BioProject

While the ruminant gut archaeome regulates the gut microbiota and hydrogen balance, it is also a major producer of the greenhouse gas methane. However, the ruminant gut archaeome’s diversity within the gastrointestinal tract (GIT) of ruminant animals worldwide remains largely underexplored. Here, we construct a catalogue of 998 unique archaeal genomes recovered from the GITs of ruminants, utilizing 2,270 metagenomic samples across 10 different ruminant species. Most of the archaeal genomes (669/998=67.03%) belong to Methanobacteriaceae and Methanomethylophilaceae (198/998=19.84%). We recover previously undescribed 47/279 archaeal genomes at the strain level with completeness of >80% and contamination of <5%. We also investigate the archaeal gut biogeography across various ruminants, demonstrating that archaeal compositional similarities vary significantly by breed and gut location. The catalogue contains 42,691 protein clusters, and the clustering and methanogenic pathways analysis reveal strain and host-specific dependencies among ruminant animals. We also find that archaea potentially carry antibiotic and metal resistance genes, mobile genetic elements, virulence factors, quorum sensors, and complex archaeal viromes. Overall, this catalogue stands as a substantial repository for ruminant archaea recourses, providing potential for advancing our understanding of archaeal ecology and discovering strategies to regulate methane production in ruminants.