Inflammatory bowel disease (IBD), including Crohn’s disease and ulcerative colitis, is characterized by chronic relapsing intestinal inflammation. It has been a worldwide health-care problem with a continually increasing incidence. It is thought that IBD results from an aberrant and continuing immune response to the microbes in the gut, catalyzed by the genetic susceptibility of the individual. Although the etiology of IBD remains largely unknown, it involves a complex interaction between the genetic, environmental or microbial factors and the immune responses. Of the four components of IBD pathogenesis, most rapid progress has been made in the genetic study of gut inflammation. The latest internationally collaborative studies have ascertained 163 susceptibility gene loci for IBD. The genes implicated in childhood-onset and adult-onset IBD overlap, suggesting similar genetic predispositions. However, the fact that genetic factors account for only a portion of overall disease variance indicates that microbial and environmental factors may interact with genetic elements in the pathogenesis of IBD. Meanwhile, the adaptive immune response has been classically considered to play a major role in the pathogenesis of IBD, as new studies in immunology and genetics have clarified that the innate immune response maintains the same importance in inducing gut inflammation. Recent progress in understanding IBD pathogenesis sheds lights on relevant disease mechanisms, including the innate and adaptive immunity, and the interactions between genetic factors and microbial and environmental cues. In this review, we provide an update on the major advances that have occurred in above areas.

Inflammatory bowel disease (IBD) has been a global healthcare problem with a sustained increasing incidence^[1]. It includes two major forms, Crohn’s disease (CD) and ulcerative colitis (UC), which are distinct chronic bowel-relapsing inflammatory disorders. CD can cause transmural inflammation and affect any part of the gastrointestinal tract (most commonly, the terminal ileum or the perianal region) in a non-continuous type. Unlike UC, CD is commonly associated with complications such as abscesses, fistulas and strictures. In contrast, UC is typified by mucosal inflammation and limited to the colon^[2]. Although the etiology of IBD remains largely unknown, recent research indicated that the individual’s genetic susceptibility, external environment, intestinal microbial flora and immune responses are all involved and functionally integrated in the pathogenesis of IBD^[3-5]. The main purpose of this review is to offer an update that have occurred in each of the above four areas, and to highlight the future work to find a clear understanding of IBD pathogenesis.

Over the past decades, there have been huge advances in our understanding of genetic contributions to IBD^[6]. This is due to the technological advances in DNA analysis and sequencing and the use of huge multinational databases^[7]. Advances in genetic testing and analyzing technologies have allowed for the completion of many genome-wide association studies (GWAS) which identify single nucleotide polymorphisms (SNPs). Recent studies have brought the number of IBD-associated gene loci to 163, of which 110 are associated with both diseases, 30 CD specific and 23 UC specific^[8]. Studies of gene loci shared by UC and CD may provide new way to find their common pathogenesis.

The era of modern IBD genetic research began in 2001 with the discovery of NOD2 (nucleotide-binding oligomerization domaincontaining 2), the first susceptibility gene for CD^[9]. The NOD2 gene codes for a protein that was originally described as an intracellular receptor recognizing the muramyl dipeptide (MDP), a conserved motif present in peptidoglycan from both Gram-positive and -negative bacteria^[10]. MDP stimulation induces autophagy which controls bacterial replication and antigen presentation^[11,12], and modulates both innate and adaptive immune responses^[13]. NOD2 participates in distinct MDP-independent pathways such as the regulation of the T-cell response^[14]. The association between CD and NOD2 has already been replicated at the genome-wide significance level^[15].

Genetic analyses have shown an indispensable role for autophagy in immune responses in IBD, and reported two autophagy-related genes named ATG16L1 and IRGM^[16-18]. Autophagy is involved in intracellular homeostasis, contributing to the degradation and recycling of cytosolic contents and organelles, as well as to the resistance against infection and removal of intracellular microbes^[19]. ATG16L1 is essential for all forms of autophagy, and the coding mutation T300A is associated with an increased risk of CD. IRGM belongs to the p47 immunity-related GTPase family. CD-associated polymorphisms in IRGM lead to reduced protein expression. Epithelial cells and dendritic cells containing ATG16L1 and NOD2 variants show defects in antibacterial autophagy^[12,20].

