The involvement of the intestinal microbiome in IBD progression has been proven by previous studies. Large scale data demonstrated differences in the intestinal flora composition of IBD patients in comparison with healthy controls. There have been few studies on the bacterial microbiome profiles of inflamed mucosa in comparison with noninflamed mucosa in Crohn’s disease patients.
In this study, we analyzed the composition and differences of intestinal bacteria from the inflamed mucosa of active CD patients in comparison with their own noninflamed mucosa. Beta diversity and alpha diversity analyses demonstrated that there was no significant difference in the biodiversity of the bacterial microbiota in the inflamed mucosa compared with its noninflamed mucosa control. In a study of 14 patients with UC and 14 heathy controls, Hirano et al. have discovered that microbial alpha diversity in both inflamed and noninflamed sites was significantly lower in UC patients than in non-IBD controls [13]. Therefore, we inferred that it was plausible there was no significant difference in the biodiversity of bacterial microbiota between the inflamed and noninflamed sites of the CD patients analyzed in this study. If the diversity of inflamed and noninflamed sites of CD patients was lower than that of heathy controls, which is the case in UC patients, then their difference might not be great enough to be statistically significant. In the current study, the intestinal mucosa of CD patients was rich in Bacteroidaceae (Bacteroides), Prevotellaceae (Prevotell), Fusobacteriaceae (Fusobacterium), and Enterobacteriaceae (Escherichia). There was no significant difference in the community compositions at the family level between inflamed tissues and noninflamed tissues (Fig. 2). The Wilcox test results identified Methylobacterium, Rothia, Capnocytophaga, Shinella, Actinomyces, Gardnerella, Leucobacter, and Bifidobacterium as significantly different genera between inflamed and noninflamed mucosa of CD patients. The abundance of these genera was increased in the inflamed mucosa of CD patients relative to their noninflamed counterparts (Fig. 4D). There were no reports associated with Shinella and Leucobacter on CD. Similar or contradictory reports exist for other differentially abundant genera that were found in the inflamed mucosa of CD patients from this study.
Increased abundance of Actinomyces was found in patients with immune-mediated inflammatory disease (including CD, UC, multiple sclerosis and rheumatoid arthritis) and Crohn’s-like appendicitis[14–18]. Generally, Actinomyces were considered commensal microorganisms in previous studies, and caused opportunistic infections [19]. Therefore, we inferred that Actinomyces could invade the inflamed mucosa of patients with CD. Gardnerella is considered to be a conditioned pathogen of vaginitis. A higher frequency of Gardnerella vaginalis biofilms was discovered in the urine of IBD patients (CD 38%, UC 43%) than in that of the control group (16%)[20].Compared with CD patients, patients with UC were significantly more enriched in Gardnerella in their fecal samples [17]. In this study, Gardnerella was discovered to be significantly more enriched in the inflamed mucosa of CD patients compared with their respective noninflamed mucosa. These data indicated that Gardnerella may participate in CD progression as a conditioned pathogen.
The relative abundance of Methylobacterium was increased in creeping fat taken from patients with Crohn’s disease (CD) [21]. Rodrick et al. discovered that the abundance of Methylobacterium was specifically increased 6.1-fold in the submucosa compared with the mucosa in CD patients.[22]. One study by wang et al. on pediatric CD patients discovered that a sustained response to IFX therapy was associated with a higher abundance of Methylobacterium[23]. Methylobacterium may play important roles in trigging immune responses. Methylobacterium spp. are fastidious microorganisms that grow slowly, and are tolerant to high temperatures, drying, cleaning and disinfecting agents. Therefore, they are able to form biofilms and are predominant in hospital environments, particularly in endoscope channels and tap water [24]. In our study, the abundance of Methylobacterium was enriched in the inflamed mucosa of CD patients compared with their respective noninflamed mucosa. CD patients frequently received endoscopic inspection, which may lead to opportunistic colonization of Methylobacterium. CD is a disease characterized by persistent and overactive immune responses. Thus, the function of Methylobacterium in immune regulation should be further studied.
The genera Capnocytophaga and Rothia are opportunistic pathogens isolated frequently from oral cavities [25, 26]. There are few reports on the mechanisms by which Capnocytophaga may participate in immune regulation. Sun’s study reported that patients with both CD and periodontitis had a relatively higher abundance of Rothia, while healthy individuals had a relatively lower abundance of Capnocytophaga [27]. Our results indicated increased abundance of Rothia and Capnocytophaga in the inflamed mucosa of CD patients compared with the same patients’ noninflamed mucosa. Rothia play important roles in immunomodulation. Macrophages[28] or lymphocytes[29] can be activated by Rothia or antigens from Rothia in periodontal disease. Specific strains of Rothia such as R. dentocariosa ATCC14189 and ATCC14190 can induce TNF-alpha production in macrophages[30]. There was persistent activation of lymphocytes and higher expression levels of TNF-alpha in CD patients. Accordingly, we inferred a similar immunomodulatory function of Rothia in CD.
Reports on the abundance of Bifidobacterium in IBD patients vary. Generally, the abundance of Bifidobacterium in patients with intestinal diseases is much lower than healthy controls [31]. The load of Bifidobacterium in fecal samples (ileum and colon) of patients with CD was decreased compared to that in heathy people[32, 33]. Forbes et al. reported that the abundance of Bifidobacterium was higher in stool samples of patients with UC [16]. An increased proportion of Bifidobacterium was discovered to be higher in fecal and biopsy samples of active CD patients or UC patients[34]. In this study, there were no flora distribution data of mucosa from healthy people. However, the abundance of Bifidobacterium in the inflamed mucosa of CD patients was discovered to be relatively increased compared with that in their own noninflamed mucosa. Few studies have revealed the load of Bifidobacterium in patients with CD compared with their own noninflamed mucosa.
In a randomized trial, a diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) reduced specific symptoms, thereby reporting adequate symptom relief in quiescent IBD. Patients on the low FODMAP diet had a significantly lower abundance of Bifidobacterium adolescentis and Bifidobacterium longum in stool samples [35]. Numerous studies have indicated that Bifidobacterium are capable protecting against intestinal inflammation by enhancing the intestinal epithelial tight junction barrier and reducing inflammatory cytokine expression [36] [37]. Bifidobacterium strains were discovered to induce IL-10, IL-6 and MCP-1 expression in peripheral blood mononuclear cells [38]. Therefore, we inferred a complex function of Bifidobacterium in CD progression. In this study, the load of Bifidobacterium in the inflamed mucosa of patients with CD was higher than that in their noninflamed mucosa. Bifidobacterium in inflamed mucosa may play a protective role by enhancing epithelial the tight junction barrier and inducing IL-10 expression. On the other hand, Bifidobacterium may promote inflammation by inducing proinflammatory cytokine secretion (IL-6, MCP-1 etc.).