollutants and heavy metals in a reasonable and effective process: collection of the dredged materials, liquid and solid separation, and treatment of organic compounds and heavy metals. In this study we have developed a continuous bioreactor system that can treat a mixture of silt and particulate organic matter using a microbial consortium (BM-S-1). The steady-state operation conditions were: pH (7.4-7.5), temperature (), DO (7.5-7.9), and salt concentration (3.4-3.7%). The treatment efficiencies of SCOD, T-N and T-P of the mixture were 95-96%, 92-99%, and 79-97%. The system was also effective in removal of heavy metals such as Zn, Ni, and Cr. Levels of MLSS during three months operation period were 11,000-19,000 mg/L. Interestingly, there was little sludge generated during this period of operation. The augmented microbial consortium seemed to be quite active in the removal of the organic component (30%) present in the dredged material in association with indigenous bacteria. The dominant phyla in the treatment processes were Proteobacteria and Bacteroidetes while dominant genii were Marinobacterium, Flaviramulus, Formosa, Alteromonadaceae_uc, Flavobacteriaceae_uc. These results will contribute to a development of a successful bioremediation technology for various coastal and river sediments with a high content of organic matter, inorganic nutrients and heavy metals, leading to a successful reuse of the polluted dredged sediments.

Comparative Genomic Analysis of Pseudomonas chlororaphisPCL1606 Reveals New Insight into antifungal Compounds Involved in Biocontrol
Calderón CE et al . Mol Plant Microbe Interact. 2015 Mar;28(3):249-60. doi: 10.1094/MPMI-10-14-0326-FI.
Abstract -
Pseudomonas chlororaphis PCL1606 is a rhizobacterium that has biocontrol activity against many soilborne phytopathogenic fungi. The whole genome sequence of this strain was obtained using the Illumina Hiseq 2000 sequencing platform and was assembled using SOAP denovo software. The resulting 6.66-Mb complete sequence of the PCL1606 genome was further analyzed. A comparative genomic analysis using 10 plant-associated strains within the fluorescent Pseudomonas group, including the complete genome of P. chlororaphis PCL1606, revealed a diverse spectrum of traits involved in multitrophic interactions with plants and microbes as well as biological control. Phylogenetic analysis of these strains using eight housekeeping genes clearly placed strain PCL1606 into the P. chlororaphis group. The genome sequence of P. chlororaphis PCL1606 revealed the presence of sequences that were homologous to biosynthetic genes for the antifungal compounds 2-hexyl, 5-propyl resorcinol (HPR), hydrogen cyanide, and pyrrolnitrin; this is the first report of pyrrolnitrin encoding genes in this P. chlororaphis strain. Single-, double-, and triple-insertional mutants in the biosynthetic genes of each antifungal compound were used to test their roles in the production of these antifungal compounds and in antagonism and biocontrol of two fungal pathogens. The results confirmed the function of HPR in the antagonistic phenotype and in the biocontrol activity of P. chlororaphis PCL1606.
Eco-friendly remediation and odor control of a contaminated urban stream using beneficial microorganisms
Chang et al . Korean Journal of Microbiology (2015) Vol. 51, No. 4, pp. 389-397.
Abstract -
Dongchun, one of the representative streams in urban area, is a downstream that is connected to Hogyechun, Bujeonchun, Jeonpochun, Danggamchun, and Gayachun as its upstream. Hogyechun has been mostly covered with concrete structures for decades, causing sewage pollution from the upstream, overflow of the downstream region and other serious pollution that gave rise to many civil complaints from the residents nearby. In this study, we analyzed 3 stations, including control station for water quality and malodor changes of Hogyechun after applying the microbial augmentation (BM-2) for a few months including the rainy season. Amounts (g/h) of DO in the middle site (Middle) and the downstream site (Borim) increased by 1.7 times compared with the upstream site (Chuhae) after augmentation for about 2 months. Amounts (g/h) of COD and NO₃ N decreased by 2 and 1.7 times, respectively, in the middle and downstream sites while SS increased by 7.5 and 22 times in the middle and downstream sites, respectively. Moreover, odor removal efficiencies at the middle and downstream sites were 65% and 19%, respectively, indicating the microbial activity in reduction of malodor in the polluted stream. The dominant microbial species of the sampling sites were Hydrogenophaga caeni, Sphaerotilus natans, Acidovorax radicis, Acidovorax delafieldii, and Cloacibacterium rupense. Densities of the two species Sphaerotilus natans and Acidovorax delafieldii were significantly increased in the middle site after augmentation which possessed potential odor removal and denitrification activity, respectively. Potential pathogens (e.g., Arcobacter cryaerophilus) were also removed from the middle site after the implementation.

Science Walden: new horizons of combined ecological sanitation with separated urine/feces and treatment wetlands
Jongkwan Park et al . Desalination and Water Treatment, 54:4-5, 1353-1360. DOI: 10.1080/19443994.2014.903528
Abstract -
A new engineering concept, designed with separated urine/feces and graywater recovery, was proposed, and the first steps in taking this concept from the planning stage to implementation have been taken using pilot experiments within a small village. The village employs ecological toilet, equipped with 24 h ventilation, and constructed treatment wetlands consisting of both vertical and horizontal subsurface wetlands for graywater recovery. The quality of recovered graywater was similar to that of the water found in the adjacent stream, which is a concept of zero discharge system with graywater. Separated urine, in either fresh or stored form, was diluted with collected rainwater and with reused water without any detergent from a sink, to be supplied to vegetable garden as fertilizer. Separated dried feces were composted in the garden for approximately 3 months and then used as fertilizer. Dried and composted feces, together with stored urine, were characterized in terms of microbial community using pyrosequencing, to identify the presence of any potential pathogens, in order to confirm the system provides safe hygiene. Hypothesized idea of a micro-algae farm within the village might be proposed with separated urine serving as nutrients for algae that could in turn be cultivated as biofuel (diesel) produced from extracted lipids of algae. Through this pilot village test, we have taken a great stride towards practical realization of experimental concepts, in the form of this new urban water management model with ecological sanitation.
Analysis of Soil Properties and Microbial Communities for Mine Soil Vegetation
Park et al . Journal of Soil and Groundwater Environment. 2015. Jun, 20(3): 83-91
Abstract -
Mine soil contamination by high levels of metal ions that prevents the successful vegetation poses a serious problem. In the study presented here, we used the microbial biocatalyst of urease producing bacteriumSporosarcina pasteurii or plant extract based BioNeutro-GEM (BNG) agent. The ability of the biocatalysts to bioremediate contaminated soil from abandoned mine was examined by solid-state composting vegetation under field conditions. Treatment of mine soil with the 2 biocatalysts for 5 months resulted in pH increase and electric conductivity reduction compared to untreated control. Further analyses revealed that the microbial catalysts also promoted the root and shoot growth to the untreated control during the vegetation treatments. After the Sporosarcina pasteurii or plant extract based BNG treatment, the microbial community change was monitored by culture-independent pyrosequencing. These results demonstrate that the microbial biocatalysts could potentially be used in the soil bioremediation from mine-impacted area.

The Effect of Probiotics on Gut Microbiota during the Helicobacter pylori Eradication: Randomized Controlled Trial
Oh B et al . Helicobacter. 2016 Jun;21(3):165-74. doi: 10.1111/hel.12270. Epub 2015 Sep 23.
Abstract -

BACKGROUND:

Helicobacter pylori causes chronic gastritis, gastroduodenal ulcers, and gastric cancer, and has been treated with two antibiotics (amoxicillin and clarithromycin) and proton-pump inhibitors (PPIs). However, antibiotic treatment alters the indigenous gut microbiota to cause side effects. Therefore, the effects of probiotic supplementation on therapy have been studied. Although several studies have covered the probiotics' effects, details about the gut microbiota changes after H. pylori eradication have not been evaluated. Therefore, we analyzed the influences of antibiotics and their combination with probiotics on the composition of the gut microbiota using high-throughput sequencing.

METHODS:

Subjects were divided into two groups. The antibiotics group was treated with general therapy, and the probiotics group with general therapy and probiotic supplementation. Fecal samples were collected from all subjects during treatments, and the influences on gut microbiota were analyzed by 16S rRNA gene-pyrosequencing.

RESULTS:

Three phyla, Firmicutes, Bacteroidetes, and Proteobacteria, were predominant in the gut microbiota of all subjects. After treatment, the relative abundances of Firmicutes were reduced, whereas those of Proteobacteria were increased in both groups. However, the changed proportions of the gut microbiota in the antibiotics group were higher than those in the probiotics group. In addition, the increase in the levels of antibiotic-resistant bacteria was higher in the antibiotics group than in the probiotics one.

CONCLUSION:

Probiotic supplementation can reduce the antibiotic-induced alteration and imbalance of the gut microbiota composition. This effect may restrict the growth of antibiotic-resistant bacteria in the gut and improve the H. pylori eradication success rate.

Analysis of Rhizosphere Soil Bacterial Communities on Seonginbong, Ulleungdo Island
YJ Nam et al . Journal of Life Science. 2015. Mar, 25(3): 323-328 DOI : http://dx.doi.org/10.5352/JLS.2015.25.3.323
Abstract -
The study of microbial diversity and richness in soil samples from a volcanic island named Ulleungdo, located east of South Korea. The soil bacterial communities on the Ulleungdo were analyzed using pyrosequencing method based on 16S rRNA gene. There were 1,613 operational taxonomic units (OUT) form soil sample. From results of a BLASTN search against the EzTaxon-e database, the validated reads (obtained after sequence preprocessing) were almost all classified at the phylum level. Proteobacteria was the most dominant phylum with 48.28%, followed by acidobacteria (26.30%), actionbacteria (6.89%), Chloroflexi (4.58), Planctomycetes (4.56%), Nitrospirae (1.83%), Bacteroidetes (1.51%), Verrucomicrobia (1.48%), and Gemmatimonadetes (1.11%). α-proteobacteria was the most dominant class with 36.07% followed by Acidobacteria_c (10.65%), Solibacteres (10.64%), δ-proteobacteria (4.42%), γ-proteobacteria (4.29%), Planctomycetacia (4.16%), Actinobacteria_c (4.00%), Betaproteobacteria (3.50%), EU686603_c (2.97%), Ktedonobacteria (2.91%), Acidimicrobiia (1.32%), Verrucomicrobiae (1.27%), Gemmatimonadetes_c (1.11%), Sphingobacteria (1.09%), and GU444092_c (1.06%). Bradyrhizobiaceae was the most dominant family with 22.83% followed by Acidobacteriaceae (10.62%), EU445199_f (5.72%), Planctomycetaceae (4.03%), Solibacteraceae (3.63%), FM209092_f (3.58%), Steroidobacter_f (2.81%), EU686603_f (2.73%), Hyphomicrobiaceae (2.33%), Ktedonobacteraceae (1.75%), AF498716_f (1.46%), Rhizomicrobium_f (1.03%), and Mycobacteriaceae (1.01%). Differences in the diversity of bacterial communities have more to do with geography than the impact on environmental factors and also the type of vegetation seems to affect the diversity of bacterial communities.

Microbial profiling of a suppressiveness-induced agricultural soil amended with composted almond shells lead to isolation of new biocontrol agents
Carmen Vida et al . Front Microbiol. 2016; 7: 4. Published online 2016 Jan 22. doi: 10.3389/fmicb.2016.00004
Abstract -
This study focused on the microbial profile present in an agricultural soil that becomes suppressive after the application of composted almond shells (AS) as organic amendments. For this purpose, we analyzed the functions and composition of the complex communities present in an experimental orchard of 40-year-old avocado trees, many of them historically amended with composted almond shells. The role of microbes in the suppression of Rosellinia necatrix, the causative agent of avocado white root rot, was determined after heat-treatment and complementation experiments with different types of soil. Bacterial and fungal profiles obtained from natural soil samples based on the 16S rRNA gene and ITS sequencing revealed slight differences among the amended (AS) and unamended (CT) soils. When the soil was under the influence of composted almond shells as organic amendments, an increase in Proteobacteria and Ascomycota groups was observed, as well as a reduction in Acidobacteria and Mortierellales. Complementary to these findings, functional analysis by GeoChip 4.6 confirmed these subtle differences, mainly present in the relative abundance of genes involved in the carbon cycle. Interestingly, a group of specific probes included in the “soil benefit” category was present only in AS-amended soils, corresponding to specific microorganisms previously described as potential biocontrol agents, such as Pseudomonas spp., Burkholderia spp., or Actinobacteria. Considering the results of both analyses, we determined that AS-amendments to the soil led to an increase in some orders of Gammaproteobacteria, Betaproteobacteria, and Dothideomycetes, as well as a reduction in the abundance of Xylariales fungi (where R. necatrix is allocated). The combination of microbial action and substrate properties of suppressiveness are discussed.

Changes in human gut microbiota influenced by probiotic fermented milk ingestion
Unno T et al . J Dairy Sci. 2015 Jun;98(6):3568-76. doi: 10.3168/jds.2014-8943. Epub 2015 Apr 8.
Abstract -
We investigated the effect of consuming probiotic fermented milk (PFM) on the microbial community structure in the human intestinal tract by using high-throughput barcoded pyrosequencing. Six healthy adults ingested 2 servings of PFM daily for 3 wk, and their fecal microbiota were analyzed before and after 3 wk of PFM ingestion period and for another 3 wk following the termination of PFM ingestion (the noningestion period). Fecal microbial communities were characterized by sequencing of the V1-V3 hypervariable regions of the 16S rRNA gene. All subjects showed a similar pattern of microbiota at the phylum level, where the relative abundance of Bacteriodetes species increased during the PFM ingestion period and decreased during the noningestion period. The increase in Bacteroidetes was found to be due to an increase in members of the families Bacteroidaceae or Prevotellaceae. In contrast to PFM-induced adaptation at the phylum level, the taxonomic composition at the genus level showed a considerable alteration in fecal microbiota induced by PFM ingestion. As revealed by analysis of operational taxonomic units (OTU), the numbers of shared OTU were low among the 3 different treatments (before, during, and after PFM ingestion), but the abundance of the shared OTU was relatively high, indicating that the majority (>77.8%) of total microbiota was maintained by shared OTU during PFM ingestion and after its termination. Our results suggest that PFM consumption could alter microbial community structure in the gastrointestinal tract of adult humans while maintaining the stability of microbiota.

Analysis of the Microbial Community in an Acidic Hollow-Fiber Membrane Biofilm Reactor (Hf-MBfR) Used for the Biological Conversion of Carbon Dioxide to Methane
Hyun Chul Shin et al . PLoS One. 2015; 10(12): e0144999.
Abstract -
Hydrogenotrophic methanogens can use gaseous substrates, such as H2 and CO2, in CH4 production. H2 gas is used to reduce CO2. We have successfully operated a hollow-fiber membrane biofilm reactor (Hf-MBfR) for stable and continuous CH4 production from CO2 and H2. CO2 and H2 were diffused into the culture medium through the membrane without bubble formation in the Hf-MBfR, which was operated at pH 4.5–5.5 over 70 days. Focusing on the presence of hydrogenotrophic methanogens, we analyzed the structure of the microbial community in the reactor. Denaturing gradient gel electrophoresis (DGGE) was conducted with bacterial and archaeal 16S rDNA primers. Real-time qPCR was used to track changes in the community composition of methanogens over the course of operation. Finally, the microbial community and its diversity at the time of maximum CH4 production were analyzed by pyrosequencing methods. Genus Methanobacterium, related to hydrogenotrophic methanogens, dominated the microbial community, but acetate consumption by bacteria, such as unclassified Clostridium sp., restricted the development of acetoclastic methanogens in the acidic CH4 production process. The results show that acidic operation of a CH4production reactor without any pH adjustment inhibited acetogenic growth and enriched the hydrogenotrophic methanogens, decreasing the growth of acetoclastic methanogens.
Characteristics and functional analysis of Bacillus strains from the fermented soybean products, Cheonggukjang
Moon et al . Korean Journal of Microbiology (2015) Vol. 51, No. 3, pp. 300-307.
Abstract -
For selecting Bacillus strains producing high-quality Cheonggukjang, 8 strains were isolated from the different Cheonggukjang samples. Seven of them exhibited the highest 16S rRNA gene sequence similarity value of over 99.9% to Bacillus subtilis subsp. subtilis and one of them showed the similarity to B. licheniformis. All the strains showed positive activities for amylase, cellulase, protease and lipase, and 6 strains are positive for fibrinolytic activity. To confirm the safety of the strains isolated from the samples of Cheonggukjang which are manufactured by traditional method, strains were analyzed for the presence of seven toxin genes of Bacillus cereus and results were found negative. And 7 strains did not produce at all or merely produce both histamine and tyramine, the representative biogenic amines. Biogenic amine degradation analysis by HPLC revealed that, most of them exhibited tyramine degradation activity. For Cheonggukjang fermented by artificial inoculation of selected strains, fermentation property, sensory test, volatile basic nitrogen production and metabolic profiles by  were tested. Seven strains were confirmed to make high-quality Cheonggukjang.

Diversity and Identification of Halophilic Bacteria by Pyrosequencing in a Solar Salterns of Jeungdo
Park SH et al . Korean Journal of Nature Conservation, 9(2), 149-156.
Abstract -
This research is on the halophilic bacteria inhibiting in solar salterns. It was conducted by measuring the composition of cultivating ground in each step of salt production and targeting solar salterns during 2012 and 2013 in Jeungdo, Shinangun, JeollaNam-do, Korea. In each step of salt production, the succession of the group has been studied using pyrosequencing method and the new halophile variety has been separately identified in solar salterns. The results are as follows; The decomposition ability of protein, lipid, cellulose, and starch, has been experimented with separately identifying 33 bacteria that appeared as dominants in solar salterns. Overall, the bacteria with decomposition capability of all 4 components were Micrococcus luteus, Nocardioides daejeonensis in Actinobacteria group, Halobacillus trueperi whb45 in Firmicutes group, and Aurantimonas coralicida, Lutibacterium anuloederans, Nesiotobacter exalbescens in Alphaproteobacteria group. Analysis in the diversity of bacteria community of diluted solution with concentration of 3%, 6%, 11%, 20%, and 30% has been made using pyrosequencing method. In the Order level, SAR 11 dominated in 3% salt solution, Rhodobacterales group (18.9%) in 6% solution, Micrococcales group showed the highest ratio in 11% and 20% solutions, and Rhodobacterales group was dominant in the solution of 30%. In Phylum level, Proteobacteria group showed dominancy in 3% and 6% salt solutions, Actinobacteria group was dominant in 11% and 20% solutions, and Proteobacteria group was dominant in 30% solution. Among the isolated strains, seven novel strains (Kmb21, Kmb26, Kmb27, Kmb32, Kmb42, Kmb64, and Kmb80) were donate registered to NCBI and KCTC, JCM, each as new variety candidate.

The unified ICE-CBF pathway provides a transcriptional feedback control of freezing tolerance during cold acclimation in Arabidopsis.
Kim YS et al . Plant Mol Biol. 2015 Sep;89(1-2):187-201. doi: 10.1007/s11103-015-0365-3. Epub 2015 Aug 27.
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During cold acclimation, C-repeat binding factors (CBFs) activate downstream targets, such as cold-regulated genes, leading to the acquisition of freezing tolerance in plants. Inducer of CBF expression 1 (ICE1) plays a key role by activating CBF3 expression in shaping the cold-induced transcriptome. While the ICE1-CBF3 regulon constitutes a major cold acclimation pathway, gene regulatory networks governing the CBF signaling are poorly understood. Here, we demonstrated that ICE1 and its paralog ICE2 induce CBF1, CBF2, and CBF3 by binding to the gene promoters. ICE2, like ICE1, was ubiquitinated by the high expression of osmotically responsive gene 1 (HOS1) E3 ubiquitin ligase. Whereas ICE2-defective ice2-2 mutant did not exhibit any discernible freezing-sensitive phenotypes, ice1-2 ice2-2/+ plant, which is defective in ICE1 and has a heterozygotic ice2 mutation, exhibited significantly reduced freezing tolerance. Accordingly, all three CBF genes were markedly down-regulated in the ice1-2 ice2-2/+ plant, indicating that ICE1 and ICE2 are functionally redundant with different implementations in inducing CBF genes. Together with the negative regulation of CBF3 by CBF2, we propose that the unified ICE-CBF pathway provides a transcriptional feedback of freezing tolerance to sustain plant development and survival during cold acclimation.

