Enterobacteriaceae community dynamics in sleepy lizards: Richness, prevalence and co-occurrence over time

Animal gut microbiomes can be very diverse, and enteric bacteria can profoundly affect the physiology of their host. The gut microbiome can be related to host health and digestion, which ultimately contribute to host body condition. However, we have a limited understanding of the co-occurrence patterns of gut bacteria in their host, and how co-occurrence and bacterial diversity change over time. This notion is especially important to animals living in groups as bacteria can transmit through social interactions. We investigated the co-occurrence patterns of gut bacteria in a lizard host. We repeatedly collected cloacal swabs from 87 sleepy lizards (Tiliqua rugosa) from two different study sites over their activity season. We determined the richness and prevalence of 82 enteric bacterial strains and used a probabilistic model to investigate their co-occurrence. At both study sites, richness and prevalence generally increased over time. We suggest that the lizards acquire strains throughout their activity season by moving through the landscape and inspecting conspecific scats. Lizards continuously tongue-flick while moving, and thereby ingest bacteria when they move through areas where other animals defaecated. Temperature, rainfall and diet change seasonally, influencing lizard activity, and may influence the observed increase in enterobacterial richness and prevalence. Further, albeit with some exceptions, most strain pairs did not occur significantly more often or less often than expected by chance. This finding shows a lack of structured co-occurrence, which may imply that most bacterial strains did not facilitate or inhibit each other. The absence of a co-occurrence pattern could also be driven by random encounters of bacteria shed by other lizards within the habitat. Our results suggest that behaviour (movement patterns, tongue-flicking), activity patterns and environmental factors collectively drive the temporal pattern of the gut bacterial community in sleepy lizards and potentially other wild reptiles.