It has been hypothesized that a subset of patients with IBS may have an intolerance of dietary triggers such as gluten and highly FODMAP-containing foods, which can alter the gut microbiota and the metabolome of patients with IBS leading to worsening of their symptoms [25-27]. This has led researchers to recommend GFD and low-FODMAP diet as the most widely adopted diets to improve IBS symptoms [28-30]. Despite the growing popularity of the GFD and low-FODMAP diet in patients with IBS, the beneficial impact of such dietary interventions on restoration of intestinal microbiota dysbiosis has been lacking in this population.
In this 6-week, controlled, dietary intervention study, a clinically significant improvement in IBS-SSS was observed after the dietary intervention compared to the baseline. Several other clinical trials have also shown that a low-FODMAP diet associates with an improvement in IBS symptom scores and effectively increased quality of life in patients with IBS [19, 27, 31-34]. It is now well documented that IBS is a condition in which several pathophysiological mechanisms are involved in its development and symptom severity. Among them, a distinct fecal microbiota composition and microbiome dysbiosis has been proposed as one of the key factors associated with the disease symptom severity [14, 35, 36]. Data obtained from a recent systematic review demonstrated that phylum Proteobacteria, phylum Bacteroidetes, family Enterobacteriaceae, and family Lactobacillaceae increased in patients with IBS [14]. On the other hand, it was also documented that uncultured Clostridiales I, genus Faecalibacterium (including Faecalibacterium prausnitzii), and genus Bifidobacterium were decreased in patients with IBS. Moreover, it was revealed that the overall microbiota diversity was either decreased or not changed in IBS patients in comparison with healthy controls [14]. However, conflicting results of cumulative evidence for Firmicutes, Bacteroidetes, and Actinobacteria were observed among different studies [37-39].
There is increasing evidence that dietary interventions using low-FODMAP diets could improve functional gastrointestinal symptoms in IBS patients particularly through interactions with the gut microbiota [15, 19, 40]. Furthermore, another study suggested that reduction of FODMAPs intake in a GFD consistently and significantly improved the gastrointestinal symptoms in IBS patients who were finally classified as non-celiac gluten sensitivity (NCGS) [41]. In our study, we found that the relative abundance of phylum Firmicutes were higher prior to the start of dietary interventions compared to the phylum Bacteroidetes in patients with IBS. However, there was a clear tendency to increased Bacteroidetes after the dietary interventions, and subsequently the F/B ratio was significantly decreased. In a recent study by Dieterich et al., clinical and neurological symptoms of NCGS patients who consumed low-FODMAP diet and especially the GFD significantly improved [42]. In addition, they reported a significant increase in the numbers of Bacteroidetes following a 2-week GFD compared to the low-FODMAP diet (P <0.01). Furthermore, data obtained from a randomized clinical trial in childhood IBS demonstrated that individuals who respond to a low-FODMAP diet have a greater capacity for saccharolytic metabolism mainly due to higher proportions of Bacteroidaceae, Erysipilotrichaceae and Clostridiales species than non- responders [33]. Rajilić-Stojanović et al. also reported an approximately 2-fold increase in the F/B ratio as the major bacterial phyla in 62 IBS patients (Rome II criteria) compared with 46 healthy subjects [43]. This finding has been observed in several other studies, in which the abundance of Firmicutes was enriched together with a reduced abundance of Bacteroidetes in the IBS subjects compared to healthy individuals [44-46]. In contrast, other studies reported an increase in the content and abundance of Bacteroidetes members in the IBS patients compared to non-IBS subjects [47, 48]. Bacteroidetes are known as complex carbohydrate digesters which are specialized in degrading specific types of dietary fibers in order to maximize energy intake from these kinds of carbohydrates [49, 50].
