Habitual exercise modulates the composition of the intestinal microbiota. We examined whether transplanting fecal microbiota from trained mice improved skeletal muscle metabolism in high-fat diet-fed mice. The recipient mice that received fecal samples from trained donor mice for 1 week showed elevated levels of metabolic signalings in skeletal muscle. Glucose tolerance was improved by fecal microbiota transplantation after 8 weeks of HFD administration. Intestinal microbiota may mediate exercise-induced metabolic improvement in mice. We performed a microarray analysis to compare the metabolic gene expression profiles in the skeletal muscle from each mouse. Overall design: Male germ-free mice were administered fecal samples from sedentary or training donor mice. After 1 week, 6 mice from each recipient group were used for microarray analysis. Total RNA was extracted from the gastrocnemius muscle. cRNA and target hybridization preparations were performed according to the Affymetrix GeneChip Technical Protocol. Affymetrix GeneChip Mouse Gene 1.0 ST arrays were stained and washed in an Affymetrix Fluidics Station 450 and scanned using a GeneChip Scanner 3000.