Traumatic brain injuries (TBI) manifest into post-traumatic stress disorders such as anxiety comorbid with gut ailments. The perturbations in gut microbial communities are often linked to intestinal and neuropsychological disorders. We have previously reported anxiety and abnormalities in gut function in mild TBI (MTBI)-exposed rats. The current study demonstrates the changes in gut microbiome of MTBI-exposed animals and discusses its implications in intestinal health and behaviours. The rats were subjected to repeated MTBI (rMTBI) and microbial composition in jejunum was examined after 6 h, 48 h and 30 days of rMTBI. Significant reduction in bacterial diversity was observed in the rMTBI-exposed animals at all the time points. Principal coordinate analysis based on weighted UniFrac distances indicated substantial differences in gut microbial diversity and abundances in rMTBI-exposed animals as compared to that in healthy controls. The abundance of Proteobacteria increased dramatically with reciprocal decrease in Firmicutes after rMTBI. At the genus level, Helicobacter, Lactobacillus, Campylobacter, and Streptococcus were found to be differentially abundant in the jejunum of rMTBI-exposed rats as compared to sham controls indicating profound dysbiosis from the healthy state. Furthermore, substantial depletion in butyrate-producing bacterial communities was observed in rMTBI-exposed animals. These results suggest that the traumatic stress alters the gut microbiome with possible implications in gut health and neuropsychopathology.