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A unified catalog of 204,938 reference genomes from the human gut microbiome.

Author information

Affiliations

  • 1. European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.
      Authors
    • Almeida A 1
    • Boland M 1
    • Beracochea M 1
    • Sakharova E 1
    • Finn RD 1
    (5 authors)
  • 2. US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.
      Authors
    • Nayfach S 2
    • Kyrpides NC 2
    (2 authors)
  • 3. Enterome Bioscience, Paris, France.
      Authors
    • Strozzi F 3
    (1 author)
  • 4. Gladstone Institutes, San Francisco, CA, USA.
      Authors
    • Shi ZJ 4
    • Pollard KS 4
    (2 authors)
  • 5. Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.
      Authors
    • Parks DH 5
    • Hugenholtz P 5
    (2 authors)
    • Show all (6)

ORCIDs linked to this article

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Nature Biotechnology, 20 Jul 2020, 39(1):105-114
https://doi.org/10.1038/s41587-020-0603-3 PMID: 32690973 PMCID: PMC7801254

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Abstract 

Comprehensive, high-quality reference genomes are required for functional characterization and taxonomic assignment of the human gut microbiota. We present the Unified Human Gastrointestinal Genome (UHGG) collection, comprising 204,938 nonredundant genomes from 4,644 gut prokaryotes. These genomes encode >170 million protein sequences, which we collated in the Unified Human Gastrointestinal Protein (UHGP) catalog. The UHGP more than doubles the number of gut proteins in comparison to those present in the Integrated Gene Catalog. More than 70% of the UHGG species lack cultured representatives, and 40% of the UHGP lack functional annotations. Intraspecies genomic variation analyses revealed a large reservoir of accessory genes and single-nucleotide variants, many of which are specific to individual human populations. The UHGG and UHGP collections will enable studies linking genotypes to phenotypes in the human gut microbiome.

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Read article at publisher's site: https://doi.org/10.1038/s41587-020-0603-3

Read article for free, from open access legal sources, via Unpaywall: https://www.nature.com/articles/s41587-020-0603-3.pdfUnpaywall

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Funding 

Funders who supported this work.

Biotechnology and Biological Sciences Research Council (2)

European Research Council (1)