Gut Microbiome as a Target of Intervention in Inflammatory Bowel Disease Pathogenesis and Therapy

Abstract

Inflammatory bowel disease (IBD) is a chronic complicated inflammatory gut pathological disorder and is categorized into ulcerative colitis (UC) and Crohn’s disease (CD). Although the cause of IBD is unclear, dysbiosis of the gut microbiota is thought to be a key factor in the disease’s progression. The gut microbiome serves as a metabolic organ and promotes wellness by carrying out several biological activities. Any modification in the makeup of the gut microbiome leads to several pathological conditions, including IBD. In this review, we emphasize the key metabolic processes that control host–microbiome interaction and its impact on host health. We also discuss the association between microbiome dysbiosis (bacteriome, virome, and mycobiome) and the progression of IBD. Finally, we will highlight microbiome-based therapy as a novel and promising strategy to treat and manage IBD.

1. Introduction

The gut microbiome, defined as the microorganisms that inhabit the human gut, contains billions of organisms, perhaps outnumbering our cells [1]. The human bowel is inhabited by a variety of microorganisms, such as fungi, viruses, and protozoa in addition to the bacterial communities that form up a large proportion of the gut microbiome [2]. The host receives significant advantages from the gut microbiome, such as improved digestion, vitamin production [3], and protection against pathogen colonization [4], and in exchange, they may get vital nutrients from the host. Although humans and the gut microbiome cohabit primarily in symbiosis, this interaction can become pathogenic and result in diseases [2,5]. Since all gut microbiomes exist in the same host habitats, competition and parasitism may arise between species and affect the host in addition to the commensal and symbiotic connection. When the long-term homeostasis of the gut microbiome is interrupted, the risk of developing multiple illnesses increases [6].

Inflammatory bowel disease (IBD) is a relapsing and chronic inflammatory disease of the digestive system, influenced by the interplay between the immune system, gut microbiome, intestinal barrier, and diet in genetically predisposed persons [7,8,9,10,11]. IBD is categorized into two subtypes, ulcerative colitis (UC) and Crohn’s disease (CD), depending on affected regions and involved layers. UC typically affects the colon and rectum only [12], but CD can affect any part of the gastrointestinal tract (GIT) from mouth to anus [13,14]. UC is restricted to the mucosal layer and causes superficial destruction to the intestinal wall, in contrast to CD, which is characterized by inflammation across the whole intestinal wall. Furthermore, the inflamed area in UC appears as continuous, while in CD it appears as patches alternating with healthy areas [15] (Figure 1). Pathological and clinical symptoms of these two illnesses, such as diarrhea, rectal bleeding, weight loss, bloody stools, abdominal discomfort, severe anemia, and recurrent inflammation, largely overlap [16].

IBD is widely disseminated around the world and affects millions of people, according to epidemiological studies, creating a global health threat [8,17,18]. The exact pathogenesis of IBD is not clear until now, but the literature has proved that IBD is a multifactorial disease in which environmental factors, in genetically susceptible persons, may enhance dysbiosis in the gut microbiome [19,20,21,22]. The microbiome–immune system interaction enhances the activation of the inflammatory cascade and immune activation that is responsible for clinical presentation in IBD patients [8,23].

This review exclusively highlights the implementation of the gut microbiome in normal health and modifications that occur in IBD to give critical insight into the inquiry of IBD etiology. It also sheds light on the emergence of microbiome-based therapy techniques as a viable method to treat, manage, and finally cure IBD.

2. Immunopathogenesis of IBD

Although the exact mechanism of pathophysiology and development is not fully clarified, it is believed that an excessive mucosal immune response against gut bacteria plays a significant role in genetically predisposed individuals [24]. The microbial dysbiosis and reduced microbial diversity seen in IBD patients support the theory that the gut microbiome is linked to illness development [25,26]. Dysbiosis in the gut microbiome enhances the thinning of the mucus layer and destruction of tight junctions. So, this increases the permeability of the gut wall to different pathogens with subsequent stimulation of different inflammatory and immune responses.

2.1. Role of Innate Immunity

The mucous layer and intestinal epithelium act as the first barrier that encounters intestinal bacteria, pathogens, and food antigens [27]. It has been reported that the mucosal barrier abnormalities and alterations in IBD patients increase intestinal permeability and initiate inflammatory cascades [28].

