Assessing the Impacts of Dairy Farm Antimicrobial Use on the Bovine Fecal Microbiome

Rising rates of antimicrobial-resistant infections have prompted increased scrutiny on antimicrobial use (AMU) in livestock agriculture. Dairy farms primarily use antimicrobials to maintain animal health and welfare by treating and preventing infectious diseases. However, the impact of dairy farm AMU practices on the cattle fecal microbiome remains largely unclear, partly due to difficulties in quantifying AMU. This study leveraged quantitative AMU data from 40 large commercial dairy farms to identify farms with low (n = 4) and high (n = 4) AMU. Using 16S rRNA gene amplicon sequencing, we compared the fecal bacterial communities of dairy calves and cows (healthy, cull, sick) by both AMU designation (high/low) and by individual farm AMU, summarized by animal defined daily dose (DDD) and mg/kg. We found significant differences in beta-diversity between cattle from high- and low-AMU groups using either method and found that Corynebacterium and Clostridium abundances increased with farm AMU. Additionally, we found fecal bacterial communities differed across farms within high- and low-AMU groupings, highlighting the need to account for farm-to-farm variation when assessing AMU impacts. These findings suggest that dairy farm AMU influences the fecal microbiome and identifies specific taxa that warrant further investigation as potential reservoirs for antimicrobial resistance genes.