Generalized Soil ThaumarchaeotaCommunity in Weathering Rock and Saprolite
Dong K et al . Microb Ecol. 2015 Feb;69(2):356-60. doi: 10.1007/s00248-014-0526-y. Epub 2014 Nov 5.
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Relatively little is known of the archaeal communities associated with endolithic environments, compared to other microbial groups such as bacteria and fungi. Analyzing the pyrosequenced archaeal 16S ribosomal RNA (rRNA) gene V1-V3 region, we investigated the archaeal community associated with aboveground-exfoliated weathering layers of a granite gneiss, and of the saprolite derived from this rock at 1 m depth below the soil surface, in a forested hilly area south of Seoul, South Korea. In both these sites, an archaeal community dominated by the phylum Thaumarchaeota was identified. The archaeal community in all cases closely resembled that of the surface layer of acidic soils in temperate climates of Korea. It appears that there is no clear distinction in archaeal community composition between a soil and a rock and a saprolite despite a tremendous difference in the concentration of total nitrogen and organic carbon. Of the chemical properties we measured, pH was the best predictor of the archaeal community composition and relative abundance of thaumarchaeal subphyla. These findings reinforce the view that soil archaea are mostly generalists, whose ecology is not closely dependent on nitrogen concentration or soil organic matter status, the presence of living roots, or the abundant presence of any other biota.

Analysis of the nasal vestibule mycobiome in patients with allergic rhinitis.
Won Hee Jung et al . Mycoses. 2015 Mar;58(3):167-72. doi: 10.1111/myc.12296. Epub 2015 Feb 10.
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Advances in culture-independent sequencing methods have been utilised in recent studies to understand the phylogenetic composition of the human microbiome of healthy and diseased skin. Allergic rhinitis (AR) is an inflammatory condition of the nasal cavity caused by environmental allergens. Although nasal microbial communities have been considered important contributors in human health, no studies to date have comprehensively compared fungal communities (mycobiome) of the nasal vestibule using the culture-independent pyrosequencing method. This study aimed to investigate how fungal communities of the nasal vestibule skin surface are influenced by AR. The phylogenetic composition of the nasal vestibule mycobiome of patients with AR was analysed by culture-independent pyrosequencing methods and compared with healthy individuals. A total of 69 fungal genera were identified from both AR samples and healthy controls, and the genus Malassezia predominated in the nasal vestibule. Species-level analysis classified eight different Malassezia species including M. pachydermatis and M. cuniculi, which were normally isolated from animals, and revealed M. restricta to be the most abundant species in the nasal vestibule. Although high interpersonal variation was observed, some of the AR samples displayed significantly higher diversities than healthy controls at both the genus and species level.

Microbiota-Independent Ameliorative Effects of Antibiotics on Spontaneous Th2-Associated Pathology of the Small Intestine
Han D et al . PLoS One. 2015 Feb 17;10(2):e0118795.
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We have previously generated a mouse model of spontaneous Th2-associated disease of the small intestine called TRAF6ΔDC, in which dendritic cell (DC)-intrinsic expression of the signaling mediator TRAF6 is ablated. Interestingly, broad-spectrum antibiotic treatment ameliorates TRAF6ΔDC disease, implying a role for commensal microbiota in disease development. However, the relationship between the drug effects and commensal microbiota status remains to be formally demonstrated. To directly assess this relationship, we have now generated TRAF6ΔDC bone marrow chimera mice under germ-free (GF) conditions lacking commensal microbiota, and found, unexpectedly, that Th2-associated disease is actually exacerbated in GF TRAF6ΔDC mice compared to specific pathogen-free (SPF) TRAF6ΔDC mice. At the same time, broad-spectrum antibiotic treatment of GF TRAF6ΔDC mice has an ameliorative effect similar to that observed in antibiotics-treated SPF TRAF6ΔDC mice, implying a commensal microbiota-independent effect of broad-spectrum antibiotic treatment. We further found that treatment of GF TRAF6ΔDC mice with broad-spectrum antibiotics increases Foxp3+ Treg populations in lymphoid organs and the small intestine, pointing to a possible mechanism by which treatment may directly exert an immunomodulatory effect. To investigate links between the exacerbated phenotype of the small intestines of GF TRAF6ΔDC mice and local microbiota, we performed microbiotic profiling of the luminal contents specifically within the small intestines of diseased TRAF6ΔDC mice, and, when compared to co-housed control mice, found significantly increased total bacterial content characterized by specific increases in Firmicutes Lactobacillus species. These data suggest a protective effect of Firmicutes Lactobacillus against the spontaneous Th2-related inflammation of the small intestine of the TRAF6ΔDC model, and may represent a potential mechanism for related disease phenotypes.

First report on the whole genome sequence of Pseudomonas cichoriistrain JBC1 and comparison with otherPseudomonasspecies
G. et al . Plant Pathology, Volume 64, Issue 1, pages 63–70, February 2015
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Pseudomonas cichorii, a plant pathogen that infects a wide range of host plants worldwide, causes several diseases in economically important vegetable crops. Availability of the genome sequences of pathogens can greatly enhance research necessary for the advancement of disease management programmes. Despite the significance of P. cichorii, its whole genome sequence has not been reported previously. The genome sequence of P. cichorii JBC1, described for the first time in this study, is 5 986 012 bp with an average GC content of 58·1% and has 5174 coding sequences (CDS). The genes related to virulence, transport mechanisms, phytotoxic compounds, and secondary metabolite products were analysed and the genome was compared to eight other Pseudomonas species to understand the diversity at species level. Despite the high similarity (up to 80·85%), significant diversity was found among the different Pseudomonas species at the genome level. A comparison of JBC1 pathogenicity island (PAI) regions indicated that the P. viridiflava UASWS0038 PAI has more similarity than the P. syringae PAI region, and the analysis revealed significant divergence at PAI regions among the Pseudomonas species, providing an insight into the differences in host specificity and degree of virulence. In addition, JBC1 encodes antibiotic resistance and tolerance to heavy metals, and two different prophage segments were inserted at three different regions. The genome sequence of JBC1, which was deposited into the NCBI GenBank (accession no. CP007039), will be a reference sequence for other P. cichorii strains and a useful resource for further research.

Saxitoxin-Producing cyanobacteria in Lake Baikal
O. I. Belykh et al . Contemp. Probl. Ecol. (2015) 8: 186. doi:10.1134/S199542551502002X
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Cyanobacteria containing neurotoxic saxitoxin synthesis genes were found in the coastal zone of Lake Baikal near the village of Turka for the first time. Phylogenetic analysis showed that the sequences of saxitoxin synthesis genes belong to the genus Anabaena Bory. Saxitoxin concentration in the water according to ELISA was 1.93 ± 0.64 mg/L. The genetic and taxonomic composition of the bacterial community of the central part of Lake Baikal was characterized using 16S rRNA gene pyrosequencing. It was established that the phylum Cyanobacteria dominated in the composition of summer bacterioplankton in both littoral and pelagic zones of the lake, but higher species diversity was found in the plankton of littoral zone.

Halocynthiibacter arcticus sp. nov., isolated from Arctic marine sediment
Baek K et al . Int J Syst Evol Microbiol. 2015 Aug 4. doi: 10.1099/ijsem.0.000507
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A Gram-staining-negative, oxidase- and catalase- positive, non-motile, producing white colonies, aerobic and rod-shaped bacterium, PAMC 20958T, was isolated from a marine sediment of the Arctic. Strain PAMC 20958T grew at 10-27 °C (optimally at 21 °C), at pH 5.5-9.5 (optimally at 7.0-7.5) and in the presence of 0.5-7.5 % (w/v) (optimally at 2.0 %) of NaCl. Strain PAMC 20958T showed 97.5 % of 16S rRNA sequence similarity with Halocynthiibacter namhaensis KCTC 32362T and formed a robust phylogenetic clade with this species. Average nucleotide identity value between strain PAMC 20958T and H. namhaensis KCTC 32362T was 79.7 % and the genome-to-genome distance was 13.0 % on average. The genomic DNA G+C content calculated from the genome sequence was 53.2 mol%. The major fatty acids were C18:1 ω7c and/or C18:1 ω6c. The major respiratory isoprenoid quinone was ubiquinone-10 (Q-10) and major polar lipids were phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid and two unidentified lipids. On the basis of phylogenetic analysis and genotypic and phenotypic data obtained in this study, strain PAMC 20958T (= KCTC 42129T = JCM 30530T) represents the type strain of a novel species of the genus Halocynthiibacter, for which the name Halocynthiibacter arcticus sp. nov. is proposed.
Streptomyces mangrovi sp. nov., isolated from mangrove forest sediment
Yousif G et al . Antonie Van Leeuwenhoek. 2015 Sep;108(3):783-91. doi: 10.1007/s10482-015-0533-0. Epub 2015 Jul 18.
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A Streptomyces strain isolated from a mangrove sediment was classified using a polyphasic approach. The organism, isolate GY1(T), was found to have chemical and morphological properties typical of members of the genus Streptomyces. The isolate was shown to form a distinct phyletic line within the Streptomyces radiopugnans 16S rRNA gene subclade and to be closely related to the type strain of Streptomyces fenhuangensis (98.7 % similarity). It is also closely related to the type strain of Streptomyces bakulensis which was also closely related to members of the Streptomyces glaucosporus 16S rRNA gene subclade. Isolate GY1(T) was distinguished readily from the S. barkulensis type strain and from species classified in the S. radiopugnans clade using a combination of morphological and physiological properties, including a requirement for seawater for growth. Based on the genotypic and phenotypic data, it is proposed that isolate GY1(T) (=NCIMB 14980(T), NRRL B-69296(T)) be classified in the genus Streptomyces as Streptomyces mangrovi sp. nov.

Complete genome sequence of Novosphingobium pentaromativoransUS6-1T
Yun Sik Choi et al . Sci Rep. 2016; 6: 29186. Published online 2016 Jul 7. doi: 10.1038/srep29186
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Oral lichen planus (OLP) is a chronic T cell-mediated mucocutaneous disease of unknown etiopathogenesis. Although various antigens have been considered, what actually triggers the inflammatory response of T cells is unknown. In the present study, we propose that intracellular bacteria present within tissues trigger T cell infiltration and provide target antigens. Sections of OLP (n = 36) and normal (n = 10) oral mucosal tissues were subjected to in situ hybridization using a universal probe targeting the bacterial 16S rRNA gene and immunohistochemistry with anti-CD3, anti-CD4, anti-CD8, and anti-macrophage-specific antibodies. Bacteria were abundant throughout the epithelium and the lamina propria of OLP tissues, which exhibited positive correlations with the levels of infiltrated CD3+, CD4+, and CD8+ cells. Furthermore, bacteria were detected within the infiltrated T cells. Pyrosequencing analysis of the mucosal microbiota from OLP patients (n = 13) and control subjects (n = 11) revealed a decrease in Streptococcus and increases in gingivitis/periodontitis-associated bacteria in OLP lesions. Using the selected bacterial species, we demonstrated that certain oral bacteria damage the epithelial physical barrier, are internalized into epithelial cells or T cells, and induce production of T cell chemokines CXCL10 and CCL5. Our findings provide insights into the pathogenesis of OLP.

Domibacillus tundrae sp. nov., isolated from active layer soil of tussock tundra in Alaska, and emended description of the genusDomibacillus
Gyeong HR et al . Int J Syst Evol Microbiol. 2015 Oct;65(10):3407-12. doi: 10.1099/ijsem.0.000429. Epub 2015 Jul 9.
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A novel Gram-stain-positive, spore-forming, aerobic, motile and rod-shaped bacterium designated strain PAMC 80007T was isolated from an active layer soil sample of Council, Alaska. Optimal growth of strain PAMC 80007T was observed at 30 °C, pH 7.0 and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain PAMC 80007T belonged to the genus Domibacillus. This strain was closely related to Domibacillus enclensis (98.3 %), Domibacillus robiginosus (98.3 %) and Domibacillus indicus (97.2 %). Genomic DNA G+C content was 43.5 mol% and genomic relatedness analyses based on the average nucleotide identity and the genome-to-genome distance showed that strain PAMC 80007T is clearly distinguished from the closely related species of the genus Domibacillus. The major fatty acids (>5 %) were iso-C15 : 0 (24.7 %), C16 : 1ω11c (16.8 %), anteiso-C15 : 0 (16.5 %), C16 : 0 (15.6 %) and anteiso-C17 : 0 (8.7 %). The major respiratory isoprenoid quinones were menaquinone-6 (MK-6) and menaquinone-7 (MK-7), and the polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid, phospholipid and two unidentified lipids. meso-Diaminopimelic acid (type A1γ) was present in the cell-wall peptidoglycan, and the major whole-cell sugar was ribose with a minor quantity of glucose. Results from a polyphasic study suggested that strain PAMC 80007T represents a novel species of the genus Domibacillus for which the name Domibacillus tundrae sp. nov. is proposed. The type strain is PAMC 80007T ( = JCM 30371T = KCTC 33549T = DSM 29572T). An emended description of the genus Domibacillus is also provided.

Emission of Carbon Dioxide and Methane from Duckweed Ponds for Stormwater Treatment
Dai J et al . Water Environ Res. 2015 Sep;87(9):805-12. doi: 10.2175/106143015X14362865226310.
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This study determined the greenhouse gas emission from two laboratory-scale duckweed ponds for stormwater treatment. The rate of carbon dioxide (CO2) emission from the two duckweed systems was 1472 ± 721 mg/m(2)·d and 626 ± 234 mg/m(2)·d, respectively. After the removal of duckweeds, CO2 emissions decreased to 492 ± 281 mg/m(2)·d and 395 ± 53 mg/m(2)·d, respectively. The higher CO2 emissions in the duckweed systems were attributed to duckweed biomass decay on the pond soil surface. A thin-film model was able to predict the increasing CO2 concentrations in the closed static chamber during 2 weeks of sampling. The initial methane fluxes from the duckweed systems were 299 ± 74 mg/m(2)·d and 180 ± 91 mg/m(2)·d, respectively. After the removal of duckweeds, the flux increased to 559 ± 215 mg/m(2)·d and 328 ± 114 mg/m(2)·d, respectively.