The lamina propria’s dendritic cells (DCs) and macrophages are crucial for maintaining gut homeostasis [29,30]. They help to carry food and microbial antigens and present them to the mesenteric lymph nodes (MLNs), where they develop tolerance to nutrients and the commensal microbiome by shifting T lymphocytes in the direction of a regulatory phenotype (Tregs) [29,30,31]. In IBD patients, different types of DCs are increased in MLNs as myeloid and plasmacytoid DCs [32]. They induce Th1/Th17 inflammatory responses, which suggests that DCs and macrophages are important in the pathogenesis of inflammatory diseases like IBD [33,34]. Additionally, mucosal DCs and macrophages exhibit higher levels of TLR2, TLR4, CD40, and the chemokine receptor CCR7, which promotes the production of pro-inflammatory cytokines such IL-1β, IL-6, IL-18, and TNF-α [35,36,37].

TNF-α promotes chronic inflammation in IBD by activating pro-inflammatory cytokines, enhancing endothelial adhesion molecules, and promoting macrophage phagocytic activity [37]. IL-6 is a multi-faceted cytokine that regulates leucocyte trafficking and has a role in CD4⁺ [38] and CD8⁺ T cell activation, proliferation, and differentiation via activating the JAK-STAT signaling pathway [39]. IL-1β stimulates Th17 activity and facilitates granulocyte migration [37].

2.2. Role of Adaptive Immunity

The development of IBD’s chronic inflammatory symptoms is dependent on adaptive immune responses. Th0, a naïve CD4⁺ T cell, is activated to effector T helper cells—Th1, Th2, Th17, and Treg—upon the influence of an antigen-specific signal from an antigen-presenting cell (APC) and existing cytokines [37,40].

Th0 is differentiated into Th1 upon the influence of IL-12 and IL-27 and secretes IL-2, TNFα, and IFNγ [41,42]. On the other hand, Th0 can be differentiated into Th2, upon the influence of IL-4, which secretes IL-13 and IL-5 [42] (Figure 2).

Th17 is critical for the defense against microbial and fungal infections of the mucosa, mainly activated through the triggering of IL-1, IL-6, IL-13, and transforming growth factor β (TGFβ). Activated Th17 secretes pro-inflammatory IL-17A, IL-17F, IL-21, and IL-22, which are important in the pathogenesis of IBD [43,44] (Figure 2).

Treg cells control the production and activity of pro-inflammatory cytokines produced by effector T cell. These unique T cell are essential for maintaining self-tolerance, which guards against autoimmune and inflammatory illnesses as they secrete anti-inflammatory cytokines such as IL-10 and TGFβ [45].

Activated T cell can penetrate the gut mucosa through a process known as homing that is regulated by gut-homing markers on the T cell surface. α4β7 is considered one of the important homing markers. T cells expressing α4β7 can penetrate the gut mucosa by attaching to the mucosal addressin cell-adhesion molecule 1 (MADCAM1) that is expressed by an endothelial cell in the blood vessels of the intestinal tract [46] (Figure 3).

It was also reported that cytokine receptors are linked to JAK protein, which engages in signal transduction by binding to ligands and activating transcription factors (STAT proteins) to promote the expression of genes [47].

3. Gut Microbiome and Association with a Normal Health Condition

The GIT system is a habitat to a complex ecosystem that contains trillions of microorganisms including bacteria, viruses, fungi, and protozoans, together termed as the gut microbiome. The bacterial species (called bacteriome) form around 99% of this ecosystem, more than 100 folds of the human genome, with 1000 to 1150 species. Four phyla make up nearly 99% of the gut bacteriome: Firmicutes (60%), Bacteroidetes (20%), Proteobacteria, and Actinobacteria [48,49], and other lesser ones are divided into the phyla of Verrucomicrobia, Fusobacteria, and Cyanobacteria [50]. During birth, the gut microbiome is less diverse and becomes more complicated as it engages with foods [51,52]. The bacterial burden is lower in the upper GI tract and steadily raises from the terminal ileum to the colon (10² vs. 10¹² CFU/gram content) [53]. The most prevalent fungus genera that cohabit with bacteria in the GIT include Galactomyces, Bullera, Rhodotorula, Trametes, Pleospora, Sclerotinia, Candida, and Aspergillus, whilst bacteriophages make up the majority of the virome community [54,55,56,57]. Several parts of the intestine have various communities, beginning in the duodenum with aerobic Lactobacillus and Streptococcus spp. and ending towards the colon with strong anaerobic organisms like Bifidobacterium, Bacteroides, and clostridial clusters [57]. This diversity may be explained by variations in available nutrients, O₂ concentration, pH, as well as other factors at various regions of the GIT. It is well known that the gut bacteriome greatly differs from person to person. Furthermore, it has been demonstrated that the same person’s gut microorganisms undergo continual temporal fluctuation due to infection, alteration in immunological status, or any other environmental changes [58,59]. Nonetheless, the gut microbiota accommodates these transient alterations and reverts to its initial form after the gut’s physiological and physical situations have cleared up. This is referred to as the gut microbial ecosystem’s resilience [59].

