Altered microbiota, antimicrobial resistance genes, and functional enzyme profiles in the rumen of yak calves fed with milk replacer

ABSTRACT

The use of milk replacer (MR) is a modern strategy to ensure the health and growth of neonatal ruminants. Some studies have confirmed that dietary factors have significant effects on ruminal antimicrobial resistance genes (ARGs), which, as a potential threat to livestock, have received more attention. However, the effect of different milk sources (milk or MR) on the rumen resistome of yaks is still largely unknown. Here, using metagenome technology, we investigated the occurrence of ruminal ARGs in yaks and their relationship with rumen bacteria in response to different milk sources. The metagenomic result showed that MR feeding significantly increased the abundance of Prevotella members compared to milk feeding. A total of 138 rumen resistome-conveying ARGs to 17 different classes of antimicrobials were detected, of which tetracycline resistance was the predominant. MR feeding also drove the changes in the rumen resistome, and the predicted bacterial origins of ARGs had complex and various manifestations. Moreover, enzymes of butyrate metabolism and carbohydrate-active enzymes encoding carbohydrate and cellulose degradation were increased. This study revealed that MR feeding increased the abundance of beneficial bacteria Prevotella members, changed the microbial resistome, and promoted the metabolic function of volatile fatty acid biosynthesis in the rumen of yaks, which could provide beneficial evidence for the regulation of the rumen microbiome and the intervention of antimicrobial resistance in ruminants by dietary or nutritional methods.