The resistome of the bovine gastrointestinal tract

The gastrointestinal tracts of beef and dairy cattle are reservoirs of antimicrobial-resistant bacteria, and our knowledge of the ecology of resistance in these animals has changed with the advent of novel molecular technologies. Application of metagenomics and qPCR to the study of bovine gut ecology has demonstrated that there is overlap, with some differences, between beef and dairy cattle fecal resistomes, that treatment with antimicrobials often transiently influences the resistome, and young calves carry a high abundance of ARGs. Future work should harness emerging metagenome sequencing technologies to better describe the taxa harboring ARGs and collocated non-resistance genes and use these data along with identifying the multiplicity of factors driving resistance to develop strategies to reduce AMR carriage in cattle.