The host provides a nutrient-rich environment and residence for the gut bacteria, and in turn, they contribute to the host by producing short-chain fatty acids and essential vitamins. This mutual relationship between the host and the gut bacteria is called symbiosis. Recent advancement of next-generation sequencing techniques has enabled culture-independent analysis of the gut microbiota, revealing that an altered balance of the gut microbiota constituents, rather than specific pathogens, is involved in the pathophysiology of several diseases. This shift in the balance of the gut microbiota is referred to as dysbiosis.
More than 90 % of the human gut microbiota is composed of four major phyla. The Firmicutes (49–76 %) and Bacteroidetes (16–23 %) phyla dominate, followed to a much less extent by the Proteobacteria and Actinobacteria phyla [5, 6]. The Firmicutes phylum is mainly composed of the Clostridium XIV and IV groups.
Various alterations of the gut microbiota have been reported in IBD patients (Table 1). Most studies have shown reduced diversity of the gut microbiota in IBD patients [6–9]. The most consistent observations of altered composition of the gut microbiota in IBD patients are a reduction in Firmicutes and an increase in Proteobacteria [6, 7, 10–12]. The reduced diversity of the gut microbiota observed in IBD patients is largely due to a decline in the diversity of Firmicutes. Among Firmicutes, a decrease in the Clostridium leptum groups, especially Faecalibacterium prausnitzii, has been reported in many studies [7, 13, 14]. Results related to Enterobacteriaceae, Bacteroides, Bifidobacteria species, Lactobacillus species, and Escherichia coli are not consistent among studies [15, 16]. Various factors may explain the between-study discrepancies: (1) sample source (biopsy or stool), (2) sampling location (inflammatory or noninflammatory sites), (3) disease activity (active or quiescent), (4) medication, (5) diet, (6) age, (7) smoking, and (8) methods used to analyze the microbiota.
While the gut microbiota in healthy subjects shows little temporal change, the gut microbiota in IBD patients is unstable. The composition of the gut microbiota differs between active and quiescent stages. Furthermore, a study that longitudinally examined the gut microbiota in IBD patients for a year demonstrated that the gut microbiota was unstable even in UC patients in remission . Before relapse of UC, normal anaerobic bacteria such as Bacteroides, Escherichia, Eubacterium, Lactobacillus, and Ruminococcus are decreased and the diversity of the gut microbiota is also reduced . In CD patients, dysbiosis is observed even in patients with remission. Medication also affects the composition of the gut microbiota. Mesalazine, for example, reduces the total bacterial number to almost half . Bowel rest, which is a treatment option in CD, changes the composition of the gut microbiota. Antibiotics dramatically amplify the dysbiosis of CD .
The distribution of the gut microbiota should be taken into account when interpreting dysbiosis. For example, the composition of the microbiota is significantly different between fecal and mucosal samples [5, 21]. Mucosal samples are reported to be superior in order to detect dysbiosis . The mucosa-associated microbiota is increased in IBD compared with healthy subjects [22, 23]. It is tempting to speculate that the mucosa-associated microbiota is physiologically more important in IBD than luminal microbiota because of the close contact of mucosa-associated bacteria with the intestinal surface. It has also been reported that the gut microbiota is different in the same individual between inflammatory and noninflammatory sites . The dysbiosis observed in noninflammatory sites may be more representative of a causative composition because the dysbiosis observed in inflammatory sites may be affected by inflammation.
It remains controversial whether dysbiosis is a cause or consequence of intestinal inflammation in IBD. Comparison of the gut microbiota composition of IBD patients with that of their unaffected relatives, who are likely to share genetic and environmental background, is useful to provide evidence relevant to this fundamental question. Compositional change of the gut microbiota was not consistent between UC patients and their unaffected twins . In contrast, a decrease in F. prausnitzii was reported to be observed in both UC patients and their first-grade relatives . Unaffected relatives of CD patients also had dysbiosis, although it was different from the dysbiosis observed in CD patients . Furthermore, it was reported that the genetic status of NOD2 and ATG18L genes, which are two major CD susceptibility genes, was associated with alteration of the gut microbiota . These results suggest that dysbiosis is caused by genetic and environmental factors, rather than being a consequence of inflammation.
