This dataset is a combination of data obtained from a longitudinal live trapping study of wild rodents in Wytham Woods, Oxford (51.796 N,-1.367 W); October 2015-18), a dissection study of rodents caught in the same woodland (October 2017-18), and a diet shift experiment on a captive colony of wood mice housed at the University of Edinburgh (May 2017). The longitudinal live trapping study dataset contains trapping data and data on the gut microbiome composition, diet and gut parasite infection of individually-identifiable rodents. Three species of rodents were trapped with Sherman live-traps fortnightly for 3 years: wood mice (Apodemus sylvaticus), yellow-necked mice (Apodemus flavicollis) and bank voles (Myodes glaerolus). Upon capture, they were injected with a passive integrated transponder (PIT) tag, measured, weighted, sexed, aged and a faecal sample was collected from individuals for microbiome, diet and parasite analyses. All rodents were released to their location of capture. The dissection study contains trapping data, gut microbiome and parasite infection data. Wood mice were trapped fortnightly for one year with Sherman live-traps at least 300m away from the longitudinal sampling grid. Individuals that had been captured and marked with a PIT tag as part of the longitudinal study were released along with other rodents species and juvenile or pregnant individuals (only non-marked adult wood mice were sampled). Wood mice were euthanized (with ethical approval) and their gastrointestinal tract dissected for counts of gut helminths. Samples from along the gastrointestinal tract were taken for gut microbiome analysis. The diet shift experiment dataset contains data on experimental diet treatments and gut microbiome composition of wood mice captively bred in a facility at the University of Edinburgh. Wood mice were given diets varying in the ratio of food supplementation (dried mealworm and/or peanut) and faecal samples taken periodically over 30 days to measure changes in gut microbiome composition and function. Samples for microbiome and diet characterization were stored without buffer at -80̊C. Samples for parasite detection were stored in 10% formalin and refrigerated at 4̊C. This work was funded by a NERC independent Research Fellowship. Full details about this dataset can be found at https://doi.org/10.5285/4f454849-0d30-4c27-ad5b-d285e461bedc