Genome sequence analysis of potential probiotic strain Leuconostoc lactis EFEL005 isolated from kimchi.
Moon JS et al . J Microbiol. 2015 May;53(5):337-42. doi: 10.1007/s12275-015-5090-8. Epub 2015 May 3.
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Leuconostoc lactis EFEL005 (KACC 91922) isolated from kimchi showed promising probiotic attributes; resistance against acid and bile salts, absence of transferable genes for antibiotic resistance, broad utilization of prebiotics, and no hemolytic activity. To expand our understanding of the species, we generated a draft genome sequence of the strain and analyzed its genomic features related to the aforementioned probiotic properties. Genome assembly resulted in 35 contigs, and the draft genome has 1,688,202 base pairs (bp) with a G+C content of 43.43%, containing 1,644 protein-coding genes and 50 RNA genes. The average nucleotide identity analysis showed high homology (≥ 96%) to the type strain L. lactis KCTC3528, but low homology (≤ 95%) to L. lactis KCTC3773 (formerly L. argentinum). Genomic analysis revealed the presence of various genes for sucrose metabolism (glucansucrases, invertases, sucrose phosphorylases, and mannitol dehydrogenase), acid tolerance (F1F0 ATPases, cation transport ATPase, branched-chain amino acid permease, and lysine decarboxylase), vancomycin response regulator, and antibacterial peptide (Lactacin F). No gene for production of biogenic amines (histamine and tyramine) was found. This report will facilitate the understanding of probiotic properties of this strain as a starter for fermented foods.
Bacterial communities along stratified water columns at the Chukchi Borderland in the western Arctic Ocean
Dukki Hana et al . http://doi.org/10.1016/j.dsr2.2015.01.018
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An expedition of the IBRV ARAON took place in the Arctic Ocean during the summer of 2010. To investigate the hydrographic features and bacterial variations in water columns, we categorized 16 water samples collected from distinct water masses at the Chukchi Borderland in the western Arctic Ocean. Bacterial diversity, relative abundance, and community composition were determined based on a pyrosequencing approach, and their relationship with water mass properties was considered. Alphaproteobacteria (43.2%), Gammaproteobacteria (16.7%), Flavobacteria (13.7%), and Deltaproteobacteria (12.0%) were the most common bacteria found in all samples, and the relative abundance of these predominant taxa represent the population dynamics of bacterial communities in different water masses (from the euphotic to the sub-euphotic zone) in the Arctic Ocean. Furthermore, the relative abundance of Alphaproteobacteria and its subgroup, SAR11 group I, were significantly related to depth change in water columns, suggesting that environmental heterogeneity caused by changes in depth may play an important role in bacterial population dynamics. In this study, bacterial communities in the Arctic Ocean exhibit biogeographic patterns according to the type of water mass. The halocline layer between the Pacific winter water and Atlantic water exhibits a variation in the composition of bacterial communities, which may be influenced by mixing of Pacific winter water and Atlantic water.
High-throughput nucleotide sequence analysis of diverse bacterial communities in leachates of decomposing pig carcasses
Seung Hak Yang et al . http://dx.doi.org/10.1590/S1415-475738320140252
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The leachate generated by the decomposition of animal carcass has been implicated as an environmental contaminant surrounding the burial site. High-throughput nucleotide sequencing was conducted to investigate the bacterial communities in leachates from the decomposition of pig carcasses. We acquired 51,230 reads from six different samples (1, 2, 3, 4, 6 and 14 week-old carcasses) and found that sequences representing the phylum Firmicutes predominated. The diversity of bacterial 16S rRNA gene sequences in the leachate was the highest at 6 weeks, in contrast to those at 2 and 14 weeks. The relative abundance of Firmicutes was reduced, while the proportion of Bacteroidetes and Proteobacteria increased from 3–6 weeks. The representation of phyla was restored after 14 weeks. However, the community structures between the samples taken at 1–2 and 14 weeks differed at the bacterial classification level. The trend in pH was similar to the changes seen in bacterial communities, indicating that the pH of the leachate could be related to the shift in the microbial community. The results indicate that the composition of bacterial communities in leachates of decomposing pig carcasses shifted continuously during the study period and might be influenced by the burial site.
Archaeal community diversity and abundance changes along a natural salinity gradient in estuarine sediments
Sonia Michail et al . https://doi.org/10.1093/femsec/fiu002
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Obesity is becoming the new pediatric epidemic. Non-alcoholic fatty liver disease (NAFLD) is frequently associated with obesity and has become the most common cause of pediatric liver disease. The gut microbiome is the major metabolic organ and determines how calories are processed, serving as a caloric gate and contributing towards the pathogenesis of NAFLD. The goal of this study is to examine gut microbial profiles in children with NAFLD using phylogenetic, metabolomic, metagenomic and proteomic approaches. Fecal samples were obtained from obese children with or without NAFLD and healthy lean children. Stool specimens were subjected to 16S rRNA gene microarray, shotgun sequencing, mass spectroscopy for proteomics and NMR spectroscopy for metabolite analysis. Children with NAFLD had more abundant Gammaproteobacteria and Prevotella and significantly higher levels of ethanol, with differential effects on short chain fatty acids. This group also had increased genomic and protein abundance for energy production with a reduction in carbohydrate and amino acid metabolism and urea cycle and urea transport systems. The metaproteome and metagenome showed similar findings. The gut microbiome in pediatric NAFLD is distinct from lean healthy children with more alcohol production and pathways allocated to energy metabolism over carbohydrate and amino acid metabolism, which would contribute to development of disease.
Complete genome sequence of bacteriophage P8625, the first lytic phage that infects Verrucomicrobia
Ahyoung Choi et al . DOI: 10.1186/s40793-015-0091-0
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Bacteriophage P8625 is a lytic bacteriophage that infects the verrucomicrobial strain IMCC8625, a marine bacterium affiliated with Verrucomicrobia subdivision 4. Both the bacteriophage and the host bacterial strain were isolated from surface seawater samples collected off the east coast of Korea. The phage particle has an icosahedral capsid with a diameter of ~47 nm and a long tail of ~75 nm in length, showing the distinctive morphology of the Siphoviridae family. The complete genome sequence of phage P8625 is 32,894 bp long with 51.0 % G + C content. This is the first report of the complete genome sequence of a lytic phage that infects the Verrucomicrobia, for which the name “verrucophage” is proposed.
Draft genome sequence of the extremely halophilic archaeonHaladaptatus cibariustype strain D43Tisolated from fermented seafood
Hae-Won Lee et al . DOI: 10.1186/s40793-015-0051-8
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An extremely halophilic archaeon, Haladaptatus cibarius D43T, was isolated from traditional Korean salt-rich fermented seafood. Strain D43T shows the highest 16S rRNA gene sequence similarity (98.7 %) with Haladaptatus litoreus RO1-28T, is Gram-negative staining, motile, and extremely halophilic. Despite potential industrial applications of extremely halophilic archaea, their genome characteristics remain obscure. Here, we describe the whole genome sequence and annotated features of strain D43T. The 3,926,724 bp genome includes 4,092 protein-coding and 57 RNA genes (including 6 rRNA and 49 tRNA genes) with an average G + C content of 57.76 %.
Plant-specific effects of sunn hemp (Crotalaria juncea) and sudex (Sorghum bicolor×Sorghum bicolorvar. sudanense) on the abundance and composition of soil microbial community
Jinu Eo et al . http://doi.org/10.1016/j.agee.2015.07.025
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We investigated the effect of sunn hemp (leguminous) and sudex (non-leguminous) on the abundance and composition of microbial community in soil with a low nutrient content for two years. Abundance of microbial groups was determined by phospholipid fatty acid (PLFA) analysis. Pyrosequencing analysis was used to compare the composition of bacterial communities in the rhizosphere with that in the bulk soil of the unplanted control. The concentration of microbial PLFA increased during cultivation period and decreased after incorporation of plant residues, which implies that the responses depended on living plants. Overall, the bacterial PLFA concentration was lower with sunn hemp than sudex, despite the above-ground biomass was about five times greater with the former than with the latter crop. This indicates that the increase in bacterial PLFA with sudex is plant-specific. Pyrosequencing analysis revealed that the abundance of Arthrobacter, Bacillus, and Sphingomonas were the highest in the bulk soil and decreased in the rhizospheres of the cover plants. The proportions of Gaiella and the nitrogen fixing bacteria Mesorhizobium increased with sunn hemp, while those of cyanobacteria, including Calothrix, Leptolyngbya, and Nostoc, increased greatly with sudex. Our results indicated that the high level of bacterial PLFA with sudex could be primarily explained by the colonization of cyanobacteria. We show that the impacts of cover plants on the abundance and composition of the microbial communities depend more on the plant species than on the aboveground plant biomass, both during growth and incorporation stages. Our results also suggest that non-leguminous as well as leguminous plants harbor beneficial microbes such as nitrogen-fixing bacteria to cope with nutrient-poor environments.
Genomic Analysis of the Moderately Haloalkaliphilic Bacterium Oceanobacillus kimchiiStrain X50Twith Improved High-Quality Draft Genome Sequences
Dong Wook Hyun et al . http://www.papersearch.net/thesis/article.asp?KEY=3375036
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Oceanobacillus kimchii is a member of the genus Oceanobacillus within the family Bacillaceae. Species of the Oceanobacillus possess moderate haloalkaliphilic features and originate from various alkali or salty environments. The haloalkaliphilic characteristics of Oceanobacillus advocate they may have possible uses in biotechnological and industrial applications, such as alkaline enzyme production and biodegradation. This study presents the draft genome sequence of O. kimchii X50(T) and its annotation. Furthermore, comparative genomic analysis of O. kimchii X 5 0T was performed with two previously reported Oceanobacillus genome sequences. The 3,822,411 base-pair genome contains 3,792 protein-coding genes and 80 RNA genes with an average G+C content of 35.18 mol%. The strain carried 67 and 13 predicted genes annotated with transport system and osmoregulation, respectively, which support the tolerance phenotype of the strain in high-alkali and high-salt environments.
WolbachiaSequence Typing in Butterflies Using Pyrosequencing
Sungmi Choi et al . J. Microbiol. Biotechnol.2015 ; Vol.25-9
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Wolbachia is an obligate symbiotic bacteria that is ubiquitous in arthropods, with 25–70% of insect species estimated to be infected. Wolbachia species can interact with their insect hosts in a mutualistic or parasitic manner. Sequence types (ST) of Wolbachia are determined by multilocus sequence typing (MLST) of housekeeping genes. However, there are some limitations to MLST with respect to the generation of clone libraries and the Sanger sequencing method when a host is infected with multiple STs of Wolbachia. To assess the feasibility of massive parallel sequencing, also known as next-generation sequencing, we used pyrosequencing for sequence typing of Wolbachia in butterflies. We collected three species of butterflies (Eurema hecabe, Eurema laeta, and Tongeia fischeri) common to Korea and screened them for Wolbachia STs. We found that T. fischeri was infected with a single ST of Wolbachia, ST41. In contrast, E. hecabe and E. laeta were each infected with two STs of Wolbachia, ST41 and ST40. Our results clearly demonstrate that pyrosequencing-based MLST has a higher sensitivity than cloning and Sanger sequencing methods for the detection of minor alleles. Considering the high prevalence of infection with multiple Wolbachia STs, next-generation sequencing with improved analysis would assist with scaling up approaches to Wolbachia MLST.
Complete Genomic and Lysis-Cassette Characterization of the Novel Phage, KBNP1315, which Infects Avian Pathogenic Escherichia coli(APEC)
Jung Seok Lee et al . https://doi.org/10.1371/journal.pone.0142504
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Avian pathogenic Escherichia coli (APEC) is a major pathogen that causes avian colibacillosis and is associated with severe economic losses in the chicken-farming industry. Here, bacteriophage KBNP1315, infecting APEC strain KBP1315, was genomically and functionally characterized. The evolutionary relationships of KBNP1315 were analyzed at the genomic level using gene (protein)-sharing networks, the Markov clustering (MCL) algorithm, and comparative genomics. Our network analysis showed that KBNP1315 was connected to 30 members of the Autographivirinae subfamily, which comprises the SP6-, T7-, P60-, phiKMV-, GAP227- and KP34-related groups. Network decomposition suggested that KBNP1315 belongs to the SP6-like phages, but our comparison of putative encoded proteins revealed that key proteins of KBNP1315, including the tail spike protein and endolysin, had relative low levels of amino acid sequence similarity with other members of the SP6-like phages. Thus KBNP1315 may only be distantly related to the SP6-like phages, and (based on the difference in endolysin) its lysis mechanism may differ from theirs. To characterize the lytic functions of the holin and endolysin proteins from KBNP1315, we expressed these proteins individually or simultaneously in E. coli BL21 (DE3) competent cell. Interestingly, the expressed endolysin was secreted into the periplasm and caused a high degree of host cell lysis that was dose-dependently delayed/blocked by NaN3-mediated inhibition of the SecA pathway. The expressed holin triggered only a moderate inhibition of cell growth, whereas coexpression of holin and endolysin enhanced the lytic effect of endolysin. Together, these results revealed that KBNP1315 appears to use a pin-holin/signal-arrest-release (SAR) endolysin pathway to trigger host cell lysis.
Alteration of gut microbiota by vancomycin and bacitracin improves insulin resistance viaglucagon-like peptide 1 in diet-induced obesity
Injae Hwang et al . doi:10.1096/fj.14-265983
Abstract -
Firmicutes and Bacteroidetes, 2 major phyla of gut microbiota, are involved in lipid and bile acid metabolism to maintain systemic energy homeostasis in host. Recently, accumulating evidence has suggested that dietary changes promptly induce the alteration of abundance of both Firmicutes and Bacteroidetes in obesity and its related metabolic diseases. Nevertheless, the metabolic roles of Firmicutes and Bacteroidetes on such disease states remain unclear. The aim of this study was to determine the effects of antibiotic-induced depletion of Firmicutes and Bacteroidetes on dysregulation of energy homeostasis in obesity. Treatment of C57BL/6J mice with the antibiotics (vancomycin [V] and bacitracin [B]), in the drinking water, before diet-induced obesity (DIO) greatly decreased both Firmicutes and Bacteroidetes in the gut as revealed by pyrosequencing of the microbial 16S rRNA gene. Concomitantly, systemic glucose intolerance, hyperinsulinemia, and insulin resistance in DIO were ameliorated via augmentation of GLP-1 secretion (active form; 2.03-fold, total form; 5.09-fold) independently of obesity as compared with untreated DIO controls. Furthermore, there were increases in metabolically beneficial metabolites derived from the gut. Together, our data suggest that Firmicutes and Bacteroidetes potentially mediate insulin resistance through modulation of GLP-1 secretion in obesity.—Hwang, I., Park, Y. J., Kim, Y. -R., Kim, Y. N., Ka, S., Lee, H. Y., Seong, J. K., Seok, Y.-J., Kim, J. B. Alteration of gut microbiota by vancomycin and bacitracin improves insulin resistance via glucagon-like peptide 1 in diet-induced obesity. 
Complete Genome Sequence of Martelella endophyticaYC6887, Which Has Antifungal Activity Associated with a Halophyte
Ajmal Khan et al . doi: 10.1128/genomeA.00366-15
Abstract -
Martelella endophytica YC6887, which produces antifungal compounds against fungal and oomycete pathogens, was isolated from the root of a halophyte, Rosa rugosa, collected at a tidal flat in South Korea. Its full-genome sequence shows that it is a circular DNA, without a plasmid, of about 4.8 Mb in size. 
Barcoded pyrosequencing-based metagenomic analysis of the faecal microbiome of three purebred pig lines after cohabitation
Edward Alain B. Pajarillo et al . DOI: 10.1007/s00253-015-6408-5
Abstract -
The microbial communities in the pig gut perform a variety of beneficial functions. Along with host genetics and diet, farm management practices are an important aspect of agricultural animal production that could influence gut microbial diversity. In this study, we used barcoded pyrosequencing of the V1–V3 regions of the 16S ribosomal RNA (rRNA) genes to characterise the faecal microbiome of three common commercial purebred pig lines (Duroc, Landrace and Yorkshire) before and after cohabitation. The diversity of faecal microbiota was characterised by employing phylogenetic, distance-based and multivariate-clustering approaches. Bacterial diversity tended to become more uniform after mixing of the litters. Age-related shifts were also observed at various taxonomic levels, with an increase in the proportion of the phylum Firmicutes and a decrease in Bacteroidetes over time, regardless of the purebred group. Cohabitation had a detectable effect on the microbial shift among purebred pigs. We identified the bacterial genus Parasutterella as having utility in discriminating pigs according to time. Similarly, Dialister and Bacteroides can be used to differentiate the purebred lines used. The microbial communities of the three purebred pigs became more similar after cohabitation, but retained a certain degree of breed specificity, with the microbiota of Landrace and Yorkshire remaining distinct from that of their distant relative, Duroc.
Microbial community changes in Makgeolliduring brewing
Changhoon Chai et al . DOI: 10.1002/jib.227
Abstract -

Makgeolli, a traditional Korean alcoholic beverage, is produced from the simultaneous saccharification and fermentation of glutinous rice by microbes introduced through nuruk (fermentation starter). The microbial community in Makgeolli is complex, and changes in the community are important for quality control and product development of Makgeolli. In this study, changes in the microbial community of Makgeolli during brewing were monitored by pyrosequencing. Pyrosequencing of microbes in Makgeolli illustrated dynamic changes in the populations and species of bacteria and fungi during brewing. Saccharomyces, a fungal genus, dominated the fungal community in Makgeolli throughout brewing, and produced alcohol after sufficient production of reducing sugars. As the bacterial genera Pediococcus, Weissella, Lactobacillus and Enterococcus, categorized as lactic acid bacteria, grew in Makgeolli, the pH decreased. The fungal community in Makgeolli was not significantly changed during brewing, but there were dynamic changes in the bacterial community, especially during the first 2 days of brewing. Copyright © 2015 The Institute of Brewing & Distilling

