Research progress on the relationship between intestinal microecology and intestinal bowel disease

Abstract

Intestinal microecology is the main component of human microecology. Intestinal microecology consists of intestinal microbiota, intestinal epithelial cells, and intestinal mucosal immune system. These components are interdependent and establish a complex interaction network that restricts each other. According to the impact on the human body, there are three categories of symbiotic bacteria, opportunistic pathogens, and pathogenic bacteria. The intestinal microecology participates in digestion and absorption, and material metabolism, and inhibits the growth of pathogenic microorganisms. It also acts as the body's natural immune barrier, regulates the innate immunity of the intestine, controls the mucosal barrier function, and also participates in the intestinal epithelial cells' physiological activities such as hyperplasia or apoptosis. When the steady‐state balance of the intestinal microecology is disturbed, the existing core intestinal microbiota network changes and leads to obesity, diabetes, and many other diseases, especially irritable bowel syndrome, inflammatory bowel disease (IBD), and colorectal malignancy. Intestinal diseases, including tumors, are particularly closely related to intestinal microecology. This article systematically discusses the research progress on the relationship between IBD and intestinal microecology from the pathogenesis, treatment methods of IBD, and the changes in intestinal microbiota.

The article systematically discussed the research progress of the relationship between inflammatory bowel disease and intestinal microecology from the pathogenesis and treatment methods of inflammatory bowel disease and the changes in intestinal flora.

1. INTRODUCTION

It is currently known that as many as 10¹⁴ microorganisms aggregate in the nutrient‐rich gut, which together constitutes the microbiota with very diverse characteristics. ¹ These microbes perform many functions in the gut, such as preventing pathogen infection, aiding digestion, providing nutrients, and forming a mucosal barrier to the immune system. ² Some researchers believe that the microbial diversity of the human gut is the result of the co‐evolution of the microbial community and its host. ³ Human Microecology Project and the Human Intestinal System Genome Project (MetaHIT) have focused on the function and structure of gut microbes. ⁴ , ⁵ Studies between obese and non‐obese individuals in twins have shown that obese individuals have reduced diversity in their gut microbiota and altered characterization of metabolic pathways. ⁶ , ⁷ Between the host epithelial cells and immune cells and specific gut microbes there are pattern receptors can mutual recognition, microbes through Pregnane X receptor (PXR) and Toll‐like receptors (TLR) control the mucosal barrier function modulates gut innate immunity and affects gut community structure. ⁸ After the microbiota and metabolites bind to receptors, they activate signaling pathways and interact with related key proteins, thereby participating in the regulation of macrophage polarization by host immune cells and the destruction and regeneration of intestinal epithelial cells. ⁹

Pathogen recognition by immunoglobulins (Ig) is an important aspect in immune adaptation, and microbial symbionts increase the frequency of antimicrobial IgM + IgD + and B cells in the gut. This enrichment affects follicular B cells, and microbial symbionts influence host immunity by enriching antibacterial‐specific frequencies in the pre‐immune B cell pool, thereby affecting the mucosal immune system. ¹⁰ Bifidobacterium, Faecacterium, Ruminococcus, and Prevotella were negatively associated with markers of chronic inflammation such as hsCRP and interleukin (IL)‐6. Gut microbiota may control chronic inflammatory response and thus participate in the pathogenesis of atherosclerotic cardiovascular disease (ACVD). ¹¹ Studies show that the progression of myocarditis to fatal heart disease depends on cardiac myosin‐specific TH17 cells tagged in the gut by commensal Bacteroidetes peptidomimetics, involved in immune responses to exacerbate myocardial inflammation. ¹² Studies in obese patients have shown reduced diversity of gut microbiota and abundance of lactobac in obese individuals, and although the causal role of altered gut microbiome and obesity is controversial, animal and human studies have shown that gut metabolites (such as butyrate) can be used to prevent and treat obesity and its complications. ¹³ A metagenomic study demonstrated a significant reduction in gut bacterial diversity in patients with autoimmune liver disease (AILD), in whom functional analyses revealed altered metabolic pathways in the gut microbiome of AILD patients. ¹⁴ A study of pregnant women with gestational diabetes found that the microbes in pregnant women and newborns changed significantly at almost the same time, mainly Firmicutes and Proteobacteria. ¹⁵ Studies have shown that the gut microbiota is involved in the early stages of Rheumatoid Arthritis (RA). The results of the analysis found that, compared with healthy controls, the diversity of RA patients led to dysbiosis, and especially genes related to Bacteroidetes and synthetic lipopolysaccharide were enriched in RA. ¹⁶

In this review, the intestinal epithelial‐mucosal barrier is considered to be spatiotemporally controlled and organized by commensal bacteria, and intestinal epithelial cells and effector molecules. ¹⁷ To avoid the attack of pathogenic bacteria, viruses, and sometimes opportunistic pathogenic bacteria, the immune barrier in the intestinal tract is composed of epithelial cell layer and mucus layer, and active and passive immunity with symbiotic bacteria together forms the intestinal barrier system.

1.1. The relationship between gut bacteria and the mucus layer

The intestinal mucus layer is divided into inner and outer mucus layers. The outer mucus layer has a loose structure, a thin and thick texture, and is in direct contact with the microbiota. it is distributed in the small intestine and colon, but the mucus layer on the surface of the small intestine does not completely cover the epithelial cells of the small intestine. he mucus layer in the colon is more complex than that in the small intestine, one of the main locations the immune response occurs where the mechanical barrier of mucus layer in the colon while providing energy to maintain microbial symbiosis. ¹⁸ How the host controls mucus barrier integrity and maintains symbiosis is unclear. A major function of the intestinal mucus layer is the production of mucin secreted by intercrypt goblet cells (icGCS) on the colon surface. ¹⁹ Dense O‐glycosylated mucin 2 (MUC2) is the core molecule in the mucus layer. ²⁰ Deficiency of MUC2 results in a thinner mucus layer in the colon, which is less likely to colonize commensal bacteria. ²¹

