Bacteria sheltered in gut impact on the physiology and function of several distant organs such as liver, adipose tissue or brain1. A functional cross talk between gut microbiota and skeletal muscle has also been recently discussed in the literature2. However this hypothesis requires more experimental support. Here we investigated in mice whether skeletal muscle remodeling could affect gut microbiota signature and pertinent intestinal mRNA genes expression related to muscle metabolism. We showed that mice invalidated for myostatin, a lean model presenting hypertrophic fatigable muscles3,4, display a specific microbiota signature characterized notably by a decrease of Firmicutes and Proteobacteria phyla. We also highlighted in the distal intestine an over-expression of Fiaf mRNA, a fat storage inhibitor5 and this could contribute to the specific lean phenotype of myostatin KO mice. Furthermore, 4 weeks of aerobic endurance training was associated with a normalization of gut microbiota signature (and phyla abundance) of KO-myostatin mice towards the WT profile. Interestingly, we also observe a normalization of expression of some intestinal mRNA markers including Fiaf. Altogether our results suggest a cross-talk between muscle remodeling and gut microbiota. Further understanding of the underlying mechanisms could open new therapeutic strategies for muscle- related disorders.