Genome Sequence of Arthrobactersp. MWB30, Isolated from a Crude Oil-Contaminated Seashore
Jonghyun Kim et al . doi: 10.1128/genomeA.00013-15
Abstract -
We report here the draft genome sequence of Arthrobacter sp. MWB30 strain, isolated from a crude oil-contaminated seashore in Tae-an, South Korea, which is able to degrade the crude oil and its derivatives. The draft genome sequence of 4,647,008 bp provides a resource for the identification of crude oil-degrading mechanisms in strain MWB30.
Complete Genome Sequence of Mycobacterium bovisClinical Strain 1595, Isolated from the Laryngopharyngeal Lymph Node of South Korean Cattle
Narae Kim et al . doi: 10.1128/genomeA.01124-15
Abstract -
Mycobacterium bovis strain 1595 was isolated from the lymph node of South Korean native cattle. The complete genome sequence of strain 1595 was determined in 2 contigs and was found to be 4,351,712 bp in size, with a 65.64% G+C content and 4,358 predicted protein-coding genes. 
Developmental Dynamic Analysis of the Excreted Microbiome of Chickens Using Next-Generation Sequencing
Lim S et al . doi.org/10.1159/000430865
Abstract -
Poultry contamination can be largely attributed to the presence of chicken feces during the production process. Fecal contamination is often found in raw chicken products sold for human consumption. Quantitative analysis of the fecal microbial community of chickens using next-generation sequencing techniques is the focus of this study. Fecal samples were collected from 30 broiler chickens at two time points: days 1 and 35 of development. 454 pyrosequencing was conducted on 16S rRNA extracted from each sample, and microbial population dynamics were investigated using various automated bioinformatics pipelines. Diversity of the microbial community at the genus level increased during the 5-week growth period. Despite this growth, only a few dominant bacteria groups (over 80%) were identified in each fecal sample, with most groups being unique and only a few were shared between samples. Population analysis at the genus level showed that microbial diversity increased with chicken growth and development. Classification and phylogenetic analysis of highly represented microbes (over 1%) clearly showed high levels of sequence similarity between groups such as Firmicutes and Proteobacteria. These results suggest that the chicken fecal excreted microbiome is a dynamic system with a differentiated population structure that harbors a highly restricted number of higher taxa.
Study of the microbiome of the intestine of the Comephorus dybowskikorotneff, 1904
N. L. Bel’kova et al . DOI: 10.1134/S1062359015050039
Abstract -
Data on metagenomic analysis of the microbial community of the intestine of the Comephorus dybowski are presented for the first time. It was established that the bacterial community is characterized by a significant species diversity. In its composition 301 phylotypes (OTU) belonging to 23 phyla (out of which six are candidate, including the Thermobaculum, Gracilibacteria, Candidatus Saccharibacteria, TM6, Latescibacteria, and Parcubacteria) were detected. It was demonstrated that species richness estimated by means of the nonparametric ACE and Chao1 criteria was 568 and 504, respectively; and the species diversity by the Shannon index was 4.05. The analysis of unique peculiarities of the C. dybowski ecology and biology allows us to explain some of the data obtained on the intestinal microbiome of this specie.
Identification of toxic Cyanobacteria in Lake Baikal
O. I. Belykh et al . DOI: 10.1134/S1607672915040067
Abstract -
Cyanobacteria of the genera Anabaena and Microcystis, containing genes for the synthesis of-microcystins (hepatotoxic cyanotoxins) were found for the first time in the coastal zone of Lake Baikal near-the village of Turka, where a tourism and recreational complex were constructed. According to the enzyme-immunoassay, microcystin concentration in water was 0.17 ± 0.01 µg/L. Using 16S rRNA gene pyrosequencing, we found 3936 sequences in the eubacterial community of central basin of Lake Baikal. The summer bacterioplankton in both littoral and pelagic areas of the lake was dominated by the phylum Cyanobacteria, whereas a higher diversity of cyanobacteria was recorded in the plankton of the littoral zone. Moreover, the-potentially toxic Anabaena and Microcystis were detected in this area.
Complete genome sequence of Mycobacterium tuberculosisK from a Korean high school outbreak, belonging to the Beijing family
Seung Jung Han et al . DOI: 10.1186/s40793-015-0071-4
Abstract -
Mycobacterium tuberculosis K, a member of the Beijing family, was first identified in 1999 as the most prevalent genotype in South Korea among clinical isolates of M. tuberculosis from high school outbreaks. M. tuberculosis K is an aerobic, non-motile, Gram-positive, and non-spore-forming rod-shaped bacillus. A transmission electron microscopy analysis displayed an abundance of lipid bodies in the cytosol. The genome of the M. tuberculosis K strain was sequenced using two independent sequencing methods (Sanger and Illumina). Here, we present the genomic features of the 4,385,518-bp-long complete genome sequence of M. tuberculosis K (one chromosome, no plasmid, and 65.59 % G + C content) and its annotation, which consists of 4194 genes (3447 genes with predicted functions), 48 RNA genes (3 rRNA and 45 tRNA) and 261 genes with peptide signals.
Whole-Genome Sequence of Mycobacterium bovisW-1171, Isolated from the Laryngopharyngeal Lymph Node of a Wild Boar in South Korea
Narae Kima et al . doi: 10.1128/genomeA.01464-15
Abstract -
Mycobacterium bovis W-1171 was isolated from a wild boar living in a free-ranging field in Gyeonggido, South Korea. The whole-genome sequence of this strain was determined in 50 contigs, which was 4,304,865 bp with a 65.57% G+C content. In total 3,945 protein-coding genes were predicted from this assembly. 
Complete genome sequence of bacteriophage P26218 infecting Rhodoferaxsp. strain IMCC26218
Kira Moon et al . DOI: 10.1186/s40793-015-0090-1
Abstract -
Bacteriophage P26218 is a virus that thrives in freshwater and infects Rhodoferax sp. strain IMCC26218, both of which were isolated from Soyang Lake, Korea. The bacterial host, IMCC26218, belongs to the genus Rhodoferax and is closely related to R. saidenbachensis, with 98.7 % 16S rRNA gene sequence similarity. Bacteriophage P26218 has an icosahedral head structure with a diameter of ~52 nm and short tail of ~9 nm, which is a typical morphology of the Podoviridae family. Its complete dsDNA genome was 36,315 bp with 56.7 % G + C content. This is the first genome sequence reported for a lytic phage of the genus Rhodoferax.
Microbial Forensic Analysis of Bacterial Fingerprint by Sequence Comparison of 16S rRNA Gene
So-Yeon Lee1 et al . doi:10.4172/2157-7145.1000297
Abstract -
Human have the microorganisms in the skin, gut and mouth. Human skin microbiome based on the 16S rRNA encoding gene can reveal bacterial species diversity. Also bacterial species in the skin have diverse and unique composition between individuals. We thought that a bacterial fingerprint obtained from surfaces including computer keyboards aids forensic individual identification in case of evidence deficiency. Next generation sequencing was used to analyze the bacterial community on objects and fingertips to match the object to the individual. The 16S rRNA gene sequence was submitted to EMBL SRA with accession number PRJEB8760. Higher similarity of bacterial community between public computer keyboards and laboratory member’s fingertips were evident than between other locations including doorknobs. Here we studied the challenges that bacterial fingerprint can be used as a human identification tool in forensic fields.
Genome sequence of the haloarchaeon Haloterrigenajeotgali type strain A29Tisolated from salt-fermented food
In-Tae Cha et al . DOI: 10.1186/s40793-015-0047-4
Abstract -
Haloterrigena jeotgali is a halophilic archaeon within the family Natrialbaceae that was isolated from shrimp jeotgal, a traditional Korean salt-fermented food. A29T is the type strain of H. jeotgali, and is a Gram-negative staining, non-motile, rod-shaped archaeon that grows in 10 %–30 % (w/v) NaCl. We present the annotated H. jeotgali A29T genome sequence along with a summary of its features. The 4,131,621 bp genome with a GC content of 64.9 % comprises 4,215 protein-coding genes and 127 RNA genes. The sequence can provide useful information on genetic mechanisms that enable haloarchaea to endure a hypersaline environment.
Effect of genetically modified rice producing resveratrol on the soil microbial communities
Soo-In Sohn et al . DOI: 10.1007/s13765-015-0106-y
Abstract -
Cultivation of genetically modified (GM) crops has rapidly increased in the global agricultural area. However, cultivation of GM crops in the field evoked the concern of the possibility of unintentional consequences from transgenic plant into environment. In our present study, we have assessed the effects of RS526, GM rice producing resveratrol on the surrounding soil microbial community. The effects of RS526 on the soil microbial community in its field of growth were assessed using a conventional culture technique and culture-independent molecular methods. Three replicate field plots were planted with single GM rice and a non-GM counterpart, Dongjin. The soil microbial communities around these plants were compared using colony counting, denaturing gradient gel electrophoresis (DGGE), pyrosequencing analysis, and community-level physiological profiling during the growing periods. The bacterial, fungal, and actinomycetes population densities of the RS526 soils were found to be within the range of those of the non-GM rice cultivar. The DGGE banding patterns of the GM and non-GM soils were also similar, suggesting that the bacterial community structures were stable within a given month and were unaffected by the presence of a GM plant. The data obtained from pyrosequencing analysis showed that the bacterial community distribution at the phylum level were highly similar to DGGE patterns between two tested groups. The substrate utilization pattern of RS526 and Dongjin rice soil was quite similar between each sampling time. These results indicate that soil microbial communities are not significantly affected by the cultivation of RS526 within the experimental time frame.
Seasonal Dynamics of Marine Microbial Community in the South Sea of Korea
Sung-Suk Suh et al . doi.org/10.1371/journal.pone.0131633
Abstract -
High-resolution 16S rRNA tag pyrosequencing was used to obtain seasonal snapshots of the bacterial diversity and community structure at two locations in Gosung Bay (South Sea, Korea) over a one year period. Seasonal sampling from the water column at each site revealed highly diverse bacterial communities containing up to 900 estimated Operational Taxonomic Units (OTUs). The Alphaproteobacteria and Gammaproteobacteria were the most abundant groups, and the most frequently recorded OTUs were members of Pelagibacter and Glaciecola. In particular, it was observed that Arcobacter, a genus of the Epsilonproteobacteria, dominated during summer. In addition, Psedoalteromonadaceae, Vibrionaceae and SAR11-1 were predominant members of the OTUs found in all sampling seasons. Environmental factors significantly influenced the bacterial community structure among season, with the phosphate and nitrate concentrations contributing strongly to the spatial distribution of the Alphaproteobacteria; the Gammaproteobacteria, Flavobacteria, and Actinobacteria all showed marked negative correlations with all measured nutrients, particularly silicon dioxide and chlorophyll-a. The results suggest that seasonal changes in environmental variables contribute to the dynamic structure of the bacterial community in the study area.
Temporal Changes in Soil Bacterial Diversity and Humic Substances Degradation in Subarctic Tundra Soil
Ha Ju Park et al . DOI: 10.1007/s00248-014-0499-x
Abstract -
Humic substances (HS), primarily humic acids (HA) and fulvic acids (FA), are the largest constituent of soil organic matter. In microcosm systems with subarctic HS-rich tundra soil (site AK 1-75; approximately 5.6 °C during the thawing period) from Council, Alaska, the HA content significantly decreased to 48 % after a 99-day incubation at 5 °C as part of a biologically mediated process. Accordingly, levels of FA, a putative byproduct of HA degradation, consistently increased to 172 % during an identical incubation process. Culture-independent microbial community analysis showed that during the microcosm experiments, the relative abundance of phyla Proteobacteria (bacteria) and Euryarchaeota (archaea) largely increased, indicating their involvement in HS degradation. When the indigenous bacteria in AK 1-75 were enriched in an artificial mineral medium spiked with HA, the changes in relative abundance were most conspicuous in Proteobacteria (from 60.2 to 79.0 %), specifically Betaproteobacteria-related bacteria. One hundred twenty-two HA-degrading bacterial strains, primarily from the genera Paenibacillus (phylum Firmicutes) and Pseudomonas (class Gammaproteobacteria), were cultivated from AK 1-75 and nearby sites. Through culture-dependent analysis with these bacterial isolates, we observed increasing HS-degradation rates in parallel with rising temperatures in a range of 0 °C to 20 °C, with the most notable increase occurring at 8 °C compared to 6 °C. Our results indicate that, although microbial-mediated HS degradation occurs at temperature as low as 5 °C in tundra ecosystems, increasing soil temperature caused by global climate change could enhance HS degradation rates. Extending the thawing period could also increase degradation activity, thereby directly affecting nearby microbial communities and rhizosphere environments.
Comparative analysis of gut microbiota in elderly people of urbanized towns and longevity villages
Se-Hoon Park et al . DOI: 10.1186/s12866-015-0386-8
Abstract -
To understand differences in the gut microbiota between elderly people of urbanized town communities (UTC) and longevity village communities (LVC), we analyzed fecal microbiota collected from individuals living in 2 UTC (Seoul and Chuncheon) and 3 LVC (Gurye, Damyang, and Soonchang) selected on the basis of indices for superlongevity (the ratio of centenarians to the total population) and longevity (the ratio of those aged 85 years or greater to those aged 65 years or greater) in South Korea by 454 pyrosequencing.
Metagenomic Insights into the Bioaerosols in the Indoor and Outdoor Environments of Childcare Facilities
Su-Kyoung Shin et al . doi.org/10.1371/journal.pone.0126960
Abstract -
Airborne microorganisms have significant effects on human health, and children are more vulnerable to pathogens and allergens than adults. However, little is known about the microbial communities in the air of childcare facilities. Here, we analyzed the bacterial and fungal communities in 50 air samples collected from five daycare centers and five elementary schools located in Seoul, Korea using culture-independent high-throughput pyrosequencing. The microbial communities contained a wide variety of taxa not previously identified in child daycare centers and schools. Moreover, the dominant species differed from those reported in previous studies using culture-dependent methods. The well-known fungi detected in previous culture-based studies (Alternaria, Aspergillus, Penicillium, and Cladosporium) represented less than 12% of the total sequence reads. The composition of the fungal and bacterial communities in the indoor air differed greatly with regard to the source of the microorganisms. The bacterial community in the indoor air appeared to contain diverse bacteria associated with both humans and the outside environment. In contrast, the fungal community was largely derived from the surrounding outdoor environment and not from human activity. The profile of the microorganisms in bioaerosols identified in this study provides the fundamental knowledge needed to develop public health policies regarding the monitoring and management of indoor air quality.
An Appropriate Cutoff Value for Determining the Colonization of Helicobacter pyloriby the Pyrosequencing Method: Comparison with Conventional Methods
Jaeyeon Kim et al . DOI: 10.1111/hel.12214
Abstract -

Sequencing of 16S ribosomal RNA (rRNA) gene has improved the characterization of microbial communities. It enabled the detection of low abundance gastric Helicobacter pylori sequences even in subjects that were found to be H. pylori negative with conventional methods. The objective of this study was to obtain a cutoff value for H. pylori colonization in gastric mucosa samples by pyrosequencing method.

Characterization of the Fecal Microbial Communities of Duroc Pigs Using 16S rRNA Gene Pyrosequencing
Edward Alain B. Pajarillo et al . doi: 10.5713/ajas.14.0651
Abstract -
This study characterized the fecal bacterial community structure and inter-individual variation in 30-week-old Duroc pigs, which are known for their excellent meat quality. Pyrosequencing of the V1–V3 hypervariable regions of the 16S rRNA genes generated 108,254 valid reads and 508 operational taxonomic units at a 95% identity cut-off (genus level). Bacterial diversity and species richness as measured by the Shannon diversity index were significantly greater than those reported previously using denaturation gradient gel electrophoresis; thus, this study provides substantial information related to both known bacteria and the untapped portion of unclassified bacteria in the population. The bacterial composition of Duroc pig fecal samples was investigated at the phylum, class, family, and genus levels. Firmicutes and Bacteroidetes predominated at the phylum level, while Clostridia and Bacteroidia were most abundant at the class level. This study also detected prominent inter-individual variation starting at the family level. Among the core microbiome, which was observed at the genus level, Prevotella was consistently dominant, as well as a bacterial phylotype related to Oscillibacter valericigenes, a valerate producer. This study found high bacterial diversity and compositional variation among individuals of the same breed line, as well as high abundance of unclassified bacterial phylotypes that may have important functions in the growth performance of Duroc pigs.
Complete Genome Sequence of Bacillus amyloliquefacienssubsp. plantarum CC178, a Phyllosphere Bacterium Antagonistic to Plant Pathogenic Fungi
Byung-Yong Kim et al . doi: 10.1128/genomeA.01368-14
Abstract -

Bacillus amyloliquefaciens subsp. plantarum strain CC178 is a phyllosphere bacterium with antagonistic activity against a wide range of plant fungal pathogens. The genome of strain CC178 is 3,916,828 bp in size and harbors 3,972 genes. Six giant gene clusters are dedicated to the nonribosomal synthesis of antimicrobial polypeptides and polyketides. 

Effects of probiotic Enterococcus faeciumNCIMB 11181 administration on swine fecal microbiota diversity and composition using barcoded pyrosequencing
Edward Alain B. Pajarilloa et al . doi.org/10.1016/j.anifeedsci.2015.01.011
Abstract -
Although our understanding of probiotics is increasing, basic information regarding their effect on the composition of the gut microbiome is scarce. The purpose of this study was to characterize the fecal microbiota of weaned piglets before and after probiotic intervention. The probiotic bacterium Enterococcus faecium NCIMB 11181 was administered to pigs for 2 weeks and fecal bacterial diversity using 16S rRNA gene pyrosequencing was analyzed. A more stable bacterial community, as indicated by increased bacterial diversity and richness, was observed after administration of the probiotic, compared with the control group. Regardless of the diet, Firmicutes and Bacteroidetes were found to be the dominant bacterial phyla in the pigs; however, inhibition of Proteobacteria was clearly evident in the probiotic group. In addition, the probiotic-fed group featured elevated levels of Lactobacillus, Enterococcus, Oscillibacter, Succinivibro, and Clostridium genera and decreased levels of Escherichia and Dialister genera, compared with the control group. This study demonstrated that the probiotic E. faecium NCIMB 11181 modulates the fecal microbiota of weaned piglets. This modulation is characterized by an increase in other bacterial species including L. johnsonii, L. fermentum, and L. kimchii and several Clostridium spp., which might be beneficial to the health of weaned piglets.
The association of uterine cervical microbiota with an increased risk for cervical intraepithelial neoplasia in Korea
H.Y. Oh et al . doi.org/10.1016/j.cmi.2015.02.026
Abstract -
Recent studies have suggested potential roles of the microbiome in cervicovaginal diseases. However, there has been no report on the cervical microbiome in cervical intraepithelial neoplasia (CIN). We aimed to identify the cervical microbiota of Korean women and assess the association between the cervical microbiota and CIN, and to determine the combined effect of the microbiota and human papillomavirus (HPV) on the risk of CIN. The cervical microbiota of 70 women with CIN and 50 control women was analysed using pyrosequencing based on the 16S rRNA gene. The associations between specific microbial patterns or abundance of specific microbiota and CIN risk were assessed using multivariate logistic regression, and the relative excess risk due to interaction (RERI) and the synergy index (S) were calculated. The phyla Firmicutes, Actinobacteria, Bacteroidetes, Proteobacteria, Tenericutes, Fusobacteria and TM7 were predominant in the microbiota and four distinct community types were observed in all women. A high score of the pattern characterized by predominance of Atopobium vaginae, Gardnerella vaginalis and Lactobacillus iners with a minority of Lactobacillus crispatus had a higher CIN risk (OR 5.80, 95% CI 1.73‒19.4) and abundance of A. vaginae had a higher CIN risk (OR 6.63, 95% CI 1.61‒27.2). The synergistic effect of a high score of this microbial pattern and oncogenic HPV was observed (OR 34.1, 95% CI 4.95‒284.5; RERI/S, 15.9/1.93). A predominance of A. vaginae, G. vaginalis and L. iners with a concomitant paucity of L. crispatus in the cervical microbiota was associated with CIN risk, suggesting that bacterial dysbiosis and its combination with oncogenic HPV may be a risk factor for cervical neoplasia.
Molecular Analysis of Bacterial Microbiota on Brazilian Currency Note Surfaces
Tairacan Augusto Pereira da Fonseca et al . doi:10.3390/ijerph121013276
Abstract -
Currency notes have been implicated as a vehicle for transmitting community-acquired bacterial infections. However, the overall diversity of the bacterial population residing on banknotes is still unknown in Brazil. In this study, we aimed to investigate the overall bacterial population from 150 different Brazilian Rial (R$) notes in circulation using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Samples were randomly collected from three different street markets or “feiras” in the metropolitan region of São Paulo. Taxonomical composition revealed the abundance of Proteobacteria phyla, followed by Firmicutes and Streptophyta, with a total of 1193 bacterial families and 3310 bacterial genera. Most of these bacterial genera are of human, animal, and environmental origins. Also, our analysis revealed the presence of some potential pathogenic bacterial genera including Salmonella, Staphylococcus, and Klebsiella. The results demonstrate that there is a tremendous diversity of bacterial contamination on currency notes, including organisms known to be opportunistic pathogens. One of the factors that may contribute to the richness of bacterial diversity in currency notes is personal hygiene. Thus, our results underscore the need to increase public awareness of the importance of personal hygiene of money handlers who also handle food. 
Genome sequence of the moderately halophilic bacterium Salinicoccus carnicancri type strain CrmT(= DSM 23852T)
Dong-Wook Hyun et al . DOI: 10.4056/sigs.3967649
Abstract -
Salinicoccus carnicancri Jung et al. 2010 belongs to the genus Salinicoccus in the family Staphylococcaceae. Members of the Salinicoccus are moderately halophilic and originate from various salty environments. The halophilic features of the Salinicoccus suggest their possible uses in biotechnological applications, such as biodegradation and fermented food production. However, the genus Salinicoccus is poorly characterized at the genome level, despite its potential importance. This study presents the draft genome sequence of S. carnicancri strain CrmT and its annotation. The 2,673,309 base pair genome contained 2,700 protein-coding genes and 78 RNA genes with an average G+C content of 47.93 mol%. It was notable that the strain carried 72 predicted genes associated with osmoregulation, which suggests the presence of beneficial functions that facilitate growth in high-salt environments.
Fermented Green Tea Extract Alleviates Obesity and Related Complications and Alters Gut Microbiota Composition in Diet-Induced Obese Mice
Seo Dae-Bang et al . doi:10.1089/jmf.2014.3265.
Abstract -
Obesity is caused by an imbalance between caloric intake and energy expenditure and accumulation of excess lipids in adipose tissues. Recent studies have demonstrated that green tea and its processed products (e.g., oolong and black tea) are introduced to exert beneficial effects on lipid metabolism. Here, we propose that fermented green tea (FGT) extract, as a novel processed green tea, exhibits antiobesity effects. FGT reduced body weight gain and fat mass without modifying food intake. mRNA expression levels of lipogenic and inflammatory genes were downregulated in white adipose tissue of FGT-administered mice. FGT treatment alleviated glucose intolerance and fatty liver symptoms, common complications of obesity. Notably, FGT restored the changes in gut microbiota composition (e.g., the Firmicutes/Bacteroidetes and Bacteroides/Prevotella ratios), which is reported to be closely related with the development of obesity and insulin resistance, induced by high-fat diets. Collectively, FGT improves obesity and its associated symptoms and modulates composition of gut microbiota; thus, it could be used as a novel dietary component to control obesity and related symptoms.
Bacterial Community Diversity in Soil Under two Tillage Practices as Determined by Pyrosequencing
Aditi Sengupta et al . DOI: 10.1007/s00248-015-0609-4
Abstract -
The ability of soil to provide ecosystem services is dependent on microbial diversity, with 80–90 % of the processes in soil being mediated by microbes. There still exists a knowledge gap in the types of microorganisms present in soil and how soil management affects them. However, identification of microorganisms is severely limited by classical culturing techniques that have been traditionally used in laboratories. Metagenomic approaches are increasingly becoming common, with current high-throughput sequencing approaches allowing for more in-depth analysis. We conducted a preliminary analysis of bacterial diversity in soils from the longest continuously maintained no-till (NT) plots in the world (52 years) and in adjacent plow-till (PT) plots in Ohio, USA managed similarly except for tillage. Bacterial diversity was determined using a culture-independent approach of high-throughput pyrosequencing of the 16S rRNA gene. Proteobacteria and Acidobacteria were predominant in both samples but the NT soil had a higher number of reads, bacterial richness, and five unique phyla. Four unique phyla were observed in PT and 99 % of the community had relative abundance of <1 %. Plowing and secondary tillage tend to homogenize the soil and reduces the unique (i.e., diverse) microenvironments where microbial populations can reside. We conclude that tillage leads to fewer dominant species being present in soil and that these species contribute to a higher percentage of the total community.
Comparison of the gut microbiota profile in breast-fed and formula-fed Korean infants using pyrosequencing
Sang A Lee et al . doi.org/10.4162/nrp.2015.9.3.242
Abstract -
Feeding in infancy is the most significant determinant of the intestinal microbiota in early life. The aim of this study was to determine the gut microbiota of Korean infants and compare the microbiota obtained between breast-fed and formula-fed Korean infants.

The Effect of Probiotics on Gut Microbiota during the Helicobacter pylori Eradication Randomized Controlled Trial.
Bumjo Oh et al . DOI: 10.1111/hel.12270
Abstract -

Background

Helicobacter pylori causes chronic gastritis, gastroduodenal ulcers, and gastric cancer, and has been treated with two antibiotics (amoxicillin and clarithromycin) and proton-pump inhibitors (PPIs). However, antibiotic treatment alters the indigenous gut microbiota to cause side effects. Therefore, the effects of probiotic supplementation on therapy have been studied. Although several studies have covered the probiotics’ effects, details about the gut microbiota changes after H. pylori eradication have not been evaluated. Therefore, we analyzed the influences of antibiotics and their combination with probiotics on the composition of the gut microbiota using high-throughput sequencing.

Methods

Subjects were divided into two groups. The antibiotics group was treated with general therapy, and the probiotics group with general therapy and probiotic supplementation. Fecal samples were collected from all subjects during treatments, and the influences on gut microbiota were analyzed by 16S rRNA gene-pyrosequencing.

