Hidden palette: Culturing the sauropsid gut microbiome reveals a high prevalence and diversity of bacteria that undergo carotenoid biosynthesis.

Pigments play essential roles in communication, physiology, and ecological adaptation in taxa across the tree of life and are especially important for animals, where carotenoid pigments contribute to diverse functions including coloration, antioxidant defense, and immune function. One potentially important yet largely overlooked source of carotenoids is host-associated microbes. Microbially derived carotenoids may influence host phenotype and physiology, but the extent to which they occur or vary across hosts remains largely unknown. To begin to address this gap, we isolated gut-associated bacteria from multiple wild sauropsids. We cultured 157 distinct bacterial isolates from 25 individuals representing eight host species; 21% of isolates were yellow- or orange-pigmented and 40% exhibited absorbance spectra consistent with the presence of carotenoids. 16S rRNA gene sequencing revealed that isolates spanned four phyla and 35 genera. Isolates that were consistent with the presence of carotenoids were found across all four phyla, with Pantoea being the most common carotenoid-associated genus. Host species did not significantly explain variation in isolate community composition. These results demonstrate that carotenoid-capable bacteria are both taxonomically diverse and widespread among gut-associated bacteria from wild sauropsids. More broadly, our findings provide insight into a hidden dimension of host-microbe interactions and their potential function.