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

By Alexandre Almeida, Stephen Nayfach, M. Boland, F. Strozzi, Martin Beracochea, Z. Shi, Katherine S. Pollard, Ekaterina A. Sakharova, Donovan H. Parks, Philip Hugenholtz and 3 more. Nature Biotechnology, 2020

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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. More than 200,000 gut prokaryotic reference genomes and the proteins they encode are collated, providing comprehensive resources for microbiome researchers.

Subfields: Food Science, Infectious Diseases, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/40faa55438449b0240f01ffc306dd067fad0fd26

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Citations in the corpus

MGnify: the microbiome sequence data analysis resource in 2023 (2022, background): “This approach has been applied extensively in the most-sampled biome, namely the human gut, where the Unified Human Gastrointestinal Genome catalogue provided draft genomes for 4644 prokaryotic species of which 70% lacked cultured representative genomes (9).”
CoverM: read alignment statistics for metagenomics (2025, positive): “…sequencing reads into metagenome assembled genomes (MAGs) has become increasingly common and high-throughput, with recovery of tens to hundreds of thousands of genomes from a diverse array of environments (Pasolli et al. 2019, Almeida et al. 2021, Nishimura and Yoshizawa 2022, Schmidt et al. 2024).”
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 (2020, background): “Studies of microbial community biology continue to be enriched by the growth of culture-independent sequencing and high-throughput isolate genomics (Almeida et al., 2020, 2019; Forster et al., 2019; Parks et al., 2017; Pasolli et al., 2019; Poyet et al., 2019; Zou et al., 2019) .”
InStrain enables population genomic analysis from metagenomic data and sensitive detection of shared microbial strains (2021, background): “By mapping reads to all 4,644 representative genomes in the Unified Human Gastrointestinal Genome (UHGG) collection 24 , inStrain detected the eight bacterial taxa known to be present in each of the three Zymo metagenomes.”
Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4 (2023, methodology): “From a collection of 1.01 M bacterial and archeal MAGs and isolate genomes integrating the most recent genome cata-logs 37–45 and additional newly assembled MAGs spanning multiple environments, we first expanded the definition of 54,596 SGBs and then defined SGB-specific unique marker genes (that…”