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Nat Biotechnol. 2019 Feb;37(2):186-192. doi: 10.1038/s41587-018-0009-7. Epub 2019 Feb 4.

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

Author information

1
Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK. sf15@sanger.ac.uk.
2
Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia. sf15@sanger.ac.uk.
3
Department of Molecular and Translational Sciences, Monash University, Clayton, Victoria, Australia. sf15@sanger.ac.uk.
4
Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
5
Microbiology and Infection Unit, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK.
6
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
7
Bacterial Genomics and Evolution Laboratory, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
8
Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada.
9
Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK. tl2@sanger.ac.uk.

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.

PMID:
30718869
DOI:
10.1038/s41587-018-0009-7

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