Microbiota diversity and association with performance phenotypes in beef bulls

Feed efficiency, nutrient utilization, and methane emission are highly dependent on the gastrointestinal microbiota, implying an influence of these microorganisms on economically important traits (e.g., carcass traits and meat quality). The interaction between microbial composition, diet, and host performance suggests that microbiota-targeted strategies may increase production in livestock animals. However, little is known about this interaction in beef cattle. We aimed to characterize the gastrointestinal microbiota and identify taxa associated with performance phenotypes in Nellore bulls. We identified 1,268 bacterial and 75 archaeal amplicon sequence variants (ASVs). For both bacteria and archaea, alpha diversity showed significant within-year variation. No statistical differences were found for the Shannon index for bacteria in 2019 versus 2021 or archaea in 2019-2020 and 2021-2022. Except for 2022 (bacteria), no clusters were observed for bacteria or archaea beta diversity across years. Ten different bacteria ASVs were found to affect ribeye area (RA), whereas only five did so for metabolic weight (MW). For archaea, eight ASVs had a significant effect on RA, whereas 15 were found to affect MW. Coefficients of the regression of phenotype on ASV ranged from (± SE, in SD units) -0.40 ± 0.08 (ASV 892, Bacteroidales RF16 spp.) to 0.36 ± 0.11 (ASV 605, Marvinbryantia spp.) for MW, and from -0.72 ± 0.20 (ASV 188, Faecalibacterium spp.) to 0.65 ± 65 (ASV 457, Christensenellaceae R-7 spp.) for RA. Our study revealed significant associations between ASV and traits of economic importance in beef cattle, including carcass, feed efficiency, and morphology, indicating that the microbiome influences animal performance. Further research is needed to elucidate the biological mechanisms behind these associations.