Metagenomic sequencing provides insights into the location of microbial detoxification in the gut of a small mammalian herbivore

Abstract Microbial detoxification of plant defense compounds influences the use of certain plants as food sources by herbivores. The location of microbial detoxification along the gut could have profound influences on the distribution, metabolism, and tolerance to toxic compounds. Stephen’s woodrats (Neotoma stephensi) specialize on juniper, which is heavily defended by numerous defensive compounds, such as oxalate, phenolics, and monoterpenes. Woodrats maintain two gut chambers harboring dense microbial communities: a foregut chamber proximal to the major site of toxin absorption, and a cecal chamber in their hindgut. First, we conducted a trial with antibiotics to determine whether the gut microbiota is important in allowing N. stephensi to consume juniper. Antibiotic-treated animals lost significantly more body mass while feeding on juniper, relative to those feeding on rabbit chow. Next, we measured levels of toxins throughout the gut. Oxalate concentrations were immediately lower in the foregut chamber, while concentrations of terpenes remain high in the foregut, and are lowest in the cecal chamber. Finally, we conducted metagenomic sequencing of the foregut and cecal chambers. We found that the majority of genes associated with detoxification functions were more abundant in the cecal chamber. However, some genes associated with degradation of oxalate and phenolic compounds were more abundant in the foregut. Thus, it seems that microbial detoxification may take place in various chambers depending on the class of chemical compound. We hypothesize that the location of microbial detoxification could impact the tolerance of animals to these compounds, which may have ecological and evolutionary consequences. ImportanceFor decades, ecologists have investigated how partnerships with fermentative microbes have contributed to the success of mammalian herbivores. The location of these partnerships in the gut (foregut vs. hindgut fermentation) can have large implications for host ecology, such as limiting body size or dietary niche breadth. Mammalian herbivores also host microbial communities that aid in the detoxification of plant defensive compounds, though the location of these functions in the gut has not been studied thoroughly. Here, we used metagenomic sequencing to investigate the location of detoxification functions in the gut of a small mammalian herbivore, Stephen’s woodrat, which has both a foregut and a hindgut chamber. We found that most detoxification genes exhibited higher abundance in the hindgut, though genes associated with oxalate degradation were enriched in the foregut. We hypothesize that similar to microbial fermentation, the location of microbial detoxification may also have implications for host ecology.