There have been attempts to utilize dysbiosis as a diagnostic tool or biomarker . To date, there are no microbial constituents specific to UC or CD, because interindividual variations are much larger than inter-disease differences . Several studies have suggested the possibility of using the gut microbiota as a biomarker. Firmicutes, for example, was increased in UC patients who responded to mesalazine . The relapse rate was lower in postoperative CD patients who had a similar composition of gut microbiota to healthy controls than in those with dysbiosis . In the largest CD microbiota cohort so far, comparing 447 newly diagnosed pediatric CD patients with 221 healthy controls, Gevers et al. proposed a “dysbiosis index,” which was shown to be associated with clinical disease severity assessed using the Pediatric Crohn’s Disease Index . They also reported that profiles of the gut microbiota were able to be utilized as a diagnostic marker of CD and were also useful to predict the severity at 6 months. This report encourages further efforts to use gut microbial profiles as a diagnostic tool or biomarker for disease activity, prognosis, and response to treatment.
Specific bacteria associated with IBD
There have been no specific pathogens yet identified that fulfill Koch’s postulates. There are, however, several specific bacteria that are associated with IBD. Mycobacterium avium subspecies paratuberculosis (MAP) causes chronic granulomatous ileitis (Johne’s disease) in cattle and sheep, which shares some pathological features with CD. In addition, because MAP has been found in commercial milk, it is suspected as a causative pathogen of CD. MAP was detected in CD patients using mucosal PCR, and the positive rates of serum anti-MAP antibody were higher in CD patients than in healthy controls or UC patients . However, a clinical trial of a 2-year administration of antituberculosis drugs to CD patients showed no efficacy . Adhesive-invasive E. coli (AIEC), which can adhere to and invade the intestinal epithelial cells, colonize the ileal mucosa of CD . AIEC also replicate in macrophages and stimulate TNFα production from macrophages. It was observed that Fusobacterium varium attaches to inflamed regions in UC and invades the mucosa at ulcers . Serum titers for anti-F. varium antibodies were higher in UC patients compared with healthy controls . F. varium produces butyrate, and rectal administration of butyrate has been shown to cause mucosal damage in mice . The pathological consequence of butyrate production by F. varium, however, needs to be examined more extensively because butyrate has diverse effects on the intestinal homeostasis including Treg induction in the gut and energy supply to the intestinal epithelial cells. The combination therapy of amoxicillin, tetracycline, and metronidazole (to which F. varium is sensitive) for 2 weeks showed efficacy in active UC patients, suggesting the possible pathogenic role of F. varium .
The role of the gut microbiota in IBD revealed by susceptibility genes
The association of IBD susceptibility genes with bacteria has recently been highlighted. The development of the genome-wide association study has contributed greatly to the identification of more than 160 IBD susceptibility genes to date . The physiological functions of these genes are categorized into several groups relating to (1) acquired immunity (IL23R, IL12B, JAK2, STAT3), (2) bacterial recognition and processing (NOD2/CARD15), (3) autophagy (ATG16L, IRGM, ATG5), and (4) mucosal barrier (ECM1, CDH1, LAMB1) . Many of the CD susceptibility genes are associated with bacterial recognition and processing, and many of the UC susceptibility genes are related to mucosal barrier function, suggesting that impaired handling of bacteria or disruption of the mucosal barrier function leads to breakdown of tolerance against the commensal bacterial in the gut in CD and UC, respectively.
NOD2/CARD15 was the first reported CD susceptible gene and shows the strongest association with CD. The function of the NOD2 protein has been extensively studied. NOD2 is an intracellular receptor for muramyl dipeptide (MDP), a component of the cell wall of gram-positive bacteria, and is expressed in intestinal epithelial cells and monocytes/macrophages. While Nod2-deficient mice do not develop spontaneous colitis, the bacterial load in the gut is increased in these mice. CD patients with NOD2 mutations demonstrate diminished production of antimicrobial peptides (AMPs) from Paneth cells  as well as reduced production of the anti-inflammatory cytokine IL-10 from peripheral mononuclear cells . NOD2 stimulation with MDP induces autophagy , which regulates replication of intracellular bacteria and is also involved in bacterial antigen presentation in the infected cells.
Several autophagy-related genes have also been reported as CD susceptibility genes. Autophagy is an intracellular process that is involved in degradation and recycling of proteins when cells are in starvation. Autophagy is also involved in the handling of intracellular pathogens. ATG16L is a susceptibility gene for CD and is essential for autophagosome formation. Interestingly, it has been shown that NOD1 and NOD2 sense bacterial invasion into the cell and recruit ATG16L to the site of bacterial entry, which triggers autophagy. The intracellular bacteria are then processed through autophagy . This close association between NOD2 and ATG16L suggests the importance of this pathway in the pathophysiology of CD.
