Animal Microbiomes and Disease: Pathogenesis to Treatments

Animal-associated microbiomes play a pivotal role in maintaining host homeostasis, influencing immune responses, nutrient absorption, and resistance to pathogens. However, disruptions in microbial community composition—whether due to infection, antibiotic exposure, diet, or environmental stress—can lead to dysbiosis, a condition linked to increased disease susceptibility, chronic inflammation, and reduced treatment efficacy. Recent advances in sequencing technologies and multi-omics approaches have revolutionized our understanding of microbiota dynamics and their bidirectional interactions with pathogens and host systems. This emerging knowledge is reshaping classical paradigms in infectious disease research and paving the way for a new generation of microbiome-based diagnostics and therapeutics. In veterinary contexts, microbiome research spans livestock, companion animals, and wildlife, with significant implications for health, productivity, animal welfare, and zoonotic risk. Moreover, alterations in animal microbiota may influence the emergence, persistence, or control of foodborne pathogens, underscoring their indirect yet critical role in food safety and public health.

This Research Topic aims to elucidate the functional and mechanistic links between animal microbiomes and disease pathogenesis. We seek to investigate how pathogenic organisms alter microbial communities and, conversely, how the microbiota modulates host responses—whether by enhancing resistance or increasing susceptibility. Additionally, this Topic highlights the therapeutic and diagnostic potential of microbiome-targeted strategies in veterinary medicine, particularly in the context of rising antimicrobial resistance and the urgent need for alternative interventions.

We welcome submissions that explore the relationship between animal microbiomes and infectious or chronic diseases, with particular emphasis on mechanistic insights, experimental validation, and translational potential. Topics of interest include, but are not limited to:

- Dynamics of the microbiota during infection or antibiotic treatment
- Microbial biomarkers for disease diagnosis or prognosis
- Immunomodulatory effects of the microbiota or their metabolites
- Microbiota-targeted therapies, including probiotics, postbiotics, bacteriophages, and FMT/MMT
- Impact of pathogens on microbial ecology and resilience
- Multi-omic and computational approaches to model microbiome–pathogen–host interactions
- Influence of animal microbiota on foodborne pathogens and associated control strategies

Contributions addressing domestic animals, wildlife, or One Health interfaces are especially encouraged. We welcome preclinical, in vivo, in vitro, or in silico studies that investigate the complexity of the microbiome in the context of infection, disease management, and implications for food safety.