Early-life and host-associated animal microbiomes: biodiversity, function, and One Health management strategies

Animal-associated microbiomes are increasingly recognised as integral components of host biology and ecosystem functioning. This thesis investigates host-associated animal microbiomes as dynamic ecological systems embedded within interconnected biological, environmental and anthropogenic contexts. Using a comparative framework integrating culture-dependent and culture-independent approaches, metagenomic analyses, and strain-resolved genomics, this work examines how microbiomes are structured by ecological context, developmental stage and management-related pressures, within a One Health perspective. Part I focuses on how ecological context plays a greater role than host taxonomy alone in shaping microbiome composition. Diet, habitat characteristics, social structure and anthropogenic exposure emerge as primary drivers of microbial community assembly, highlighting the microbiome as an interface linking host biology and environmental conditions.Part II focuses on early life as a critical window for microbial assembly and host-microbe adaptation. Analyses of bifidobacteria associated with human infants and pre-weaning calves reveal substantial strain-level diversification, with functional traits consistent with adaptation to milk-derived substrates and host-specific physiological conditions. These findings indicate that host-driven selection during early development plays a key role in shaping the functional structuring of the microbiome.Part III addresses the microbiome as an ecological node in antimicrobial resistance dynamics. In livestock systems, animal-associated microbiomes and derived waste streams act as reservoirs and redistribution points for resistance determinants. Through resistome and mobilome analyses, as well as in vivo intervention studies, this work shows that non-antibiotic strategies and targeted waste treatments can modulate microbial community trajectories and reduce selective pressure without compromising ecosystem functionality. Overall, this thesis proposes an integrated view of the animal microbiome as an ecological interface shaped by assembly processes, developmental constraints and anthropogenic influences. Within a One Health framework, sustainable animal production and antimicrobial resistance mitigation require not only reduced antimicrobial inputs, but also an improved understanding and ecological modulation of microbial ecosystems across the host-environment continuum.