Among the selected studies, 2 publications analyzed the microbiota from the duodenum, with duodenal biopsies used in one study and duodenal aspirates used in the other. Li et al. (17) identified 56 genera in duodenal biopsies from patients with IBS-D that increased and 36 that decreased, with the most prevalent genera having increased and decreased frequencies being Bacillus and Faecalibacterium, respectively. Meanwhile, analysis of the duodenal aspirates by Giamarellos-Bourboulis et al. (27) detected significant changes for 12 genera, including the overrepresentation of Escherichia/Shigella and Aeromonas and the underrepresentation of Acinetobacter, Citrobacter, Microvirgula, Flavobacterium, Enhydrobacter, Weissella, Leuconostoc, Chryseobacterium, and Lactococcus.
Two studies focused on mucosal microbiota from the proximal jejunum, with one study using single-balloon enteroscopy and the other using sterile Watson capsules to biopsy the jejunum. Chung et al. found a higher Firmicutes:Actinobacteria ratio in patients with IBS compared to that in HCs. Increased Prevotellaceae and decreased Mycobacteriaceae and Neisseriaceae at the family level, and higher proportions of Streptococcus, Prevotella, Helicobacter, Brevibacterium and a lower proportion of Neisseria at the genus level were also observed in patients with IBS (25). In contrast, Dlugosz et al. (28) found no statistical differences among major phyla or genera between patients with IBS and HCs. Regardless, some operational taxonomic units exhibited a trend toward differential expression with increased levels of Carnobacteriaceae, Prevotella, and Leptotrichia and decreased levels of Escherichia and Streptococcus.
Other studies searched for alterations of mucosal microbiota in the colon or rectum. Durbán et al. (32) reported that mucosal biopsies from the ascending and descending colon in patients with IBS presented with higher counts of Bacteroidaceae. Tap et al. (19) failed to report significant differences between patients and controls regarding the mucosal microbiota from the sigmoid colon. As for the mucosal microbiota in the rectum, Li et al. (17) showed 21 genera in patients with IBS-D with increased levels and 79 genera with decreased levels, with the most common genera having increased and decreased frequencies being Ochrobactrum and Faecalibacterium, respectively. Ng et al. (29) detected some members that differed significantly between the 2 groups with increased levels of Bacteroidetes and Synegitestes and reduced levels of Actinobacteria and Cyanobacteria in patients with IBS. And the differences in abundance at the lower taxonomic levels are shown in detail in Table 4.
Numerous studies have focused on gut microbiota alterations in patients with IBS. A better understanding of microbial signatures is an important prerequisite if intervention is to be used in managing the disease (34). In the current study, we choose 16S rRNA-targeted sequencing as the single method in the inclusion criteria to avoid methodology-based heterogeneity. Results from the eligible studies showed both inconsistencies and several common trends pertaining to microbial alterations of patients with IBS.
Microbial diversity is a crucial property of communities because it is a primary descriptor of the community structure and a major determinant of community function (35). In this review, we found that most of the studies observed a lower microbial α-diversity in both fecal and mucosal samples from patients with IBS compared to those from HCs. Similar findings have also been confirmed by other microbial detection methods, including terminal-restriction fragment length polymorphism (36), DNA microarrays (37) and metagenomic gene-targeted approach (38). Given these findings, it can be easily speculated that microbial dysbiosis may be a result of increases or decreases of specific microbial groups and the disappearance of global homeostasis (39), which are thought to be markers for negative conditions in patients with IBS.
As noted above, the reports from different studies on fecal microbial profiles in patients with IBS are mixed but include several consistent trends. For instance, increased levels of Firmicutes, decreased levels of Bacteroidetes, and increased F/B ratio were found. The phylum Firmicutes makes up the largest portion of the human gut microbiota and has been shown to be associated with energy extraction and potentially related to obesity and diabetes (9). In contrast, the phylum Bacteroidetes generally produces butyrate, which is suggested to reduce inflammation and plays a role in the normal development of the gut (6,9). In general terms, the F/B ratio is regarded to be of significant relevance in signaling human gut microbiota status (40). Altered F/B ratio has been reported in connection with diet and some chronic diseases such as obesity (41,42). A 2-fold higher F/B ratio was also found in patients with IBS compared to that in HCs in the study of Rajilić-Stojanović et al. (43), in which fecal samples were analyzed using a human intestinal tract chip. However, even with these findings, at this time there remains no clear consensus on how the changes are associated with IBS. Clemente et al. (44) proposed that the shift in abundances of Firmicutes and Bacteroidetes in obese individuals resulted in an increased capacity for harvesting energy from food and producing low-grade inflammation. The fatty acids in high-fat diets have been shown to increase the F/B ratio, which is associated with increased gut epithelial permeability and low-grade inflammation (18). Therefore, we can speculate that the alterations in bacterial phyla of patients with IBS may be related to alterations in epithelial permeability and low-grade inflammation, which have been implicated as possible components of the pathogenesis of IBS (45). In contrast, 2 of the studies detected increases in Bacteroidetes and decreases in Firmicutes in patients with IBS. The divergence in the results may be attributed to different dietary habits, geographical environments, or even methodological heterogeneity.
