There are several reports regarding the effects of various nutrients and diet patterns on human gut microbiota [
23,
44,
45] but, recently, physical exercise was disclosed as yet another factor affecting the composition, diversity, and metabolic activity of the gut microbiota [
15,
17,
18]. However, the impact of physical exercise associated with diet pattern and type of exercise training on the gut microbiota is not fully understood. Our findings, in contrast to recent studies, indicate that type of exercise training and the diet pattern associated with specific sports did not make a difference in the beta diversity of gut microbiota, but they did affect the relative abundance of certain intestinal microbes. In particular, bodybuilders’ high fat intake made
Sutterella more abundant, while significantly reducing the abundance of
Bifidobacterium. Cani et al. (2007) reported that a high fat diet caused a decrease in
Bifidobacterium [
46], and
Bifidobacterium has a negative correlation with the concentration of lipopolysaccharide (LPS), an endotoxin, in the blood [
46]. A high protein, low carbohydrate (HP-LC) diet in conjunction with a high fat diet causes a decrease in
Bifidobacterium [
47,
48]. The lack of
Bifidobacterium resulting from an HP-LC diet could be due to a shortage of carbohydrate-based substrates, the detrimental effects of protein-fermentative metabolites, or competitive exclusion by protein-fermenting microbes in the gut [
49]. Several reports have accentuated the significance of
Bifidobacterium in modulating intestinal homeostasis, regulating local and systemic immune responses, and defending against inflammatory diseases and infections [
50,
51]. In addition, acetate-producing bacteria (e.g.,
Blautia wexlerae,
Bifidobacterium adolescentis group, and
Bifidobacterium longum group) and lactate-producing bacteria (e.g.,
Lactobacillus sakei group) appeared less in bodybuilders, which may have led to the observed decrease in butyrate-producing
Eubacterium hallii, which use acetate and lactate as substrates.
Eubacterium hallii is one of the most abundant butyrate-producing bacteria in the human intestine (followed by
Faecalibacterium prausnitzii,
E. rectale,
E. hallii, and
Anaerostipes hadrus) [
52,
53]; it uses glycerol to produce reuterin, an antimicrobial substance that regulates the homeostasis of intestinal microbial metabolism and inhibits pathogens [
54]. As a result, the HP-LC and high fat diet of the bodybuilders is expected to lower the relative abundance of
Bifidobacterium and, in particular, to lower the relative abundance of acetate-producing bacteria and lactate-producing bacteria, thus influencing the substrate supply of butyrate-producing bacteria.
Sutterella, highly expressed in athletes, is a genus of Gram-negative, anaerobic, nonspore-forming bacteria that is associated with autism, Down’s syndrome, and inflammatory disease [
55,
56].
Sutterella is augmented by a high-fat diet as well as by a low-fiber diet [
57]. The mechanism of the increase of
Sutterella may due to the decrease in mucosal thickness caused by the lack of luminal butyrate, because it can adhere to epithelial cells [
58]. Therefore, the increase of
Sutterella in athletes may be associated with the lack of butyrate-producing bacteria such as
Bifidobacterium adolescentis group,
Bifidobacterium longum group,
Blautia wexlerae,
Lactobacillus sakei group, and
Eubacterium hallii.
Athletes who had adapted to certain exercise training practices and diet regimens for long time periods did not have the high gut microbiota diversity found in controls who did not engage in regular exercise training. Specifically, in the case of low carbohydrate and dietary fiber intake of distance runners, gut microbiota diversity tended to decrease as protein intake increased. However, Clarke et al. (2014) reported that as protein intake in rugby athletes increased, the gut microbiota diversity also increased. This inconsistency between our results and those of Clarke et al. seems to be caused by the differences in nutrition status of the athletes [
18]. The rugby athletes of Clarke et al.’s study met all of the recommended intake requirements, while the athletes of our study had insufficient carbohydrate and dietary fiber intake. Carbohydrates and dietary fiber are the main nutrients that provide carbon and energy to the intestinal microorganisms. In particular, adequate intake of dietary fiber increases the diversity of gut microbiota [
59,
60]. Therefore, inadequate intake of carbohydrates and dietary fiber by athletes seem to counteract the benefits of exercise and a high protein diet that tend to increase gut microbiota diversity. Taken together, our results suggest that high-protein diets may have a negative impact on gut microbiota diversity for athletes in endurance sports who consume low carbohydrates and low dietary fiber, while athletes in resistance sports that carry out the HP-LC and high fat diet demonstrate a decrease in short chain fatty acid-producing commensal bacteria. Additional studies should be conducted to determine the effects of external stimuli on the gut microbiota characteristics, exercise performance, and physical condition in athletes.