If the microbiota is imbalanced, many bacteria and metabolites can disrupt the mucus layer and affect its recovery of the mucus layer. A study has shown that the toxins produced by Akkermansia municiphila and Bacteroides fragilis release dissolved proteolytic enzymes of the mucus layer. ²² Sulfate‐reducing bacteria can also degrade mucin proteins, and the mucus layer also provides energy for the activity of the microbiota. ²³ Goblet cells secrete a large amount of mucin. When pathogenic bacteria invade, Toll receptors receive a signal to instruct MUC2 protein to encapsulate pathogenic bacteria and opportunistic bacteria and metabolites out of the inner mucus layer and then secrete new mucin to form renewal. ²⁴ , ²⁵ When the intestinal mucosal barrier is destroyed, the Paneth cells in the small intestinal crypts undergo gene mutations or contain abnormal transcription factors, and the Nod2 gene mutation in the antibacterial peptide subgroup will reduce the secretion of mucin and antibacterial substances after being stimulated by the microbiota. ²⁶ , ²⁷ However, symbiotic bacteria also have a protective effect on the mucus layer. Studies shows that intestinal microbiota metabolites produce short‐chain fatty acids (SCFA) and butyric acid, and these products can upregulate the secretion of MUC2. ²⁸ Mucin also participates in the anti‐pathogen invasion and protects the crypt stem cells at the base of Paneth cells in the crypts of the small intestine and colon to normally maintain the renewal of intestinal epithelial cells. ²⁹ , ³⁰ WFDC2 is an anti‐protease molecule expressed by goblet cells and inhibits bacterial growth. In vivo, WFDC2 maintains the integrity of tight junctions (TJ) between epithelial cells and prevents the invasion of commensal bacteria and mucosal inflammation, a role in mucosal barrier homeostasis. ³¹

1.2. The relationship between gut bacteria and intestinal epithelial cells

Intestinal epithelial cells are the second immune barrier of the intestine and complete a renewal cycle every 3–6 days. To maintain intestinal homeostasis, colonic epithelial cells are covered by a thick inner and outer mucus layer, which contains some symbiotic bacteria (eg. Bacteroidetes. Fermicutes, etc). The inner mucus layer does not contain commensal bacteria. ¹⁹ , ³² Although the mucus layer serves as a physical barrier to the large microbiota present in the large intestine, the mechanism that separates bacteria from the colonic epithelium has not been fully elucidated. Secretory fragments and IgA of intestinal epithelial cells assemble into sIgA; the sIgA found on the surface of the intestinal mucosa can recognize the intestinal microbiota, especially gram‐negative facultative anaerobic bacilli, encapsulate the bacteria, avoid bacterial colonization in the intestinal epithelium, block the junction between bacteria and mucus, and activate autophagy to clear bacteria and metabolites. ³³ The mechanism of maintaining intestinal epithelial barrier homeostasis has not yet been elucidated. Some studies have found that if Lypd8 gene expression is blocked, bacteria can directly bind to receptors on the cell membrane. Lypd8^−/− mice show spontaneous inflammatory response than normal mice or high‐fat diet (HFD) mice. ³⁴ Lypd8 gene is selectively expressed in the uppermost epithelial cells of the colorectal glands, possibly. It is in the Ly6/PLAUR domain containing eight (Lypd8) proteins, which can bind to the flagella of gram‐negative bacilli or Proteus mirabilis to inhibit the movement of the flagella, thereby preventing bacteria from entering the inner mucus layer, inhibiting the inflammatory response of epithelial cells, and separating bacteria and epithelial cell layer. ³⁵ , ³⁶

The intestinal mucosal barrier is capable of secreting antimicrobial proteins, some of which are activated only when the barrier is attacked. An example is SPRR2A protein that can work in low salt concentration and acidic environment. SPRR2A binds with negatively charged lipids and can destroy liposomes of negatively charged lipids. After intestinal microbiota colonization or pathogen infection, the expression of small protein 2A is significantly upregulated through the activation of the TLR‐MyD88 signaling pathway. ³⁷ The intestinal microbiota of SPRR2A knockout mice was altered, and 16sRNA gene sequence analysis showed an increase in the abundance of gram‐positive bacteria in the intestine, indicating that SPRR2A knockout increased the susceptibility of gram‐positive bacteria in the intestine. The researchers observed that the SPRR2A protein is induced through STAT6. Intraperitoneal injection of IL‐13 into the wild‐type mice also increased SPRR2A expression. STAT6 acts downstream of IL‐4 and IL‐13 to induce type 2 immunity. This indicated that SPRR2A could be upregulated through the IL‐4/13‐STAT6 pathway, thereby eliminating pathogenic bacteria and protecting the integrity of the epithelial barrier. ³⁸

Clostridium difficile toxin A (TcdA) is a major exotoxin that contributes to the destruction of the colonic epithelium during C. difficile infection and is thought to be a major contributor to colonic inflammation. A study used untransformed NCM460 human colon cells, in which C. difficile toxin A activated the PGE2 pathway through EP1 receptor agonists to activate FasL transcription in enterocytes, and FasL perforated the mitochondrial outer membrane, leading to apoptosis, destroying epithelial cells. ³⁹ In addition, TcdA contains a carbohydrate‐binding combinatorial repeat oligopeptide (CROPs) domain that mediates its attachment to the cell surface. TcdA binds with sulfated groups in sulfated glycosaminoglycans (sGAG) by recognizing low‐density lipoproteins receptor (LDLR) and enters epithelial cells; while cells lacking LDLR show reduced sensitivity to TcdA. ⁴⁰