The phylum Actinobacteria is proportionally less abundant phyla (3%) of the human gut microbiota, and notably represented by the probiotic containing genera such as Bifidobacterium and Collinsella [36, 51]. Several studies have reported a significant depletion in Actinobacteria in the gut of patients with IBS [43, 45, 52]. On the other hand, other studies reported an increase in the relative abundance of Actinobacteria among IBS patients compared to healthy controls [39, 44, 53]. In our study the relative abundance of Actinobacteria was increased, although not statistically significant, after the GFD and low-FODMAP dietary intervention. In line with our results, McIntosh et al. also reported that a 3-week low-FODMAP diet increased Actinobacteria richness and diversity in patients with IBS [27]. In contrast, a recent study had demonstrated that gut bacteria such as Actinobacteria, Bifidobacterium, and Faecalibacterium prausnitzii were significantly decreased in IBS patients throughout a 9-week low-FODMAP diet along with reduction in total SCFAs, n-butyric acid, and serum levels of proinflammatory cytokines (IL-6 and IL-8) as compared to baseline [54]. However, the overall inconsistency and differences in the abovementioned results contribute to the difference among study populations, IBS subtypes, duration of dietary intervention, level of dietary adherence, washout period in crossover studies, and variations in taste or other contents outside of FODMAP carbohydrates that may affect the dysbiotic gut microbiota and disease outcomes.
In fact, the majority of studies on gut microbiota analysis in IBS patients that used either q-PCR or non-quantitative methods reported a decrease in the abundance of Bifidobacterium and Lactobacillus [55, 56]. However, Maccaferri et al. exceptionally reported an increase in the relative abundance of Lactobacilli and Bifidobacteria among IBS subjects [57]. A number of studies have shown that the low-FOMAPs diet decreases the abundance of Bifidobacterium in the gut of IBS patients [16, 20, 27, 31, 34, 54]. Collectively, previous studies have also demonstrated that GFD induced a decrease in Bifidobacterium spp. in the intestinal microbiome of healthy human subjects, celiac disease (CD) and NCGS patients, raising potential concerns after the consumption of a GFD [42, 58, 59]. However, Collado et al. reported increased prevalence of certain Bifidobacterium species including B. adolescentis, B. lactis and B. dentium after a GFD in CD subjects [60]. In another study from Brazil, the fecal counts of Bifidobacteria were significantly higher in GFD treated-CD (T-CD) patients compared to the healthy subjects [59, 61]. Interestingly, we observed that the relative abundances of lactate-producing bacteria Bifidobacterium and Lactobacillus were increased after the GFD and low-FODMAP dietary intervention in IBS patients. To our knowledge, no previous studies have evaluated effects of the GFD and low-FODMAP dietary intervention simultaneously on IBS patients. Our findings propose that at least in patients with IBS implementing simultaneous GFD and low-FODMAP diet may lead to an increase in the relative abundances of Bifidobacterium and Lactobacillus, although contrary to the other studies which applied these dietary interventions separately. Therefore, it is noteworthy to administrate the diet or a combination of diets of choice for gut microbiota-associated disorders such as IBS in order to normalize the dysbiotic communities of microbiota.
The family Enterobacteriaceae (phylum Proteobacteria), contains several pathogenic genera such as Escherichia, Shigella, Salmonella, and Campylobacter. Generally, these aerobes were found to be slightly enriched in IBS patients and significantly correlated with IBS symptoms. Moreover, an increase in some of these pathogenic microbiota may contribute to the low rate of mucosal inflammation through overexpression of proinflammatory cytokines IL-6 and IL-8 as seen in IBS patients [14, 43, 57, 62]. In contrast, Tana et al. found no difference in Enterobacteriaceae count between IBS patients and healthy controls. In another study by De Palma et al., Enterobacteriaceae were increased in a group of healthy adult subjects who were on a one-month GFD [63]. In our study, we found no difference in the relative abundance of Enterobacteriaceae before and after the dietary intervention.
The genus Streptococcus is among the dominant bacterial groups present in the upper gastrointestinal tract [64]. Some reports have also showed high fecal amounts of Streptococcus spp., pathogenic bacteria which causes increased expression levels of IL-6 [65], in IBS patients [43], and particularly in IBS-D subtypes [46, 66]. We found no difference in relative abundance of Streptococcus after the dietary intervention compared to the baseline. Our results are in agreement with another study which found no difference in relative abundance of Streptococcus species for the low FODMAP diet compared with sham diet [31]. Furthermore, Bennet et al. also demonstrated no difference in abundance of Streptococcus between responders and non-responders patients with IBS after a 4-week low-FODMAP diet [34].
Our data suggest that there is a correlation between consuming a low-FODMAP diet combined with GFD and decrease of FC which is in line with a study performed by Shulman et al. [67], but are in contrast with a few previous studies which suggested that FC concentration was not increased in IBS patients compared with control subjects [68-70]. However, these controversial findings in the above-mentioned studies may be due to differences in the study design and population.