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The One Health concept, introduced at the beginning of the 2000s, is a worldwide strategy for promoting multidisciplinary partnerships and information in all facets of health care sciences, perceiving the interrelationship between humans, animals, plants, and their common environment. Recent advances in DNA sequencing technology and computational biology have revolutionized the field of the microbiome. Information surrounding uncultured microorganisms provides a comprehensive analysis of the relationships between an animal, the environment, and human's microbiota, including various disease correlations. In this Research Topic, we are interested in exploring how environmental stress effects bacterial communities, and how those changes relate to human health and pathobiont transmission in experimental and big data analysis.