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Fungi are major players in many ecosystems, including soil, food and human skin. Even though the identification of fungi in nature has been improved by the introduction of molecular phylogenetic markers such as the ITS of rRNA operon, deciphering whole communities of existing fungal species in a given sample has been a challenge to scientists who are trying to understand their role in nature. Next generation sequencing (NGS), particularly used for the long reads it generates, can provide massive sequencing of each phylogenetic marker, therefore dissecting the actual community structure of fungal species in multiple samples under consideration. Here, we introduce easy yet comprehensive NGS coupled with bioinformatics service solutions for fungal community analysis.
ChunLab provides 3 options for fungal community analysis to meet your needs
Our end-to-end service allows us to ensure quality control at every step of the process to provide clients with the highest rate of success and meaningful downstream results. Just send us your metagenomic DNA sample and we will do the rest. Our full service solution includes:
  • Library preparation / PCR amplification using barcoded fusion primers
  • Pyrosequencing using Roche 454, which are known for providing long, high quality reads
  • Pyrosequencing performed on the internal transcribed spacer (ITS2) region, which has been recommended as the universal fungal barcode (Schoch et al., 2012).
  • Average of 5,000 reads per sample with reads lengths of >300 bp to provide precise taxonomic assignments
  • Superior phylogenetic identification and taxonomic assignment of each read at the species level based on the highly curated EzFungi database*
  • Comprehensive bioinformatics: Chimera checks, alpha and beta diversity indices, rarefaction curves, environmental correlations, UniFrac multivariate analysis, etc.
  • Dedicated software tool, CLcommunity™, that allows you to browse your taxonomic compositions, perform high quality comparative analysis and create publication ready charts and figures instantaneously.

*EzFungi Database: the EzFungi database is specifically designed for routine identification of fungal strains using fungal ITS sequences. EzFungi has 17,000+ fungi species as of Feb. 2014.
ChunLab’s Full Service Fungal Community Analysis Workflow
If you have several samples and are looking for a cheaper option, you can carry out PCR amplification yourself and simply send us the pooled PCR products for sequencing and bioinformatics. We recommend multiplexing 10-15 samples per run on the Roche 454 platform. For amplicon sequencing, PCR products have to be linked with certain adaptors to generate appropriate libraries for next generation sequencing. Our recommended procedure for amplification library preparation can be found here.

Keep in mind, PCR amplification requires some skill and experience as improper protocols that contaminate reagents can produce false and misleading results. Therefore, unless you have extensive experience with PCR amplification for fungal community analysis, we do not recommend that you perform PCR amplification yourself.
If you have raw pyrosequenced data (sff file), from Roche 454 Junior or GS FLX, that you would like to browse and analyze using our CLcommunity software, contact us to get your data analyzed and converted for our software. Contact us at to see how we can help you more easily discover your data.
Publications related to microbial community analysis using NGS
Fungal Community Analysis
Fungal community analysis by high-throughput sequencing of amplified markers – a user's guide
Lindahl et al. New Phytol. 2013 July; 199(1): 288–299. Published online 2013 March 28. doi: 10.1111/nph.12243

Improved Selection of Internal Transcribed Spacer-Specific Primers Enables Quantitative, Ultra-High-Throughput Profiling of Fungal Communities
N. Bokulich et al. Appl Environ Microbiol. 2013 April; 79(8): 2519–2526. doi: 10.1128/AEM.03870-12

Soil Ecology/Science
Light Structures Phototroph, Bacterial and Fungal Communities at the Soil Surface
L. O. Davies et al. PLoS One. 2013; 8(7): e69048.

Differences in Soil Fungal Communities between European Beech (Fagus sylvatica L.) Dominated Forests Are Related to Soil and Understory Vegetation
T. Wubet et al. PLoS One. 2012; 7(10): e47500.

Human Skin Microbiome
Human Skin Fungal Diversity
K. Findley et al. Nature. 2013 June 20; 498(7454): 367–370.

Skin microbiome: genomics-based insights into the diversity and role of skin microbes
Heidi H. Kong Trends Mol Med. 2011 June; 17(6): 320–328.
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Data generated by ChunLab is for research purposes only. It is not intended for diagnostic use.
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