According to reports, the gut microbiome of healthy people engages in a symbiotic association and participates in critical biological processes like breakdown and absorption of nutrients, construction of the GIT’s immune system, as well as protection versus harmful organisms [60]. It participates in the breakdown of undigestible food debris including complex carbs, bile acids, plant glycans, and choline [61]. Therefore, by the degradation of polysaccharides, the gut bacteriome can manufacture 90% of the advantageous short-chain fatty acids (SCFAs), such as acetate, butyrate, and propionate, which are considered vital sources of energy for the intestinal epithelium cell and promote cell growth [62,63,64]. Moreover, earlier research has demonstrated that the gut microbiome has a vital role in lipid metabolism by promoting lipoprotein lipase activity and can breakdown the protein into amino acids, through its peptidases and proteases, and then transport these into the inside through amino acid transporters at the cell wall where they can be processed into signaling molecules, bacteriocins, or formed into microbial proteins [65]. Additionally, the gut microbiome is responsible for the de novo synthesis of vital vitamins such as vitamin K and some vitamin B [66].

3.1. Production of Beneficial Short-Chain Fatty Acids (SCFAs)

The digestion and breakdown of complex carbohydrates produces SCFAs such as acetate, butyrate, and propionate. This digestion process is achieved in the colon by anaerobic microbiomes like Firmicutes and Bacteroidetes with the aid of other bacterial species, Bifidobacterium, employed in oligosaccharide fermentation [67,68]. SCFAs are considered energy suppliers, as they are the major energy supply to colonocytes and supply humans with 10% of the total energy supply [69]. Acetate serves as a substrate for lipogenesis and gluconeogenesis, whereas butyrate and propionate can control immunological and intestinal physiology [70]. SCFAs suppress the proliferation of gram-negative facultative anaerobic Enterobacteriaceae like E. coli and Salmonella spp. [71]. The colon’s predominance of obligatory anaerobes (Firmicutes and Bacteroidetes) is directly related to a strict anaerobic environment. This anaerobic condition is established through the hypoxic condition of colonocytes (1% of O₂ vs. 3 to 10% in other tissues) that is generated by their own oxygen consumption, which is mediated via mitochondrial β-oxidation of butyrate from bacteria to carbon dioxide [72,73] (Figure 4).

SCFAs, notably butyrate, exert potent anti-inflammatory actions by regulating the synthesis of inflammatory mediators in gut epithelial cells [74]. These effects are conducted through the suppression of histone deacetylase (HDAC) activity. It is noted that butyrate promotes a hyperacetylation of both histone and nonhistone proteins by suppressing HDAC activity [75,76]. Histone hyperacetylation results in a highly relaxed chromatin architecture, which makes it easier for transcription factors to engage the promoter regions of particular genes [77]. Furthermore, butyrate alters gene expression and prevents the activation of some transcription factors, such as NF-κB [78]. Moreover, it is investigated that butyrate participates in the formation of tight junctions and intestinal integrity and promotes the release of mucin [79].

On the other hand, some studies have shown that SCFAs could negatively affect the gut barrier, particularly in the presence of inflammatory stimuli, and may even be detrimental in such conditions [80,81]. Further studies are urgently required to clarify this confusion.

3.2. Metabolism of Bile Acids

One important mechanism for maintaining GIT homeostasis is the breakdown of bile acids by the gut microbiome. Primary bile acids (PBAs) produced by the liver, for instance cholic acid and chenodeoxycholic acid (CDCA), facilitate lipid processing and absorption in the small intestine due to their amphipathic characteristics. PBAs are initially conjugated with taurine or glycine to improve their water solubility. Gut microbiomes participate in the conversion of PBA to secondary bile acid (SBA) through two important steps, bile acid deconjugation followed by 7α-dehydroxylation to metabolize conjugated PBAs [82,83,84]. The first step is the deconjugation step which is mediated by bile salt hydrolases that are present in both gram-positive and gram-negative gut bacteria, such as Clostridium, Bifidobacterium, Bacteroides, Lactobacillus, and Enterococcus species. A total of 5% of deconjugated PBAs enter the colon and act as a substrate for the second step [85]. The second stage involves 7α-dehydroxylation in the distal ilium and colon, where deconjugated PBAs are transformed into SBAs like lithocholic acid, deoxycholic acid, and ursodeoxycholic acid [82,83].

Current research indicates that SBAs generated by the microbiome are crucial for T cell development. According to one study, SBAs regulate the number of ROR-expressing Tregs, and the removal of the microbial bile acid metabolic pathways reduced the number of these Tregs [86]. In a different investigation, two bile acid derivatives with distinct functions were identified: 3-oxo-LCA, which inhibits the growth of Th17 cells, and isoalloLCA, which promotes the growth of Tregs. [87]. Another study of UC patients with ileal pouches similarly found lower levels of lithocholic and deoxycholic acids, as well as fewer microbial bile acid-converting genes. Also, this study found that there is an association present between SBA deficiency and a reduced number of Ruminococcaceae in UC patients [83]. These results imply that microbial metabolites play a significant part in regulating the homeostasis of the immune system.

