Microbial detoxification of plant defense compounds influences the use 27 of certain plants as food sources by herbivores. The location of microbial 28 detoxification along the gut could have profound influences on the distribution, 29 metabolism, and tolerance to toxic compounds. Stephen's woodrats (Neotoma 30 stephensi) specialize on juniper, which is heavily defended by numerous defensive 31 compounds, such as oxalate, phenolics, and monoterpenes. Woodrats maintain two 32 gut chambers harboring dense microbial communities: a foregut chamber proximal 33 to the major site of toxin absorption, and a cecal chamber in their hindgut. First, we 34 conducted a trial with antibiotics to determine whether the gut microbiota is 35 important in allowing N. stephensi to consume juniper. Antibiotic-treated animals 36 lost significantly more body mass while feeding on juniper, relative to those feeding 37 on rabbit chow. Next, we measured levels of toxins throughout the gut. Oxalate 38 concentrations were immediately lower in the foregut chamber, while 39 concentrations of terpenes remain high in the foregut, and are lowest in the cecal 40 chamber. Finally, we conducted metagenomic sequencing of the foregut and cecal 41 chambers. We found that the majority of genes associated with detoxification 42 functions were more abundant in the cecal chamber. However, some genes 43 associated with degradation of oxalate and phenolic compounds were more 44 abundant in the foregut. Thus, it seems that microbial detoxification may take place 45 in various chambers depending on the class of chemical compound. We hypothesize 46 that the location of microbial detoxification could impact the tolerance of animals to 47 Importance -For decades, ecologists have investigated how partnerships with 50 fermentative microbes have contributed to the success of mammalian herbivores. 51The location of these partnerships in the gut (foregut vs. hindgut fermentation) can 52 have large implications for host ecology, such as limiting body size or dietary niche 53 breadth. Mammalian herbivores also host microbial communities that aid in the 54 detoxification of plant defensive compounds, though the location of these functions 55 in the gut has not been studied thoroughly. Here, we used metagenomic sequencing 56 to investigate the location of detoxification functions in the gut of a small 57 mammalian herbivore, Stephen's woodrat, which has both a foregut and a hindgut 58 chamber. We found that most detoxification genes exhibited higher abundance in 59 the hindgut, though genes associated with oxalate degradation were enriched in the 60 foregut. We hypothesize that similar to microbial fermentation, the location of 61 microbial detoxification may also have implications for host ecology. 62 63 64 65 66 67 68 69 70 71 72in the gut, then toxins concentrations in the foregut would be significantly lower 132 compared to food material. Last, we conducted a series of metagenomic analyses to 133 inventory and compare the functions of microbial communities. We first c...