This study investigated the effects of exercise preconditioning‐induced modification in gut microbiota composition and host responses to cecal ligation and puncture (CLP)‐induced sepsis. Four‐week‐old C57BL/6N male mice were randomly assigned to either CLP (n = 30) or CLP‐exercise (CLP+Exe; n = 30) groups. Prior to CLP‐induced sepsis, the CLP+Exe mice were subjected to 8 wk of treadmill running. Fecal samples were collected and analyzed by 16S rRNA amplification sequencing to assess gut microbiota composition. Diversity analyses such as principal coordinates analysis and rarefaction curves showed that exercise preconditioning was associated with differences in gut microbiota community structure and species richness. Exercise preconditioning‐induced differences in gut microbiota composition were also evident at the family level of taxonomic analysis, with the dominant phyla being Bacteriodetes, Firmicutes, Verrucomicrobia, and, to a lesser extent, Cyanobacteria. Compared with control mice, preconditioned mice had a higher survival rate and less organ damage during the acute phase of sepsis, secondary to attenuation of the host response to septic shock. The current findings suggest that exercise preconditioning‐induced modification in gut microbiota composition may lead to an attenuated host response to CLP‐induced sepsis in wild‐type mice, as shown by increased survival and less organ damage, as well as the establishment of a balance between pro‐ and anti‐inflammatory responses.—Kim, D., Kang, H. Exercise training modifies gut microbiota with attenuated host responses to sepsis in wild‐type mice. FASEB J. 33, 5772–5781 (2019). http://www.fasebj.org