Parikh et al. discovered a new absorptive cell, BEST4+/OTOP2+ cells, which help goblet cells repair barrier damage by regulating the GC‐C signaling pathway. ³¹ Guillermin et al. found that Wnt/β‐catenin signaling is an important pathway for epithelial cell proliferation in intestinal crypts. ⁴¹ TcdA destroys intestinal epithelial cells by inhibiting Wnt/β‐catenin signaling. ⁴² Wnt signaling is responsible for proliferation of intestinal crypt stem cell and cooperates with Scr‐YAP signaling to inhibit inflammatory damage and promote intestinal epithelial regeneration. ⁴¹ , ⁴³ Metabolites are produced by intestinal microbiota through fermentation. Among them, SCFA families, including acetate, propionate, butyrate, play a role in protecting the intestinal mucosal barrier in the intestine. SCFAs can be directly taken up by epithelial cells into the lamina propria, and sometimes can also pass through the lamina propria. As transporter, SCFAs have a stronger affinity with SMCT‐1 (sodium‐coupled monocarboxylate transporter 1) than MCT‐1 (monocarboxylate transporter 1). ⁴⁴ , ⁴⁵ SCFAs can also activate inflammasomes to produce a large number of protective cytokines by regulating the expression of TLRs, and improving the self‐repair ability of epithelial cells. ⁴⁶ , ⁴⁷ Shao et al. found that the transplantation of B. fragilis into germ‐free mice could restore cell oxidative phosphorylation and increase ATP levels, and maintain epithelial cell integrity through increased colon epithelial cell metabolism. ⁴⁸

1.3. The relationship between intestinal microbiota and TJs

TJs are multiprotein complexes composed of regulatory molecules, including kinases, transmembrane proteins, and peripheral membrane proteins, which protect the intestinal epithelial barrier and regulate intestinal permeability. ⁴⁹ , ⁵⁰ The TJs family mainly includes claudins, occludins, and JAM, ZO‐1, ZO‐2, and zonulin. ⁵⁰ Enteropathogenic bacteria can release toxic proteins through their secretion system or direct secretion, transport them to the transport system in the host cell, and deliver them into the intestinal epithelial cells, affecting the expression and localization of TJ proteins and destructing intestinal epithelial cells. At the same time, dendritic cells release dendrites through epithelial cells to directly capture bacteria, identify invasive bacteria in advance, and strengthen the expression of TJ proteins to protect barrier integrity. ⁵¹ It is known that enteropathogenic Escherichia coli (EPEC) causes enteritis to destroy the TJs of the intestinal epithelium. The experiment found that after infection with EPEC, it will accumulate near the TJ proteins, encoding specific type III secreted effector proteins through the effector EspG1 to induce consumption of tricellulin. ⁵² Shigella flexneri also affects the expression and distribution of ZO‐1, Cldn1, and occludin, disrupting the epithelial barrier. ⁵³ Intestinal bacteria can also directly secrete some enzymes or toxic proteins into the extracellular space, such as zonula occluden toxin (ZOT), which can activate intracellular signaling pathways leading to mislocalization of TJ proteins and damage to the intestinal mucosal barrier. ⁵⁴ In contrast, intestinal epithelial cells contain protective antimicrobial proteins, and in a mouse model of inflammatory bowel disease (IBD), it was found that REG3A and Resistin‐like molecule‐beta can bind with negatively charged lipids to form pore membranes and lead to the destruction of liposomes to control inflammation. ⁵⁵ , ⁵⁶ In vivo, in the absence of the antibacterial protein WFDC2 secreted by goblet cells, epithelial cells separate and pathogenic bacteria cross the barrier, and normal expression of WFDC2 maintains the integrity of TJs between epithelial cells and prevents the invasion of commensal bacteria and mucosal inflammation. ³¹ In addition, the quinone oxidoreductase 1 (NQO1) protein involved in the formation of TJs is itself resistant to the acute inflammatory response induced by C. difficile toxin A, and Wang et al. found that NQO1 knockout mice spontaneously showed weak intestinal inflammation, marked loss of colonic epithelial TJ proteins, mucosal barrier disruption, and higher levels of epithelial cell apoptosis. ⁵⁷ Studies have found that bacterial metabolite SCFAs can also regulate TJ proteins to protect the integrity of the barrier and have shown that higher levels of SCFAs in the gut can regulate NFκB and AMPK signaling pathway phosphorylation, upregulate the expression of ZO‐1 and claudin TJ protein, and enhance epithelial cell transmembrane resistance (TER). ⁵⁸ Interestingly, some intestinal epithelial TJs are receptors for bacterial toxins. Saitoh et al. have shown that Claudin3 and Claudin4 were the earliest discovered Clostridium perfringens enterotoxin (CPE) receptors, and the C‐terminal region can bind to Claudin3/4, acting as cytotoxin and perforin, and break down TJ structures and increase the permeability of paraepithelial pathways, trigger epithelial cell apoptosis, and affect the physiological activities of intestinal epithelial cells. ⁵⁹ C. difficile gets attached to the epithelium in the intestine through the action of C. difficile transferase (CDT). ⁶⁰ There is evidence that a lipolysis stimulated lipoprotein receptor (LSR), which exists between consecutive epithelial cells, mediates the entry of CDT into target cells and is considered to be the host recognition receptor for CDT. ⁴² , ⁶¹ Tube cell binding promotes Clostridial adhesion and colonization, ultimately resulting in cell death that disrupts intestinal mucosal barrier integrity. ⁶² , ⁶³

In conclusion, the relationship between gut microflora and gut barrier is a complex and intimate one. Although the aforementioned studies have demonstrated the interregulation between intestinal flora and intestinal barrier under physiological conditions, there are some potential mechanisms of action that need to be elucidated by more research evidence.

2. INTESTINAL MICROECOLOGY AND IBD

IBD is usually divided into two categories: ulcerative colitis (UC) and Crohn's disease (CD). IBD is considered to be caused by genetic susceptibility, diet, environmental and microbial factors that drive and trigger immune responses in genetically susceptible individuals. ⁶⁴ , ⁶⁵

2.1. IBD and microbial homeostasis

The current study puts the core of the pathogenesis of IBD seems to be all point to the interaction between the gut microbiota and the gut epithelium. Increased epithelial permeability in the colon is one of the indicators of the severity of IBD. Goblet cells in gastrointestinal epithelial cells regulate that defects in the mucus secretion can lead to changes in the expression of TJ proteins, resulting in the destruction of TJs in epithelial cells and in the imbalance of intestinal homeostasis and the termination of symbiosis (Figure 1).