Studies on IBD susceptibility genes have revealed the essential role of Paneth cells in CD. Paneth cells reside at the bottom of the intestinal crypts and produce AMPs. The important role of Paneth cells in the regulation of the gut microbiota and the intestinal immune system is shown by the observation that genetically engineered mice overexpressing α-defensin, one of the AMPs, in intestinal epithelial cells had a reduced number of segmented filamentous bacteria (SFB) in the gastrointestinal tract, resulting in impaired Th17 development in the gut . Abnormalities in the size, number, and distribution of granules in Paneth cells, which contain AMPs, have been observed in CD. These morphological abnormalities were reported to be more frequent in CD patients with NOD2 or ATG16L mutations . Mice harboring the same Atg16l mutation as CD patients develop similar morphological abnormalities of Paneth cells after murine Norovirus infection and become susceptible to dextran sodium sulfate (DSS)-induced colitis . These results provide a good example of the complex interaction between a genetic factor and an environmental factor in the development of intestinal inflammation. Mice deficient in Xbp1, which is an essential molecule for endoplasmic reticulum stress and is a CD susceptibility gene, also have impaired autophagy induction in Paneth cells and develop spontaneous ileitis . These results suggest that autophagy in Paneth cells is critical for maintaining gut homeostasis, probably through regulation of the gut microbiota by AMP production. Impaired Paneth cell function may be an essential element in the development and perpetuation of intestinal inflammation in CD.
How does dysbiosis lead to intestinal inflammation?
It is well known that different commensal bacteria induce distinct types of colitis in IL-10-deficient mice. A mono-association study, in which a single strain of bacteria was inoculated into germ-free IL-10-deficient mice, demonstrated that E. coli induced cecal inflammation, Enterococcus faecalis induced distal colitis, and Pseudomonas fluorescens did not cause colitis . It was also reported that the presence of Helicobacter hepaticus, a species of commensal bacteria, exacerbated colitis in IL-10-deficient mice. These results show that alteration of the composition of the gut microbiota can cause distinct intestinal immune responses even in a host with the same genetic background, suggesting that dysbiosis can modulate the immune response in the gut.
Garrett et al.  reported that mice deficient in both Tbx21/T-bet, which is an essential transcription factor for Th1 differentiation, and Rag, which is indispensable for the acquired immune system, developed spontaneous UC-like colitis, which was ameliorated by the administration of antibiotics. Importantly, wild-type mice co-housed with colitic T-bet/Rag double knockout mice also developed similar colitis, suggesting that a dysbiotic gut microbiota is communicable and can cause intestinal inflammation without genetic manipulation.
Functional changes in the gut microbiota resulting from dysbiosis may be involved in the pathophysiology of IBD. The number of genes harbored in the gut microbiota is 100 times greater than that in the human genome [5, 47, 48]. Metabolites of the gut microbiota contribute to epithelial cell function, energy balance, and the immune system of the host. A metagenomic analysis of the gut microbiota showed a decrease in genes responsible for carbohydrate and amino acid metabolism and an increase in those in the oxidative stress pathway, in IBD patients , raising the possibility that oxidative stress from the gut microbiota causes intestinal inflammation in IBD patients. A specific metabolite of the gut microbiota is also likely to be involved in the pathophysiology of IBD. The gut microbiota metabolizes nonabsorptive dietary fiber and produces short-chain fatty acids such as butyrate and propionate. Commensal bacteria-derived butyrate induces the differentiation of colonic regulatory T cells in mice . Butyrate is also an important energy source for intestinal epithelial cells and increases production of mucin and AMPs . The concentrations of butyrate in feces have consistently been shown to be decreased in IBD patients. Consistently, F. prausnitzii, a species of butyrate-producing bacteria, has also been observed to be decreased in IBD . It is possible that the decreased level of butyrate in the gut contributes to inducing intestinal inflammation. Another example of a functional alteration of the gut microbiota in IBD is the increase of sulfate-reducing bacteria (SRB) in UC . SRB produce hydrogen sulfide, which is toxic to the intestinal epithelial cells and can cause mucosal inflammation.
Recent studies have revealed that specific bacteria control the intestinal immune system. SFB, for example, induce Th17 cells in the murine intestine . Although the human counterpart of SFB has not yet been identified, SFB-like organisms were observed in six out of six surgical specimens from UC patients . These SFB-like organisms were not observed in surgical specimens from CD patients. In non-IBD controls, SFB-like organisms were observed in three out of six specimens, with a much lower density compared with UC. These are interesting observations because Th17 cells were reported to be increased in IBD. The physiological role of these SFB-like organisms requires further investigation.
The number of bacteria in the mucus layer is increased in IBD , suggesting impaired mucosal barrier function. This is consistent with the fact that many of the UC susceptibility genes are related to mucosal barrier function. Furthermore, bacteria that can degrade mucins in the mucus layer and utilize it as an energy source, for example Ruminococcus gnavus and Ruminococcus torques, are increased in IBD. These bacteria help other bacteria reside in the mucus layer by providing degraded mucins as nutrients.