Microbial drivers of divergent butyrate and methane pathways in dairy cows with contrasting methane intensity

While the relationship between microbial composition and feed efficiency has been explored, less is known about microbial metabolic activity in animals with differing feed efficiency. This study aimed to investigate metagenomic and metatranscriptomic differences in dairy cows classified by feed efficiency. No significant differences were observed in alpha or beta diversity. However, annotation of 424 recovered MAGs revealed functional differences: butyrate-related KEGG orthologs were enriched in high-efficiency animals, while methanogenesis-related orthologs were more abundant in the low-efficiency group. Similarly, CAZyme analysis showed increased fructan degradation in the LMI group and pectin degradation in the HMI group. These results suggest a shift toward butyrate-producing microbes driven by fructan utilization in efficient cows, and increased methanogenesis potentially linked to pectin-derived methyl group release in inefficient cows.