3.3. Metabolism of Tryptophan

Tryptophan is crucial for maintaining the balance between intestinal immune tolerance and the health of the gut microbiome. The gut microbiome can transform tryptophan into beneficial indole-containing compounds such as indole, indolic acid, skatole, and tryptamine [88]. Indole derivatives activate the aryl hydrocarbon receptor (AhR) and enhance immune homeostasis mechanisms in the host. AhR activation stimulates IL-22 secretion from CD4⁺ and intestinal innate lymphoid organs. IL-22 modifies the microbial structure and can provoke the release of antimicrobial peptides. Additionally, innate lymphoid cells and intraepithelial lymphocyte production are mediated by AhR signaling, which also has anti-inflammatory effects. Moreover, the mucus-using bacterium, Peptostreptococcus, produces an indole derivative, indole acrylic acid, which promotes gene expression of mucin. This suggests that a tryptophan derivative generated by the gut microbiome improves the formation of mucus while lowering the release of inflammatory cytokines [89].

3.4. Sphingolipids Production

Sphingolipids, a group of organic compounds generated by the host and microorganisms, frequently vary between individuals with IBD and those without IBD [90]. The pathogenesis of IBD has been linked to host-derived sphingolipids, which are significant signaling molecules that control immunity and inflammation [91]. Yet, the gut microbiome can also create sphingolipids, which can control host immunological reactions. Sphingolipids made by Bacteroides, for instance, prevent chemically induced colitis and suppress the growth of invariant NKTs [92]. It was demonstrated that IBD patients had lower production of sphingolipids obtained from the microbiome, which might be balanced off by higher synthesis of sphingolipids derived from the host [90].

3.5. Balancing Immune and Inflammatory Reactions

The development and maturity of the immune system are influenced by the gut microbiome. In comparison with normal mice, germ-free mice displayed abnormal lymphoid tissues in the gut, fewer mesenteric lymph nodes, Peyer’s patches, intraepithelial lymphocytes and CD4⁺ T cell, cellular lamina propria, as well as decreased expression of TLRs and class II MHC molecules [93]. Tregs protect against autoimmune illness and maintain tolerance to self-antigens. Normally, these cells inhibit effector T cell growth and activation [94]. Prior research has shown that Clostridium can strongly stimulate Tregs by producing butyrate. As a result, the homeostasis of the mucosa may be disturbed if the proportion population of butyrate-producing bacteria diminishes [94,95,96,97,98] (Figure 5).

4. Dysbiosis in IBD

4.1. Gut Bacteriome Dysbiosis

Individual health status is determined by the interaction of the microbiome, gut epithelium, and gut immune system; any disruption in this relationship may lead to chronic intestinal inflammatory diseases like IBD. Numerous studies on IBD patients have shown changes in the composition and activity of the gut microbiome, along with alterations in the metabolite levels and the pathways that are linked to them, which have served as support for this hypothesis [99,100]. According to metabolomics research, some types of metabolites, including bile acids, SCFAs, and tryptophan, have been linked to the pathophysiology of IBD [101]. Animal models of colitis were initially used to establish the link between IBD and microbiome dysbiosis. Colitis does not occur in germ-free IL 10-/- mice until enteric bacteria have colonized them [102]. Earlier research utilizing fecal samples demonstrated dysbiosis in IBD, which is characterized by an elevation in Enterobacteriaceae, Bifidobacteriaceae, Fusobacteria, and Pasteurellaceae and a decrease in the phylum Firmicutes (including Faecalibacterium, Roseburia, and Ruminococcus) [64,103,104,105]. Clinical findings indicate that IBD patients had decreased overall diversity, an available microbiome that possesses anti-inflammatory properties, such as Bacteroides, Suterella, Feacalibacterium prausnitzii, Roseburia, Bifidobacterium spp., and Clostridium groups IV and XIVa, and an increase in abundance of bathogenic organisms, such as Veillonellaceae, adherent invasive E. coli (AIEC), as well as Pasteurellaceae [64,106,107]. In comparison to healthy persons, UC patients exhibit decreased diversity of species at all stages of the disease [108]. UC patients also demonstrated an elevation in E. coli and a decrease in F. prausnitzii, which is similar to CD patients [109]. It is reported that bacteriome alteration and dysbiosis are more predominant in CD compared to UC [103,110]. It is still unknown how precisely dysbiosis and inflammation relate to one another in IBD, whether inflammation results from dysbiosis or vice versa [111]. According to certain experimental studies, dysbiosis may contribute to IBD. For instance, mice exposed to the feces of colitis-affected mice exhibit more aggressive colitis than control mice [64].