FIGURE 1.

Factors influencing dysbiosis and intestinal inflammation in intestinal bowel disease.

On the one hand, the Integrative Human Microbiome Project (HMP2 or iHMP) tracks patients and analyzes the relationship between gut microbial activity and host disease activity through a multi‐omics approach. On the other hand, substantial evidence has demonstrated that microbial taxa enriched in IBD patients have similar pro‐inflammatory roles, such as Bacteroidetes, Firmicutes, and Proteobacteria. Furthermore, disturbances in the microbiota‐metabolic network with different subtypes of bacteria group‐characterized in patients interaction networks behave differently, including a balance of Lachnospira and Ruminococcus gnavus. ⁶⁶ The study found that some gut‐derived microbiota differed in classification and function between enteritis‐susceptible samples and healthy samples. Enterococcus faecium, as the most different species, was positively correlated with the disease severity of patients. Transplant feces Enterococcus strains, compared with healthy people, the strains transplanted from UC patients can cause the increased expression of inflammatory factors related to UC in IL‐10 knockout mice. ⁶⁷ .

However, currently no evidence directly demonstrates a causal relationship between gut microbe‐host symbiosis and IBD. Qian et al. observed that HLA‐B27 transgenic rats housed in a non‐sterile environment developed spontaneous immune‐mediated colonic inflammation. ⁶⁸ Im et al. also found that in a mouse model deficient in IL‐2 and IL‐10 genes, mice with defective cell receptor genes in a non‐sterile environment developed symptoms of colitis. ⁶⁹ , ⁷⁰ Therefore, the changes in intestinal microbiota in the intestinal mucosa or the organ cavity may be secondary to intestinal inflammation. The intestinal environment with IBD may alter the metabolic activities of the strains, making it difficult for the strains to colonize, and then stimulate the intestinal mucosa to destroy the intestinal immune barrier. To reconstruct the gut microbial environment in IBD, the intestinal commensal microbiota forms a unique dominant microbiota. In addition, it was found that the dynamically changing microbiota in healthy people highly overlapped with the gut microbiota that was reduced in CD patients, and it was also observed that alleles of CD in patients were highly correlated with changes in colonic mucosal microbial composition. ⁷¹ In addition, a systematic review found that the amount of Faecalibacterium prausnitzii was significantly reduced in both CD patients and UC patients, indicating that the expression level of F. prausnitzii was negatively correlated with the degree of IBD. ⁷² The immune mechanism of the intestinal mucosal barrier in IBD is still unclear. Studies have found that if there is an inflammatory damage to the intestinal mucosa, the stimulated intestinal epithelial barrier can adapt to a certain degree of inflammation without causing an immune cascade. ⁷³

The production of indopoacrylic acid (IA) by the Peptostreptococcus species can regulate intestinal immune responses through the xenobiotic sensor pregnane X receptor(PXR). ⁷⁴ Metagenomic studies have found reduced biosynthetic gene clusters of IA in IBD patients, resulting in an inability to mitigate the inflammatory response to restore the intestinal epithelial barrier. ⁷⁵ Statistics show that the level of bile salt hydrolases (BSH) in the gut microbiota of IBD patients is significantly lower than that in healthy individuals, especially in Firmicutes in CD patients. Lower BSH level fails to inhibit NF‐B signaling by activating farnesoid‐activated X receptor (FXR). ⁷⁶

Colonic inflammation activates the immune response, produces IFNγ, and then generates reactive oxygen species (ROS) through phagocytic innate immune cells. These free radicals eventually provide a suitable environment for anaerobic microorganisms, reduce microbial diversity, reduce the abundance of inhibiting inflammatory microbiota, and fail to activate inhibiting inflammatory pathways to relieve inflammation, disrupted the balance of microbial homeostasis in IBD patients. 77In particular, in the colonization of germ‐free mice with microbiota from IBD patients, research shows that microbial adhesion to epithelial cells stimulates the production of Th17 cells and reduces the number of RORγt⁺ Tregs to break the regulatory process of inflammation, providing evidence for disease mechanisms in the gut microbiota of IBD (Table 1).

TABLE 1.

Major dysbiosis of gut microbiome during intestinal bowel disease

Microorganism	Type	Dysbiosis	Model	References
Bifidobacteria, Firmicutes, Firmicutes prausnitzii	CD/UC	Decrease	Humans	72
Firmicutes	2‐, 4‐ and 6‐ Trinitrobenzenesul fonic acid (TNBS) colitis	Decrease	Animal (rats and mice)	66
Bacteroidetes, Bacteroides, Enterobacteriaceae		Increase		91
Helicobacteraceae, Mucispirillum, Desulfovibrio	Experimental colitis	Increase	T‐bet(−/−), Rag2(−/−) mice	117
Enterobacteriaceae and adherent/invasive E. coli	Experimental colitis	Increase	IL‐10(−/−)mice	69, 86
Akkermansia muciniphila, Bacteroides distasonis, Enterobacteriaceae, Clostridium ramnosum	DSS‐colitis	Increase	F1Mice	88
Porphyromonas genera, Bacteroides	Experimental colitis	Increase	F11r(−/−), Rag1(−/−)mice	73
Lachnospira and Ruminococcus	DSS‐colitis/TNBS colitis	Decrease	Animal (rats and mice)	66
Enterococcus faecium	Experimental colitis	Increase	IL‐10(−/−)mice	67
Fusobacterium nucleatum	Experimental colitis	Increase	Humans	90
Faecalibacterium, Roseburia	CD	Decrease	Humans	82

Abbreviations: CD, Crohn's disease; DSS, dextran sodium sulfate; UC, ulcerative colitis.

