Turtle Assemblage Composition and Body Site Shape Microbiome Structure in Native and Non-Native Freshwater Turtles

Abstract Biological invasions are increasingly recognised as drivers of ecological change. However, the consequences for host-associated microbiomes have been neglected. The coexistence of native and non-native freshwater turtles provides a useful ecological system for evaluating whether turtle assemblage composition is associated with variation in host-associated microbiomes. In this study, we characterised the microbial communities associated with native and non-native freshwater turtles in isolated and mixed assemblages. External-shell and cloaca samples were analysed using 16 S rRNA metabarcoding to assess microbial diversity, composition, and abundance patterns. Alpha and Beta diversity were evaluated in relation to body site, turtle assemblage composition, sex and body size. Alpha diversity differed consistently between body sites, while turtle assemblage composition was associated with Shannon diversity but not with Simpson diversity or Faith’s phylogenetic diversity. Beta diversity analyses revealed significant differences between body sites and turtle assemblage compositions across all distance metrics, with a body site × assemblage interaction detected for Bray–Curtis dissimilarity. Taxonomic composition of the most represented microbial taxa also differed markedly between external-shell and cloaca, with body site consistently emerging as the main driver of microbial community structure. Differential abundance analyses supported these findings, identifying several phyla and genera that were significantly increased in each body site. A total of 19 taxa were identified as closely related to human-associated pathogens. These taxa were absent in communities only containing non-native turtles but were present in native only and mixed communities. Overall, our results highlight the importance of body site and turtle assemblage in shaping turtle microbiomes and underscore the potential implications of biological invasions.