The anaerobic environment in the colon is disrupted in the case of mucosal abnormalities that are associated with bleeding and increased permeability, which results in a decrease in anti-inflammatory activity due to the reduction in the prevalence of butyrate-producing obligate anaerobes. Reduced quantities of butyrate-producing bacteria cause surface colonocytes to switch to anaerobic glycolysis and boost oxygen diffusion into the lumen, which in turn causes the expansion of luminal aerobes and facultative anaerobes through aerobic respiration [73] (Figure 4). It has been shown that F. prausnitzii abundance is significantly decreased in CD and UC biopsies. Furthermore, there is a link between a low percentage of F. prausnitzii and a higher risk of IBD recurrence [112], and its restoration is related to maintaining clinical improvement of UC [113]. Therefore, a complex interplay between a reduction in butyrate-producing bacteria, a rise in epithelial oxygenation, O₂ transfer into the lumen, and the growth of facultative aerobic bacteria such as Proteobacteria may be responsible for the bacteriome dysbiosis observed in IBD. The gut microbiome can induce the proliferation of effector T cell and inflammatory cytokines in the inflamed intestine. This could be attributed to increased adhesive properties of intestinal cells as the protective mucus layer thins. Increased adhesive properties of intestinal cells induce Th17 cells in the mucosa and inflammatory cascade [95,114] (Figure 5).

Moreover, studies have shown that proinflammatory sulfur-reducing bacteria, which turn sulfur and sulfur-containing substances into hydrogen sulfide (H₂S), are more prevalent in IBD patients than in healthy people [115,116]. High levels of H₂S decrease the oxidation of essential SCFAs like acetate, L-glutamine, and n-butyrate which reduce the cell’s bioenergetic efficiency and prevent colonocytes from using butyrate [117,118,119]. Ohkusa et al. found that Fusobacterium varium, isolated from UC patients, may kill Vero cells and cause UC-like lesions in mice when administered rectally via an enema. They proved that this toxic effect is due to the production of butyric acid by F. varium [120]. This suggests that certain metabolites produced in dysbiosis can encourage the initiation and development of IBD.

4.2. Gut Virome Dysbiosis

The gut virome is a significant element of the gut microbiome and is made up of viruses that infect both prokaryotes and eukaryotes [121,122]. The majority of the enteric virus is composed of bacteriophages [123]. Bacteriophages affect gut homeostasis and pathologic states by interacting with the gut bacteriome [124,125]. Phages multiply and propagate within the bacterial-infected cells before being liberated through cell bursts (the lytic cycle). The lytic cycle modifies bacterial strain ratios and has a substantial impact on the gut bacteriome. However, some phages actively integrate their genetic element into the infected cells’ genomes, transmitting this information to the next generation of host cells (lysogenic cycle) [126,127]. Numerous phages are conserved as prophages within the bacterial genome and are present in the gut in a lysogenic or latent state [124]. This process could change bacterial activities like antibiotic resistance and toxin production, or it could change the immunogenicity of bacteria, which would affect interactions between bacteria and hosts [125,126]. Generally, a change in the gut virome implies bacteriome dysbiosis in IBD patients [123]. Pérez-Brocal et al. proved that IBD patients had a higher proportion of bacteriophages infecting Clostridium acetobutylicum, Clostridiales, Alteromonadales, and the Retroviridae family when compared to healthy people [128]. It is well established that patients with IBD have significantly higher levels of the Caudovirales phage families such as Myoviridae, Siphoviridae, and Podoviridae [125,129]. In another study, Zuo et al. found an increase in the abundance of Caudovirales bacteriophages, elevation in phage/bacteria pathogenicity, as well as loss in viral–bacterial associations in the mucosa of UC patients [130]. Moreover, UC patients were shown to have a high prevalence of phages that infect Enterobacteria and Escherichia [130]. Gogokhia et al. conducted a germ-free mice study and stated that several phages, including those infecting Bacteroides, Escherichia, and Lactobacillus, as well as phage DNA, showed to aggravate inflammation of the GIT and participate in the progression of IBD by elevating the release of IFNγ through a TLR9-dependent pathway [131].

Furthermore, because phages can invade and integrate into eukaryotic (human) cells, they play a crucial role in the onset of IBD. Phage integration into the human genome can modify the integrity of intestinal cells [132,133]. Not only do bacteriophages have the risk of developing IBD but also other viruses can infect the human GIT. For instance, there is evidence that a norovirus infection raises the danger of colitis progression by inducing intestinal inflammation [134,135]. Another study showed that patients with CD and UC had high levels of Hepeviridae and Hepadnaviridae, respectively, in their intestinal mucosa [136].

