Linking pathogens and antibiotic resistance in microbial communities: Insights from omics and isotopic tracing

The accelerating emergence of antibiotic-resistant pathogens is driven by widespread antibiotic use and escalating environmental disturbances, with resistance and virulence shaped by both genetic determinants and interspecies interactions. Traditional culture-based methods remain insufficient to capture the ecological and functional dynamics of these processes in situ. High-throughput multi-omics, including metagenomics, metatranscriptomics, metaproteomics, and metabolomics, has revealed remarkable taxonomic and functional diversity of resistance and virulence determinants across ecosystems. Yet, these approaches often fall short in pinpointing the specific taxa actively expressing functional traits within complex communities. Stable isotope probing (SIP) addresses this gap by linking microbial identity with metabolic activity, enabling direct detection of organisms that degrade antibiotics or express resistance genes under native conditions. Here, we synthesize advances in omics and isotopic tracing to uncover ecological and mechanistic bases of resistance and virulence, highlighting new insights into horizontal gene transfer, community-level selective pressures, and real-time microbial responses to antimicrobial compounds.