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Abstract The gut microbial communities of mammals provide numerous benefits to their hosts. However, given the recent development of the microbiome field, we still lack a thorough understanding of the variety of ecological and evolutionary factors that structure these communities across species. Metabarcoding is a powerful technique that allows for multiple microbial ecology questions to be investigated simultaneously. Here, we employed DNA metabarcoding techniques, predictive metagenomics, and culture-dependent techniques to inventory the gut microbial communities of several species of rodent collected from the same environment that employ different natural feeding strategies [granivorous pocket mice (Chaetodipus penicillatus); granivorous kangaroo rats (Dipodomys merriami); herbivorous woodrats (Neotoma albigula); omnivorous cactus mice (Peromyscus eremicus); and insectivorous grasshopper mice (Onychomys torridus)]. Of particular interest were shifts in gut microbial communities in rodent species with herbivorous and insectivorous diets, given the high amounts of indigestible fibers and chitinous exoskeleton in these diets, respectively. We found that herbivorous woodrats harbored the greatest microbial diversity. Granivorous pocket mice and kangaroo rats had the highest abundances of the genus Ruminococcus and highest predicted abundances of genes related to the digestion of fiber, representing potential adaptations in these species to the fiber content of seeds and the limitations to digestion given their small body size. Insectivorous grasshopper mice exhibited the greatest inter-individual variation in the membership of their microbiomes, and also exhibited the highest predicted abundances of chitin-degrading genes. Culture-based approaches identified 178 microbial isolates (primarily Bacillus and Enterococcus), with some capable of degrading cellulose and chitin. We observed several instances of strain-level diversity in these metabolic capabilities across isolates, somewhat highlighting the limitations and hidden diversity underlying DNA metabarcoding techniques. However, these methods offer power in allowing the investigation of several questions concurrently, thus enhancing our understanding of gut microbial ecology. 

Abstract Measurements of fecal pellet size can provide important information about wild mammals, such as body size and demographic information. Previous studies have not rigorously tested whether diet can confound these measurements. Furthermore, it is unknown whether diet might alter fecal dimensions directly or through changes in animal physiology. Here, we studied three closely related rodent species that differ in natural feeding strategies. Individuals were fed diets that varied in protein and fiber content for 5 weeks. We then measured body size, fecal widths and lengths, and the radius of the large intestine. Diet composition significantly changed fecal widths in all species. High-fiber content significantly increased fecal widths and would cause overestimations of body size if applied to wild feces. Using path analysis, we found that fiber can increase fecal widths both directly and indirectly through increasing the large intestine radius. Protein affected each species differently, suggesting that protein effects vary by species feeding strategy and existing physiology. Overall, diet and large intestine morphology can alter fecal pellet measurements. Studies using fecal measurements therefore must consider these effects in their conclusions.