Diet is a recognized factor in microbial diversity of the gut microbiome but is seldom investigated thoroughly outside of captive animal studies. In fecal samples where the signal of evolutionary history is weak, diet is often suggested as an alternative driving factor, but this assertion is not supported by data on an individual level. Here I propose to connect the gut microbiota of individual insectivorous bats to a precise account of their diet using 16S rRNA sequencing of the bacterial community and DNA barcoding of the COI mitochondrial gene. Several alternative hypotheses are presented to account for variation in the gut microbiota of bats with similar prey composition, including species level variation, sex, reproductive state, foraging habitat, and white nose syndrome survivorship. This study incorporates field collection and identification of bat subjects, laboratory methods including DNA extraction, amplification of three markers, and sequencing on the MiSeq Illumina platform. Analysis includes an extensive bioinformatics toolbox, spatial analysis, and mathematical modeling in a generalized hidden markov model framework.