In addition to bacterial microbes, the microbiome includes both fungi and viruses. In 1988, an antibody to the cell wall component of Saccharomyces cerevisiae was linked to CD. ⁷⁸ Studies have demonstrated that S. cerevisiae colonization can promote purine metabolism in mice, leading to elevated uric acid levels to enhance the inflammatory response. ⁷⁹

2.2. Intestinal microecological imbalance and IBD

At present, a large number of studies have indicated that metabolites regulate the interaction between the gut microbiota and the host. Among these metabolites, bile acids, SCFAs, and tryptophan metabolites are closely related to the pathogenesis of IBD. ⁸⁰ CARD9 is one of the IBD susceptibility genes that integrate signals downstream of the pattern recognition receptor. When Card9^−/− mice fail to normally mediate p38‐JNK signaling and Toll‐like receptor signaling, then the microbiota of mice is unable to normally metabolize tryptophan to a ligand for the aromatic hydrocarbon receptor and fails to activate the IL‐22 pathway, leading to an increase in the number of proinflammatory microorganisms and aggravating the inflammatory response. ⁸¹ Roseburia hominis and F. prausnitzii are currently recognized acetic acid‐butyric acid converters, which are enriched in the mucus layer and play an important role in producing anti‐inflammatory effects. In some studies R. hominis and other SCFA‐producing bacteria decreased, and the levels of SCFA and unconjugated bile acids in feces decreased. ⁸² , ⁸³ However, there are a large number of butyric acid metabolites in the human intestine, such as Clostridium and methanogens. Butyrate promotes Treg development and specifically regulates MUC expression in goblet cells, and the increased secretion of mucus enhances the mucosal barrier; the reduction in butyric acid synthesis leads to the slowdown of reconstitution of intestinal mucosal barrier. ⁸⁴

Pathogens and viruses and some opportunistic bacteria in the gut microbiota may promote inflammatory damage, but commensal bacteria also play a protective role in the gut against inflammatory damage. Different microbiota plays different roles in IBD. Studies have shown that when the number of anaerobic bacteria in the intestine is high, the inflammatory damage is the most serious, the adhesion is strong, and the exudation and infiltration of mononuclear cells are the main factors. ⁸⁵ Adherent/invasive E. coli (AIEC) isolated from IBD patients and non‐IBD patients express different virulence factors, and the virulence factors of non‐IBD patient strains are absent in AIEC. ⁸⁶ AIEC is a typical opportunistic pathogen. AIEC avoids the immune system, invasion into epithelial cells and macrophages. In addition to the autophagy machinery that impairs the IBD host, it can avoid macrophage phagocytosis. Persistent replication of macrophages leads to increased TNFα levels and excessive colonization of AIEC, leading to a sustained immune response. ⁸⁷ Some studies have also suggested that Mycobacterium paratuberculosis, Helicobacter pylori, Myxobacterium, Desulfovibrio, and Porphyromonas may play a role in promoting the pathogenesis of IBD, but there is still a lack of sufficient experimental evidence. ⁸⁸ , ⁸⁹

Fusobacterium nucleatum targeted by NOD2 in colonic epithelial cells' upregulation of CARD3 activates the IL‐17F/NF‐κB signaling pathway, promotes intestinal inflammation, and causes relapse in patients. ⁹⁰ On the contrary, Lactobacillus can reduce the receptors of pro‐inflammatory factors, and reduce the expression of IL‐6, TNF‐α,and Bcl‐2 family proteins, thereby reducing the inflammatory response. ⁹¹ Recent studies have indicated that AIEC bacteria can invade epithelial cells and induce TNF‐α to activate downstream signals of the T‐like receptor transduction pathway, thereby activating NF‐κB to initiate abnormal immune responses, through the adhesion of CEACAM‐6 (carcinoembryonican‐tigen associated cell adhesion molecule‐6) on the mucosa. ⁹² This abnormal immune response leads to changes in the integrity of the intestinal mucus‐epithelial barrier, which in turn enhances IBD susceptibility. Intestinal microbiota imbalance reduces mucus secretion and exposes the intestinal epithelium to damage by intestinal toxic metabolites. However, animal experiments have shown that germ‐free mice have reduced plasma cells, lymphoid follicles, T cells, and Paneth cells, resulting in mucosal damage. IgA was also reduced, and IgG‐producing lymphocytes in the intestinal mucosa of IBD patients significantly increased compared with controls. ⁹³ It indicates that symbiotic microbiota can also increase anti‐inflammatory factors, and symbiotic microbiota can promote 5‐fluorouracil‐induced mucus secretion in rat goblet cells, constituting an important part of the mucus‐epithelial barrier. ⁹⁴ The occurrence of abnormal immune responses and the destruction of the mucus‐epithelial barrier are the two core links of the injury mechanism.

Recently, SARS‐CoV‐2 is known to initially affect the respiratory system, but studies have found that it may lead to multiorgan dysfunction syndrome (MODS); a study found after a patient was infected with the virus, he developed symptoms of IBD. ⁹⁵ The binding of SARS‐CoV‐2 to angiotensin‐converting enzyme receptors 2 (ACE2) hinders the absorption of nutrients, disrupts the intestinal barrier, leads to an imbalance in the microbiota of the gut microbiome, and causes symptoms of intestinal inflammation. COVID‐19‐related changes were found in the gut microbiota. Wei et al. observed that viral RNA was detected in feces in 69% of patients with diarrhea infected with COVID‐19, although only 17% of patients with diarrhea developed respiratory symptoms. ⁹⁶ At present, studies on mouse colon showed that the Bacteroidetes species can regulate ACE2 expression, and that changes in Firmicutes species can also cause variable ACE2 expression. It has been found that after respiratory symptoms have subsided for a period of time, the virus can still be detected in the feces of COVID‐19 patients. It is speculated that the gastrointestinal tract may be one of the sites for virus replication.

