Bacteria that reside in the vertebrate gut are part of a complex consortium that greatly expands the metabolic capabilities of the host, providing biochemical functions such as conversion of indigestible dietary components into usable forms, and modulation of host development, immunology, physiology and behavior. Hibernation provides a unique platform to understand the interplay among host biology, diet and the commensal microbiota, due the extended absence of dietary substrates that many gut bacteria rely on for metabolic needs. The annual hibernation cycle modifies the gut microbiota of 13-lined ground squirrels: it increases relative abundance of taxa that can degrade host glycans including Akkermansia, a dedicated mucin-degrader, and reduces abundance of many taxa that prefer plant glycans. To determine functional significance of these seasonal changes we gavaged active season squirrels and aroused hibernators with 13C-labeled substrates including inulin, a plant-derived fiber, and mannitol, a simple sugar alcohol, neither of which can be metabolized by mammalian enzymes. Subsequent measurement of δ13CO2 in breath is used an index of bacterial degradation of the substrates in vivo. Results suggest that as hibernation progresses the capacity to degrade complex plant-derived glycans, but not simpler sugars, diminishes. Maximal changes in δ13CO2 (in o/oo; mean±SE) after 13C-inulin gavage (25 mg/kg) are 160±20 in summer microbiotas and -15±2 in late winter (4 months hibernation) (n=3-5 per group). In contrast, after 13C-mannitol gavage (15 mg/kg) maximal responses average 50±10 in summer and 80±38 in hibernators (n=3-4 per group). Antibiotic manipulations of bacterial communities can reveal whether the microbiota affects seasonal cycles in hibernators. Low dose penicillin (Pen, 13.4 mg/L) given to pregnant squirrels during gestation and lactation has modest effects on total bacterial abundance of their pups but substantial effects on community composition, including greatly increased abundance of Akkermansia which persists through the hibernation season. Pen exposure in early life increases adiposity by midsummer and increases gut serotonin content. The results provide novel insights into host-microbiome interactions in natural models of extreme dietary change, with potential implications for treating microbiome alterations in patients undergoing temporary or complete bowel rest due to gastrointestinal disease.