Gut Microbiota–Driven Mechanisms of Antimicrobial Resistance: Ecological Drivers, Probiotic Interfaces, and One Health Perspectives

The gut microbiota represents an open and highly dynamic ecological system that continuously exchanges microorganisms, genetic material, and metabolites with food, water, animals, soil, and built environments. Within this interconnected ecosystem, antimicrobial resistance genes (ARGs) may emerge, persist, and disseminate independently of direct antibiotic exposure. Ecological pressures such as nutrient limitation, microbial competition, bacteriophage activity, oxidative stress, host immune signaling, and xenobiotic exposure can shape microbial fitness and promote horizontal gene transfer mediated by mobile genetic elements (MGEs), including plasmids, transposons, and integrons.Increasing evidence indicates that the gut resistome reflects long-term ecological adaptation rather than solely clinical or antibiotic-driven selection. Consequently, advancing antimicrobial resistance (AMR) research requires mechanistic and genetic analyses that resolve how resistance determinants are generated, mobilized, maintained, and suppressed within microbial communities. Descriptive phenotypic studies lacking genetic, genomic, or mechanistic resolution are therefore outside the scope of this research topic.AMR is often approached through clinical surveillance or resistance phenotyping; however, many resistance traits originate from ecological and evolutionary processes operating within the gut microbiome prior to clinical manifestation. The primary goal of this research topic is to reposition AMR as a dynamic, adaptive ecological process shaped by microbial interactions, nutrient flows, host physiology, and environmental inputs, with emphasis on molecular mechanisms underlying resistome dynamics.This collection aims to elucidate how gut microbial communities generate, stabilize, amplify, or suppress resistance determinants in response to non-antibiotic stressors. Submissions should prioritize genetic, genomic, and functional approaches that clarify causal mechanisms rather than purely observational outcomes.The One Health dimension of this research topic is grounded in tracing AMR flow across human, animal, food, and environmental compartments using comparative genomics, ARG profiling, mobile genetic element analysis, and phylogenetic or network-based frameworks. Studies integrating cross-sectoral datasets to resolve transmission routes, reservoirs, and evolutionary trajectories of resistance genes are particularly encouraged.Sub-topics of interest include, but are not limited to:• Genetic and ecological determinants of ARG emergence, maintenance, and dissemination• Mechanistic interactions between commensals, probiotics, and pathogens influencing resistome structure • Non-antibiotic ecological drivers of resistance selection and mobilization• Horizontal gene transfer mediated by plasmids, phages, and other MGEs• Host-microbiota molecular interactions shaping resistance outcomes• Probiotic, dietary, or ecological interventions evaluated using genetic or functional endpoints• One Health transmission pathways resolved through comparative genomics and molecular epidemiologyContributions integrating multi-omics, experimental models, ecological theory, comparative genomics, or cross-sectoral molecular data are particularly encouraged.This Research Topic welcomes the following article types: FAIR² DATA Direct Submission, FAIR² Data, Hypothesis and Theory, Methods, Mini Review, Opinion, Original Research, Perspective, Review, Systematic Review, and Technology and Code articles, provided they address antimicrobial resistance within the gut microbiome through genetic, genomic, mechanistic, or evolutionary frameworks rather than purely descriptive phenotypic analyses. Topic editors: Arun K B, Astghik Zaveni Pepoyan, Aravind Madhavan, Ragini Bodade, Lekshmi K. Edison Source: https://www.frontiersin.org/research-topics/76287/gut-microbiota-driven-mechanisms-of-antimicrobial-resistance-ecological-drivers-probiotic-interfaces-and-one-health-perspectives