The researchers found that nearly half of the feces of COVID‐19 infected patients were positive, and positive patients contained more high abundance of opportunistic bacteria, including Collinsella aerofaciens, Collinsella tanakaei, Streptococcus infantis, and Morganella morganii. Colonization of Coprobacillus, Clostridium ramosum, and Clostridium hathewayi is positively associated with COVID‐19 patient severity. ⁹⁷ The increase in opportunistic bacteria is more common in critically ill patients and is associated with poor prognosis. ⁹⁸ In vulnerable populations, the immune cascade generated in the short term by COVID‐19, “cytokine storm syndrome” (CRS), that mechanism possible involves that butyrate increases mucin production by goblet cells, thereby activating regulatory T cells, producing cytokines, resulting in increased ACE2 expression, enhancing SARS‐CoV‐2 in the intestine, and results in replication in the gut leading to intestinal dysbiosis and further fecal‐oral transmission. ⁹⁹ Viral infection may reflect a potentially dysregulated microbial homeostasis,as discussed earlier, colitis symptoms in COVID‐19 patients may be caused by the destruction of the intestinal mucosal layer and thus the intestinal microecological imbalance, and the reduced microbial diversity aggravates the inflammatory response.

The pathogenic role of fungi in inflammation is not well understood; a study of adult IBD patients revealed clear differences in the relative abundance of specific fungi between IBD patients and healthy individuals; especially in CD patients, fungal expansion is more conducive than bacterial expansion, but the causality is not yet clarified, and further research is needed to clarify the reasons. ⁶²

The intestinal microbiota plays both pro‐inflammatory and anti‐inflammatory roles in the pathogenesis of IBD, and there is no sufficient evidence for a causal relationship between intestinal homeostasis and IBD. In conclusion, the gut microbial homeostasis or imbalanced state plays an important role in the pathophysiological role of IBD, mainly by protecting or attacking the mucus‐epithelial barrier and affecting the immune system through commensal bacteria and metabolites.

3. REGULATION OF THE INTESTINAL MICROBIOTA TO TREAT IBD

The interaction between the intestinal microbiota and the gastrointestinal tract of the host, as well as its role in the occurrence and development of gastrointestinal diseases, provides potential therapeutic targets for the prevention and treatment of gastrointestinal diseases. ¹⁰⁰ Clinically commonly used drugs from different directions to treat IBD. Developed in 1940, sulfasalazine is decomposed by the bacterial nitrate reductase in the colon and is used for the treatment of IBD and rheumatoid arthritis. ¹⁰¹ 5‐Aminosalicylic acid (ASA) is the active part of sulfasalazine's therapeutic action as it enhances the expression of mucosal proteins, but 5‐ASA is considered a topical treatment drug, which is more effective in treating mild to moderate UC than other disease sites and ulcerseverity. ¹⁰² The most common side effects in ASA treatment are gastrointestinal symptoms, including epigastric pain, nausea, and diarrhea. ¹⁰³ Azithromycin and metronidazole are cell‐permeable and potent activators of T‐cell apoptosis, treating IBD primarily through immunomodulatory effects. ¹⁰⁴ Rifaximin is a non‐systemic bactericidal antibiotic that currently relieves symptoms in CD patients, but is ineffective against translocated bacteria. ¹⁰⁵ Its current mechanism of action still needs to be further explored, and the side effects are obvious. In addition to the aforementioned therapeutic drugs, the following ways can be used to treat IBD.

3.1. Probiotics

Probiotics and prebiotics are substances that can be selectively utilized by the host's microbiota and converted into substances beneficial to the host's health. ¹⁰⁶ , ¹⁰⁷ The American Gastroenterological Association recommends that probiotics be used to improve functional gastrointestinal symptoms in IBD. ¹⁰⁸ Multiple randomized, placebo‐controlled clinical trials provide partial evidence for the role of probiotics in relieving clinical symptoms in patients with IBD. ¹⁰⁹ , ¹¹⁰ , ¹¹¹ Szajewska et al. performed randomized controlled trials (RCT, N = 4208) in children with diarrhea with secondary to acute gastroenteritis, that those children received rhamnosus infection compared to placebo or no treatment,the clinical level of diarrhea score did not decrease, but the duration of diarrhea was significantly shorter. ¹¹² Bifidobacterium dentium regulates the glycosylation of the intestinal mucus layer, which has a unique role in regulating mucin production and can act as a mucinogenic agent. B. dentium can increase the expression of mucin genes and MUC2 protein, and its secreted metabolite acetate is also able to increase MUC2 protein expression in vitro. ¹¹³

In a study prebiotics and synbiotics significantly reduced disease activity index in patients with active UC, and probiotic supplementation could increase the quantity of Bifidobacteria in the IBD patients. ¹¹⁴ A controlled trial from Cochrane, including 22 eligible RCTs, found that probiotics were effective in preventing recurrence of quiescent UC. ¹¹⁵ Probiotic effector molecules, including fimbriae, lipoteichoic acid, exopolysaccharides and various surface proteins, alter the gastrointestinal microenvironment by reducing pH, and competing with pathogenic bacteria for nutrients and binding sites. ¹¹⁶ Wang et al. found a gene in Lactocaccus lactis I‐1631 that is specifically involved in aerobic respiration in fermented dairy products, and in the T‐bet(^−/−)Rag2(^−/−) model, in L. lactis I‐1631 the sodA gene can be made not to express. ¹¹⁷

3.2. Fecal microbiota transplantation

Fecal microbiota transplantation (FMT) involves transferring a fecal sample from a healthy donor to a recipient, either by various transplant modalities such as endoscopy, rectal enema, nasogastric/nasoenteric tube (into the upper stomach/small intestine) or by mouth. Ingestion of capsules containing fecal matter restores the microbial environment. ¹¹⁸ American Gastroenterologinal Association (AGA) suggest that FMT mainly improves mucosal inflammation rather than functional gastrointestinal symptoms. ¹¹⁹ , ¹²⁰

