Статья

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

Alexandre AlmeidaEuropean Bioinformatics Institute (EMBL–EBI), Wellcome Genome Campus, Hinxton, UKStephen NayfachEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USAMiguel BolandEuropean Bioinformatics Institute (EMBL–EBI), Wellcome Genome Campus, Hinxton, UKFrancesco StrozziEnterome Bioscience, Paris, FranceMartín BeracocheaEuropean Bioinformatics Institute (EMBL–EBI), Wellcome Genome Campus, Hinxton, UKZhou Jason ShiChan Zuckerberg Biohub, San Francisco, CA, USAKatherine S. PollardChan Zuckerberg Biohub, San Francisco, CA, USAEkaterina SakharovaEuropean Bioinformatics Institute (EMBL–EBI), Wellcome Genome Campus, Hinxton, UKDonovan H. ParksAustralian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, AustraliaPhilip HugenholtzAustralian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, AustraliaNicola SegataCIBIO Department, University of Trento, Trento, ItalyNikos C. KyrpidesEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USAROBERT FINNEuropean Bioinformatics Institute (EMBL–EBI), Wellcome Genome Campus, Hinxton, UK

2020en

ABI

Аннотация

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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Идентификаторы

DOI: 10.1038/s41587-020-0603-3

Цитирования и источники

Цитирований: 2Использованных источников: 0

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