Microbial community analysis with ribosomal gene fragments from shotgun metagenomes

Jiarong Guo, James R. Cole, Qingpeng Zhang, Charles Brown, James M. Tiedje

Research output: Contribution to journalArticle

18 Citations (Scopus)

Abstract

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. 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. The pipeline can scale to handle large amounts of soil metagenomic data (5 Gb memory and 5 central processing unit hours to process 38 Gb [1 lane] of trimmed Illumina HiSeq2500 data) and is freely available at https: //github.com/dib-lab/SSUsearch under a BSD license.

Original languageEnglish (US)
Pages (from-to)157-166
Number of pages10
JournalApplied and Environmental Microbiology
Volume82
Issue number1
DOIs
StatePublished - Jan 1 2016

Fingerprint

Metagenome
Firearms
microbial communities
microbial community
ribosomal RNA
rRNA Genes
gene
Verrucomicrobia
Genes
Metagenomics
genes
Soil
chimerism
Actinobacteria
chimera
Licensure
community structure
soil sampling
analysis
ordination

ASJC Scopus subject areas

  • Biotechnology
  • Food Science
  • Applied Microbiology and Biotechnology
  • Ecology

Cite this

Microbial community analysis with ribosomal gene fragments from shotgun metagenomes. / Guo, Jiarong; Cole, James R.; Zhang, Qingpeng; Brown, Charles; Tiedje, James M.

In: Applied and Environmental Microbiology, Vol. 82, No. 1, 01.01.2016, p. 157-166.

Research output: Contribution to journalArticle

Guo, Jiarong ; Cole, James R. ; Zhang, Qingpeng ; Brown, Charles ; Tiedje, James M. / Microbial community analysis with ribosomal gene fragments from shotgun metagenomes. In: Applied and Environmental Microbiology. 2016 ; Vol. 82, No. 1. pp. 157-166.
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