Universes within universes: microbiome diversity associated with different body parts of the sand lizard (Lacerta agilis)

The bodies of animals host millions of microbial communities collectively known as the microbiome. The microbiome plays a crucial role in various processes related to the host’s health and well-being. Although our understanding of the microbiome’s importance to host functioning is growing rapidly, many aspects remain poorly understood. One such aspect is the role of the microbiome in chemical communication. To address this question, we used the sand lizard (Lacerta agilis), a reptile with well-developed chemosensory abilities and commonly distributed in Central Europe. Our first goal was to characterize the bacterial microbiome associated with different body parts potentially involved in chemical signalling (e.g., femoral glands, cloaca, and skin). Additionally, we examined sex-related differences in the microbiome that could be connected to intraspecific communication. Over two years, a total of 274 samples were collected. Amplicon sequencing of the 16S rRNA V3–V4 region revealed significant variation in microbial diversity across body parts, with the skin hosting the most diverse and balanced communities. In contrast, the cloaca and femoral glands contained less diverse but more specialised assemblages. No differences in microbial diversity between sexes were observed, but the year of sampling was an important factor, suggesting a highly dynamic microbiome in sand lizards. There was minimal overlap in the number of unique operational taxonomic units (OTUs) between body parts, indicating a small core microbiome (∼1% of shared taxa). Sex differences in tissue-specific bacteria were more pronounced in the cloaca, supporting the idea that the cloacal microbiome is highly specialised. Our findings suggest that microbial communities vary significantly among body parts, with strong tissue specificity, indicating that each region provides a distinct ecological niche. This study offers promising directions for future research into how host-associated microbiomes could influence chemical communication in vertebrates.