With the widespread use of GWAS and SNPs, a significant association between IBD and the IL23R gene has recently been described^[21]. The IL23R gene encodes a subunit of the receptor for the pro-inflammatory cytokine interleukin (IL)-23, a peptide involved in the generation of Th17 cells. The Th17 and IL-23 pathway is well established in the pathogenesis of IBD, with susceptibility gene loci IL23R, IL12B, JAK2, and STAT3 having been identified in both UC and CD^[22,23]. Variants in IL12B, which encodes the p40 subunit of IL-12 and IL-23, have been associated with IBD and other immune disorders. Defects in the function of IL-10 have also been associated with CD and UC^[24]. Other susceptibility genes that regulate immune function include CARD9, IL1R2, REL, SMAD3 and PRDM1.

Recent progress in the genetics of IBD holds several key messages in regard to the underlying mechanism of the disease. On one hand, the expanding number of susceptibility gene loci described in IBD indicates that genetic influences are critical components of the disease pathogenesis; while on the other hand, explainable susceptibility loci discovered so far account for only 20%-25% of the heritability found in the above-mentioned studies. This is not only true for IBD, but also true for many other polygenetic diseases, and the phenomenon has been called “the mystery of missing heritability of common traits” or “genetic vacuum”^[25]. This issue is further proved by GWAS that has failed to add new susceptibility gene loci to fill the “genetic vacuum”^[26,27]. The possibility was then proposed that, instead of missing genes, the interactions among genes and their products could explain much of the apparent vacuum and account for a considerable number of IBD^[25]. These new insights into genetics and heritability of IBD implicate that future explorations of gene-gene interactions, gene-pathway interactions and gene-environment interactions are likely to give us more insights into IBD pathogenesis than finding new rare variants.

There is no doubt that environmental factors play an important role in the pathogenesis of IBD. A large number of environmental factors are considered risk factors for IBD, including smoking, diet, drugs, geography, social stress, and psychological element^[28]. Among them, smoking remains the most widely studied and replicated environmental prompter for IBD. Since the first described inverse association between UC and smoking in 1982, subsequent studies have confirmed the protective effect of heavy smoking on the development of UC with a lower rate of relapse^[29-31]. Contrary to its effect on UC, smoking increases the risk of CD and is associated with a higher rate of postoperative disease^[32].

Traditional conception for vitamin D’s role is concentrated in calcium metabolism and bone health. Nowadays, there has been increasing recognition of the immunologic role of vitamin D^[33]. Recent literature suggests that the role of vitamin D is multifarious and associated with diverse diseases including IBD. Leslie et al^[34] found that vitamin D deficiency had been common in diagnosed IBD patients and pointed out that low vitamin D had contributed to the increased risk of IBD. In mouse models, vitamin D deficiency is associated with an increased susceptibility to dextran sodium sulfate-induced colitis and 1,25(OH)₂D3 supplementation ameliorates the severity of intestinal inflammation^[35].

The effect of aspirin and nonsteroidal anti-inflammatory drugs (NSAIDs) in the gastrointestinal tract is well recognized. However, limited high quality evidence is available to support the notion that aspirin and NSAIDs have an effect in triggering onset or relapse of IBD. Ananthakrishnan et al^[36] found no association between the dose, duration, or frequency of aspirin use and the risk for CD or UC; but the high dose, prolonged using duration, and frequent use of NSAIDs had been associated with an increased risk of CD and UC. A recent study has found that the use of antibiotics is an important environmental factor, influencing the risk of IBD through their effect on the microbiome. Antibiotic use within the first year of life is more common among pediatric IBD cases compared to controls^[37].

Stress has long been proposed to play a role in the pathogenesis of CD and UC^[38-40]. Bitton et al^[41] suggested that individuals with lower levels of stress had a reduced risk of the disease onset. Mood components of perceived stress, including depression and anxiety, may play a strong role in mediating the deterioration of IBD^[42]. A retrospective study by Goodhand et al^[43] found a reduction in the number of symptomatic relapses in participants, and the antidepressants beneficially impact the course of IBD. However, a Cochrane review shows no benefit of psychological interventions in IBD^[44].

