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

被引：375

作者：

Forster, Samuel C. ^{[1
,2
,3
]}

Kumar, Nitin ^{[1
]}

Anonye, Blessing O. ^{[1
,7
]}

Almeida, Alexandre ^{[4
,5
]}

Viciani, Elisa ^{[1
]}

Stares, Mark D. ^{[1
]}

Dunn, Matthew ^{[1
]}

Mkandawire, Tapoka T. ^{[1
]}

Zhu, Ana ^{[1
]}

Shao, Yan ^{[1
]}

Pike, Lindsay J. ^{[1
]}

Louie, Thomas ^{[6
]}

Browne, Hilary P. ^{[1
]}

Mitchell, Alex L. ^{[4
]}

Neville, B. Anne ^{[1
]}

Finn, Robert D. ^{[4
]}

Lawley, Trevor D. ^{[1
]}

机构：

[1] Wellcome Sanger Inst, Hostmicrobiota Interact Lab, Wellcome Genome Campus, Hinxton, England

[2] Hudson Inst Med Res, Ctr Innate Immun & Infect Dis, Clayton, Vic, Australia

[3] Monash Univ, Dept Mol & Translat Sci, Clayton, Vic, Australia

[4] European Bioinformat Inst, European Mol Biol Lab, Wellcome Genome Campus, Hinxton, England

[5] Wellcome Sanger Inst, Bacterial Genom & Evolut Lab, Wellcome Genome Campus, Hinxton, England

[6] Univ Calgary, Dept Microbiol & Infect Dis, Calgary, AB, Canada

[7] Univ Warwick, Warwick Med Sch, Div Biomed Sci, Microbiol & Infect Unit, Coventry, W Midlands, England

来源：

NATURE BIOTECHNOLOGY | 2019年 / 37卷 / 02期

基金：

英国医学研究理事会; 英国生物技术与生命科学研究理事会; 英国惠康基金;

关键词：

MINIMUM INFORMATION; READ ALIGNMENT; MICROBIOTA; TRANSMISSION; DIVERSITY; REVEALS; TREE; EVOLUTION; VERSATILE; SOFTWARE;

D O I：

10.1038/s41587-018-0009-7

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

引用

页码：186 / +

页数：9

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