The tendencies for the change of Firmicutes and Bacteroidetes in patients with IBS persisted at the lower taxonomic levels with higher abundances of Clostridia and Clostridiales and lower abundances of Bacteroidia and Bacteroidales. Clostridia is a wide and heterogenic class that includes species degrading various organic compounds and are devoted to acid production (46). Disturbed metabolism of intestinal short-chain fatty acids has been associated with IBS (11), so it is intriguing to speculate that bacteria of the class Clostridia may play a role in the development of IBS as a result of its capacity to produce acids. As for decreased levels of Bacteroidia and Bacteroidales in patients with IBS, it remains unclear about their relationship with IBS. Nevertheless, using an animal model of experimental colitis, a previous study showed that Bacteroides fragilis, which is one of the most important species within the order Bacteroidales, protected its host from inflammation and that this beneficial activity required polysaccharide A, a natural antiinflammatory molecule of Bacteroides fragilis (47).
Increased Proteobacteria, as well as the order Enterobacteriales and family Enterobacteriaceae within the phylum were found in patients with IBS, which encompass many known pathogenic species with potential inflammation causing mechanisms such as Escherichia coli (6). Thus, it is likely that these bacteria are among the potential pathogens that contribute to the progression of IBS (14).
Thus far, there have been 2 meta-analyses focusing on gut microbiota alterations in patients with IBS, and all of the studies included in these 2 meta-analyses were based on culture or real-time quantitative polymerase chain reaction methods (48,49). The first meta-analysis found increased levels of Escherichia coli and Enterobacter and decreased levels of Bifidobacteria and Lactobacillus in patients with IBS from China compared with those in HCs. In addition, Bacteroides and Bifidobacteria were shown to be increased and decreased, respectively in patients with IBS from other regions of the world. (48) The second meta-analysis pooled seven studies that were based on quantitative polymerase chain reaction and showed significant decreases in the levels of Lactobacillus, Bifidobacterium, and Faecalibacterium prausnitzii in patients with IBS compared with those in HCs (49). In these 2 studies, there was a trend with patients with IBS showing decreased levels of Lactobacillus and Bifidobacterium, the 2 most widely used probiotics. Most of the previous clinical trials demonstrated that the probiotics Lactobacillus spp. and Bifidobacterium spp. have positive effects on the overall symptoms of IBS by altering the composition of gut microbiota (50,51), suggesting a preventive role for these microorganisms in IBS. However, this finding is not universal with some studies recording no significant improvement or even unfavorable effects on patient symptoms (52,53). Our current review indicated that the previous reports on the 2 probiotics are limited and inconsistent. Thus, it remains unclear whether there are IBS-specific effects related to Lactobacillus and Bifidobacterium.
Most studies on gut microbiota of patients with IBS carried out to date have drawn conclusions by analyzing fecal samples since they are easily collected in a noninvasive manner. In contrast, mucosal samples must be obtained through an endoscopic procedure (54). However, there is increasing evidence that the mucosa-associated microbiota significantly differs from the feces-associated microbiota (55). The microbial composition in feces does not necessarily reflect the organisms directly related to disorders (54), which may be partly explained by the fact that amplification of DNA from feces also identifies nonviable and transient microbes that may not be biologically active (27). The mucosa-associated microbiota may play a more prominent pathogenic role due to their closer contact with host epithelial, immune, and enteroendocrine cells (32,56). However, studies analyzing mucosal microbiota composition are limited, and their results are not comparable because of the difference in sampling and the heterogeneity of methodologies. Hence, more studies concerning mucosa-associated microbiota in patients with IBS should be included in future research.
Considering that IBS is a multifactorial disorder with many putative causes and a wide range of symptoms, it can be reasonably stated that results from these studies might not represent patients with IBS as a whole, but rather as only a portion of patients. In addition, a variety of factors may affect the microbial identification, such as sample size, geographical environment, dietary habits, diagnostic criteria, and sample sources (11). Furthermore, the specific processes of the 16S rRNA sequencing method may also drastically affect the quality of results, including the DNA extraction techniques, primers used for amplicon generation, bioinformatic pipelines, data transformations, and statistical approaches (14). Thus, it is difficult to compare the results from various studies and make a general inference on microbial profiles in patients with IBS. From this point of view, our work depicting alterations of gut microbiota in patients with IBS based on 16S rRNA sequencing may be viewed as a preliminary study.
We acknowledge several limitations regarding this systematic review. First, we only listed alterations in fecal microbiota according to limited studies involving subtypes, because most of the studies were based on the assessment of various subtypes of patients with IBS, making subgroup analysis difficult. Therefore, additional studies considering IBS subtypes are needed in the future. Second, because this was a qualitative review and we only included peer-reviewed published studies, it is impossible to comment on the likelihood of publication bias.
In conclusion, our systematic review found that based on 16S rRNA-targeted sequencing, there are alterations in the gut microbiota of patients with IBS compared with that in HCs. Patients with IBS had a lower α-diversity than HCs in both fecal and mucosal samples. Relatively consistent changes in fecal microbiota for patients with IBS included increased Firmicutes, decreased Bacteroidetes, and increased F/B ratio at the phylum level, as well as increased Clostridia and Clostridiales and decreased Bacteroidia and Bacteroidales at lower taxonomic levels. Results for mucosal microbiota were inconsistent. Further studies, especially studies regarding mucosa-associated microbiota and studies based on IBS subtype analyses, are needed to draw conclusions about the alterations of gut microbiota in patients with IBS.
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