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

Nat Biotechnol. 2021 Jan;39(1):105-114. doi: 10.1038/s41587-020-0603-3. Epub 2020 Jul 20.


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bacteria / classification
  • Bacteria / genetics
  • Databases, Genetic*
  • Gastrointestinal Microbiome / genetics*
  • Genome, Bacterial / genetics*
  • Humans
  • Metagenome / genetics*
  • Metagenomics
  • Phenotype
  • Phylogeny