Emerging Resistomes in Non-Conventional Environmental Bacterial Phyla

The global expansion of antimicrobial resistance (AMR), recognized as a critical public health threat by the World Health Organization, has traditionally been investigated within clinically relevant bacterial groups, particularly members of the Pseudomonadota , Bacillota , and Actinobacteriota . However, advances in genomics, environmental metagenomics, and single-cell approaches have increasingly revealed that antimicrobial resistance genes (ARGs) are widely distributed across diverse and largely underexplored environmental bacterial lineages.This Research Topic seeks to explore the concept of the “emerging resistome” within non-canonical, environmentally widespread bacterial lineages, such as: i) Candidate Phyla Radiation (CPR), ii) the PVC superphylum ( Planctomycetota , Verrucomicrobiota , Chlamydiota ), iii) deep-branching thermophilic lineages (e.g. Aquificota , Thermotogota ), and iv) recently described or rare phyla (e.g. Gemmatimonadota , Nitrospirota ). These taxa are often overlooked due to cultivation challenges and limited representation in reference databases. Despite these limitations, they may contribute to the resistome through previously uncharacterized resistance determinants, ancestral gene variants, alternative genetic architectures, and novel mechanisms of microbial adaptation and interaction. Furthermore, horizontal gene transfer (HGT) plays an important role in shaping resistome dynamics, enabling the movement of ARGs across taxa and environments. In this context, mobile genetic elements (MGEs), such as plasmids, transposons, integrons, and bacteriophages, act as key mediators of resistance gene dissemination. These processes are especially relevant in complex ecosystems where non-canonical bacterial phyla coexist with clinically relevant organisms, creating opportunities for genetic exchange and the emergence of novel resistance traits.We welcome studies investigating the diversity, evolution, and functional significance of resistance traits in these organisms, including intrinsic resistance mechanisms, novel ARGs, and horizontal gene transfer pathways linking environmental reservoirs to clinically relevant bacteria. Emphasis is placed on integrative approaches such as comparative genomics, metagenomics, transcriptomics, epigenomics, and experimental validation of resistance phenotypes. Investigations into ecological drivers, such as anthropogenic pollution, antibiotic residues, wastewater discharge, and climate-related stressors, that may shape resistome dynamics in non-model phyla are also encouraged. Conceptual and evolutionary frameworks that examine resistomes as ancient adaptive systems rather than solely anthropogenic phenomena are of special interest.By expanding the scope of AMR research beyond conventional model organisms and pathogens within the One Health framework, this article collection aims to deepen our understanding of environmental reservoirs as critical interfaces for the circulation of resistance determinants, uncover novel resistance mechanisms, and refine the evolutionary narrative of antimicrobial resistance in the less explored microbial world.Sub-topics of interest include, but are not limited to:• Diversity and distribution of antimicrobial resistance genes (ARGs) in non-canonical bacterial phyla• Emerging resistomes in underexplored bacterial lineages• Role of horizontal gene transfer (HGT) in resistome evolution• Mobile genetic elements (MGEs) as drivers of antimicrobial resistance dissemination• Environmental reservoirs of AMR within a One Health framework• Comparative genomics and metagenomics of non-model bacterial phyla• Novel resistance mechanisms and ancestral ARG variants• Ecological and evolutionary drivers shaping resistome dynamics• Impact of anthropogenic pressures (e.g., pollution, antibiotics, wastewater) on environmental resistomes• Functional validation of resistance phenotypes in uncultured or difficult-to-culture bacteriaThis 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. Topic editors: Sandra Quinteira, Olga Lage, Lise Øvreås Source: https://www.frontiersin.org/research-topics/80271/emerging-resistomes-in-non-conventional-environmental-bacterial-phyla