Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart

Mouse is the most used model for studying the impact of microbiota on its host, but the repertoire of species from the mouse gut microbiome remains largely unknown. Accordingly, the similarity between human and mouse microbiomes at a low taxonomic level is not clear. We construct a comprehensive mou...

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Bibliographic Details
Published in:PLoS computational biology 2022-03, Vol.18 (3), p.e1009947-e1009947
Main Authors: Kieser, Silas, Zdobnov, Evgeny M, Trajkovski, Mirko
Format: Article
Language:English
Subjects:
Animals
Bacteria - genetics
Biology and Life Sciences
Body fat
Cold
Computer and Information Sciences
Digestive system
Digestive tract
Feces
Gastrointestinal Microbiome - genetics
Gene mapping
Genes
Genetic aspects
Genomes
Humans
Intestinal microflora
Metagenome - genetics
Metagenomics
Mice
Microbiomes
Microbiota
Microbiota (Symbiotic organisms)
Microbiota - genetics
New families
New genera
New orders
Phylogenetics
Phylogeny
Physiological aspects
Plasmids
Research and Analysis Methods
Species
Taxonomy
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Summary:Mouse is the most used model for studying the impact of microbiota on its host, but the repertoire of species from the mouse gut microbiome remains largely unknown. Accordingly, the similarity between human and mouse microbiomes at a low taxonomic level is not clear. We construct a comprehensive mouse microbiota genome (CMMG) catalog by assembling all currently available mouse gut metagenomes and combining them with published reference and metagenome-assembled genomes. The 41'798 genomes cluster into 1'573 species, of which 78.1% are uncultured, and we discovered 226 new genera, seven new families, and one new order. CMMG enables an unprecedented coverage of the mouse gut microbiome exceeding 86%, increases the mapping rate over four-fold, and allows functional microbiota analyses of human and mouse linking them to the driver species. Comparing CMMG to microbiota from the unified human gastrointestinal genomes shows an overlap of 62% at the genus but only 10% at the species level, demonstrating that human and mouse gut microbiota are largely distinct. CMMG contains the most comprehensive collection of consistently functionally annotated species of the mouse and human microbiome to date, setting the ground for analysis of new and reanalysis of existing datasets at an unprecedented depth.
ISSN:1553-7358
1553-734X
1553-7358
DOI:10.1371/journal.pcbi.1009947