A human gut bacterial genome and culture collection for improved metagenomic analyses

Samuel C. Forster, Nitin Kumar, Blessing O. Anonye, Alexandre Almeida, Elisa Viciani, Mark D. Stares, Matthew Dunn, Tapoka T. Mkandawire, Ana Zhu, Yan Shao, Lindsay J. Pike, Thomas Louie, Hilary P. Browne, Alex L. Mitchell, B. Anne Neville, Robert D. Finn, Trevor D. Lawley

Research output: Contribution to journalArticleResearchpeer-review

Abstract

Understanding gut microbiome functions requires cultivated bacteria for experimental validation and reference bacterial genome sequences to interpret metagenome datasets and guide functional analyses. We present the Human Gastrointestinal Bacteria Culture Collection (HBC), a comprehensive set of 737 whole-genome-sequenced bacterial isolates, representing 273 species (105 novel species) from 31 families found in the human gastrointestinal microbiota. The HBC increases the number of bacterial genomes derived from human gastrointestinal microbiota by 37%. The resulting global Human Gastrointestinal Bacteria Genome Collection (HGG) classifies 83% of genera by abundance across 13,490 shotgun-sequenced metagenomic samples, improves taxonomic classification by 61% compared to the Human Microbiome Project (HMP) genome collection and achieves subspecies-level classification for almost 50% of sequences. The improved resource of gastrointestinal bacterial reference sequences circumvents dependence on de novo assembly of metagenomes and enables accurate and cost-effective shotgun metagenomic analyses of human gastrointestinal microbiota.

Original languageEnglish
Pages (from-to)186-192
Number of pages7
JournalNature Biotechnology
Volume37
Issue number2
DOIs
Publication statusPublished - 1 Feb 2019

Cite this

Forster, S. C., Kumar, N., Anonye, B. O., Almeida, A., Viciani, E., Stares, M. D., ... Lawley, T. D. (2019). A human gut bacterial genome and culture collection for improved metagenomic analyses. Nature Biotechnology, 37(2), 186-192. https://doi.org/10.1038/s41587-018-0009-7
Forster, Samuel C. ; Kumar, Nitin ; Anonye, Blessing O. ; Almeida, Alexandre ; Viciani, Elisa ; Stares, Mark D. ; Dunn, Matthew ; Mkandawire, Tapoka T. ; Zhu, Ana ; Shao, Yan ; Pike, Lindsay J. ; Louie, Thomas ; Browne, Hilary P. ; Mitchell, Alex L. ; Neville, B. Anne ; Finn, Robert D. ; Lawley, Trevor D. / A human gut bacterial genome and culture collection for improved metagenomic analyses. In: Nature Biotechnology. 2019 ; Vol. 37, No. 2. pp. 186-192.
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abstract = "Understanding gut microbiome functions requires cultivated bacteria for experimental validation and reference bacterial genome sequences to interpret metagenome datasets and guide functional analyses. We present the Human Gastrointestinal Bacteria Culture Collection (HBC), a comprehensive set of 737 whole-genome-sequenced bacterial isolates, representing 273 species (105 novel species) from 31 families found in the human gastrointestinal microbiota. The HBC increases the number of bacterial genomes derived from human gastrointestinal microbiota by 37{\%}. The resulting global Human Gastrointestinal Bacteria Genome Collection (HGG) classifies 83{\%} of genera by abundance across 13,490 shotgun-sequenced metagenomic samples, improves taxonomic classification by 61{\%} compared to the Human Microbiome Project (HMP) genome collection and achieves subspecies-level classification for almost 50{\%} of sequences. The improved resource of gastrointestinal bacterial reference sequences circumvents dependence on de novo assembly of metagenomes and enables accurate and cost-effective shotgun metagenomic analyses of human gastrointestinal microbiota.",
author = "Forster, {Samuel C.} and Nitin Kumar and Anonye, {Blessing O.} and Alexandre Almeida and Elisa Viciani and Stares, {Mark D.} and Matthew Dunn and Mkandawire, {Tapoka T.} and Ana Zhu and Yan Shao and Pike, {Lindsay J.} and Thomas Louie and Browne, {Hilary P.} and Mitchell, {Alex L.} and Neville, {B. Anne} and Finn, {Robert D.} and Lawley, {Trevor D.}",
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Forster, SC, Kumar, N, Anonye, BO, Almeida, A, Viciani, E, Stares, MD, Dunn, M, Mkandawire, TT, Zhu, A, Shao, Y, Pike, LJ, Louie, T, Browne, HP, Mitchell, AL, Neville, BA, Finn, RD & Lawley, TD 2019, 'A human gut bacterial genome and culture collection for improved metagenomic analyses', Nature Biotechnology, vol. 37, no. 2, pp. 186-192. https://doi.org/10.1038/s41587-018-0009-7

A human gut bacterial genome and culture collection for improved metagenomic analyses. / Forster, Samuel C.; Kumar, Nitin; Anonye, Blessing O.; Almeida, Alexandre; Viciani, Elisa; Stares, Mark D.; Dunn, Matthew; Mkandawire, Tapoka T.; Zhu, Ana; Shao, Yan; Pike, Lindsay J.; Louie, Thomas; Browne, Hilary P.; Mitchell, Alex L.; Neville, B. Anne; Finn, Robert D.; Lawley, Trevor D.

In: Nature Biotechnology, Vol. 37, No. 2, 01.02.2019, p. 186-192.

Research output: Contribution to journalArticleResearchpeer-review

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AU - Kumar, Nitin

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AU - Stares, Mark D.

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AU - Louie, Thomas

AU - Browne, Hilary P.

AU - Mitchell, Alex L.

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AU - Finn, Robert D.

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