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

Miller, Ian J.; Weyna, Theodore R.; Fong, Stephen S.; Lim-Fong, Grace E.; Kwan, Jason C.

doi:10.1038/srep34362

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

Journal Article · Thu Sep 29 00:00:00 EDT 2016 · Scientific Reports

DOI:https://doi.org/10.1038/srep34362· OSTI ID:1378482

Miller, Ian J. ^[1]; Weyna, Theodore R. ^[1]; Fong, Stephen S. ^[2]; Lim-Fong, Grace E. ^[3]; Kwan, Jason C. ^[1]

Univ. of Wisconsin, Madison, WI (United States). Division 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

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.

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Research Organization:: 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 Organization:: USDOE Office of Science (SC); National Science Foundation (NSF)

Grant/Contract Number:: 0910812

OSTI ID:: 1378482

Journal Information:: Scientific Reports, Vol. 6, Issue 1; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 26 works

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