Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes

Guo, Jiarong; Cole, James R.; Zhang, Qingpeng; Brown, C. Titus; Tiedje, James M.

doi:10.1128/AEM.02772-15

Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes

Journal Article · Fri Oct 16 04:00:00 EDT 2015 · Applied and Environmental Microbiology

DOI:https://doi.org/10.1128/AEM.02772-15· OSTI ID:1470720

Guo, Jiarong ^[1]; Cole, James R. ^[2]; Zhang, Qingpeng ^[2]; Brown, C. Titus ^[3]; Tiedje, James M. ^[2]

Michigan State Univ., East Lansing, MI (United States); Michigan State Univ., East Lansing, MI (United States)
Michigan State Univ., East Lansing, MI (United States)
Michigan State Univ., East Lansing, MI (United States); Univ. of California, Davis, CA (United States)

Shotgun metagenomic sequencing does not depend on gene-targeted primers or PCR amplification; thus, it is not affected by primer bias or chimeras. However, searching rRNA genes from large shotgun Illumina data sets is computationally expensive, and no approach exists for unsupervised community analysis of small-subunit (SSU) rRNA gene fragments retrieved from shotgun data. We present a pipeline, SSUsearch, to achieve the faster identification of short-subunit rRNA gene fragments and enabled unsupervised community analysis with shotgun data. It also includes classification and copy number correction, and the output can be used by traditional amplicon analysis platforms. Shotgun metagenome data using this pipeline yielded higher diversity estimates than amplicon data but retained the grouping of samples in ordination analyses. We applied this pipeline to soil samples with paired shotgun and amplicon data and confirmed bias against Verrucomicrobia in a commonly used V6-V8 primer set, as well as discovering likely bias against Actinobacteria and for Verrucomicrobia in a commonly used V4 primer set. In conclusion, this pipeline can utilize all variable regions in SSU rRNA and also can be applied to large-subunit (LSU) rRNA genes for confirmation of community structure.

View Accepted Manuscript (DOE)

Research Organization:: Michigan State Univ., East Lansing, MI (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: SC0004601

OSTI ID:: 1470720

Journal Information:: Applied and Environmental Microbiology, Journal Name: Applied and Environmental Microbiology Journal Issue: 1 Vol. 82; ISSN 0099-2240

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

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