Despite all these investigations, it remains unclear exactly what role virome dysbiosis plays in IBD. It will be hoped to fully understand the relationship between virome and IBD development by discovering and screening viruses that infect IBD patients at the earliest stages of intestinal inflammation.

4.3. Gut Mycobiome Dysbiosis

The gut mycobiome has a significant role in the pathogenesis of IBD. The mycobiome may affect the composition of the gut microbiome or boost the production of pro-inflammatory cytokines [137]. Mycobiome dysbiosis is another issue with IBD [55]. According to reports, CD patients have greater levels of fungal variety compared to healthy controls [138]. One distinguishing aspect of the fungal composition in IBD is a high Basidiomycota/Ascomycota ratio [139]. Additionally, IBD patients have lower levels of Saccharomyces cerevisiae than healthy controls [140]. In a mouse model of colitis, Chiaro et al. demonstrated that the presence of S. cerevisiae increases gut barrier permeability and worsens intestinal illness [141]. On the other hand, Tiago et al. found that S. cerevisiae UFMG A-905 exhibited protective effects in the mouse model of acute UC [142]. In another study, S. cerevisiae CNCM I-3856 was confirmed to reduce AIEC-induced colitis by preventing its adherence to enterocytes and reestablishing barrier integrity [143].

Patients with CD and IBD have noticeably higher levels of Candida spp. [144,145,146]. Moreover, IBD patients have significantly higher levels of C. albicans [140,144,146,147]. Specific-pathogen-free Clec7a-/- mice have been shown to develop more severe colitis after being infected with C. tropicalis than uninfected Clec7a-/- mice or infected mice of the wild type [148,149]. Standaert-Vitse et al. reported that patients with familial CD showed greater C. albicans colonization [150]. Besides this, several investigations indicated that CD patients had elevated amounts of C. glabrata as well as C. albicans [151].

In addition to Candida spp., CD patients also have much more Malassezia restricta, a normal skin fungus, that exacerbates colitis in animal models through pathways that involve CARD9, a signaling protein involved in antifungal immunity [152].

In IBD patients, the interaction of fungus and bacteria may be of critical importance. A prior study revealed a positive association between Serratia marcescens, E. coli, and C. tropicalis [153]. Significantly, the relationship between the severity of IBD in patients and mycobiome-bacterial dysbiosis may point to the effect of the gut mycobiome in IBD.

5. Therapeutic Approaches for IBD That Address the Gut Microbiome

Many clinical trials have already been undertaken on the use of antibiotics for IBD [154,155]. Antibiotics are frequently recommended to lower the number of IBD-related bacteria in the host’s gut since current theories on the pathophysiology of IBD mainly involve intestinal microflora. Yet, receiving antibiotics might also have unfavorable effects [156]. Moreover, the effects of antibiotic therapy are not always reliable. Research has demonstrated how antibiotics have a negative effect on the microbial communities in the gut. Continual use of antibiotics at higher doses affects the activity of the gut microbiome [157]. Growing research on the impact of microbiomes in treating IBD suggests that it may be possible to control the ecosystem and stop the inflammatory process [158]. Fast development in metagenomics and molecular investigations has not only helped to understand the pathophysiology of IBD but has also aided in the investigation of potential treatments for IBD by changing the gut microbiome [159]. Probiotics, prebiotics, and their synbiotic methods, as well as fecal microbiota transplantation (FMT), are new emerging treatments for IBD that affect the gut microbiome, slow the disease’s progression, and enhance intestinal health. [160,161] (Figure 6).

5.1. Probiotics

Probiotics are live bacteria that promote health when taken in sufficient doses. They have a beneficial effect on the gut because they regulate immune responses, boost the level of mucosal IgA, and outcompete pathogenic bacteria [162,163]. According to prior research, providing particular probiotic strains (such as Lactobacillus and Bifidobacterium) is an effective strategy for controlling IBD [164,165,166]. Probiotics may slow the evolution of IBD in a variety of different ways, through affecting the composition and operation of the gut microbiota, interacting with enterocytes, and regulating immune processes (such as stimulating IgA and β-defensins synthesis), non-immune functions (such as mucus thickness and gut permeability), as well as regulating cytokine response by B and T cell. [167,168]. Probiotics can alter the architecture of the microbiome through boosting the development of beneficial forms while suppressing the growth of harmful species. Nevertheless, only clinical research in adults and children is suggested for their usage in the management of IBD [169]. Live probiotics need to be able to enter the gut and contribute to the preservation of homeostasis. The prominent modes of action depend on the strain but generally involve the production of antimicrobial substances including bacteriocins, lactic acid, and hydroperoxides, overexpressing tight junction proteins in the intestinal barrier, blocking binding sites on intestinal cells, destroying toxin receptors, competing for essential nutrients, and adjusting favorable pH [170,171,172] (Figure 7).

