Host traits and environmental variation shape gut microbiota diversity in wild threespine stickleback

Abstract

BackgroundDespite the growing recognition of the importance of gut microbiota in host ecology and evolution, our understanding of the relative contributions of host-associated and environmental factors shaping gut microbiota composition within and across wild populations remains limited. Here, we investigate how host morphology, sex, genetic divergence, and environmental characteristics influence the gut microbiota of threespine stickleback fish populations from 20 lakes on Vancouver Island, Canada. ResultsOur findings reveal substantial variation in gut microbiota composition and diversity among populations, with host traits exerting a stronger influence on bacterial alpha diversity than environmental characteristics. Host morphology, which is indicative of trophic ecology, was linked to gut microbiota divergence among populations, suggesting that dietary specialization may play a role in shaping the stickleback gut microbiota. Within and across populations, we only observed a weakly defined core microbiota and limited sharing of ASVs among hosts, indicating that gut microbiota composition is individualized. Additionally, we detected sex-dependent differences in microbial diversity, opening avenues for future research into the mechanisms driving this variation. ConclusionsIn sum, our study emphasizes the need to consider both host-associated and environmental factors in shaping gut microbiota dynamics and highlights the complex interplay between host organisms, their associated microbial communities, and the environment in natural settings. Ultimately, these insights enhance our understanding of host-microbiota interactions and their eco-evolutionary implications.