Shotgun metagenomics analysis of rumen microbiota following spent mushroom substrate infusion in beef cattle

This study aimed to evaluate how the infusion of spent mushroom substrate (SMS) into the rumen altered fermentation dynamics and microbial composition in Angus beef cattle. Rumen samples were collected from Angus beef cows following controlled SMS infusion, and shotgun metagenomic sequencing was used to characterize taxonomic and functional shifts in the rumen microbiome. SMS infusion did not alter total volatile fatty acids, rumen pH, or ammonia-nitrogen concentrations; However, SMS increased the acetate-to-propionate ratio (P=0.043) and decreased propionate (P=0.016). Fibrolytic taxa, including Actinobacteria and Fibrobacteres, were enriched, while saccharolytic Bacteroidetes declined, and Proteobacteria had minor increases. Functional pathway analysis showed that hydrogenotrophic methanogenesis from H2 and CO2 remained active, with Methanobrevibacter ruminantium as the dominant archaeal taxon. Additional functional pathways, including galactose degradation, glycolysis, pyruvate fermentation, and the pentose phosphate pathway, highlighted the continued contributions of Prevotella, Ruminococcus, Butyrivibrio, and Fibrobacter to carbohydrate metabolism and fiber utilization. These microbial and functional shifts suggest that SMS infusion supported fibrolytic activity and rumen stability but with limited potential for methane mitigation due to persistent methanogenic pathways. Future strategies may require combining SMS with plant secondary metabolites, dietary lipids, or specific methanogenesis inhibitors to redirect metabolic hydrogen toward propionate formation and improve feed efficiency.