Results

Three phyla, Firmicutes, Bacteroidetes, and Proteobacteria, were predominant in the gut microbiota of all subjects. After treatment, the relative abundances of Firmicutes were reduced, whereas those of Proteobacteria were increased in both groups. However, the changed proportions of the gut microbiota in the antibiotics group were higher than those in the probiotics group. In addition, the increase in the levels of antibiotic-resistant bacteria was higher in the antibiotics group than in the probiotics one.

Conclusion

Probiotic supplementation can reduce the antibiotic-induced alteration and imbalance of the gut microbiota composition. This effect may restrict the growth of antibiotic-resistant bacteria in the gut and improve the H. pylori eradication success rate.


Draft genome sequence of the extremely halophilic archaeon Halococcus sediminicola CBA1101T isolated from a marine sediment sample
Kyung June Yim et al . Mar Genomics. 2014 Oct 22;18PB:145-146. doi: 10.1016/j.margen.2014.10.003
Abstract -
Halococcus sediminicola CBA1101T (=CECT 8275T, JCM 18965T) is an extremely halophilic strain isolated from a marine sediment collected from the bay of Gangjin in the Republic of Korea. We found that the draft genome of H. sediminicola CBA1101T contains 3,764,367bp, with 62.3% G+C content. This is the one of the few genomes to be sequenced in the genus Halococcus.

In vitro evaluation of the mucin-adhesion ability and probiotic potential of Lactobacillus mucosae LM1.
V.D. Valeriano et al . J Appl Microbiol. 2014 Aug;117(2):485-97. doi: 10.1111/jam.12539. Epub 2014 Jun 2.
Abstract -

AIMS:

In this report, we characterized the probiotic potential of Lactobacillus mucosae LM1, focusing on its in vitro mucin-adhesion abilities.

METHODS AND RESULTS:

Screening assays were used to evaluate LM1. Previous studies on Lact. mucosae species have been performed, but few have examined the ability of this species to adhere to and colonize the intestinal mucosa. Thus, adhesion, aggregation and pathogen inhibition assays of LM1 along with microbial adhesion to solvents (MATS) assay were carried out in comparison with another putative probioticLactobacillusjohnsonii PF01, and the commercial strain, Lactobacillus rhamnosus GG. Based on MATS assay, the cell surfaces of the lactobacilli strains were found to be hydrophobic and highly electron-donating, but the average hydropathy (GRAVY) index of predicted surface-exposed proteins in the LM1genome indicated that most were hydrophilic. LM1 showed the highest adhesion, aggregation and hydrophobicity among the strains tested and significantly inhibited the adhesion of Escherichia coli K88 and Salmonella enterica serovar Typhimurium KCCM 40253. Correlations among adhesion, aggregation and hydrophobicity, as well as between coaggregation and displacement of E. coli, were observed.

CONCLUSIONS:

Increased adhesion may not always correlate with increased pathogen inhibition due to various strain-specific mechanisms. Nevertheless, LM1 has promising probiotic properties that can be explored further using a genomics approach.

SIGNIFICANCE AND IMPACT OF THE STUDY:

Our data on adhesion of LM1 strain showed a significant correlation between adhesion, hydrophobicity of cell surface and autoaggregation. This study gives basic knowledge for the elucidation of the adhesion mechanism of Lactobacillussp. and prediction of its adherence in specific host models.


Seasonal Dynamics of Marine Microbial Community in the South Sea of Korea
Sung-Suk Suh et al . DOI: 10.1371/journal.pone.0131633
Abstract -

High-resolution 16S rRNA tag pyrosequencing was used to obtain seasonal snapshots of the bacterial diversity and community structure at two locations in Gosung Bay (South SeaKorea) over a one year period. Seasonal sampling from the water column at each site revealed highly diverse bacterial communities containing up to 900 estimated Operational Taxonomic Units (OTUs). The Alphaproteobacteria and Gammaproteobacteria were the most abundant groups, and the most frequently recorded OTUs were members of Pelagibacter and Glaciecola. In particular, it was observed that Arcobacter, a genus of the Epsilonproteobacteria, dominated during summer. In addition, Psedoalteromonadaceae, Vibrionaceae and SAR11-1 were predominant members of the OTUs found in all sampling seasons. Environmental factors significantly influenced the bacterialcommunity structure among season, with the phosphate and nitrate concentrations contributing strongly to the spatial distribution of the Alphaproteobacteria; the Gammaproteobacteria, Flavobacteria, and Actinobacteria all showed marked negative correlations with all measured nutrients, particularly silicon dioxide and chlorophyll-a. The results suggest that seasonal changes in environmental variables contribute to the dynamic structure of the bacterial community in the study area.

Fig 4. The distribution of OTUs among the seasonal bacterial communities in Gosung Bay.

Venn diagrams demonstrating 97% OTU cluster overlap within all seasonal samples (A) or between two different seasons (B). Numbers correspond to unique OTU clusters within a subset. To highlight shared OTUs, singleton clusters were removed before analysis.

 



Comparison of the genome profiles between head and body lice
Jae Soon Kang et al . doi:10.1016/j.aspen.2015.04.010
Abstract -

The body louse (Pediculus humanus humanus) is known to have diverged from the head louse (P. humanus capitis) but genomic differences between these two subspecies still remain unexplored. To compare genomic profiles between head and body lice, whole genome sequences of head lice were determined by next generation sequencing methods based on both Illumina Genome analyzer and Roche GS FLX pyrosequencing and compared with the reference genome sequences of the body louse. Total consensuses generated by mapping to the body louse genome in conjunction with de novo assembly of head louse genome sequences revealed a head louse genome size of 110 Mbp with a 96% coverage of the body louse genome sequences. A total of 12,651 genes were predicted from the head louse genome sequences although more precise assembly and functional annotation of the genome is required for a more accurate gene count. Among the 873 genes that were putatively specific to the head louse, 15 genes were confirmed to be transcribed in both head and body lice, suggesting the previously estimated gene number of the body louse was likely underestimated. The single nucleotide polymorphism analysis showed that the nucleotide diversity of genome between head and body lice was 2.2%, which was larger than that of the transcriptome between head and body lice. An endosymbiont genome analysis showed that the composition of endosymbionts in head lice was similar to that of body lice and Candidatus Riesia pediculicola was the primary endosymbiont in both head and body lice.



Comparative analysis of gut microbiota in elderly people of urbanized towns and longevity villages.
Se-Hoon Park et al . BMC Microbiol. 2015 Feb 26;15(1):49. doi: 10.1186/s12866-015-0386-8.
Abstract -

BACKGROUND:

To understand differences in the gut microbiota between elderly people of urbanized town communities (UTC) and longevity village communities (LVC), we analyzed fecal microbiota collected from individuals living in 2 UTC (Seoul and Chuncheon) and 3 LVC (Gurye, Damyang, and Soonchang) selected on the basis of indices for superlongevity (the ratio of centenarians to the total population) and longevity (the ratio of those aged 85 years or greater to those aged 65 years or greater) in South Korea by 454 pyrosequencing.

RESULTS:

Taxonomy-based analysis showed that The relative abundance of Firmicutes, Tenericutes, and Actinobacteria was significantly lower in LVC than in UTC. Due to an increase of Firmicutes and a reduction of Bacteroidetes, the ratio of Firmicutes to Bacteroidetes in the gut microbiota was greater in UTC adults than in UTC children or LVC adults. The population levels of Bacteroides, Prevotella, and Lachnospira were significantly higher in LVC than in UTC, but the levels of Dialister, Subdoligranulum, Megamonas, EF401882_g, and AM275436_g were lower in LVC than in UTC. Although most of the species detected in LVC were detected in UTC, some Bacteroides spp. and Faecalibacterium spp. were detected only in LVC. Among Bacteroides spp., ACWH_s, EF403317_s, and EF403722_s were detected in children and LVC samples only but FJ363527_s, 4P000677_s, and 4P000015_s were detected in UTC samples. EF402172_s and EF404388_s, members of Faecalibacterium spp., which are known to have anti-inflammatory properties, were detected in LVC and children only (>3.9% of total sequence). In addition, the fecal lipopolysaccharides (LPS) content was significantly higher in UTC than in LVC.

CONCLUSIONS:

These findings suggest that maintaining gut microbiota, including Faecalibacterium spp. EF402172_s and EF404388_s, as well as low LPS levels may play an important role in preserving residents' health in LVC.


Characterization of bacterial communities associated with seasonal water masses from Tongyoung in South Sea of Korea
Sung-Suk Suh et al . Ocean Science Journal September 2014, Volume 49, Issue 3, pp 193-200
Abstract -
Understanding the patterns of microbial diversity and their composition in seawater is necessary to assess the impacts of microbes on marine ecosystem. Although the potential roles of microbes in the ocean have been studied, their diversity and relationship with environmental factors remain unclear. In this study, we adopted a 16S rRNA gene tag-pyrosequencing technique to investigate the bacterial communities associated with two different water masses from Tongyoung in the South Sea of Korea. Our results revealed highly diverse bacterial communities up to 900 Operational Taxonomic Units (OTUs) estimated from each seawater which was collected in the month of March and May, when the environmental conditions including temperature differed significantly: 7.2°C and 17.6°C in March and May, respectively. Altogether, 13 bacterial phyla were recovered from the seawater, of which Proteobacteria was the most dominant group. In addition, the value of the Shannon index, which measures the evenness of the distribution of individuals among OTUs, in May is higher than that in March, indicating that it displays a wider diversity of bacteria. Interestingly, the proportion of pathogenic bacteria was significantly increased in the month of May compared to March, suggesting that pathogenic bacteria were increasingly emerging in May. In particular, Pseudoalteromonas and Vibrio spp. were determined as major pathogenic bacteria from both water masses, of which Vibrio spp. were dominant.

Subgingival microbiome in smokers and non-smokers in Korean chronic periodontitis patients
J.-H. Moon et al . Mol Oral Microbiol. 2015 Jun;30(3):227-41. doi: 10.1111/omi.12086. Epub 2014 Nov 19.
Abstract -
Smoking is a major environmental factor associated with periodontal diseases. However, we still have a very limited understanding of the relationship between smoking and subgingival microflora in the global population. Here, we investigated the composition of subgingival bacterial communities from the pooled plaque samples of smokers and non-smokers, 134 samples in each group, in Korean patients with moderate chronic periodontitis using 16S rRNA gene-based pyrosequencing. A total of 17,927 reads were analyzed and classified into 12 phyla, 126 genera, and 394 species. Differences in bacterial communities between smokers and non-smokers were examined at all phylogenetic levels. The genera Fusobacterium, Fretibacterium, Streptococcus, Veillonella,Corynebacterium, TM7, and Filifactor were abundant in smokers. On the other hand, Prevotella, Campylobacter, Aggregatibacter,Veillonellaceae GQ422718, Haemophilus, and Prevotellaceae were less abundant in smokers. Among species-level taxa occupying > 1% of whole subgingival microbiome of smokers, higher abundance (≥ 2.0-fold compared to non-smokers) of seven species or operational taxonomic units (OTUs) was found: Fusobacterium nucleatum, Neisseria sicca, Neisseria oralis, Corynebacterium matruchotii, Veillonella dispar, Filifactor alocis, and Fretibacterium AY349371. On the other hand, lower abundance of 11 species or OTUs was found in smokers: Neisseria elongata, six Prevotella species or OTUs, Fusobacterium canifelinum, AggregatibacterAM420165, Selenomonas OTU, and Veillonellaceae GU470897. Species richness and evenness were similar between the groups whereas diversity was greater in smokers than non-smokers. Collectively, the results of the present study indicate that differences exist in the subgingival bacterial community between smoker and non-smoker patients with chronic moderate periodontitis in Korea, suggesting that cigarette smoking considerably affects subgingival bacterial ecology.

Profiling bacterial community in upper respiratory tracts
Hana Yi et al . BMC Infect Dis. 2014 Nov 13;14(1):583.
Abstract -

BackgroundInfection by pathogenic viruses results in rapid epithelial damage and significantly impacts on the condition of the upper respiratory tract, thus the effects of viral infection may induce changes in microbiota. Thus, we aimed to define the healthy microbiota and the viral pathogen-affected microbiota in the upper respiratory tract. In addition, any association between the type of viral agent and the resultant microbiota profile was assessed.MethodsWe analyzed the upper respiratory tract bacterial content of 57 healthy asymptomatic people (17 health-care workers and 40 community people) and 59 patients acutely infected with influenza, parainfluenza, rhino, respiratory syncytial, corona, adeno, or metapneumo viruses using culture-independent pyrosequencing.ResultsThe healthy subjects harbored primarily Streptococcus, whereas the patients showed an enrichment of Haemophilus or Moraxella. Quantifying the similarities between bacterial populations by using Fast UniFrac analysis indicated that bacterial profiles were apparently divisible into 6 oropharyngeal types in the tested subjects. The oropharyngeal types were not associated with the type of viruses, but were rather linked to the age of the subjects. Moraxella nonliquefaciens exhibited unprecedentedly high abundance in young subjects aged <6 years. The genome of M. nonliquefaciens was found to encode various proteins that may play roles in pathogenesis.ConclusionsThis study identified 6 oropharyngeal microbiome types. No virus-specific bacterial profile was discovered, but comparative analysis of healthy adults and patients identified a bacterium specific to young patients, M. nonliquefaciens.



Comparative analysis of bacterial diversity and communities inhabiting the fairy ring of Tricholoma matsutake by barcoded pyrosequencing
Kim M et al . J Appl Microbiol. 2014 Sep;117(3):699-710. doi: 10.1111/jam.12572. Epub 2014 Jul 1.
Abstract -

Aims

Comparative analysis of the soil bacterial communities inhabiting the fairy ring of Tricholoma matsutake.

Methods and Results

The bacterial communities in soil samples collected from inside, beneath and outside the T. matsutake fairy ring were investigated using barcoded pyrosequencing. A total of 15 129 reads were obtained, and 500–536 operational taxonomic units were observed at a 97% similarity level. Taxonomic analysis showed similar taxa distribution patterns inside and beneath the fairy ring. Three bacterial phyla, Proteobacteria, Acidobacteria and Actinobacteria, were dominant in all sampling sites. A heat-map analysis of the bacterial genera showed that the uncultured bacterium EU445199 was remarkably abundant outside the fairy ring, and the uncultured bacteria GU727715 and DQ451510 were more and less abundant, respectively, beneath the fairy ring than inside and outside the fairy ring.

Conclusions

The results indicated that there was no significant difference in bacterial diversity inside, beneath and outside the fairy ring even thoughT. matsutake is predominant beneath the fairy ring.

Significance and Impact of the study

This study is the first report on the numerous culturable, unculturable and unclassified bacteria in the fairy ring of T. matsutake using the pyrosequencing method.


Metagenomic analysis of fungal communities inhabiting the fairy ring zone of Tricholoma matsutake.
Miae Kim et al . J Microbiol Biotechnol. 2013 Oct 28;23(10):1347-56.
Abstract -

Tricholoma matsutake, an ectomycorrhiza that has mutual relationships with the rootlet of Pinus denisflora, forms a fruiting body that serves as a valuable food in Asia. However, the artificial culture of this fungus has not been successful. Soil fungi, including T. matsutake, coexist with many other microorganisms and plants; therefore, complex microbial communities have an influence on the fruiting body formation of T. matsutake. Here, we report on the structures of fungal communities associated with the fairy ring of T. matsutake through the pyrosequencing method. Soil samples were collected inside the fairy ring zone, in the fairy ring zone, and outside the fairy ring zone. A total of 37,125 sequencing reads were obtained and 728 to 1,962 operational taxonomic units (OTUs) were observed in the sampling zones. The fairy ring zone had the lowest OTUs and the lowest fungal diversity of all sampling zones. The number of OTUs and fungal taxa inside and outside the fairy ring zone was, respectively, about 2 times and 1.5 times higher than the fairy ring. Taxonomic analysis showed that each sampling zone has different fungal communities. In particular, out of 209 genera total, 6 genera in the fairy ring zone, such as Hemimycena, were uniquely present and 31 genera, such as Mycena, Boletopsis, and Repetophragma, were specifically absent. The results of metagenomic analysis based on the pyrosequencing indicate a decrease of fungal communities in the fairy ring zone and changes of fungal communities depending on the fairy ring growth of T. matsutake.



First report on the whole genome sequence of Pseudomonas cichorii strain JBC1 and comparison with other Pseudomonas species
G. Ramkumar et al . DOI: 10.1111/ppa.12259
Abstract -

Pseudomonas cichorii, a plant pathogen that infects a wide range of host plants worldwide, causes several diseases in economically important vegetable crops. Availability of the genome sequences of pathogens can greatly enhance research necessary for the advancement of disease management programmes. Despite the significance of P. cichorii, its whole genome sequence has not been reported previously. The genome sequence of P. cichorii JBC1, described for the first time in this study, is 5 986 012 bp with an average GC content of 58·1% and has 5174 coding sequences (CDS). The genes related to virulence, transport mechanisms, phytotoxic compounds, and secondary metabolite products were analysed and the genome was compared to eight other Pseudomonas species to understand the diversity at species level. Despite the high similarity (up to 80·85%), significant diversity was found among the differentPseudomonas species at the genome level. A comparison of JBC1 pathogenicity island (PAI) regions indicated that the P. viridiflavaUASWS0038 PAI has more similarity than the P. syringae PAI region, and the analysis revealed significant divergence at PAI regions among the Pseudomonas species, providing an insight into the differences in host specificity and degree of virulence. In addition, JBC1 encodes antibiotic resistance and tolerance to heavy metals, and two different prophage segments were inserted at three different regions. The genome sequence of JBC1, which was deposited into the NCBI GenBank (accession no. CP007039), will be a reference sequence for other P. cichorii strains and a useful resource for further research.



A Vanillin Derivative Causes Mitochondrial Dysfunction and Triggers Oxidative Stress in Cryptococcus neoformans
Jin Hyo Kim et al . PLoS One. 2014 Feb 20;9(2):e89122. doi: 10.1371/journal.pone.0089122. eCollection 2014.
Abstract -

Vanillin is a well-known food and cosmetic additive and has antioxidant and antimutagenic properties. It has also been suggested to have antifungal activity against major human pathogenic fungi, although it is not very effective. In this study, the antifungal activities of vanillin and 33 vanillin derivatives against the human fungal pathogen Cryptococcus neoformans, the main pathogen of cryptococcal meningitis in immunocompromised patients, were investigated. We found a structural correlation between the vanillin derivatives and antifungal activity, showing that the hydroxyl or alkoxy group is more advantageous than the halogenated or nitrated group in benzaldehyde. Among the vanillin derivatives with a hydroxyl or alkoxy group, o-vanillin ando-ethyl vanillin showed the highest antifungal activity against C. neoformanso-Vanillin was further studied to understand the mechanism of antifungal action. We compared the transcriptome of C. neoformans cells untreated or treated with o-vanillin by using RNA sequencing and found that the compound caused mitochondrial dysfunction and triggered oxidative stress. These antifungal mechanisms of o-vanillin were experimentally confirmed by the significantly reduced growth of the mutants lacking the genes involved in mitochondrial functions and oxidative stress response.



