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, sexual signaling, and ecological adaptation in taxa across the tree of life and are especially important for animals, which often rely on carotenoid pigments for their coloration. One potentially important yet largely overlooked source of pigments is host-associated microbes. Microbial carotenoids may influence host coloration or other fitness-related traits, but the extent to which they occur or vary across associations with host species remains largely unknown. To begin to address this gap, we used culture-based techniques to isolate gut-associated bacteria from multiple wild sauropsid species. We cultured 157 morphologically distinct bacterial isolates from 25 individuals representing eight host species; 17% of isolates were yellow- or orange-pigmented, and 40% of isolates exhibited absorbance spectra consistent with the presence of carotenoids. Sequencing of the 16S rRNA gene 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 frequently represented carotenoid-associated genus. These results demonstrate that carotenoid-capable bacteria are both taxonomically diverse and prevalent in the gut microbiomes of wild sauropsids. More broadly, our findings provide insight into a hidden dimension of host-microbe interactions and their potential function.