Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome

Fitzsimons, Michael S.; Novotny, Mark; Lo, Chien-Chi; Dichosa, Armand E.K.; Yee-Greenbaum, Joyclyn L.; Snook, Jeremy P.; Gu, Wei; Chertkov, Olga; Davenport, Karen W.; McMurry, Kim; Reitenga, Krista G.; Daughton, Ashlynn R.; He, Jian; Johnson, Shannon L.; Gleasner, Cheryl D.; Wills, Patti L.; Parson-Quintana, Beverly; Chain, Patrick S.; Detter, John C.; Lasken, Roger S.; Han, Cliff S.

doi:10.1101/gr.142208.112

Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome

Journal Article · Thu Mar 14 00:00:00 EDT 2013 · Genome Research

DOI:https://doi.org/10.1101/gr.142208.112· OSTI ID:1625620

Fitzsimons, Michael S. ^[1]; Novotny, Mark ^[2]; Lo, Chien-Chi ^[3]; Dichosa, Armand E.K. ^[3]; Yee-Greenbaum, Joyclyn L. ^[2]; Snook, Jeremy P. ^[3]; Gu, Wei ^[3]; Chertkov, Olga ^[3]; Davenport, Karen W. ^[3]; McMurry, Kim ^[3]; Reitenga, Krista G. ^[3]; Daughton, Ashlynn R. ^[3]; He, Jian ^[4]; Johnson, Shannon L. ^[3]; Gleasner, Cheryl D. ^[3]; Wills, Patti L. ^[3]; Parson-Quintana, Beverly ^[3]; Chain, Patrick S. ^[3]; Detter, John C. ^[3]; Lasken, Roger S. ^[2] more »

Los Alamos National Lab. (LANL), Los Alamos, NM (United States); DOE/OSTI
J. Craig Venter Institute, San Diego, CA (United States)
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Jilin Univ., Changchun (China)

The majority of microbial genomic diversity remains unexplored. This is largely due to our inability to culture most microorganisms in isolation, which is a prerequisite for traditional genome sequencing. Single-cell sequencing has allowed researchers to circumvent this limitation. DNA is amplified directly from a single cell using the whole-genome amplification technique of multiple displacement amplification (MDA). However, MDA from a single chromosome copy suffers from amplification bias and a large loss of specificity from even very small amounts of DNA contamination, which makes assembling a genome difficult and completely finishing a genome impossible except in extraordinary circumstances. Gel microdrop cultivation allows culturing of a diverse microbial community and provides hundreds to thousands of genetically identical cells as input for an MDA reaction. We demonstrate the utility of this approach by comparing sequencing results of gel microdroplets and single cells following MDA. Bias is reduced in the MDA reaction and genome sequencing, and assembly is greatly improved when using gel microdroplets. We acquired multiple near-complete genomes for two bacterial species from human oral and stool microbiome samples. A significant amount of genome diversity, including single nucleotide polymorphisms and genome recombination, is discovered. Gel microdroplets offer a powerful and high-throughput technology for assembling whole genomes from complex samples and for probing the pan-genome of naturally occurring populations.

View Accepted Manuscript (DOE)

Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: Alfred P. Sloan Foundation; National Human Genome Research Institute (NHGRI); National Institute of Allergy and Infectious Diseases (NIAID); National Institutes of Health (NIH); US Department of Health and Human Services (HHS); USDOE Laboratory Directed Research and Development (LDRD) Program; USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC52-06NA25396

OSTI ID:: 1625620

Journal Information:: Genome Research, Journal Name: Genome Research Journal Issue: 5 Vol. 23; ISSN 1088-9051

Publisher:: Cold Spring Harbor Laboratory PressCopyright Statement

Country of Publication:: United States

Language:: English

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