Rumen microbiota play a key role in the digestion and utilization of plant materials by the ruminant species, which have important implications for greenhouse gas emission. Yet, little is known about the key taxa and potential gene functions involved in the digestion process. Here, we performed a genome-centric analysis of rumen microbiota attached to six different lignocellulosic biomasses in rumen-fistulated cattle. Our metagenome sequencing provided novel genomic insights into functional potential of 523 uncultured bacteria and 15 mostly uncultured archaea in the rumen. The assembled genomes belonged mainly to Bacteroidota, Firmicutes, Verrucomicrobiota, and Fibrobacterota and were enriched for genes related to the degradation of lignocellulosic polymers and the fermentation of degraded products into short chain volatile fatty acids. We also found a shift from copiotrophic to oligotrophic taxa during the course of rumen fermentation, potentially important for the digestion of recalcitrant lignocellulosic substrates in the physiochemically complex and varying environment of the rumen. Differential colonization of forages (the incubated lignocellulosic materials) by rumen microbiota suggests that taxonomic and metabolic diversification is an evolutionary adaptation to diverse lignocellulosic substrates constituting a major component of the cattle’s diet. Our data also provide novel insights into the key role of unique microbial diversity and associated gene functions in the degradation of recalcitrant lignocellulosic materials in the rumen.

Domesticated buffaloes have been integral to rice-paddy agro-ecosystems for millennia, yet relatively little is known about the buffalo genomics. Here, we sequenced and assembled reference genomes for both swamp and river buffaloes and we re-sequenced 230 individuals (132 swamp buffaloes and 98 river buffaloes) sampled from across Asia and Europe. Beyond the many actionable insights that our study revealed about the domestication, basic physiology and breeding of buffalo, we made the striking discovery that the divergent domestication traits between swamp and river buffaloes can be explained with recent selections of genes on social behavior, digestion metabolism, strengths and milk production.

The attachment of rumen microbes to feed particles is critical to feed fermentation, degradation and digestion. However, the extent to which the physicochemical properties of feeds influence the colonization by rumen microbes is still unclear. We hypothesized that rumen microbial communities may have differential preferences for attachments to feeds with varying lignocellulose properties. To this end, the structure and composition of microbial communities attached to six common forages with different lignocellulosic compositions were analyzed following in situ rumen incubation in male Taleshi cattle. The results showed that differences in lignocellulosic compositions significantly affected the inter-sample diversity of forage-attached microbial communities in the first 24 h of rumen incubation, during which the highest dry matter degradation was achieved. However, extension of the incubation to 96 h resulted in the development of more uniform microbial communities across the forages. Fibrobacteres were significantly overrepresented in the bacterial communities attached to the forages with the highest neutral detergent fiber contents. Ruminococcus tended to attach to the forages with low acid detergent lignin contents. The extent of dry matter fermentation was significantly correlated with the populations of Fibrobacteraceae, unclassified Bacteroidales, Ruminococcaceae and Spirochaetacea. Our findings suggested that lignocellulosic compositions, and more specifically the cellulose components, significantly affected the microbial attachment to and thus the final digestion of the forages.