In the present study, fecal samples of the three major GI disease patients were analyzed for the gut microbiota and there was a significant difference in Firmicutes, Bacteroidetes, Bifidobacterium spp., and Lactobacillus spp. in CD patients. In addition, the relative abundance of Bifidobacterium spp. and Lactobacillus spp. in IBS patients and Bacteroidetes in NCGS were statistically lower than HC group. Furthermore, Firmicutes to Bacteroidetes ratio assessment was another goal of this study, which was statistically higher in NCGS and CD patients than HCs.
Recent studies suggested that the alteration of gut microbiota composition is associated with CD [27–29]. It was observed that increased abundance of Bacteroidetes and reduced abundance of Bifidobacterium spp. and Lactobacillus spp. are the most often hallmarks of CD microbiota [30]. As it has been discussed in several studies, Bifidobacterium spp. and Lactobacillus spp. have protective effects on the intestinal epithelial cells from gliadin damage [31], it was suggested that the fecal transplant which can cause an increment in Bifidobacterium spp. could reverse the inflammatory pathway in CD patients [32]. In the study of Golfetto et al., the concentration of Bifidobacterium spp. in CD patients was significantly lower in compare to the HCs [33]. In contrast, Nylund et al. suggested a higher abundance of Bifidobacterium spp. in CD patients compared with HCs that was associated with the higher fecal acetate in HCs [34]. In the study of Nistal et al., Firmicutes, Proteobacteria, and Bacteroidetes were the most frequent gut microbiota [35]. Furthermore, in the study of Bodkhe et al., Actinobacteria, Bacteroides, Euryarchaeota, Firmicutes and Proteobacteria were the major phyla in the duodenal microbiota of CD patients [36]. The current study was largely associated with the previous results. In our study, Firmicutes phylum was dominant in the gut microbiota of all studied groups. In addition, Bacteroidetes, Bifidobacterium spp. and Lactobacillus spp. had significantly lower abundance in CD patients compared to the HCs. The cause of lower abundance of Bacteroidetes in this study that is inconsistent with the previous results may be associated with genetic determinants, ethnic background, geographical diversity, and different diet habits which can affect the gut microbiota composition [37–39].
Gut microbiota dysbiosis in the IBS patients has been reported in several studies [40–42]. In fact, gastrointestinal dysbiosis in these patients is associated with the intestinal hypersensitivity, mucosal immune activation and chronic inflammation, which are the three important pathophysiology factors in this disease [43, 44]. Several studies suggested the higher amounts of Bacteroidetes and the lower amounts of Firmicutes in the IBS patients in compare to HCs [45, 46]. In addition, it has been suggested that IBS is associated with the lower relative abundance of Bifidobacterium spp. and Lactobacillus spp. [47, 48]. This study was completely in line with the previous results. It was demonstrated that the relative abundance of Bifidobacterium spp. and Lactobacillus spp. in the IBS patients is significantly lower in compare to HCs. However, Maccaferri et al. observed an increase in the relative abundance of Bifidobacterium spp. and Lactobacillus among IBS subjects [49]. It seems that further evidences are needed for confirming these results.
Dysbiosis in the NCGS patients is one of the important issues which can cause constipation, diarrhea, chronic inflammation, intestinal hypersensitivity and immune dysfunction [50]. Garcia-Mazcorro et al. reported a high relative abundance of Firmicutes and low relative abundance of Bacteroidetes in the fecal microbiota of the NCGS individuals [51]. Furthermore, Dieterich et al. suggested low relative abundance of Porphyromonadaceae (from Bacteroidetes phylum) in the NCGS patients and high relative abundance of Sphingobacteria (from Bacteroidetes phylum) in the HCs [52]. This study was in line with the previous results. The relative abundance of Bacteroidetes phylum in the NCGS patients was significantly lower in compare to the HCs.
The human gut microbiota is majorly composed of two bacterial phyla and their subdominants that included in Firmicutes and Bacteroidetes [53]. The Firmicutes/Bacteroidetes ratio has an important role in gastrointestinal homeostasis. In fact, increased or decreased F/B ratio which states as dysbiosis, can observe in the chronic intestinal conditions like inflammatory bowel disease (IBD) [54, 55]. In this study, F/B ratio was significantly higher in the CD and NCGS patients compared to other studies groups. This issue has been discussed in the previous studies, especially for the CD therapeutic purpose. In the study of Quagliariello et al., three-month administration of Bifidobacterium breve significantly decreased the F/B ration in the CD patients [56]. In addition, in the study of Primec et al., three months of treatment with probiotic had a significant effect on F/B ratio in the CD patients [57]. The results of this study suggested an F/B abnormality in the CD and NCGS patients, which is a useful factor for the assessment of the outcomes of the CD and NCGS treatment.
Analysis of the dissimilarity in this study suggested that CD patients have more dysbiosis as compared to the other chronic GI patients. This issue can justify the alteration in the symptoms in this disease in comparison with the other GI diseases. Furthermore, it has been suggested that the microbiome composition in the IBS and NCGS patients are similar to the healthy microbiome and this issue can suggest better outcome of this disease in comparison to the CD.
Easy access to the patients and conducting the study in a referral center for gastrointestinal disease was one of the positive points of this study. In fact, accurate diagnosis of the diseases such as NCGS requires a gluten challenge test, which may not be available in many medical centers. On the other hand, low sample size and lack of mucosal microbiome evaluation were the major limitation of this study. It would be better for future studies to conduct in a larger sample size and as multicentric studies and examination of fecal microbiome and mucosal microbiome simultaneously to have a better prospective for the differences between mucosal microbiome and fecal microbiome.