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Title: Single sample resolution of rare microbial dark matter in a marine invertebrate metagenome

Abstract

Direct, untargeted sequencing of environmental samples (metagenomics) and de novo genome assembly enable the study of uncultured and phylogenetically divergent organisms. However, separating individual genomes from a mixed community has often relied on the differential-coverage analysis of multiple, deeply sequenced samples. In the metagenomic investigation of the marine bryozoan Bugula neritina, we uncovered seven bacterial genomes associated with a single B. neritina individual that appeared to be transient associates, two of which were unique to one individual and undetectable using certain “universal” 16S rRNA primers and probes. We recovered high quality genome assemblies for several rare instances of “microbial dark matter,” or phylogenetically divergent bacteria lacking genomes in reference databases, from a single tissue sample that was not subjected to any physical or chemical pre-treatment. One of these rare, divergent organisms has a small (593 kbp), poorly annotated genome with low GC content (20.9%) and a 16S rRNA gene with just 65% sequence similarity to the closest reference sequence. Lastly, our findings illustrate the importance of sampling strategy and de novo assembly of metagenomic reads to understand the extent and function of bacterial biodiversity.

Authors:
 [1];  [1];  [2];  [3];  [1]
  1. Univ. of Wisconsin, Madison, WI (United States). Division of Pharmaceutical Sciences
  2. Virginia Commonwealth Univ., Richmond, VA (United States). Dept. of Chemical and Life Science Engineering
  3. Randolph-Macon College, Ashland, VA (United States). Dept. of Biology
Publication Date:
Research Org.:
Univ. of Wisconsin, Madison, WI (United States). Div. of Pharmaceutical Sciences; Virginia Commonwealth Univ., Richmond, VA (United States). Dept. of Chemical and Life Science Engineering; Randolph-Macon College, Ashland, VA (United States). Dept. of Biology
Sponsoring Org.:
USDOE Office of Science (SC); National Science Foundation (NSF)
OSTI Identifier:
1378482
Grant/Contract Number:
0910812
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 6; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Miller, Ian J., Weyna, Theodore R., Fong, Stephen S., Lim-Fong, Grace E., and Kwan, Jason C. Single sample resolution of rare microbial dark matter in a marine invertebrate metagenome. United States: N. p., 2016. Web. doi:10.1038/srep34362.
Miller, Ian J., Weyna, Theodore R., Fong, Stephen S., Lim-Fong, Grace E., & Kwan, Jason C. Single sample resolution of rare microbial dark matter in a marine invertebrate metagenome. United States. doi:10.1038/srep34362.
Miller, Ian J., Weyna, Theodore R., Fong, Stephen S., Lim-Fong, Grace E., and Kwan, Jason C. 2016. "Single sample resolution of rare microbial dark matter in a marine invertebrate metagenome". United States. doi:10.1038/srep34362. https://www.osti.gov/servlets/purl/1378482.
@article{osti_1378482,
title = {Single sample resolution of rare microbial dark matter in a marine invertebrate metagenome},
author = {Miller, Ian J. and Weyna, Theodore R. and Fong, Stephen S. and Lim-Fong, Grace E. and Kwan, Jason C.},
abstractNote = {Direct, untargeted sequencing of environmental samples (metagenomics) and de novo genome assembly enable the study of uncultured and phylogenetically divergent organisms. However, separating individual genomes from a mixed community has often relied on the differential-coverage analysis of multiple, deeply sequenced samples. In the metagenomic investigation of the marine bryozoan Bugula neritina, we uncovered seven bacterial genomes associated with a single B. neritina individual that appeared to be transient associates, two of which were unique to one individual and undetectable using certain “universal” 16S rRNA primers and probes. We recovered high quality genome assemblies for several rare instances of “microbial dark matter,” or phylogenetically divergent bacteria lacking genomes in reference databases, from a single tissue sample that was not subjected to any physical or chemical pre-treatment. One of these rare, divergent organisms has a small (593 kbp), poorly annotated genome with low GC content (20.9%) and a 16S rRNA gene with just 65% sequence similarity to the closest reference sequence. Lastly, our findings illustrate the importance of sampling strategy and de novo assembly of metagenomic reads to understand the extent and function of bacterial biodiversity.},
doi = {10.1038/srep34362},
journal = {Scientific Reports},
number = 1,
volume = 6,
place = {United States},
year = 2016,
month = 9
}

Journal Article:
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