99 Differential rumen microbial taxa in Charolais bulls with divergent residual feed intake-expected progeny difference.

Abstract This study aimed to investigate the rumen microbiome of Charolais bulls with divergent RFI-EPD values to identify microbial taxa associated with feed efficiency. Forty Charolais bulls (443 ± 64 kg body weight) were evaluated for feed intake and growth performance over 60 days, and RFI values were determined. Vytelle (Vytelle Insight Beef Genetics) conducted genetic evaluation of the bulls for residual feed intake-expected progeny difference (RFI-EPD). The 10 most feed-efficient (NegRFI) and 10 least feed-efficient (PosRFI) bulls were selected and ranked based off their RFI-EPD coefficients for microbiome analysis. Rumen fluid samples were collected using an orally administered stomach tube and analyzed via 16S rRNA gene sequencing. Growth performance data showed that NegRFI bulls consumed less dry matter (9.39 kg/d, p = 0.006) compared to PosRFI bulls (10.55 kg/d), with no significant difference in average daily gain (p = 0.073). Microbial analysis revealed no significant differences in alpha (p = 0.92) or beta diversity (p = 0.397) between groups, but differential abundance analysis identified 20 operational taxonomic unit (OTU) as more prevalent in NegRFI bulls, including Clostridiales OTU 133719, Ruminococcus OTU 823658, and S24-7 OTU 4479793. Fifteen OTUs, such as Oscillospira OTU 290253 and F16 OTU 277519, were more abundant in PosRFI bulls. Two OTUs from key genus Prevotella showed different relative abundance in the two RFI-EPD groups. NegRFI bulls had 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, suggesting a rumen community optimized for fiber degradation and energy utilization. In contrast, PosRFI bulls had a higher abundance of OTUs from Oscillospira and F16, both linked to butyrate production. These findings highlight the potential of targeting the rumen microbiome to improve feed efficiency in cattle breeding programs. Further research is needed to clarify the functional roles of these microbial taxa.