Many investigations have been carried out to determine the value of probiotics in IBD patients for inducing or maintaining remission. Garcia Vilela et al. proved that Saccharomyces boulardii therapy improved bowel healing and remission maintenance in CD patients [173]. It has been shown that the strains of Lactobacillus acidophilus, Bifidobacterium breve, Bifidobacterium bifidum, and E. coli Nissle1917 have a promising effect on keeping UC patients in the remission stage [174,175]. Tamaki and colleagues demonstrated that the use of Bifidobacterium longum 536 in the management of mild-to-moderate UC patients produced a clinical remission as well as a significant decrease in the disease activity index and rectal bleeding. [163]. Moreover, Hegazy et al. found that, when Lactobacillus fermentum was given to UC patients, NF-κB regulation was lowered, and the levels of IL-6 and TNF-alpha were also reduced [176]. Palumbo et al. discovered that probiotic therapy appears to be more successful than probiotics alone, especially when combined with anti-inflammatory drugs. In their study, they demonstrated the effect of co-administration of mesalazine with a probiotic mixture (Lactobacillus acidophilus, Lactobacillus salivarius, and Bifidobacterium bifidum strain BGN4) in UC patients and found that patients administered combinatorial therapy had a quicker recovery period, less disease activity, and an improved endoscopic image [177]. VSL#3 is the most prevalent probiotic cocktail with established effectiveness. There are around 900 billion lyophilized bacteria in this mixture, including one strain of Streptococcus thermophilus, three strains of Bifidobacterium (B. infantis, B. longum, and B. breve), as well as four strains of Lactobacillus (L. plantarum, L. paracasei, L. delbrueckii subspecies bulgaricus, and L. acidophilus). The efficacy of VSL#3 was studied and proved in both animal models and UC patients. In a clinical trial, Sood et al. proved that UC patients administering VSL#3 experienced a marked reduction in rectal bleeding, frequency of stools, look of mucosa, and overall physician assessment [178]. On the other hand, Wang et al. studied the effect of VSL#3 combined with 5-aminosalicylic acid on a DDS-induced colitis animal model. They demonstrated that the treated animal model experienced a marked reduction in TNF-α and IL-6, boosting the prevalence of Bifidobacterium and other non-pathogenic bacteria in the gut mucosa and decreasing the number of pathogenic types [179]. Moreover, Fedorak et al. reported the earlier study on utilizing VSL#3 to avoid the relapse of endoscopic CD. These results demonstrated that long-term VSL#3 use is strongly associated with positive and useful effects for reducing IBD [180]. In a most recent study, Min et al. studied the effect of VSL#3 on leaky epithelium, and demonstrated that VSL#3 can boost bacterial cell colonization on the mucosal surface and greatly improve barrier integrity, tight junction protein localization, and mucus production [181]. Additionally, VSL#3 possesses an anti-inflammatory effect and reduces the production of proinflammatory cytokines [181].

It should be emphasized that various bacterial strains may operate and interact with the host in different ways. Probiotics can have an impact on many IBD symptoms, according to a prior study. IBD is a multi-factor illness; thus, it is important to note that it would appear to be impossible to identify a particular strain that would be favorable for all individuals. Both the dosage and strain of probiotics have a significant impact on the anti-inflammatory effect. It is apparent that there is no one, all-purpose treatment that will be good for all inflammatory illnesses, so it is necessary to perform more investigation to discover the best probiotic-based therapy. Obviously, this situation calls for tailored medication. It is critical to consider the type of the inflammatory reactions, the seriousness of the disease, the composition of the microbiome, as well as environmental and genetic factors. These factors contribute to the varying information on the effectiveness of the live strains among patients.

