Metagenomic Insights into the Fecal Microbiome, Resistome, and Mobilome of Beef Cattle in Cow-Calf Operations in Florida, United States

Predicted plasmids carried 23.9% of 1,054 curated antimicrobial resistance gene (ARG) hits in fecal metagenomes from Florida beef cow-calf operations, with higher ARG hit rates in calves than cows.

• Why it matters: Antimicrobial resistance in food animals is a One Health concern, but how fecal microbiomes, ARG abundance, and mobile genetic elements vary by animal age and operation size remains unclear.
• What they did: Metagenomic sequencing of fecal samples from 162 cows and calves was pooled into 54 composite samples by age group; ARGs were profiled across 14 resistance classes and mapped to predicted plasmid, viral, and insertion-sequence contigs.
• The result: Normalized ARG hit rates were higher in small operations (0.444) than medium (0.278) and large (0.222; P = 0.088), and calves had higher estimated marginal mean normalized ARG hit rates than cows (0.383 vs. 0.247 hits/million reads; P < 0.001).

AI summary of the abstract · may contain errors · not medical advice · read the paper.