Cited by 1,367Genomics and Phylogenetic StudiesGut microbiota and healthMicrobial Community Ecology and Physiology

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

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Almeida, Alexandre, Nayfach, Stephen, Boland, Miguel, Strozzi, Francesco, Beracochea, Martin, Shi, Zhou Jason, Pollard, Katherine S., Sakharova, Ekaterina +5 more·2021·Nature Biotechnology

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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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  • Microbiome members of individuals from non-westernized populations are underrepresented by current cultivation-based genomic catalogs, causing metagenomic profiling to miss large fractions of microbial diversity.

    “Microbiome members of individuals from non-westernized populations are particularly underrepresented by current cultivation-based genomic catalogs causing metagenomic profiling approaches to miss large fractions of the microbial diversity in the samples.”
  • Metagenomic assembly can partially mitigate the underrepresentation of non-westernized microbiome members in genomic catalogs.

    “Recent efforts showed that metagenomic assembly can partially mitigate this problem,23,25,33,34”

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Authors
Almeida, A., Nayfach, S., Boland, M., Strozzi, F., Beracochea, M., Shi, Z. J., Pollard, K. S., Sakharova, E., Parks, D. H., Hugenholtz, P., Segata, N., Kyrpides, N. C., & Finn, R. D.
Affiliations
  • European Bioinformatics Institute (GB)
  • Lawrence Berkeley National Laboratory (US)
  • Enterome (France) (FR)
  • Gladstone Institutes (US)
  • The University of Queensland (AU)
  • University of Trento (IT)
Corresponding author
  • Almeida, Alexandre
  • Finn, Robert D.
Venue
Nature Biotechnology
Published
2020-07-20
Volume
39
Issue
1
Pages
105-114
ISSN
  • 0733-222X (ISSN-L)
  • 1087-0156
  • 1546-1696
OpenAlex
W3042305844
Cited by
1,367
References
80
Citations by year
2026: 216 · 2025: 308 · 2024: 279 · 2023: 209 · 2022: 175 · 2021: 144 · 2020: 30 · 2019: 2
FWCI
46.15
Type
journal article
Language
en
Open access
Locations
  • Nature Biotechnology (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Institutional Research Information System (Università degli Studi di Trento) (submittedVersion, cc-by)
  • eScholarship (California Digital Library) (submittedVersion)
  • OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
Funders
  • U.S. Department of Energy (-AC02-05CH11231, 05CH11231, DE AC02 05CH11231, DE-AC02-)
  • European Molecular Biology Laboratory
  • Joint Genome Institute (AC02-05CH11231, DE–AC02–05CH11231)
  • National Energy Research Scientific Computing Center (DE–AC02–05CH11231, 05CH11231, AC02-05CH11231)
  • Directorate for Biological Sciences
  • Office of Science (DEAC02–05CH11231, AC02-05CH11231, DE-AC02, 05CH11231)
  • Biotechnology and Biological Sciences Research Council (BB/N018354/1, BB/R015228/1)
  • H2020 European Research Council (716575)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
  • Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Keywords
human gut microbiome, reference genome, prokaryotic genomes, accessory genes, single nucleotide variants, genotype-phenotype correlation, taxonomic assignment
MeSH terms
Gastrointestinal Microbiome, Bacteria, Humans, Phenotype, Phylogeny, Genome, Bacterial, Databases, Genetic, Metagenome, Metagenomics

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