Rodents consuming the same toxic diet harbor a unique taxonomic and functional core microbiome

Abstract Gut microbiota are intrinsic to an herbivorous lifestyle, but very little is known about how plant secondary compounds (PSCs), which are often toxic, influence these symbiotic partners. Using 16S rRNA gene and shotgun metagenomic sequencing, we investigated the possibility of a unique taxonomic and functional core microbiome in populations of two species of woodrats ( Neotoma lepida and bryanti ) that have independently converged to feed on the same toxic diet (creosote bush; Larrea tridentata ). In each gut region (foregut, cecum, and hindgut) sampled, we found a distinct taxonomic core set of microbes in the populations feeding on creosote that were not designated as core members in noncreosote-feeding populations. The core members in creosote feeders were significantly enriched and occurred more frequently than predicted by chance, suggesting that they may benefit the host. Some of the functions identified within the functional core include the metabolism of aromatic rings and thus may be involved in the degradation of PSCs. Overall, our results characterize the functional profiles of the gut microbiota in a wild herbivore and identify key taxa that may aid herbivores in subsisting on their toxic diet.