Differential Rumen Microbial Taxa in Charolais Bulls with Divergent Residual Feed Intake

The rumen microbiome impacts beef cattle feed efficiency, a key economic factor in production systems. This study investigated the rumen microbiome of Charolais bulls with divergent residual feed intake-expected progeny difference (RFI-EPD) values to identify microbial taxa associated with feed efficiency. Forty Charolais bulls were evaluated for feed intake and growth over 60 days, and RFI values were determined. The 10 most efficient (NegRFI) and 10 least efficient (PosRFI) bulls were selected for microbiome analysis. Rumen fluid samples were collected and analyzed via 16S rRNA gene sequencing. Microbial analysis revealed no significant differences in alpha or beta diversity between groups, but differential abundance analysis identified 20 operational taxonomic units (OTUs) as more prevalent in NegRFI bulls, while 15 OTUs were more abundant in PosRFI bulls. Two OTUs from the key genus Prevotella showed different relative abundances in the two RFI-EPD groups. NegRFI bulls had a higher relative abundance of Prevotella OTU 109358, while PosRFI bulls had more Prevotella OTU 626329. Additionally, OTUs from Ruminococcus, a genus involved in fiber degradation and volatile fatty acid (VFA) production, were more abundant in NegRFI bulls. In contrast, PosRFI bulls had a higher abundance of OTUs from Oscillospira and F16, both linked to butyrate production. The results of this study support the need for further exploration into the role of microbial taxa associated with feed efficiency. A deeper understanding of the functional profile of the microbiota could aid in the development of microbiome-informed strategies to enhance nutrient utilization and performance in beef cattle.