Recent ecological and epidemiologic evidence suggests that air pollution may contribute to the risk of CD and UC. The rising incidence of CD and UC in developing countries parallels the development of industrialization^[45]. Elevated air pollution is associated with an augment in circulating polymorphonuclear leukocytes and plasma cytokines^[46,47]. Kaplan et al^[48] using The Health Improvement Network Database in the United Kingdom, found that high levels of NO₂ and SO₂ correlate with the increased risk of CD and UC. In another study, total pollutant emission has been linked to increased rates of hospitalizations for both CD and UC, suggesting that ambient air pollution may also influence these established diseases^[49].

The whole human gut microbiome consists of approximately 1150 bacterial species, with each individual host having roughly 160 species^[50]. Gut microbiome is established within the first 2 wk of life and then usually remains remarkably stable thereafter. Although it is only possible to culture 20%-30% of the gut microbiome, the association between the changes in the microbiome and IBD has been established^[51]. Many studies have examined the gut flora in CD and UC in both inflamed and non-inflamed segments, and found that there is a significantly reduced biodiversity in faecal microbiome in IBD patients compared to that in healthy controls^[52]. Other research has also found that the microbiota in IBD patients is unstable than that in healthy individual^[53]. In healthy intestine, the Firmicutes and Bacteroidetes phyla predominate, and contribute to the production of epithelial metabolic substrates. In contrast, the microbiota is characterized by a relative lack of Firmicutes and Bacteroidetes, and an over-representation of enterobacteria in CD; meanwhile, a reduction in Clostridium spp. and an increase in Escherichia coli (E. coli) have been reported in UC^[54].

In healthy colon, there is a continuous mucus coating consisting of two layers of sub-structures: the outer is a loosely adherent layer, good for bacterial growth; while the inner is a tightly adherent layer, normally sterile. In IBD, particularly CD, there is a marked increase in bacteria associated with the colonic adherent mucus layer^[55,56]. In CD, a consistent increase in mucosa-associated E. coli and reduction in Firmicutes are reported^[57,58]. There is strong evidence for an increase in mucosa-associated E. coli in both the ileum and colon, and their presence within the granulomas in CD implicates a primary pathogenic role^[59]. An adherent and invasive E. coli (AIEC) phenotype has been found in CD, which is typified by bacterial invasion into epithelial cells and replication within macrophages^[60]. AIEC has also been shown to induce granuloma in vitro and granulomatous colitis in Boxer dogs^[61].

The investigation of IBD pathogenesis has been dominated for a long time by the studies of mucosal immunity, especially the T cell response. Available evidence suggests that the dysfunctions of innate and adaptive immune pathways contribute to the aberrant intestinal inflammatory response in patients with IBD. Most studies in the last two decades have focused on the role of abnormal adaptive immune responses in the pathogenesis of IBD. The focus on the adaptive immune response has ultimately led to the notion that the two main types of IBD represent clearly distinct forms of gut inflammation: CD has long been considered to be driven by a Th1 response and UC has been associated with a non-conventional Th2 response^[62,63]. The newly described Th17 cells are also involved in the gut inflammatory response in IBD^[64]. Immunological studies have recently focused on the mucosal innate immune responses, such as epithelial barrier integrity, innate microbial sensing, autophagy and unfolded protein response.

There is no doubt that an unprecedented progress in our understanding of IBD pathogenesis has been achieved during the past few years. The key factors responsible for IBD include genetic components, environmental elements, microbial flora and immune responses. It is hard to dispute the popular belief that IBD arises from an extremely complex interaction among genetic and environmental elements, dysregulated immune responses and alterations of the microbiome, and that none of these factors alone is likely to cause the disease. More detailed information on their composition, function, and interaction is becoming increasingly accessible through high genomic approaches, investigation of environmental changes, molecular analysis of gut bacteria flora, and a more integrated understanding of the interaction between innate and adaptive immune responses. The growing number and diversity of genetic loci associated with IBD provide major challenges to the investigation of how they impact immunity and inflammation in susceptible individuals. Future research needs to further clarify and integrate the effects of the microbiome and environment on the immune response, and it shall be essential to gain further insights into the mechanisms and pathways of how bacteria, viruses or even fungi can modulate innate and adaptive immune responses.