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Title: High-resolution phylogenetic microbial community profiling

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 communitiesmore » and predictions on their metabolic potential.« less

Authors:
 [1];  [1];  [2];  [3];  [1];  [1];  [4];  [1];  [1];  [5];  [4];  [6];  [1];  [1]
  1. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); USDA-ARS, Albanay, CA (United States)
  3. Pacific Biosciences, Menlo Park, CA (United States)
  4. Univ. of British Columbia, Vancouver, BC (Canada)
  5. Newcastle Univ. (United Kingdom). School of Biology
  6. Univ. of Queensland, St. Lucia, QLD (Australia). Australian Centre for Ecogenomics
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1379539
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
The ISME Journal
Additional Journal Information:
Journal Volume: 10; Journal Issue: 8; Journal ID: ISSN 1751-7362
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES

Citation Formats

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, Hugenholtz, Philip, Tringe, Susannah G., and Woyke, Tanja. High-resolution phylogenetic microbial community profiling. United States: N. p., 2016. Web. doi:10.1038/ismej.2015.249.
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, Hugenholtz, Philip, Tringe, Susannah G., & Woyke, Tanja. High-resolution phylogenetic microbial community profiling. United States. doi:10.1038/ismej.2015.249.
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, Hugenholtz, Philip, Tringe, Susannah G., and Woyke, Tanja. Tue . "High-resolution phylogenetic microbial community profiling". United States. doi:10.1038/ismej.2015.249. https://www.osti.gov/servlets/purl/1379539.
@article{osti_1379539,
title = {High-resolution phylogenetic microbial community profiling},
author = {Singer, Esther and Bushnell, Brian and Coleman-Derr, Devin and Bowman, Brett and Bowers, Robert M. and Levy, Asaf and Gies, Esther A. and Cheng, Jan -Fang and Copeland, Alex and Klenk, Hans -Peter and Hallam, Steven and Hugenholtz, Philip and Tringe, Susannah G. and Woyke, Tanja},
abstractNote = {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.},
doi = {10.1038/ismej.2015.249},
journal = {The ISME Journal},
number = 8,
volume = 10,
place = {United States},
year = {2016},
month = {2}
}

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