The wide diversity in gut microbiota that is found among individuals is affected by factors including environment, genetics, dietary habits, and lifestyle after birth. The gastrointestinal tract, the largest and most complicated in vivo ecosystem, is a natural habitat for microbe colonization. Gut microbiota acts as “metabolic organ” that interacts with the human host symbiotically and performs an important role in maintaining health. In addition to the above factors, microbiota distributions/proportions are affected by exercise and other forms of physical activity. However, diet, lifestyle, and nutritional supplementation may impede the actual analytic relationship in practice. Therefore, the purpose of this study is to understand the effects of several microbiota on physical fitness, exercise performance, energy metabolism, and biochemistries using the concept of gnotobiote based on a germ-free model. The microbes Eubacterium rectale, Lactobacillus plantarum TWK10, and Clostridium coccoides were separately inoculated into gnotobiotic animal models. Fecal analysis was regularly done for the entire duration of the experiment. The exercise capacities were measured repeatedly with and without aerobic exercise training using an exhaustive swimming test. Various fatigue-associated biochemical variables, including lactate, ammonia, glucose, lactic dehydrogenase (LDH), and creatine kinase (CK) were also measured to assess physiological adaption. In addition, metabolic phenotype was applied to record basal metabolic rate, diet, behavior, and activities. Body composition, glycogen content, and histopathology were further evaluated to assess the gnotobiotic effects. E. rectale engendered capacities, physiological adaption, and physical activities that were significantly better than other two microbes, possible due to energy regulation and bioavailability. In addition, L. plantarum TWK10 and C. coccoides were found to significantly increase the basal metabolic rate and to alter the body compositions, although no exercise capacity benefit was found in the gnotobiotic models. The E. rectale and L. plantarum gnotobiotic animals all showed normal histological observations with the exception of the C. coccoides gnotobiote, which showed the pathological observation of hepatic necrosis. The gnotobiotic model directly demonstrates the interactions between microbes and hosts, which are especially relevant and applicable to the field of sports science. This study supports the development of beneficial microbiota for application to exercise and fitness, which is an emerging area of health promotion.