PT  - JOURNAL ARTICLE
AU  - Alexandre Almeida
AU  - Stephen Nayfach
AU  - Miguel Boland
AU  - Francesco Strozzi
AU  - Martin Beracochea
AU  - Zhou Jason Shi
AU  - Katherine S. Pollard
AU  - Donovan H. Parks
AU  - Philip Hugenholtz
AU  - Nicola Segata
AU  - Nikos C. Kyrpides
AU  - Robert D. Finn
TI  - A unified sequence catalogue of over 280,000 genomes obtained from the human gut microbiome
AID  - 10.1101/762682
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 762682
4099  - http://biorxiv.org/content/early/2019/09/19/762682.short
4100  - http://biorxiv.org/content/early/2019/09/19/762682.full
AB  - Comprehensive reference data is essential for accurate taxonomic and functional characterization of the human gut microbiome. Here we present the Unified Human Gastrointestinal Genome (UHGG) collection, a resource combining 286,997 genomes representing 4,644 prokaryotic species from the human gut. These genomes contain over 625 million protein sequences used to generate the Unified Human Gastrointestinal Protein (UHGP) catalogue, a collection that more than doubles the number of gut protein clusters over the Integrated Gene Catalogue. We find that a large portion of the human gut microbiome remains to be fully explored, with over 70% of the UHGG species lacking cultured representatives, and 40% of the UHGP missing meaningful functional annotations. Intra-species genomic variation analyses revealed a large reservoir of accessory genes and single-nucleotide variants, many of which were specific to individual human populations. These freely available genomic resources should greatly facilitate investigations into the human gut microbiome.