Cutting-Edge Environmental Genome Monitoring Shaping a New Era of Genome-Based Safety Research for One Health and Evolution

Mutagenicity and genotoxicity research has traditionally focused on evaluating how chemicals affect genomes, particularly in relation to mutation-driven carcinogenesis. Advances in next-generation sequencing have broadened environmental applications, enabling eDNA/eRNA analysis, metagenomics, and wastewater-based surveillance for ecosystems and public health monitoring. Framed within a One Health perspective that links human, animal, and environmental health, this Global Perspective examines synergies between mutagenomics and environmental genomics aimed at maintaining organismal and ecosystem health. We review emerging trends across five domains including antimicrobial resistance genes, pathogen dynamics, biodiversity, environmental stress responses, and biological evolution and discuss how integrating mutation genomics and molecular toxicology techniques into environmental monitoring can address current gaps. Common challenges include sensitive detection of low-frequency variants in mixed environmental samples, functional interpretation and causal attribution of variants and expression changes, and the lack of cross-taxonomic reference resources. Overcoming these challenges with mutation-genomics-derived approaches could enable improved source attribution, earlier detection of emerging threats, and outcome-oriented risk assessment. Now is the time to strengthen interdisciplinary collaboration, standardize methods, and establish cross-taxonomic reference and analytical infrastructures.