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Gut eubiosis is essential for the host’s health. In athletes, the gut microbiota can be altered by several factors, including diets. While eubiotic gut microbiota in elite rugby players has been reported, our survey found that university rugby players suffered from loose stools and frequent urgency to defecate. To establish the causes of the condition, the microbiota and the concentrations of organic acids in fecal samples of university male rugby players (URP) were analyzed and compared with those of age-matching, non-rugby playing males (control). Body mass indices were significantly (<i>p</i> < 0.05) different between groups. Chao1 index was significant (<i>p</i> < 0.05) lower in URP than in control. The relative abundances of phyla Firmicutes and Bacteroidetes were significantly (<i>p</i> < 0.05) higher and lower, respectively, in URP than in control. Potential pathobiont genera <i>Collinsella</i>, <i>Enterobacter,</i> and <i>Haemophilus</i> were significantly (<i>p</i> < 0.05) abundant, whereas beneficial <i>Akkermansia</i> was lower (<i>p</i> < 0.05) in URP than in control. Succinate, a potential causative of gut inflammation, was five-fold higher in URP than in controls. Our findings all but confirmed that the dysbiotic status of gut in URP.