The Role of the Environmental Microbiome in Modulating the Spread of Antimicrobial Resistance

The environmental microbiome—the diverse communities of microorganisms in soil, water, air, plants, animals, and built environments—plays a critical role in the emergence, persistence, and spread of antimicrobial resistance (AMR). These environments act as reservoirs where bacteria naturally exchange genetic material, including antimicrobial resistance genes (ARGs), through mechanisms such as horizontal gene transfer. Human activities—especially antibiotic use in healthcare, agriculture, aquaculture, and pharmaceutical production—introduce antibiotics and resistant bacteria into environmental systems via wastewater, manure, and runoff. This creates selective pressure that favors resistant organisms and enables resistance genes to move between environmental microbes and human or animal pathogens. As a result, the environmental microbiome functions as a dynamic interface linking human, animal, and ecosystem health, reinforcing the importance of One Health approaches that integrate environmental surveillance, improved waste management, and reduced antimicrobial pollution to limit the spread of resistance.