Early Life Exposure to Manure-Fertilized Soil Shapes the Gut Antibiotic Resistome

The global rise of antimicrobial resistance (AMR) presents a pressing public health challenge with agricultural practices such as the use of manure fertilization, excessive antibiotic use in livestock, and the irrigation of crops with contaminated water contributing to the spread of antibiotic resistance genes (ARGs). Despite growing concerns, the pathways through which ARGs migrate from environmental reservoirs to animal microbiomes are poorly understood. In this study, we raised mice from birth in pig manure-fertilized red (Ultisols) and black (Mollisols) soils or unfertilized controls, sampling their gut microbiomes at 8 weeks, to show that early life exposure to manure-fertilized soil profoundly shapes the gut antibiotic resistome in mice. Application of organic manure significantly enriched tetracycline-resistant ARGs in both red and black soils. Mice living in these environments harbored markedly higher abundances of ARGs, particularly the tet-(Q) gene, compared to those in nonfertilized environments. Notably, Muribaculaceae and Bacteroidaceae were identified as key hosts of tet-(Q), with evidence suggesting a horizontal gene transfer between these families. These findings indicate that manure fertilization not only increases ARG abundance in soils but also facilitates its transfer to animal microbiomes, thereby amplifying the risk of AMR dissemination. This research underscores the importance of improved agricultural management practices to mitigate the environmental transmission of AMR.