Full-scale biological treatment of tannery wastewater using the novel microbial consortium BM-S-1
In-Soo Kim et al . J Environ Sci Health A Tox Hazard Subst Environ Eng. 2014;49(3):355-64. doi: 10.1080/10934529.2014.846707
Abstract -

In order to develop a more effective and eco-friendly treatment technology, a full-scale tannery wastewater treatment plant with a sludge digestion system was augmented with a novel microbial consortium (BM-S-1). The aim of this study was to determine if the BM-S-1 could successfully treat the tannery wastewater in a full-scale treatment system without chemical pretreatment and to investigate effect of the augmentation on sludge production. Chemical oxygen demand (COD), total nitrogen (TN), total phosphorus (TP), chromium (Cr) and mixed liquor suspended solids (MLSS) were measured to monitor treated water quality and treatment efficiency. Microbial community structures in the treatment were also examined using pyrosequencing analysis of 16S rRNA gene and quantitative PCR (qPCR) of the nitrous oxide reductase gene (nosZ). The removal efficiencies of COD, TN, TP, and Cr were estimated to be 98.3%, 98.6%, 93.6%, and 88.5%, respectively, while the system without a continuous augmentation was broken down. The pyrosequencing analysis showed Brachymonas denitrificans to be the most dominant microbial population in the buffering tank (B; 37.5%). Potential polymeric substance degraders (Clostridia), sulfate reducers (Desulfuromonas palmitatis), and sulfur oxidizers (uncultured Thiobacillus) were dominant in the sludge digestion (SD) tank. The denitrifiers assayed by nosZ qPCR were dominant in B and SD. These microbial communities appeared to play important roles in removing nutrients and odor, and reducing sludge in the wastewater treatment plant without chemical pretreatment.



Influence of Panax ginseng on obesity and gut microbiota in obese middle-aged Korean women
Mi-Young Song et al . dx.doi.org/10.1016/j.jgr.2013.12.004
Abstract -

Background

Gut microbiota is regarded as one of the major factors involved in the control of body weight. The antiobesity effects of ginseng and its main constituents have been demonstrated, but the effects on gut microbiota are still unknown.

Methods

To investigate the effect of ginseng on gut microbiota, 10 obese middle-aged Korean women took Panax ginseng extracts for 8 wk and assessment of body composition parameters, metabolic biomarkers, and gut microbiota composition was performed using 16S rRNA gene-based pyrosequencing at baseline and at 8 wk. Significant changes were observed in body weight and body mass index; however, slight changes were observed in gut microbiota. We divided the participants into two groups, the effective and the ineffective weight loss groups, depending on weight loss effect, in order to determine whether the antiobesity effect was influenced by the composition of gut microbiota, and the composition of gut microbiota was compared between the two groups.

Results

Prior to ginseng intake, significant differences of gut microbiota were observed between both at phyla and genera and the gut microbiota of the effective and ineffective weight loss groups was segregated on a principal coordinate analysis plot.

Conclusion

Results of this study indicate that ginseng exerted a weight loss effect and slight effects on gut microbiota in all participants. In addition, its antiobesity effects differed depending on the composition of gut microbiota prior to ginseng intake.


The anti-obesity effect of Ephedra sinica through modulation of gut microbiota in obese Korean women
Bong-Soo Kim et al . J Ethnopharmacol. 2014 Mar 28;152(3):532-9. doi: 10.1016/j.jep.2014.01.038.
Abstract -

Ethnopharmacological relevance

Ephedra sinica (Ma Huang) has been used in traditional Chinese medicine for more than 5000 years for treatment of various conditions, including modern-day obesity. Ephedra has been used as a supplement for weight loss and its effects have been reported. The current study investigated the influence of ephedra on the composition of gut microbiota, and its correlation with weight loss.

Materials and methods

Clinical data of subjects were measured at pre- and post-intake of ephedra (4 g of water extract, roughly equivalent of 24 g of crude herb), and analysis of the alteration of gut microbiota was performed simultaneously using 16S rRNA gene based pyrosequencing.

Results

Body weight (BW), body mass index (BMI), and body fat percentage of subjects were reduced after intake (p<0.05). In correlation analysis, SubdoligranulumOscillibacter, and Akkermansia showed an association with changes of BW and BMI (p<0.05). However, the alteration of gut microbiota varied by indigenous microbiota of each subject, and the dissimilarity between microbiota of subjects at pre- and post-intake were different.

Conclusions

The influences of gut microbiota are unique according to indigenous microbiota and differences in individual sensitivity to ephedra. Alteration of gut microbiota by ephedra intake showed correlation with loss of BW and BMI.


Comparison of Gut Microbiota between Sasang Constitutions
Bong-Soo Kim et al . Evid Based Complement Alternat Med. 2013;2013:171643. doi: 10.1155/2013/171643.
Abstract -

The Sasang constitutional medicine has long been applied to diagnose and treat patients with various diseases. Studies have been conducted for establishment of scientific evidence supporting Sasang Constitutional (SC) diagnosis. Recent human microbiome studies have demonstrated individual variations of gut microbiota which can be dependent on lifestyle and health conditions. We hypothesized that gut microbial similarities and discrepancies may exist across SC types. We compared the difference of gut microbiota among three constitutions (So-Yang, So-Eum, and Tae-Eum), along with the investigation of anthropometric and biochemical parameters. Firmicutes and Bacteroidetes were predominant phyla in all SC types. The median plot analysis suggested that Firmicutes and Bacteroidetes appeared more abundant in SE and TE, respectively, in the male subjects of 20–29 years old. At the genus level, Bifidobacterium and Bacteroides manifested the difference between SE and TE types. For anthropometry, body weight, body mass index, and waist circumference of the TE type were significantly higher than those of the other types. Overall, findings indicated a possible link between SC types and gut microbiota within a narrow age range. Further investigations are deemed necessary to elucidate the influences of age, gender, and other factors in the context of SC types and gut microbiota.



Genome sequence of type strain of Staphylococcus aureus subsp. aureus
Bong-Soo Kim et al . Gut Pathogens 2014, 6:6 doi:10.1186/1757-4749-6-6
Abstract -

Background

Staphylococcus aureus is a pathogen that causes food poisoning and community-associated infection with antibiotic resistance. This species is an indigenous intestinal microbe found in infants and not found in adult intestine. The relatively small genome size and rapid evolution of antibiotic resistance genes in the species have been drawing an increasing attention in public health. To extend our understanding of the species and use the genome data for comparative genomic studies, we sequenced the type strain of S. aureus subsp. aureus DSM 20231T.

Results

Seventeen contigs were generated using hybrid assembly of sequences derived from the Roche 454 and Illumina systems. The length of the genome sequence was 2,902,619 bases with a G + C content of 32.8%. Among the 2,550 annotated CDSs, 44 CDSs were annotated to antibiotic resistance genes and 13 CDSs were related to methicillin resistance. It is interesting to note that this strain was first isolated in 1884 before methicillin was generally used on patients.

Conclusions

The present study analyzed the genome sequence of S. aureus subsp. aureus type strain as the reference sequence for comparative genomic analyses of clinical isolates. Methicillin resistance genes found in the genome indicate the presence of antibiotic resistance mechanism prior to the usage of antibiotics. Further comparative genomic studies of methicillin-resistant strains based on this reference genome would help to understand the evolution of resistance mechanism and dissemination of resistance genes.

Keywords:
Staphylococcus aureus subsp. aureus; Genome sequencing; Type strain; Hybrid assembly

Transcriptomic Analysis of Genes Modulated by Cyclo(L-Phenylalanine-L-Proline) in Vibrio vulnificus
In Hwang Kim et al . J Microbiol Biotechnol. 2013 Dec 28;23(12):1791-801.
Abstract -
Diketopiperazine is produced by various organisms, including bacteria, fungi, and animals, and has been suggested as a novel signal molecule involved in the modulation of genes with various biological functions. Vibrio vulnificus, which causes septicemia in humans, produces cyclo(L-phenylalanine-L-proline) (cFP). To understand the biological roles of cFP, the effect of the compound on the expression of the total mRNA in V. vulnificus was assessed by nextgeneration sequencing. Based on the transcriptomic analysis, we classified the cFP-regulated genes into functional categories and clustered them according to the expression patterns resulted from treatment with cFP. From a total of 4,673 genes, excepting the genes encoding tRNA in V. vulnificus, 356 genes were up-regulated and 602 genes were down-regulated with an RPKM (reads per kilobase per million) value above 3. The genes most highly induced by cFP comprised those associated with the transport and metabolism of inorganic molecules, particularly iron. The genes negatively regulated by cFP included those associated with energy production and conversion, as well as carbohydrate metabolism. Noticeably, numerous genes related with biofilm formation were modulated by cFP. We demonstrated that cFP interferes significantly with the biofilm formation of V. vulnificus.

The Genome Sequence of ‘Mycobacterium massiliense’ Strain CIP 108297 Suggests the Independent Taxonomic Status of the Mycobacterium abscessus Complex at the Subspecies Level
Yong-Joon Cho et al . PLoS One. 2013 Nov 27;8(11):e81560. doi: 10.1371/journal.pone.0081560.
Abstract -
Members of the Mycobacterium abscessus complex are rapidly growing mycobacteria that are emerging as human pathogens. The M. abscessus complex was previously composed of three species, namely M. abscessus sensu stricto, 'M. massiliense', and 'M. bolletii'. In 2011, 'M. massiliense' and 'M. bolletii' were united and reclassified as a single subspecies within M. abscessus: M. abscessus subsp. bolletii. However, the placement of 'M. massiliense' within the boundary of M. abscessus subsp. bolletii remains highly controversial with regard to clinical aspects. In this study, we revisited the taxonomic status of members of the M. abscessus complex based on comparative analysis of the whole-genome sequences of 53 strains. The genome sequence of the previous type strain of 'Mycobacterium massiliense' (CIP 108297) was determined using next-generation sequencing. The genome tree based on average nucleotide identity (ANI) values supported the differentiation of 'M. bolletii' and 'M. massiliense' at the subspecies level. The genome tree also clearly illustrated that 'M. bolletii' and 'M. massiliense' form a distinct phylogenetic clade within the radiation of the M. abscessus complex. The genomic distances observed in this study suggest that the current M. abscessus subsp. bolletii taxon should be divided into two subspecies, M. abscessus subsp. massiliense subsp. nov. and M. abscessus subsp. bolletii, to correspondingly accommodate the previously known 'M. massiliense' and 'M. bolletii' strains.

Genomic versatility and functional variation between two dominant heterotrophic symbionts of deep-sea Osedax worms
Shana K Goffredi et al . ISME J. 2013 Nov 14. doi: 10.1038/ismej.2013.201
Abstract -
An unusual symbiosis, first observed at ~3000m depth in the Monterey Submarine Canyon, involves gutless marine polychaetes of the genusOsedax and intracellular endosymbionts belonging to the order Oceanospirillales. Ecologically, these worms and their microbial symbionts have a substantial role in the cycling of carbon from deep-sea whale fall carcasses. Microheterogeneity exists among the Osedax symbionts examined so far, and in the present study the genomes of the two dominant symbionts, Rs1 and Rs2, were sequenced. The genomes revealed heterotrophic versatility in carbon, phosphate and iron uptake, strategies for intracellular survival, evidence for an independent existence, and numerous potential virulence capabilities. The presence of specific permeases and peptidases (of glycine, proline and hydroxyproline), and numerous peptide transporters, suggests the use of degraded proteins, likely originating from collagenous bone matter, by the Osedax symbionts.13C tracer experiments confirmed the assimilation of glycine/proline, as well as monosaccharides, by Osedax. The Rs1 and Rs2 symbionts are genomically distinct in carbon and sulfur metabolism, respiration, and cell wall composition, among others. Differences between Rs1 and Rs2 and phylogenetic analysis of chemotaxis-related genes within individuals of symbiont Rs1 revealed the influence of the relative age of the whale fall environment and support possible local niche adaptation of ‘free-living’ lifestages. Future genomic examinations of other horizontally-propogated intracellular symbionts will likely enhance our understanding of the contribution of intraspecific symbiont diversity to the ecological diversification of the intact association, as well as the maintenance of host diversity.

Temporal shifts in cyanobacterial communities at different sites on the Nakdong River in Korea
Moonsuk Hur et al . Water Res. 2013 Oct 20. pii: S0043-1354(13)00823-3. doi: 10.1016/j.watres.2013.09.058.
Abstract -

The studies of cyanobacterial blooms resulting from eutrophication or climate change and investigation of changes in the cyanobacterial community in freshwater environments are critical for the management of drinking water. Therefore, we investigated the cyanobacterial communities at 6 sites along the Nakdong River in South Korea from May 2012 to October 2012 by using high-throughput sequencing techniques and studied their relationship with various geochemical factors at sampling sites. Diverse genera (total of 175 genera) were detected within the cyanobacteria, and changes in their compositions were analyzed. The genus Prochlorococcus predominated in the May samples, especially in those obtained from the upstream part of the river, whereas the relative abundance of Microcystis and Anabaena increased with increase in water temperature. The relationship between the cyanobacterial community and environmental factors was analyzed by canonical correlation analysis, and the correlation between harmful cyanobacteria and chemical factors was analyzed by nonmetric multidimensional scaling ordination. Various environmental factors such as dissolved oxygen, pH, electric conductivity, temperature were found to affect the cyanobacterial communities in the river. The results of this study could help in the management of freshwater environments and in maintenance of drinking water quality.

 

Double pie charts of typical cyanobacterial communities in samples from each month were compared. The inner pie indicates the class composition and the outer pie indicates the genus composition of the cyanobacterial communities. The names for each color appear below the figure. The nomenclature for each phylotype is based on the EzTaxon-e database (Kim et al., 2012http://eztaxon-e.ezbiocloud.net/).


An eco-friendly treatment of tannery wastewater by bioaugmentation of a novel microbial consortium
In-Soo Kim et al . J. Environ. Sci. Health, Part A. 2013, 48, 1732-1739.
Abstract -

A novel microbial consortium (BM-S-1) enriched from natural soils was successfully used to treat tannery wastewater from leather manufacturing industries in Korea on a pilot scale. The objective of this study was to determine whether augmentation with a novel microbial consortium BM-S-1could successfully treat the recalcitrant wastewater without chemical pre-treatment in a tannery wastewater treatment system. Chemical oxygen demand (COD), total nitrogen (TN) and total phosphorus (TP) were monitored for water quality. The microbial population dynamics were analyzed using pyrosequencing, and denitrifying bacteria were quantified using real-time PCR (RT-PCR). The removal efficiencies for COD, TN and TP were greater than 91%, 79%, and 90%, respectively. The dominant phyla in the buffering tank (B), primary aeration (PA), secondary aeration (SA) and sludge digestion tank (SD) were Proteobacteria, Firmicutes, Bacteroidetes, Planctomycetes and Deinococcus-Thermus. Cluster analysis based on the UniFrac distance of the species in the different stages showed that the PA is similar to the SA, whereas the B is similar to the SD. qPCR of the nosZ genes showed the highest abundance of denitrifiers in B, which was increased 734-fold compared to the influent (I). It was hypothesized that anaerobic denitrifiers and the diverse microbial community may play important roles in the biological treatment of tannery wastewater. This technology may also contribute to the full-scale treatment of industrial wastewater containing food processing wastewater and marine sediment with high organic content.

Fig. 2 Rarefaction curves of the five different samples from the pilot wastewater treatment system. I, influent; B, buffering tank; PA, primary aeration tank; SA, secondary aeration tank; SD, sludge digestion tank. The sample size was normalized by random subtraction


Identification of household bacterial community and analysis of species shared with human microbiome
Yoon-Seong Jeon et al . Curr. Microbiol.2013, Doi:10.1007/s00284-013-0401-y.
Abstract -

Microbial populations in indoor environments, where we live and eat, are important for public health. Various bacterial species reside in the kitchen, and refrigerators, the major means of food storage within kitchens, can be a direct source of food borne illness. Therefore, the monitoring of microbiota in the refrigerator is important for food safety. We investigated and compared bacterial communities that reside in the vegetable compartment of the refrigerator and on the seat of the toilet, which is recognized as highly colonized by microorganisms, in ten houses using high-throughput sequencing. Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were predominant in refrigerator and toilet samples. However, Proteobacteria was more abundant in the refrigerator, and Firmicutes was more abundant in the toilet. These household bacterial communities were compared with those of human skin and gut to identify potential sources of household bacteria. Bacterial communities from refrigerators and toilets shared more species in common with human skin than gut. Opportunistic pathogens, including Propionibacterium acnes, Bacteroides vulgatus, and Staphylococcus epidermidis, were identified as species shared with human skin and gut microbiota. This approach can provide a general background of the household microbiota and a potential method of source-tracking for public health purposes.

 

Fig. 1

The average compositions of bacterial communities obtained from the vegetable compartments of refrigerators and from toilets using culture-independent method were analyzed and compared. a The compositions of phyla detected in refrigerators and toilet samples were compared. The phylum represented by each color is defined below figure. b The compositions of the top ten genera detected in each sample were compared. The names of the genera appear below the figure. The nomenclatures of phylotypes are based on the EzTaxon-e database (Kim et al., 2012; http://eztaxon-e.ezbiocloud.net/)


Settling and dewatering characteristics of mixed microorganisms according to changes in the SRT
Kwang Ho Ahn et al . Desalination and Water Treatment 2013. doi: 10.1080/19443994.2013.780768.
Abstract -

This study was carried out to evaluate the settleability and dewaterability of mixed microorganisms according to the changes in sludge retention time (SRT) after mixing granulated methane-oxidizing bacteria and activated sludge (AS). The results of increasing SRT of microorganisms from 15 to 20 days showed that the settling rate of microorganisms increased, while specific resistance to filtration decreased. From the results of analyzing extracellular polymeric substances (EPS), no significant change was found in the bound EPS, but total soluble EPS showed a tendency to decrease as the SRT increased from 15 to 20 days. The average particle size of the mixed microorganisms was two to three times larger than that of the general AS, and as the SRT increased, the average particle size also increased, indicating that there is a close correlation between SRT and granule formation. The results of analyzing microbial community in SRT 15 and 20 days showed the dominance of Proteobacteria at long SRT.

Fig. 7 Double pie charts of bacterial communities in SRT 15 and 20 days were compared. Inner circle indicates phylum composition of community and outer circle indicates genus composition of samples. The differences of communities in SRT 15 day and 20 day were observed.


Supplementation of Lactobacillus curvatus HY7601 and Lactobacillus plantarum KY1032 in Diet-Induced Obese Mice Is Associated with Gut Microbial Changes and Reduction in Obesity
Do-Young Park et al . PLoS One 2013, e59470, doi:10.1371/journal.pone.0059470
Abstract -

Objective

To investigate the functional effects of probiotic treatment on the gut microbiota, as well as liver and adipose gene expression in diet-induced obese mice.

Design

Male C57BL/6J mice were fed a high-fat diet (HFD) for 8 weeks to induce obesity, and then randomized to receive HFD+probiotic (Lactobacillus curvatus HY7601 and Lactobacillus plantarum KY1032, n = 9) or HFD+placebo (n = 9) for another 10 weeks. Normal diet (ND) fed mice (n = 9) served as non-obese controls.

Results

Diet-induced obese mice treated with probiotics showed reduced body weight gain and fat accumulation as well as lowered plasma insulin, leptin, total-cholesterol and liver toxicity biomarkers. A total of 151,061 pyrosequencing reads for fecal microbiota were analyzed with a mean of 6,564, 5,274 and 4,464 reads for the ND, HFD+placebo and HFD+probiotic groups, respectively. Gut microbiota species were shared among the experimental groups despite the different diets and treatments. The diversity of the gut microbiota and its composition were significantly altered in the diet-induced obese mice and after probiotic treatment. We observed concurrent transcriptional changes in adipose tissue and the liver. In adipose tissue, pro-inflammatory genes (TNFα, IL6, IL1β and MCP1) were down-regulated in mice receiving probiotic treatment. In the liver, fatty acid oxidation-related genes (PGC1α, CPT1, CPT2 and ACOX1) were up-regulated in mice receiving probiotic treatment.

Conclusions

The gut microbiota of diet-induced obese mice appears to be modulated in mice receiving probiotic treatment. Probiotic treatment might reduce diet-induced obesity and modulate genes associated with metabolism and inflammation in the liver and adipose tissue.


