A study of professional rugby players, carried out by researchers in Cork and London, found the bugs in their digestive system, known as the microbiome, are primed to repair tissue.
The research also discovered that the players' microbiome is also particularly good at harnessing energy from the diet.
The findings suggest, the researchers say, that the fitness of a person is not just limited to their physical abilities, but also to their gut health.
It also found the microorganisms that reside in the gut of these full-time athletes are noticeably distinct functionally and metabolically.
Scientists from the APC Microbiome Institute, Teagasc and Imperial College London were involved in the research, results of which were published in the journal Gut.
The discoveries build on earlier findings of a study by the scientists of the microbiome of the Irish rugby squad.
It found there was a connection between the exercise and diet of individuals and their gut health.
The scientist say there is now a good reason to further explore the make-up of this exercise and diet-microbiome paradigm, which could then help with exercise and fitness programmes.
"Our earlier work, also published in Gut, had shown that the microbiome of the athletes differed in composition from that of non-athletes," said Professor Fergus Shanahan, Director of the APC Microbiome Institute in a statement.
"But now we have found that the functional behaviour of the microbiome separates the athletes and controls to an even greater degree."