The human microbiome is the totality of microorganisms along with its genes. The human gut harbors a vast array of microorganisms, the most representative of which are Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria. Microbiome affects an array of different processes in the body including host nutrition, metabolic function, gut development and immune system maturation, and has emerged as a critical regulatory factor in human physiology. The eubiosis/dysbiosis state of the gut microbiome strongly influence the health and disease conditions. Physical activity and exercise are known to improve physical fitness and mental health. Exercise has positive effects in restoring eubiosis in the gut and has a metabolic consequence in improving muscular health and mitochondrial function. Whereas dysbiosis is linked to many chronic and metabolic diseases such as type 2 diabetes, obesity, cardiovascular disease and cancer. The current knowledge, regarding the underlying mechanisms of exercise regime in shaping the microbiome, is insufficient. Therefore, we are working in this area to decipher the mechanistic details of the relationship between microbiome and exercise. The unique composition and individual responses to environmental stressors suggests a future role for gut microbiota in personalized health strategies.