Genomics and microbiome approaches to antimicrobial resistance

Bacterial pathogenesis, evolution, and genomics intersect critically with the ongoing challenge of antimicrobial resistance (AMR), which poses significant threats to public health, agriculture, and sustainable development. While traditional studies of AMR have focused on pathogenic bacteria and their mechanisms for evading antibiotics, recent research highlights the role of broader microbial communities—including commensal and environmental microbiomes—in shaping the genetic landscapes that drive resistance. Expanding knowledge from molecular bacteriology, coupled with advances in multi-omics and microbiome science, has revealed new facets of horizontal gene transfer, bacterial adaptation, and host-microbe interactions that underpin both the emergence and containment of drug resistance. Despite these advancements, unresolved questions remain regarding the interplay between pathogenic and non-pathogenic bacteria within microbiomes, the environmental and nutritional factors influencing resistance evolution, and the potential of microbiome engineering for mitigating AMR.

This Research Topic aims to integrate research that address the genetic, molecular, and ecological foundations of bacterial pathogenesis and the evolution of drug resistance. A particular objective is to showcase how new insights from molecular bacteriology and microbiome research can inform and accelerate the development of next-generation antimicrobials. We encourage submissions that explore genetic determinants of resistance, the dynamics of microbial communities in health and disease, and how microbiome-based interventions may disrupt resistance transmission and bacterial virulence.

The focus of this Research Topic encompasses bacterial pathogenesis and resistance within the context of host-associated and environmental microbiomes, with boundaries extending to both pathogenic and non-pathogenic bacterial interactions. To gather further insights in these areas, we welcome articles addressing, but not limited to, the following themes:

o Bacterial interactions within diverse microbiomes
o Health and disease implications of microbiome dynamics
o Molecular biology and evolutionary mechanisms in non-pathogenic bacteria
o Influence of nutrition and diet on the microbiome and resistance modulation
o Prebiotics and their direct or indirect effects on microbiomes and antimicrobial resistance
o Probiotics and their roles in promoting health and counteracting resistance
o Microbiome-driven cross-organ interactions and systemic implications
o Translational approaches leveraging microbiome and molecular insights for next-generation antimicrobial development

Article types and fees

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Brief Research Report
• Case Report
• Classification
• Clinical Trial
• Editorial
• FAIR² Data
• General Commentary
• Hypothesis and Theory
• Methods
• ... View all formats

Articles that are accepted for publication by our external editors following rigorous peer review incur a publishing fee charged to Authors, institutions, or funders.

Article types

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Brief Research Report
• Case Report
• Classification
• Clinical Trial
• Editorial
• FAIR² Data
• General Commentary
• Hypothesis and Theory
• Methods
• Mini Review
• Opinion
• Original Research
• Perspective
• Review
• Systematic Review
• Technology and Code

Keywords: Bacterial Pathogenesis, Antimicrobial Resistance (AMR), Microbiome, Evolutionary Genomics, Next-generation Antimicrobials

Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.