FMT is especially good at treating refractory CDI, and studies have shown that the efficacy of FMT in a single treatment of CDI can be up to 75%–90%; the efficiency rate is higher after multiple FMT treatments. ¹²¹ , ¹²² Clinical and experimental evidence also shows that the FMT treatment relieves symptoms in IBD patients. The results of double‐blind trials show that after the FMT treatment, the diversity of gut microbes in UC patients is increased, and the gut of patients is enriched with Eubacterium and Roseburia inulivorans. ¹²³ , ¹²⁴ The meta‐analysis found that for patients with CDI and IBD, the cure rate was 81%, and the overall cure rate was 89% (95% CI = 83%–93%). ¹²⁵ FMT performed through gastroscope to the distal duodenum can significantly improve abdominal distension symptoms in patients with IBS. ¹²⁶

The cure rate of FMT is lower than that of other methods of surgery in randomized trials. ¹²⁷ , ¹²⁸ However, Lima et al. believed that the choice of FMT transplantation method has a direct impact on the cure rate and recurrence rate. Colonoscopy or nasojejunal tube to transplant fresh or frozen feces is better than fecal capsules and enemas. The researchers used UC patient‐derived strains colonized germ‐free or genetically engineered mice, and metagenomic analysis found that the transferable strains could promote metabolism and participate in mucosal immunity. The induction of mucosal regulatory T cells and the strains of Odoribacter splanchnicus colonization resulted in an increase in Foxp3/RORγt tregs induction of IL‐10, and production of SCFAs, repairing of the host mucosal and epithelial barrier integrity, found in the gut of FMT mice. ¹²⁹

Yet there is substantial evidence that FMT is effective as adjunctive therapy. ¹³⁰ However, some randomized controlled studies have not found FMT as significantly effective as it lacks a treatment‐related mechanism. ¹³¹ , ¹³²

3.3. Diet intervention

Whether diet intervention can affect the structure and abundance of host intestinal microbiota species is unknown, but studies have shown that symptoms in IBD patients are triggered by some specific dietary conditions. For example, polyglycans have been observed to exacerbate inflammatory symptoms in inactive IBD patients without abdominal pain, diarrhea. ¹³³ , ¹³⁴ Dietary fiber is metabolized in the gut to SCFAs, resulting in the subsequent activation of GPCR and Treg, and resulting in a reduced inflammatory response and increased mucosal tolerance, thereby protecting CD patients. ¹³⁵ , ¹³⁶ In addition, the interaction between gut microbiota and dietary fiber and protein concentration alleviates inflammation and is also a factor that improves intestinal permeability in mice. ¹³⁷

Multiple randomized controlled trials have shown that a low‐FODMAP dietary intervention can adequately relieve symptoms in patients with IBS, accompanied by decreased abundance of Bifidobacterium adolescentis, Bifidobacterium longum, F. prausnitzii, and decreased fecal butyrate levels. ¹³⁸ , ¹³⁹ In a crossover trial of patients with remission or mild UC, researchers found that a targeted intake of either a low‐fat diet or a high‐fiber diet for 4 weeks significantly improved quality of life, a low‐fat diet significantly improved dysregulated gut microbiota. ¹⁴⁰ Studies based on animal models of IBD have found that hydrolyzed protein diets regulate bacterial abundance and metabolism, and their mechanism of action reduces the abundance of pathogenic bacteria (e.g., E. coli, C. perfringens), and the abundance of secondary bile acid–producing bacteria Clostridium hiranonis, increased associated with elevated levels of secondary bile acids (lithocholic acid, deoxycholic acid). ¹⁴¹ Based on individual differences in the composition and function of the baseline microbiota, therefore, individualized dietary interventions of patients should be considered. ¹⁴²

3.4. Traditional Chinese medicine

The active ingredients of traditional Chinese medicine (TCM) have a two‐way regulating effect on intestinal homeostasis. Some active ingredients contribute to the homeostasis of intestinal microecology, while others inhibit the growth of probiotics and destroy the homeostasis of intestinal microorganisms. Liu et al. found that the main components of Kuijieyuan decoction (KD) include emodin, and KD intervention increased the proportion of Alloprevotella, Treponema, Prevotellaceae, and Prevotella. In the experimental UC model, KD, through regulating the intestinal microbiota and reducing the level of TLR‐dependent phosphorylated PI3K/AKT/NF‐κB, protected the colonic mucosa. ¹⁴³ Emodin from Polygonum multiflorum can also protect the colonic mucosal barrier through increases in the mRNA and protein expression of the VDR and its downstream molecules, Nrf2 and HO‐1. ¹⁴⁴ Although these experiments demonstrate the protective effect of emodin, Cheng et al. have found that its long‐term administration produces toxic metabolites, because colon microorganisms convert rhubarb anthraquinones to rhein, which accumulates over time and causes melanosis coli to increase the risk of colon cancer. ¹⁴⁵ Shao et al. indicated that Sophora flavescens Aiton EtOAc extract (SFE) inhibits oxidative stress and immune inflammation in UC mice, mainly manifested as linoleic acid, arachidonic acid, and fatty acid metabolism recovery, and reduces the expression of related inflammatory markers. SFEs can construct a bacterial metabolite co‐expression network to reduce mucosal damage, suppress immune inflammation, and reduce oxidative stress in UC mice by enriching Lactobacillus, Roseburia, norank_f_Muribaculaceae, Anaerotruncus, Candidatus Saccharimona, and Parasutterella. ¹⁴⁶ Purple sweet potato anthocyanin extract (PSPAE) is also able to maintain intestinal homeostasis and reduce bacterial intestinal inflammation by modulating gut microbiota in mice with dextran sodium sulfate (DSS)‐induced chronic colitis. ¹⁴⁷ A randomized controlled clinical study demonstrated that after Ulmus macrocarpa Hance was administered, the number of Eubacterium ventriosum, Blautia faecis, and Ruminococcus gnavus in feces increased, and the ability of patients to synthesize bile acids improved. Maintaining bile acid homeostasis can protect the microbial structure and improve immunity. ¹⁴⁸

