Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

Understanding the biological functions that are carried out by microbes in the rumen is important for reducing greenhouse gas production by ruminants and enhancing the efficiency of ruminant livestock produciton. To enhance the understanding of the biology of rumen microbes a global initiative called "The Hungate 1000 Project" was conducted to cultivate a diverse range of rumen bacteria, archaea and fungi and genomically characterize these isolated cultures. This manuscript is the culmination of that effort and presents 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B12, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents ∼75% of the genus-level bacterial and archaeal taxa present in the rumen. This data will serve as a valuable resource to current and future researchers studying the rumen microbiome and is a valuable platform to direct further efforts to continue increasing the culturability of the rumen microbiome.