Gut microbiota variation in captive tortoises is associated with host species, trophic category, and growth rate

Despite the ecological and conservation importance of tortoises, their gut bacterial microbiotas remain poorly characterized, particularly across species in captivity. Associations between gut microbiota composition and tortoise age, sex, and growth rate are also poorly understood. Here, we use full-length 16S rRNA gene sequencing to characterize the gut microbiotas of 55 captive tortoises, representing seven species: red-footed tortoise (Chelonoidis carbonarius), yellow-footed tortoise (Chelonoidis denticulatus), Mojave desert tortoise (Gopherus agassizii), Texas tortoise (Gopherus berlandieri), leopard tortoise (Stigmochelys pardalis), African spurred tortoise (Centrochelys sulcata), and Russian tortoise (Testudo horsfieldii). By examining individuals maintained under consistent environmental conditions, we reduced large-scale environmental variation and evaluated associations with host characteristics. Across species, we identified a core set of 18 bacterial taxa, including cellulose degraders (Cellulosilyticum ruminicola and Ruminococcus champanellensis) and fatty-acid producers (Clostridium butyricum, and members of the families Lachnospiraceae and Christensenellaceae). Despite this shared bacterial core, microbiota composition differed by host species, age, and trophic category (herbivore vs. omnivore). Additionally, the relative abundances of two taxa-R. champanellensis, an important fiber degrader, and Anaerocella delicata, a propionate and acetate producer-were associated with variation in tortoise growth rate. Collectively, our findings suggest that although captive tortoises share a common microbial core, host species and digestive physiology shape microbiota structure, while specific bacterial taxa are associated with variation in growth rate.