Microbiome and antibiotic resistance profile of milk and faeces from cattle in an organized dairy production system

Antimicrobial resistance (AMR) represents a critical public health challenge, responsible for over one million fatalities each year. Livestock, particularly dairy cattle, significantly contribute to the AMR crisis due to the extensive use of antibiotics in the animal health sector. This study aimed to characterize the antibiotic resistome of dairy cattle by analyzing their fecal and milk metagenomes. We collected 36 milk and 36 fecal samples from three different organized dairy farms and extracted metagenomic DNA, yielding 2.58 and 2.81 billion total reads contributing 200.4 and 206.5 GB data, respectively. The majority of these reads mapped to bacterial genomes, revealing 37 bacterial phyla within the dairy production system, with greater phylum-level diversity observed in feces compared to milk. The predominant phyla identified were Bacillota (53.3%), Pseudomonadota (24.7%), Bacteroidota (11.0%), and Actinomycetota (8.4%). The most abundant genera found were Clostridium in milk and Bifidobacterium in feces. In total, we identified 290 distinct antibiotic-resistant genes spanning 27 diverse drug classes and 12 resistance mechanisms. The abundance of antibiotic-resistant genes was higher in feces than in milk, with 229 distinct antibiotic-resistant genes found in milk. Overall, aminoglycoside-resistant genes were the most prevalent and abundant in both fecal and milk metagenomes of cattle from organized dairy production systems.