Shifts in rumen prokaryotic communities of grazing beef cows with divergent feed efficiency in response to seasonal grazing

Abstract Background Cow–calf operations represent a major component of beef production, typically relying on seasonal grazing of perennial forages. While understanding the role of the rumen microbiome in improving feed efficiency in grazing systems is essential for sustainable beef production, most studies have focused on cattle in confined systems such as feedlots. There is limited understanding of how rumen microbial communities change across feeding regimens in cow-calf operations with seasonal grazing. This study characterized rumen prokaryotic communities of beef cows across four feeding regimens, drylot (DL), planted pasture (PP), summer native rangeland (SNR), and fall native rangeland (FNR) within a year-round cow–calf production cycle, aiming to determine their relationships with feed efficiency. Results Prokaryotic communities in rumen samples collected from breeding beef cows under DL, PP, SNR, and FNR were assessed using metataxonomic sequencing and quantitative PCR. Feed efficiency was evaluated using residual feed intake adjusted for backfat thickness (RFIf) under DL. The microbial profiling and quantification revealed significant shifts in microbial composition and diversity across the four regimens. Bacterial diversity was highest in DL and declined during grazing, while archaeal diversity increased in SNR compared to PP and FNR. Several taxa were differentially enriched under distinct feeding regimens: Thermobifida , Saccharomonospora , Corynebacterium , and Methanoculleus thermophilus appeared only in DL, while Patescibacteria and Olsenella were more abundant during grazing. Further analysis of microbial fermentation profiles revealed that concentrations of major volatile fatty acids (VFAs) were higher in PP than in the other regimens. Heritable bacteria ( p -251-o5 and Pirellula ) were enriched in native rangelands and negatively correlated with VFA concentrations. In FNR, the abundance of the dominant bacterial taxon Christensenellaceae R-7 group increased, while Prevotella declined. Differential abundance analysis identified RFIf-associated taxa, including Eubacterium cellulosolvens group, Colidextrobacter , and Methanosphaera sp. ISO3–F5 regardless of feeding regime variation. Conclusions This study provides a comprehensive assessment of rumen prokaryotic dynamics across seasonal feeding regimens in cow-calf production, revealing varied shifts between bacteria and archaea. We further identified feeding regimen-specific associations between microbial taxa and feed efficiency, suggesting diet-microbiome interactions influencing grazing cow’s feed efficiency. These findings enhance the understanding of host-microbe interactions in confined and grazing environments, offering insights for sustainable beef production strategies.