Bacteriophage-Driven Evolution and Genome Dynamics in Environmental and Animal-Associated Microbiomes

Bacteriophage research occupies a key position in the interconnected fields of microbial ecology, evolutionary biology, and genetics. Bacteriophages -viruses infecting bacteria, are now recognized not only as abundant predators in microbial food webs but also as powerful agents of genetic change. Recent studies have demonstrated that phages directly influence the genetic composition, adaptive capacity, and ecological roles of bacterial communities both in natural ecosystems and within animal hosts. High-throughput sequencing, comparative genomics, and metagenomic analyses have exposed the intricate and reciprocal impacts of phage infection, gene transfer, and co-evolution on bacterial diversity and function. Despite these advances, critical gaps persist: we still lack a comprehensive understanding of the mechanisms by which phages modulate bacterial genomes and shape community resilience, how these dynamics manifest differently in environmental settings versus host-associated microbiomes, and what their implications are for microbial adaptation, resistance emergence, and ecosystem stability. Key questions revolve around the evolutionary pathways enabled by phage-bacteria interactions, the role of lateral gene flow, and the potential risks and benefits for environmental and animal health.This Research Topic aims to illuminate the mechanisms, evolutionary processes, and ecological outcomes that arise from bacteriophage-bacterial genome interactions. Specifically, it seeks to uncover how these viral influences drive genetic variation, adaptation, and fitness in microbial populations in diverse settings from soil and aquatic niches to animal microbiomes. Through interdisciplinary research, this initiative hopes to elucidate not only the fundamental processes but also the applied potentials of phage dynamics, such as their role in the spread of antimicrobial resistance and virulence, and their use as tools for microbial control and biotechnology. The overarching goal is to achieve an integrated understanding of how phage-bacterial interplay shapes the evolutionary trajectory and health of microbial ecosystems.The range of this Research Topic focuses on the genetic, evolutionary, and ecological interfaces between bacteriophages and bacterial genomes, specifically at the levels of environmental biospheres and animal-associated microbiomes. Studies should emphasize evolutionary consequences, adaptation, and functional outcomes rather than organism-centric clinical or biotechnological narratives. To gather further insights in this area, we welcome articles addressing, but not limited to, the following themes:-Phage-driven evolutionary dynamics in environmental microbiomes-Phage-bacterial genetic interactions and horizontal gene transfer in animal microbiomes-The role of phages in the dissemination of antimicrobial resistance and virulence factors-Adaptive responses and genomic changes induced by lytic, temperate, or transducing phages-Innovative therapeutic, prophylactic, or biocontrol uses of phages and engineered phage elements-Co-evolutionary arms race dynamics and CRISPR-Cas mediated interactions in the phage-bacteria ecosystem Topic editors: Miryam Bonvegna, Edyta Kaczorek-Łukowska Source: https://www.frontiersin.org/research-topics/80358/bacteriophage-driven-evolution-and-genome-dynamics-in-environmental-and-animal-associated-microbiomes