Carbon nanotubes as plant growth regulators: effects on tomato growth, reproductive system, and soil microbial community.
Mariya V. Khodakovskaya et al . Small. 2013 Jan 14;9(1):115-23. doi: 10.1002/smll.201201225. Epub 2012 Sep 28.
Abstract -

Multi-walled carbon nanotubes (CNTs) can affect plant phenotype and the composition of soil microbiota. Tomato plants grown in soil supplemented with CNTs produce two times more flowers and fruit compared to plants grown in control soil. The effect of carbon nanotubes on microbial community of CNT-treated soil is determined by denaturing gradient gel electrophoresis and pyrosequencing analysis. Phylogenetic analysis indicates that Proteobacteria and Bacteroidetes are the most dominant groups in the microbial community of soil. The relative abundances of Bacteroidetes and Firmicutes are found to increase, whereas Proteobacteria and Verrucomicorbia decrease with increasing concentration of CNTs. The results of comparing diversity indices and species level phylotypes (OTUs) between samples showed that there is not a significant affect on bacterial diversity.

Figure  6 .      The analysis of common and different OTUs among control and CNT-treated samples obtained from pyrosequencing data. The upper numbers indicate the number of OTUs and numbers in the blank are total read numbers of each OTU. Most of the sequences were common among the three CNT-treated soil samples.



A defect in iron uptake enhances the susceptibility of Cryptococcus neoformans to azole antifungal drugs
Jeongmi Kim et al . Fungal Genet Biol. 2012 Nov;49(11):955-66. doi: 10.1016/j.fgb.2012.08.006. Epub 2012 Sep 4.
Abstract -

The high-affinity reductive iron uptake system that includes a ferroxidase (Cfo1) and an iron permease (Cft1) is critical for the pathogenesis of Cryptococcus neoformans. In addition, a mutant lacking CFO1 or CFT1 not only has reduced iron uptake but also displays a markedly increased susceptibility to azole antifungal drugs. Altered antifungal susceptibility of the mutants was of particular interest because the iron uptake system has been proposed as an alternative target for antifungal treatment. In this study, we used transcriptome analysis to begin exploring the molecular mechanisms of altered antifungal susceptibility in a cfo1 mutant. The wild-type strain and the cfo1 mutant were cultured with or without the azole antifungal drug fluconazole and their transcriptomes were compared following sequencing with Illumina Genome Analyzer IIx (GAIIx) technology. As expected, treatment of both strains with fluconazole caused elevated expression of genes in the ergosterol biosynthetic pathway that includes the target enzyme Erg11. Additionally, genes differentially expressed in the cfo1 mutant were involved in iron uptake and homeostasis, mitochondrial functions and respiration. The cfo1 mutant also displayed phenotypes consistent with these changes including a reduced ratio of NAD+/NADH and down-regulation of Fe–S cluster synthesis. Moreover, combination treatment of the wild-type strain with fluconazole and the respiration inhibitor diphenyleneiodonium dramatically increased susceptibility to fluconazole. This result supports the hypothesis that down-regulation of genes required for respiration contributed to the altered fluconazole susceptibility of the cfo1 mutant. Overall, our data suggest that iron uptake and homeostasis play a key role in antifungal susceptibility and could be used as novel targets for combination treatment of cryptococcosis. Indeed, we found that iron chelation in combination with fluconazole treatment synergistically inhibited the growth of C. neoformans.

Fig. 2. Sequence read mapping statistics and representative transcript signals at the CFO1 locus. (A) Each bar represents the total number of sequence reads obtained. The reads that mapped to the reference genome (Cryptococcus neoformans var. grubii H99) are shown in red and those that failed to map to the genome are shown in blue. (B) Representative RNA sequencing data from the wild-type strain (WT) or the cfo1 mutant (cfo1Δ) grown in YPD, show the expression at the CFO1 locus of each strain. Boxes with blue borders represent the RT-PCR results confirming the existence of transcript signals, and no RT-PCR signal was detected from the region of the CFO1 locus (CNAG_06241) in the cfo1 mutant (thus illustrating the reliability of the RNA-Seq data). Light blue boxes in the lower panel represent predicted open reading frames and black vertical bars represent stop codons in the reference genome. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)


Draft Genome Sequencing of Bacillus sp. Strain M2-6, Isolated from the Roots of Korean Ginseng, Panax ginseng C. A. Meyer, after High-Hydrostatic-Pressure Processing
Chong-Tai Kim et al . J. Bacteriol. December 2012 vol. 194 no. 24 7003-7004
Abstract -
A bacterium, designated M2-6, was isolated from Korean ginseng, Panax ginseng C. A. Meyer, roots after high-hydrostatic-pressure processing. On the basis of 16 rRNA gene phylogeny, the isolate was presumptively identified as a Bacillus sp. Here we report the draft genome sequence of Bacillus sp. strain M2-6 (= KACC 16563).

Effects of Crude Oil, Dispersant, and Oil-Dispersant Mixtures on Human Fecal Microbiota in an In Vitro Culture System
Jong Nam Kim et al . MBio. 2012 Oct 23;3(5). pii: e00376-12. doi: 10.1128/mBio.00376-12.
Abstract -

The Deepwater Horizon oil spill of 2010 raised concerns that dispersant and dispersed oil, as well as crude oil itself, could contaminate shellfish and seafood habitats with hazardous residues that had potential implications for human health and the ecosystem. However, little is known about the effects of crude oil and dispersant on the human fecal microbiota. The aim of this research was to evaluate the potential effects of Deepwater Horizon crude oil, Corexit 9500 dispersant, and their combination on human fecal microbial communities, using an in vitro culture test system. Fecal specimens from healthy adult volunteers were made into suspensions, which were then treated with oil, dispersant, or oil-dispersant mixtures under anaerobic conditions in an in vitro culture test system. Perturbations of the microbial community, compared to untreated control cultures, were assessed using denaturing gradient gel electrophoresis (DGGE), real-time PCR, and pyrosequencing methods. DGGE and pyrosequencing analysis showed that oil-dispersant mixtures reduced the diversity of fecal microbiota from all individuals. Real-time PCR results indicated that the copy numbers of 16S rRNA genes in cultures treated with dispersed oil or oil alone were significantly lower than those in control incubations. The abundance of the Bacteroidetes decreased in crude oil-treated and dispersedoil-treated cultures, while the Proteobacteria increased in cultures treated with dispersed oil. In conclusion, the human fecal microbiota was affected differently by oil and dispersed oil, and the influence of dispersed oil was significantly greater than that of either oil or dispersant alone compared to control cultures.

FIG 2 Comparison of fecal microbiotas from the three individuals studied in this investigation.Proportions of phyla (A), proportions of genera withinFirmicutes (B), and proportions of genera within Bacteroidetes (C). Uc_Veillonellaceae, uncultured Veillonellaceae.

FIG 3 Changes of microbial composition after exposure of three human fecal microbiota cultures to crude oil (A1, B1, and C1) or to dispersed oil(A2, B2, and C2). Relative abundance was obtained from 16S rRNA pyrosequencing. The compositions of intestinal microbiota from individual A (A1 and A2), individual B (B1 and B2), and individual C (C1 and C2) were compared with different concentrations of crude oil, crude oil-dispersant mixtures, and control incubations.


Draft Genome Sequence of Klebsiella pneumoniae subsp. pneumoniae DSM 30104T.
Je Hee Lee et al . J Bacteriol. 2012 Oct;194(20):5722-3.
Abstract -
Klebsiella pneumoniae is a Gram-negative, rod-shaped, nonmotile, and opportunistic pathogenic species with clinical importance. It is a part of natural flora of humans and animals. Here we report the draft genome sequence of the type strain of Klebsiella pneumoniae subsp. pneumoniae (DSM 30104T) to provide taxonomic and functional insights into the species.

Draft Genome Sequence of Weissella koreensis KCTC 3621T.
Je Hee Lee et al . J Bacteriol. 2012 Oct;194(20):5711-2.
Abstract -
Weissella koreensis is a Gram-positive, rod-shaped, nonmotile, and facultative anaerobic species belonging to the lactic acid bacteria (LAB). The members of this species have been repeatedly isolated from kimchi (a traditional Korean fermented food) and are known for their beneficial effects on human and animal intestinal microflora through producing various clinically important amino acids such as γ-aminobutyric acid and ornithine. Here we report the genome sequence of the type strain of W. koreensis (KCTC 3621T) to provide taxonomic and functional insights into the species.

Genome Sequence of Pectin-Degrading Alishewanella aestuarii Strain B11T, Isolated from Tidal Flat Sediment.
Jaejoon Jung et al . J Bacteriol. 2012 Oct;194(19):5476. doi: 10.1128/JB.01255-12.
Abstract -
We present the genome sequence of Alishewanella aestuarii B11T (=KCTC 22051T=DSM 19476T). This species, isolated from tidal flat sediment, was reported to be a novel species. A. aestuarii is known to degrade pectin, an important component of plant cell wall. The presence of the genes related to pectin metabolism in this strain indicates its capability to utilize pectin.

Draft Genome Sequence of Escherichia coli W26, an Enteric Strain Isolated from Cow Feces.
Mincheol Kim et al . J Bacteriol. 2012 Sep;194(18):5149-50. doi: 10.1128/JB.01180-12.
Abstract -
An enteric bacterium, Escherichia coli W26 (KACC 16630), was isolated from feces from a healthy cow in South Korea. Here, we report the draft genome sequence of the isolate, which is closely affiliated with commensal strains belonging to E. coli phylogroup B1.

Genome Sequence of Pectin-Degrading Alishewanella agri, Isolated from Landfill Soil.
Jisun Kim et al . J Bacteriol. 2012 Sep;194(18):5135-6. doi: 10.1128/JB.01129-12.
Abstract -
Alishewanella agri BL06T (= KCTC 22400T = JCM 15597T) was isolated from landfill soil in Pohang, South Korea. A. agri showed the ability to degrade pectin, a structural heteropolysaccharide present in the cell wall of plants. Here we report the genome sequence of Alishewanella agri BL06T, the second sequenced strain in the genus Alishewanella.

Genome Sequence of Lactobacillus mucosae LM1, Isolated from Piglet Feces.
Je Hee Lee et al . J Bacteriol. 2012 Sep;194(17):4766. doi: 10.1128/JB.01011-12.
Abstract -
Lactobacillus mucosae LM1, isolated from stool samples of a healthy piglet, displays good in vitro mucin adhesion and antimicrobial activity against pathogenic bacteria. To elucidate its antimicrobial effects and to find its epithelial cell and mucin adhesion genes, the genomic sequence of L. mucosae LM1 was investigated.

Elevational patterns in archaeal diversity on mt. Fuji.
Dharmesh Singh et al . PLoS One. 2012;7(9):e44494. doi: 10.1371/journal.pone.0044494. Epub 2012 Sep 6.
Abstract -

Little is known of how archaeal diversity and community ecology behaves along elevational gradients. We chose to study Mount Fuji of Japan as a geologically and topographically uniform mountain system, with a wide range of elevational zones. PCR-amplified soil DNA for the archaeal 16 S rRNA gene was pyrosequenced and taxonomically classified against EzTaxon-e archaeal database. At a bootstrap cut-off of 80%, most of the archaeal sequences were classified into phylum Thaumarchaeota (96%) and Euryarchaeota (3.9%), with no sequences classified into other phyla. Archaeal OTU richness and diversity on Fuji showed a pronounced ‘peak’ in the mid-elevations, around 1500 masl, within the boreal forest zone, compared to the temperate forest zone below and the alpine fell-field and desert zones above. Diversity decreased towards higher elevations followed by a subtle increase at the summit, mainly due to an increase in the relative abundance of the group I.1b of Thaumarchaeota. Archaeal diversity showed a strong positive correlation with soil NH4+, K and NO3. Archaeal diversity does not parallel plant diversity, although it does roughly parallel bacterial diversity. Ecological hypotheses to explain the mid diversity bulge on Fuji include intermediate disturbance effects, and the result of mid elevations combining a mosaic of upper and lower slope environments. Our findings show clearly that archaeal soil communities are highly responsive to soil environmental gradients, in terms of both their diversity and community composition. Distinct communities of archaea specific to each elevational zone suggest that many archaea may be quite finely niche-adapted within the range of soil environments. A further interesting finding is the presence of a mesophilic component of archaea at high altitudes on a mountain that is not volcanically active. This emphasizes the importance of microclimate – in this case solar heating of the black volcanic ash surface – for the ecology of soil archaea.

Figure 6. Neighbor joining tree based on the alignment of 16S rRNA gene sequences (~400 bp long) showing the relationship between archaeal phylotypes (DFT: Dominant Fuji Thaumarchaeota and DFE: Dominant Fuji Euryarchaeota) recovered from Mt. Fuji by pyrosequencing.


Draft Genome Sequence of Staphylococcus saprophyticus subsp. saprophyticus M1-1, Isolated from the Gills of a Korean Rockfish, Sebastes schlegeli Hilgendorf, after High Hydrostatic Pressure Processing
Bong-Soo Kim et al . J Bacteriol. 2012 Aug;194(16):4441-2. doi: 10.1128/JB.00848-12.
Abstract -
A bacterium designated M1-1 was isolated from the gills of a Korean rockfish, Sebastes schlegeli Hilgendorf, after high hydrostatic pressure processing. Studies of 16S rRNA phylogeny and comparative genomics demonstrated that the isolate belongs to Staphylococcus saprophyticus subsp. saprophyticus. Here, we report the draft genome sequence of S. saprophyticus subsp. saprophyticus M1-1 (KACC 16562).

Complete genome sequence of Mycobacterium intracellulare clinical strain MOTT-36Y, belonging to the INT5 genotype.
Byoung-Jun Kim et al . J Bacteriol. 2012 Aug;194(15):4141-2.
Abstract -
Here we report the complete genome sequence of the Mycobacterium intracellulare clinical strain MOTT-36Y, previously grouped into the INT5 genotype among the 5 genotypes of M. intracellulare. This genome sequence will serve as a valuable reference for understanding the disparity in virulence and epidemiologic traits between M. intracellulare-related strains.

Tropical soil bacterial communities in Malaysia: pH dominates in the equatorial tropics too
Binu M. Tripathi et al . Microb Ecol. 2012 Aug;64(2):474-84. Epub 2012 Feb 23.
Abstract -

The dominant factors controlling soil bacterial community variation within the tropics are poorly known. We sampled soils across a range of land use types—primary (unlogged) and logged forests and crop and pasture lands in Malaysia. PCR-amplified soil DNA for the bacterial 16S rRNA gene targeting the V1–V3 region was pyrosequenced using the 454 Roche machine. We found that land use in itself has a weak but significant effect on the bacterial community composition. However, bacterial community composition and diversity was strongly correlated with soil properties, especially soil pH, total carbon, and C/N ratio. Soil pH was the best predictor of bacterial community composition and diversity across the various land use types, with the highest diversity close to neutral pH values. In addition, variation in phylogenetic structure of dominant lineages (AlphaproteobacteriaBeta/GammaproteobacteriaAcidobacteria, and Actinobacteria) is also significantly correlated with soil pH. Together, these results confirm the importance of soil pH in structuring soil bacterial communities in Southeast Asia. Our results also suggest that unlike the general diversity pattern found for larger organisms, primary tropical forest is no richer in operational taxonomic units of soil bacteria than logged forest, and agricultural land (crop and pasture) is actually richer than primary forest, partly due to selection of more fertile soils that have higher pH for agriculture and the effects of soil liming raising pH.

Figure 5

a Relative abundances of dominant bacterial taxa in soils with different pH levels. b The heat map shows the relative abundances of the 30 most abundant OTUs in soils with different pH levels with a color legend and scale provided


Genome sequence of Escherichia coli J53, a reference strain for genetic studies.
Hana Yi et al . J Bacteriol. 2012 Jul;194(14):3742-3.
Abstract -
Escherichia coli J53 (F met pro Azir) is a derivative of E. coli K-12 which is resistant to sodium azide. This strain has been widely used as a general recipient strain for various conjugation experiments. Here, we report the genome sequence of E. coli J53 (=KACC 16628).

Microbial population dynamics and proteomics in membrane bioreactors with enzymatic quorum quenching
Hak-Woo Kim et al . Appl Microbiol Biotechnol. 2012 Jul 31.
Abstract -

Quorum sensing gives rise to biofilm formation on the membrane surface, which in turn causes a loss of water permeability in membrane bioreactors (MBRs) for wastewater treatment. Enzymatic quorum quenching was reported to successfully inhibit the formation of biofilm in MBRs through the decomposition of signal molecules, N-acyl homoserine lactones (AHLs). The aim of this study was to elucidate the mechanisms of quorum quenching in more detail in terms of microbial population dynamics and proteomics. Microbial communities in MBRs with and without a quorum quenching enzyme (acylase) were analyzed using pyrosequencing and compared with each other. In the quorum quenching MBR, the rate of transmembrane pressure (TMP) rise-up was delayed substantially, and the proportion of quorum sensing bacteria with AHL-like autoinducers (such asEnterobacterPseudomonas, and Acinetobacter) also decreased in the entire microbial community of mature biofilm in comparison to that in the control MBR. These factors were attributed to the lower production of extracellular polymeric substances (EPS), which are known to play a key role in the formation of biofilm. Proteomic analysis using the Enterobacter cancerogenus strain ATCC 35316 demonstrates the possible depression of protein expression related to microbial attachments to solid surfaces (outer membrane protein, flagellin) and the agglomeration of microorganisms (ATP synthase beta subunit) with the enzymatic quorum quenching. It has been argued that changes in the microbial population, EPS and proteins via enzymatic quorum quenching could inhibit the formation of biofilm, resulting in less biofouling in the quorum quenching MBR.

Fig. 5 (%) Proportions of EnterobacterPseudomonas, and Acinetobacter at a genus level in biofilm samples of control and quorum quenching MBRs


Impact of enrofloxacin on the human intestinal microbiota revealed by comparative molecular analysis
Bong-Soo Kim et al . Anaerobe. 2012 Jun;18(3):310-20. Epub 2012 Feb 3.
Abstract -

The indigenous human intestinal microbiota could be disrupted by residues of antibiotics in foods as well as therapeutically administered antibiotics to humans. These disruptions may lead to adverse health outcomes. To observe the possible impact of residues of antibiotics at concentrations below therapeutic levels on human intestinal microbiota, we performed studies using in vitro cultures of fecal suspensions from three individuals with 10 different concentrations (0, 0.1, 0.5, 1, 5, 10, 15, 25, 50 and 150 μg/ml) of the fluoroquinolone, enrofloxacin. The bacterial communities of the control and enrofloxacin dosed fecal samples were analyzed by denaturing gradient gel electrophoresis (DGGE) and pyrosequencing. In addition, changes of functional gene expression were analyzed by a pyrosequencing-based random whole-community mRNA sequencing method. Although each individual had a unique microbial composition, the communities of all individuals were affected by enrofloxacin. The proportions of two phyla, namely, Bacteroidetes and Proteobacteria, were significantly reduced with increasing concentrations of enrofloxacin exposure, while the proportion of Firmicutes increased. Principal Coordinate Analysis (PCoA) using the Fast UniFrac indicated that the community structures of intestinal microbiota were shifted by enrofloxacin. Most of the mRNA transcripts and the anti-microbial drug resistance genes increased with increasing concentrations of enrofloxacin. 16S rRNA gene pyrosequencing of control and enrofloxacin treated fecal suspensions provided valuable information of affected bacterial taxa down to the species level, and the community transcriptomic analyses using mRNA revealed the functional gene expression responses of the changed bacterial communities by enrofloxacin.

Fig. 2. Relative abundance of phyla classified from pyrosequencing data of individual samples. The phyla were selected by the abundance greater than 0.1% of total analyzed reads inany of sample.