Experiments have confirmed that the intestinal microbiota is also involved in the mechanism of Chinese herbal extracts to keep the intestinal barrier intact. Four flavonoid extracts and three astragalosides from Bunge‐Salisb (ACE) astragalus mongolica inhibit tumor growth and metastasis by modulating intestinal microbiota, inhibiting the overgrowth of opportunistic pathogens, and protecting the colonization of probiotics such as Prevotellacea. In particular, ACE by mediating the intestinal SDF‐1/CXCR4 signaling pathway through the microbiota‐metabolic network it can futher repair the integrity of the intestinal barrier and by reduce the expression of Cyclin D1 and C‐myc, increasing the level of propionic acid and butyric acid. ¹⁴⁹ Extract leaves (EL), ¹⁵⁰ Bilobalide (BI), ¹⁵¹ Rhodiola crenulata extract (RCE), ¹⁵² ginger extract, ¹⁵³ ethanol extract of Ganoderma lucidum (GL95), ¹⁵⁴ flavonoid extracts of Smilax glabra Roxb one of the functions of these extracts is to significantly increase the diversity and richness of the gut microbiota and reverse gut dysbiosis. ¹⁵⁵ Gallic acid can regulate the ratio of Firmicutes and Proteobacteria in the gut microbiota of DSS‐UC mice to induce metabolic changes; the main focus is on increasing carbohydrate metabolism (glucose‐related metabolism) and bile acid (BA) metabolism and reducing amino acid metabolism, thereby restoring intestinal microbial homeostasis. High‐fat diet (HFD)‐induced gut dysbiosis is thought to alter gene expression by improving Firmicutes/Bacteroides abundance using the flavonoid extract from Smilax glabra Roxb. ¹⁵⁶ Researchers also observed that sugar molecules and ginsenosides in the water extract of ginseng (WEG) can act as energy substrates for specific gut bacteria. Thus beneficially modulating the gut microbiota, remodeled gut microbial ecosystem subsequently triggers multiple molecular and cellular signaling pathways (such as butyrate or TGR5 signaling). ¹⁵⁷ Danggui Shaoyao powder is a TCM formula, which has been used for the treatment of Alzheimer's disease. The relative abundance of beneficial bacteria Akkermansia was upregulated, and the pathogenic bacteria Lactobacillus and Erysipelotrichaceae were downregulated in rat feces after the intervention. ¹⁵⁸

In conclusion, due to the incomplete and sufficient evidence, the efficacy and adverse effects of probiotics, FMT, dietary intervention, and TCM treatment are still controversial. Although probiotics do not significantly improve the severity of symptoms or prevent diarrhea recurrence, they can help the host to increase the number of beneficial bacteria, and their effectors can participate in the recovery of intestinal mucosal barrier integrity. Dietary intervention is particularly suitable for IBD caused by bad diet habits, such as high‐fat diet (HFB), which can directly alter gut microbes and metabolites. TCM extracts and compounds can repair the intestinal epithelial‐mucosal barrier and restore the intestinal microbial balance by activating multiple immune‐related signaling pathways. In the future, more rigorous randomized or double‐blind clinical experiments should be conducted to reduce individual differences. Although the above evidence shows that these therapies can be used to alleviate and treat the symptoms of IBD, there are still potential mechanisms of action that need further studies to elucidate.

4. CONCLUSION

The relationship between intestinal microbiota and disease is constantly being studied, but it still faces uncharted territory. An immediate question is about the causal relationship between intestinal microbiota and disease, which requires repeated validation in germ‐free animals, disease models, and clinical evidence. Therapeutic strategies targeting the intestinal microbiota have shown great potential, although the best way to “precisely” modulate the intestinal microbiota is still in the research stage. There is no doubt that the modulation of gut microbes will be more widely used for overall health improvement and adjuvant therapy. With further research, the true meaning of gut dysbiosis with disease states can be better understood, and the intestinal microbiota homeostasis that promotes overall health will be better defined, which will facilitate patient recovery and have broadly positive effects on public health.

In healthy individuals, commensal microbes perform functions that are beneficial to host health (left), in which the gut microbiota produces short‐chain fatty acid (SCFA), mainly butyrate, that help to modulate the gut microbiome. By the intestinal epithelium, the dense and complete mucus layer composed of goblet cells and tight junction (TJ) proteins can effectively prevent bacteria from invading the epithelial layer. SCFAs can provide energy for epithelial cells and help maintain the overall intestinal barrier function. SCFAs can also regulate the differentiation of T cells to provide immune cells. In contrast, gut microbiota homeostasis is disrupted in IBD patients (right), infected with viruses such as SARA‐COV‐2, or microbiota dysbiosis due to changes in the dietary environment. Microbial diversity occurs and leads to decreased immunity, including the reduction in SCFA‐producing bacteria, and in turn leads to the reduction in SCFAs, which are required for the maintenance of intestinal barrier function. This also affects the differentiation of immune cells, causing the imbalance in Treg and Teff cells, producing more pro‐inflammatory cytokines, and aggravating the intestinal inflammatory damage. The mucosal layer is damaged, and therefore the intestinal barrier function is disrupted, resulting in intestinal inflammation.

AUTHOR CONTRIBUTIONS

JC and QHF wrote the manuscript. TY S and XQM contributed to revising the manuscript . All authors gave final approval for publication.

CONFLICT OF INTEREST

The authors declare that there are no conflicts of interest to disclose.

Supporting information

Appendix S1

Fu Q, Song T, Ma X, Cui J. Research progress on the relationship between intestinal microecology and intestinal bowel disease. Anim Models Exp Med. 2022;5:297‐310. doi: 10.1002/ame2.12262