An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants

Gastrointestinal tract (GIT) microbiomes in ruminant play major roles in host health and thus animal production. However, an integrated characterization of microbial community structure and function is yet to be obtained as prior studies are predominantly biased towards the rumen. Therefore, to acquire a microbiota inventory of the discrete GIT compartments, we generated shotgun metagenomic data from 370 samples that represent 10 GIT regions of seven ruminant species. Our analyses reconstructed a GIT microbial reference catalog with >154 million nonredundant gene, and identified 8,745 uncultured candidate species from over 10,000 metagenome-assembled genomes. The integrated gene catalog across the GIT regions demonstrate spatial associations between the microbiome and physiological adaptations, and 8,745 newly characterized genomes substantially expand the genomic landscape of ruminant microbiota, particularly microbiomes from the lower gut. This substantially expands the previously known set of endogenous microbial diversity and the taxonomic classification rate of GIT microbiome. These candidate species encode hundreds of enzymes and novel biosynthetic gene clusters that improves our understanding concerning methane production and feed efficiency in ruminants. Overall, our study expands the characterization of the ruminant GIT microbiota at unprecedented spatial resolution, and offers clues for improving ruminant livestock production in the future. Having access to comprehensive gene catalog and collections of microbial genomes provide the ability to perform efficiently genome-based analysis to achieve a detailed classification of GIT microbial ecosystem composition. Our study will bring unprecedented power in future association studies to investigate the impact of the GIT microbiota in ruminant health and production.