Fig. 4. Principal coordinate analysis (PCoA) of community structures using a Fast UniFrac distance matrix. (A) All concentrations of enrofloxacin treated samples (0e150 mg/ml) fromthree individuals were compared. The samples originating from individual B were separated from those from the other two individuals. (B) Low concentrations of enrofloxacintreated samples (0e5 mg/ml) were compared.


Complete genome sequence of Mycobacterium intracellulare clinical strain MOTT-02.
Byoung-Jun Kim et al . J Bacteriol. 2012 May;194(10):2771. doi: 10.1128/JB.00365-12.
Abstract -
Here, we report the first complete genome sequence of the Mycobacterium intracellulare clinical strain MOTT-02, which was previously grouped in the INT2 genotype of M. intracellulare. This genome sequence will serve as a valuable reference for improving the understanding of the disparity in the virulence and epidemiologic traits between M. intracellulare genotypes.

Draft genome sequence of Mycobacterium abscessus subsp. bolletii BD(T).
Go-Eun Choi et al . J Bacteriol. 2012 May;194(10):2756-7. doi: 10.1128/JB.00354-12.
Abstract -
Mycobacterium abscessus subsp. bolletii is an increasing cause of human pulmonary disease and infections of the skin and soft tissues. Consistent reports of human infections indicate that M. bolletii is a highly pathogenic, emerging species of rapidly growing mycobacteria (RGM). Here we report the first whole-genome sequence of M. abscessus subsp. bolletii BDT.

Complete genome sequence of Mycobacterium intracellulare strain ATCC 13950(T).
Byoung-Jun Kim et al . J Bacteriol. 2012 May;194(10):2750. doi: 10.1128/JB.00295-12.
Abstract -
Here we report the first complete genome sequence of Mycobacterium intracellulare ATCC 13950T, a Mycobacterium avium complex (MAC) strain. This genome sequence will serve as a valuable reference for understanding the epidemiologic, biological, and pathogenic aspects of the disparity between MAC members.

Bacterial community analysis during fermentation of ten representative kinds of kimchi with barcoded pyrosequencing.
Eun-Jin Park et al . Food Microbiol. 2012 May;30(1):197-204. Epub 2011 Oct 19.
Abstract -
Park et al. investigated bacterial community in ten representative kinds of kimchi during the fermentation (4℃ for 30-35 days). They found that bacterial communities differed between starter-inoculated and non-inoculated kimchi at the early stages of fermentation, whereas there were no significant differences in the late phases. This study provides the comprehensive understanding of the factors influencing the biodiversity of the kimchi ecosystem.

Relative abundance of bacterial genera (>1% of the total sequences) obtained from pyrosequencing analysis in kimchi samples.

Genome sequence of extracellular-protease-producing Alishewanella jeotgali isolated from traditional Korean fermented seafood.
Jaejoon Jung et al . J Bacteriol. 2012 Apr;194(8):2097.
Abstract -
Alishewanella jeotgali MS1T (= KCTC 22429T = JCM 15561T) was isolated from a traditional Korean fermented seafood, gajami sikhae (jeotgal), and has been reported as a novel species. A. jeotgali was proven to have extracellular proteolytic activity, which may play an important role in the fermentation environment of food containing fish flesh. Here, we present the genome sequence of Alishewanella jeotgali MS1T as the first sequenced strain in the genus Alishewanella and its taxonomic relatives.

Distinctive phyllosphere bacterial communities in tropical trees.
Mincheol Kim et al . Microb Ecol. 2012 Apr;63(3):674-81. Epub 2011 Oct 12.
Abstract -
Kim et al. studied the phyllosphere bacterial community on leaves of six species of tropical trees at rainforest arboretum in Malaysia. Acidobacteria were one of the most abundant phyla across all samples. They found that the phyllosphere bacterial community shows a significant tendency to follow host plant phylogeny, with more similar communities on more closely related hosts.

NMDS plots showing the clustering pattern between samples based on Unifrac distance (a) and Bray-Curtis dissimilarity (b).

Comparative genomics of Neisseria weaveri clarifies the taxonomy of this species and identifies genetic determinants that may be associated with virulence
Hana Yi et al . FEMS Microbiol Lett. 2012 Mar;328(2):100-5. doi: 10.1111/j.1574-6968.2011.02485.x. Epub 2012 Jan 6.
Abstract -

A group of bacterial strains formerly known as CDC group M-5 are opportunistic pathogens to humans. In 1993, a name, Neisseria weaveri, was proposed by two independent studies to harbor CDC group M-5 strains, namely N. weaveri Holmes et al. 1993 andN. weaveri Andersen et al. 1993, with two different ‘type’ strains. However, no study has been conducted on to the relatedness of the two ‘type’ strains, although the close relationship of the two taxa has long been accepted unofficially. Formally, the status of the nameN. weaveri Andersen et al. 1993 is illegitimate because it is a later homonym of N. weaveri Holmes et al., 1993; but the name of the strain is still validly published. In this study, we attempt to resolve the confusion caused by the apparent duplication of the species N. weaveri(with different type strains) using whole genome shotgun sequencing. We also sought to gain insight into the genetic characteristics ofN. weaveri by conducting comparative genomics. On the basis of genomic similarities revealed through a comparative genomic study, we propose that N. weaveri Andersen et al. 1993 should be re-classified as a later heterotypic synonym of N. weaveri Holmes et al., 1993.

Fig. 16S rRNA gene-based neighbor-joining tree showing the evolutionary relationships among 48 Neisseria strains.


Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species.
Ok-Sun Kim et al . Int J Syst Evol Microbiol. 2012 Mar;62(Pt 3):716-21. Epub 2011 Nov 25.
Abstract -

Despite recent advances in commercially optimized identification systems, bacterial identification remains a challenging task in many routine microbiological laboratories, especially in situations where taxonomically novel isolates are involved. The 16S rRNA gene has been used extensively for this task when coupled with a well-curated database, such as EzTaxon, containing sequences of type strains of prokaryotic species with validly published names. Although the EzTaxon database has been widely used for routine identification of prokaryotic isolates, sequences from uncultured prokaryotes have not been considered. Here, we formally introduce the next generation database, named EzTaxon-e. This new database covers not only species within the formal nomenclatural system but also phylotypes that may represent species in nature. In addition to an identification function based on Basic Local Alignment Search Tool (BLAST) searches and pairwise global sequence alignments, a new objective method of assessing the degree of completeness in sequencing has been proposed. All sequences that are held in the EzTaxon-e database have been subjected to phylogenetic analysis, and this has resulted in a complete hierarchical classification system. We conclude that the EzTaxon-e database provides a useful taxonomic backbone for the identification of cultured and uncultured prokaryotes, and offers valuable means of communication among microbiologists who routinely encounter taxonomically novel isolates. The database and its analytical functions can be found at http://eztaxon-e.ezbiocloud.net/.

Figure 2. Overall workflow of the identification and completeness calculation  349 implemented in EzTaxon-e database


A hump-backed trend in bacterial diversity with elevation on Mount Fuji, Japan.
Dharmesh Singh et al . Microb Ecol. 2012 Feb;63(2):429-37. Epub 2011 Jul 7.
Abstract -
A team led by Prof. Jonathan M. Adams studied the trend of bacterial diversity with elevation on Mount Fuji in Japan. There was a significant ‘peak’ in total bacterial diversity at around 2,500 m above the tree line with a decline towards the highest elevations around 3,700 m near the summit. At the highest elevations, fewer bacterial species are capable of surviving.

Left figure presents relative abundances of dominant bacterial taxa at different elevational sampling points. Right figure presents the heatmap of relative percentage of the given 60 abundant phylotypes.

Correlation between microbial community structure and biofouling in a laboratory scale membrane bioreactor with synthetic wastewater.
SooYeon Lim et al . Desalination in press(2011) doi:10.1016/j.desal. 2011.09.030
Abstract -
Lim et al. investigated the influences of microbial community structure to the fouling process and the potential for quorum sensing in a laboratory-scale membrane bioreactor (MBR). Microbial community structure was greatly changed during continuous MBR operation. Enterobacter cancerogenus is a dominant member in both of culture-dependent and independent approaches.

Pyrosequencing-based molecular monitoring of the intestinal bacterial colonization in preterm infants.
Chang JY et al . J Pediatr Gastroenterol Nutr. (2011, Nov) 53(5):512-519.
Abstract -
A team at Department of Pediatrics, Seoul National University investigated the diversity of neonatal intestinal microbiota and monitored colonization patterns in Korean preterm infants. The results of this study could provide basic information of investigating and interpreting the role of intestinal microbiota in certain preterm infant diseases.

Effect of genetically modified poplars on soil microbial communities during the phytoremediation of waste mine tailings.
Hur M et al . Appl Environ Microbiol. 2011 Nov;77(21):7611-9. Epub 2011 Sep 2.
Abstract -
A comparative analysis of the bacterial and archaeal communities between the rhizosphere of genetically modified (GM) and wild-type (WT) poplar was performed at different growth stages of trees. Hur et al. found that poplar type and growth stages were associated with directional changes in the structure of the microbial community. A rate of metal accumulation was higher in GM poplars than in naturally occurring plants, which resulted in greater changes in soil environments and hence the microbial habitat.

Comparative approach to capture bacterial diversity of coastal waters.
Na H et al . J Microbiol. 2011 Oct;49(5):729-40. Epub 2011 Nov 9.
Abstract -
Bacterial diversity of coastal water samples using different methods were compared with each other. The comparison of common molecular and cultivation techniques detailed in this study.

Genome sequence of Lactobacillus salivarius GJ-24, a probiotic strain isolated from healthy adult intestine.
Cho YJ et al . J Bacteriol. 2011 Sep;193(18):5021-2 Epub 2011 Jul 8.
Abstract -
The draft genome sequence of Lactobacillus salivarius GJ-24 isolated from the feces of healthy adults was determined. Its properties, including milk fermentation activity and bacteriocin production, suggest its potential uses as a probiotic lactic acid bacterium and start culture for dairy products.

Genome sequence of Lactobacillus johnsonii PF01, isolated from piglet feces.
Lee JH et al . J Bacteriol. 2011 Sep;193(18):5030-1 Epub 2011 Jul 8.
Abstract -
Lactobacillus johnsonii PF01, an autochthonous bacterium of the gastrointestinal tract, was isolated from a fecal sample from a piglet. The strain adhered specifically to the duodenal and jejunal epithelial cells of the piglet and had high bile resistance activity. Here we report the genomic sequence of L. johnsonii PF01.

Genome sequence of Lactobacillus ruminis SPM0211, isolated from a fecal sample from a healthy Korean.
Lee S et al . J Bacteriol. 2011 Sep;193(18):5034. Epub Epub 2011 Jul 8.
Abstract -
Lactobacillus ruminis SPM0211 is a potential probiotic strain that shows antimicrobial activity against emerging pathogens. Here we present the draft genomic sequence of L. ruminis SPM0211, isolated from a fecal sample from a healthy Korean and describe both the common and unique features of this strain.

Draft genome sequence of Shewanella sp. strain HN-41, which produces arsenic-sulfide nanotubes.
Kim DH et al . J. Bacteriol. (2011, Sep) 193(18):5039-40.
Abstract -
A team led by Prof. Hor-Gil Hur sequenced and reported the high quality draft genome of Shewanella sp. srain HN-41. Shewanella spp. are known for their versatile electron-accepting capacities, which allow them to couple the decomposition of organic matter to the reduction of various terminal electron acceptors, such as As(V), Fe(III), Mn(IV), Se(IV), Te(IV), and U(VI), under anaerobic conditions. Strain HN-41 produces an extensive extracellular network of filamentous arsenic-sulfide (As-S) nanotubes via the reduction of As(V) and S2O32− under anaerobic conditions. This interesting strain has a potential for the production of diverse structures of nanomaterials through the reduction of metal(loid)s, and genome sequence should facilitate the understanding of its nanotube generation.

As-S nanotubes formed by Shewanella sp. strain HN-41 (Jiang et al. 2009)

Draft genome sequence of Methylophaga aminisulfidivorans MP T.
Han GH et al . J Bacteriol. 2011 Aug;193(16):4265. Epub 2011 Jun 17.
Abstract -
Methylophaga aminisulfidivorans MP(T) is a restricted facultatively marine methylotrophic bacterium that grows on methanol, methylated amines, dimethyl sulfide, and dimethyl sulfoxide. Here we present the high-quality draft genome sequence of M. aminisulfidivorans MP(T) (KCTC 12909(T) = JCM 14647(T)), consisting of a chromosome (3,092,085 bp) and a plasmid (16,875 bp).

In Vitro culture conditions for maintaining a complex population of human gastrointestinal tract microbiota.
Kim BS et al . J Biomed Biotechnol. 2011;2011:838040. Epub 2011 Jul 24.
Abstract -
Kim et al. reported the conditions to support the growth of a wide range of intestinal bacteria and maintain a complex microbial community representative of the human gastrointestinal tract using molecular methods. These conditions could be applied to several in vitro model of human gastrointestinal tract.

Genome sequence of Escherichia coli AA86, isolated from cow feces.
Yi H et al . J Bacteriol. 2011 Jul;193(14):3681. Epub 2011 May 20.
Abstract -
Escherichia coli AA86 (=KACC 15541) is an enteric bacterium that was isolated from a sample of healthy cow feces. Its genome sequence revealed that it is most closely related to the human fecal strain E. coli SE15 and could be classified under E. coli phylogenetic group B2. Here, we report the genome sequence of E. coli AA86, consisting of 3 contigs and 2 plasmids.

Analyses of bacterial communities in Meju, a Korean traditional fermented soybean bricks, by cultivation-based and pyrosequencing methods.
Kim YS et al . J Microbiol. 2011 Jun;49(3):340-8. Epub 2011 Jun 30.
Abstract -
Kim et al. studied the bacterial communities in Meju, which is raw material for Korean soy sauce and soybean paste, using both of culture-dependent and independent methods. Bacillus and lactic acid bacteria were dominant groups in different samples. The bacterial communities in Meju were very diverse and a complex microbial consortium containing various microorganisms than expected. EzTaxon-e database was used to assign taxonomic information.

Intestinal bacterial community in the food waste-reducing larvae.
Jeon H et al . Curr Microbiol. 2011 May;62(5):1390-9. Epub 2011 Jan 26.
Abstract -
Jeon et al. investigated the intestinal bacterial community in the food waste-reducing larvae of Hermetia illucens. They analyzed the bacterial community in the gut of BSF (Black Soldier Fly) larvae and their study can apply to efficient degradation of organic compounds.

Comparative genomics of clinical and environmental Vibrio mimicus.
Hasan NA et al . Proc Natl Acad Sci U S A. 2010 Dec 7;107(49):21134-9.
Epub 2010 Nov 15.
Abstract -

Pathogenicity islands found in the genome of V. mimicus.

Genome comparison of V. mimicus MB451 and reference genomes. From the outer ring to the inner ring: Vibrio fischeri MJ11, Vibrio harveyi ATCC BAA-1116, Vibrio mimicus VM223, Vibrio parahaemolyticus RIMD 2210633, Vibrio vulnificus CMCP6, Vibrio cholerae O1 El Tor N16961, and Vibrio cholerae O395. Horizontal lines are drawn to separate chromosomes and plasmid. Arrow indicates area of rearrangement or insertion. Whether Vibrio mimicus is a variant of Vibrio cholerae or a separate species has been the subject of taxonomic controversy. A genomic analysis was undertaken to resolve the issue. The genomes of V. mimicus MB451, a clinical isolate, and VM223, an environmental isolate, comprise ca. 4,347,971 and 4,313,453 bp and encode 3,802 and 3,290 ORFs, respectively. As in other vibrios, chromosome I (C-I) predominantly contains genes necessary for growth and viability, whereas chromosome II (C-II) bears genes for adaptation to environmental change. C-I harbors many virulence genes, including some not previously reported in V. mimicus, such as mannose-sensitive hemagglutinin (MSHA), and enterotoxigenic hemolysin (HlyA); C-II encodes a variant of Vibrio pathogenicity island 2 (VPI-2), and Vibrio seventh pandemic island II (VSP-II) cluster of genes. Extensive genomic rearrangement in C-II indicates it is a hot spot for evolution and genesis of speciation for the genus Vibrio. The number of virulence regions discovered in this study (VSP-II, MSHA, HlyA, type IV pilin, PilE, and integron integrase, IntI4) with no notable difference in potential virulence genes between clinical and environmental strains suggests these genes also may play a role in the environment and that pathogenic strains may arise in the environment. Significant genome synteny with prototypic pre-seventh pandemic strains of V. cholerae was observed, and the results of phylogenetic analysis support the hypothesis that, in the course of evolution, V. mimicus and V. cholerae diverged from a common ancestor with a prototypic sixth pandemic genomic backbone.

Genomic evolution of Vibrio cholerae.
Cho YJ et al . Curr Opin Microbiol. 2010 Oct;13(5):646-51. Epub 2010 Sep 17.
Abstract -
Vibrio cholera, the causal agent of cholera, also occupies an autochthonous aquatic inhabitant. The current, seventh cholera pandemic is linked to O1 El Tor biotype and O139 serogroups. In the last decades, we have witnessed a shift involving genetically and phenotypically varied pandemic clones in Asia and Africa. Recent comparative genomic studies have identified a large 'mobilome', or composed of mobile genomic islands in V. cholerae. All seventh pandemic isolates have highly related genome sequences, but they can be differentiated by set of these genomic islands. A consequence of the extensive lateral gene transfer is that classically important diagnostic markers, such as serotype and biotype, are not reliable and new methods based on genomic sequences are required.

Genome comparison of V. mimicus MB451 and reference genomes. From the outer ring to the inner ring: Vibrio fischeri MJ11, Vibrio harveyi ATCC BAA-1116, Vibrio mimicus VM223, Vibrio parahaemolyticus RIMD 2210633, Vibrio vulnificus CMCP6, Vibrio cholerae O1 El Tor N16961, and Vibrio cholerae O395. Horizontal lines are drawn to separate chromosomes and plasmid. Arrow indicates area of rearrangement or insertion.

Use of barcoded pyrosequencing and shared OTUs to determine sources of fecal bacteria in watersheds.
Unno T et al . Environ Sci Technol. 2010 Oct 15;44(20):7777-82.
Abstract -
Unno et al. developed a new library-dependent microbial source tracking (MST) methods uing pyrosequencing-derived shared operational taxonomic units (OTUs) to define sources of fecal contamination in waterways. Their results indicated the analysis of shared OTUS using pyrosequening provide the necessary resolution and discrimination to be useful MST studies. Pyroseqeuncing reads were assigned species using EzTaxon-e database in this study.

Mouse oral bacteriome has been revealed.
Chun J et al . BMC Microbiol. 2010 Apr 6;10:101.
Abstract -
A team of researchers at Seoul National University revealed the bacterial community of laboratory mice and found that there are substantial differences among different individuals even though they are maintained under controlled conditions. This is the first publication applying new version of Roche 454 GS-FLX pyrosequencing (called Titanium) and the Chunlab’s bioinformatics pipeline to the microbial community study.

Bacterial community structure of laboratory mice

Complete Genome Sequence of Strain IMCC9063, Belonging to SAR11 Subgroup 3, Isolated from the Arctic Ocean.
Hyun-Myung Oh et al . J Bacteriol. 2011 Jul;193(13):3379-80. doi: 10.1128/JB.05033-11. Epub 2011 Apr 22.
Abstract -
Strain IMCC9063 is a novel isolate of the SAR11 clade and is distantly related to other cultured representatives in this clade. The strain was isolated off the coast of Svalbard, Norway, by applying high-throughput culturing methods based on dilution to extinction. Here we present the finished genome sequence of strain IMCC9063.

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