How is animal microbiome transmitted? An integrative approach to investigate the ecological factors driving microbiome transfer using guppies

Animals and microorganisms are linked by associations that influence health, ecology and evolution. The environment and social interactions are a determining factor in the composition and alteration of the microbiota. In this thesis I addressed this topic using the guppy (Poecilia reticulata) as a model organism and applying an integrative approach combining microscopy, molecular quantification, sequencing and behavioural analysis. Optimisation of FISH visualisation revealed dense microbial localisation along the intestinal mucosa, while highlighting methodological limitations in gill tissue. Experimental conditions were established in which female individuals with simplified microbiota were co-housed with conventional males. qPCR showed that the overall bacterial load did not vary significantly between treatments, but sequencing of the 16S rRNA gene showed that exposure to sterile water reshaped community composition and reduced richness, favouring the dominance of specific taxa such as Mycobacterium. In addition, video tracking software was used to quantify the number of contacts between individuals. Taken together, these results suggest that microbiome ecology is a multifactorial process shaped by both environmental disturbances and host behaviour. They also confirm that P. reticulata is a valuable model for studying the ecological factors that drive microbiome alterations.