High-resolution phylogenetic microbial community profiling

Singer, Esther, Bushnell, Brian, Coleman-Derr, Devin, Bowman, Brett, Bowers, Robert M., Levy, Asaf, Gies, Esther A., Cheng, Jan-Fang, Copeland, Alex, Klenk, Hans-Peter, Hallam, Steven J., Hugenholtz, Philip, Tringe, Susannah G. and Woyke, Tanja (2016) High-resolution phylogenetic microbial community profiling. ISME Journal, 10 8: 2020-2032. doi:10.1038/ismej.2015.249


Author Singer, Esther
Bushnell, Brian
Coleman-Derr, Devin
Bowman, Brett
Bowers, Robert M.
Levy, Asaf
Gies, Esther A.
Cheng, Jan-Fang
Copeland, Alex
Klenk, Hans-Peter
Hallam, Steven J.
Hugenholtz, Philip
Tringe, Susannah G.
Woyke, Tanja
Title High-resolution phylogenetic microbial community profiling
Journal name ISME Journal   Check publisher's open access policy
ISSN 1751-7362
Publication date 2016-02-09
Sub-type Article (original research)
DOI 10.1038/ismej.2015.249
Open Access Status DOI
Volume 10
Issue 8
Start page 2020
End page 2032
Total pages 13
Place of publication London, United Kingdom
Publisher Nature Publishing
Collection year 2017
Language eng
Formatted abstract
Over the past decade, high-throughput short-read 16S rRNA gene amplicon sequencing has eclipsed clone-dependent long-read Sanger sequencing for microbial community profiling. The transition to new technologies has provided more quantitative information at the expense of taxonomic resolution with implications for inferring metabolic traits in various ecosystems. We applied single-molecule real-time sequencing for microbial community profiling, generating full-length 16S rRNA gene sequences at high throughput, which we propose to name PhyloTags. We benchmarked and validated this approach using a defined microbial community. When further applied to samples from the water column of meromictic Sakinaw Lake, we show that while community structures at the phylum level are comparable between PhyloTags and Illumina V4 16S rRNA gene sequences (iTags), variance increases with community complexity at greater water depths. PhyloTags moreover allowed less ambiguous classification. Last, a platform-independent comparison of PhyloTags and in silico generated partial 16S rRNA gene sequences demonstrated significant differences in community structure and phylogenetic resolution across multiple taxonomic levels, including a severe underestimation in the abundance of specific microbial genera involved in nitrogen and methane cycling across the Lake’s water column. Thus, PhyloTags provide a reliable adjunct or alternative to cost-effective iTags, enabling more accurate phylogenetic resolution of microbial communities and predictions on their metabolic potential.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: HERDC Pre-Audit
School of Chemistry and Molecular Biosciences
Institute for Molecular Bioscience - Publications
 
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Created: Fri, 12 Feb 2016, 12:15:21 EST by Mrs Louise Nimwegen on behalf of School of Chemistry & Molecular Biosciences