Molecular approaches to investigate microbiome transmission across individuals using guppies

Host-associated microbiomes are shaped by intrinsic host characteristics, environmental exposure, and social interactions, but the relative contributions of these factors to microbiome transmission remain poorly understood. To investigate contact-dependent microbial transmission and the ecological factors influencing it, we developed an experimental system using guppies (Poecilia reticulata), a tractable model for studying social interactions. Microbiome perturbation was used as an experimental tool to generate contrasting starting microbial communities, allowing transmission dynamics to be more readily detected. Environmental exposure was controlled while manipulating social contact, host sex, and population of origin through Single Origin (Botanical Garden) and reciprocal Mixed Origins (Laboratory × Botanical Garden) pairings maintained under Contact or No Contact conditions. Microbial communities were profiled via 16S rRNA sequencing across four tissues (skin, gill, gonad, intestine). Additionally, automated behavioral tracking for contact pairs quantified body contact, proximity, and side-by-side swimming to test whether specific social behaviors predicted microbiome similarity between partners. The study revealed that microbiome transmission dynamics and community composition were jointly shaped by host-associated, environmental, and behavioral factors. Environmental perturbation generated distinct microbial communities, providing the experimental contrast for examining microbiome transfer dynamics. The influence of social contact on microbiome composition depended on tissue type, sex, and origin, varying between reciprocal crosses and indicating that microbial dynamics depend considerably on partner identity. Contrary to expectations, although social contact significantly restructured microbial communities in specific tissues, higher rates of body contact, proximity, and side-by-side swimming were associated with increased rather than decreased microbiome dissimilarity between partners, suggesting that physical contact alone is insufficient to predict successful microbial convergence. The study highlights the value of integrating experimental microbiome perturbation with behavioral and microbiome profiling to disentangle the ecological processes governing microbiome transmission. Collectively, the findings demonstrated that microbiome transmission between social partners is a multifactorial process governed by host identity, behavioral context, and tissue-specific colonization dynamics, with broader implications for understanding microbiome assembly in social animals.