5.2. Prebiotics

Prebiotics are non-digestible dietary components that specifically promote the bacterial species’ development and activity in the gut so that they can improve host health [182]. “Prebiotics” have been identified by the International Scientific Association of Probiotics and Prebiotics (ISAPP) as a substrate which selectively fermented by the microbiome and provided health advantages to the host. [183,184]. The most popular prebiotics recognized for their positive effects are lactulose, inulin, glucooligosaccharides (GOSs), fructooligosaccharides (FOSs), other oligosaccharides such as arabinose and pectin, and variants of galactose and β-glucans [183,185]. Prebiotics enter the colon where they are fermented by the microbiome since endogenous enzymes in the human GIT system are not capable of their digestion [184,186]. Prebiotics found naturally in fruits and vegetables include wheat, garlic, onion, honey, bananas, tomatoes, chicory, soybeans, sugar beet, peas, beans, human and cow milk, and more recently, seaweeds and microalgae. Yet, prebiotics were frequently present in small amounts in natural sources and food [187]. Prebiotics can also be produced at a huge industrial scale from basic materials like lactose, sugar, or starch [188,189,190]. Prebiotics bind to water as they go through the intestine’s lumen, increasing the bulk of the intestinal contents. So, they form an ideal environment for bacteria to breed because of their loose structure and large surface area. Simultaneously, they prevent the formation of pathogens, hasten the regeneration and repair of the gut wall, boost mucus synthesis, keep the intestine’s pH at the ideal level to prevent the growth of harmful bacteria, boost calcium, iron, and magnesium absorption, lower blood cholesterol thresholds, and have a positive impact on the liver’s ability to metabolize carbohydrates and proteins [62,186,191,192]. Furthermore, prebiotic fermentation by specific gut bacteria produces beneficial SCFAs like acetate, lactate, propionate, and butyrate. So many systemic and colon-specific mechanisms are involved in creating these SCFAs [193]. Acetate is frequently used as a cellular energy source for the intestines and muscles. Propionate is involved in cholesterol synthesis. Particular focus is given to butyrate, as mentioned above, which helps the host in a variety of ways, including by enhancing metabolism, boosting anti-inflammatory effects, and modifying the immune system [104]. Thus, it has been demonstrated that consuming prebiotics strengthens intestinal integrity, lowers infection rates, modulates allergic reactions, and improves digestion in the host. Yet, the use of prebiotics does not immediately cause these benefits. According to recent research, prebiotic benefits are obtained indirectly since the composition of the microbiomes is changed by prebiotic fermentations [182,183].

Several studies and clinical trials were established to emphasize the effect of prebiotics on IBD patients. It has been suggested that prebiotics such as gums, inulin, pectin, resistant starch, as well as FOS are helpful in the management of IBD patients by increasing intestinal barrier functioning and defending against pathogen invasion and translocation [194]. Yet, the majority of human clinical trials have documented the use of FOS as a prebiotic for the treatment of IBD [195,196,197]. The fermentation of FOS by the gut microbiome enhances the production of SCFAs, organic acids, and butyrate, which are necessary to enhance gut immunomodulation [104,198]. Azpiroz et al. proved in their study that FOS significantly increases fecal Bifidobacterium [199]. Kanauchi et al. conducted a clinical investigation in UC patients using germinated barley foodstuff (GBF). They showed that treating UC patients with GBF significantly reduced the clinical presentation of the disease, especially nocturnal diarrhea, and blood in the stools. [200]. In a different trial, Casellas et al. evaluated the effectiveness of giving patients with mild-to-moderate acute UC supplements of inulin enhanced with FOS. A substantial drop in stool calprotectin was seen in the treatment group after 7 days of treatment [201]. Fernandez-Benares et al. evaluated the impact of Plantago ovata seeds on inactive UC patients and demonstrated that the levels of butyrate in the stool significantly increased [202]. Moreover, according to Xie et al., in the rat model, Ganoderma lucidum polysaccharide (GLP) significantly reduced the disease activity index, increased SCFA synthesis through enhancement of SCFA-producing bacteria like Ruminococcus, and decreased pathogenic bacteria like Escherichia and Shigella spp. [203].

5.3. Synbiotics

Synbiotics refer to preparations containing both prebiotics and probiotics. According to Darb Emamie et al., these preparations are referred to as “synbiotics”, which refers to the synergistic circumstances in which the probiotics metabolize the combined prebiotics to modulate dysbiosis in the gut microbiome and host wellness. Probiotics and prebiotics work together to promote the development of particular microorganisms or to activate certain processes by the gut microbiome [182,204]. Until now, there have only been a few documented investigations supporting the utilization of synbiotics in IBD. The most popular and widely utilized synbiotic combinations are Lactobacillus GG and inulin, Bifidobacteria and FOS, and Bifidobacteria and lactobacilli with either FOS or inulin [205]. In a randomized control experiment, a combination of Bifidobacterium longum psyllium and B. longum inulin-oligofructose was added to standard treatment for UC patients. When compared to using a probiotic or prebiotic alone, their combination had a positive synergistic effect and raised the clinical activity index of the disease [206]. Furthermore, it is reported that patients with UC receiving inulin-oligofructose and B. longum in combination showed a substantial decrease in levels of IL-1β and TNF-α in addition to a decrease in mucosal inflammation [207]. In a different investigation, a considerable anti-inflammatory impact was seen in mild-to-moderate UC patients when the B. breve Yakult strain and galacto-oligosaccharides were combined [208].

Even though synbiotics offer greater health advantages than prebiotics or probiotics separately, researchers have had difficulty making a definitive finding because of the benefits’ variability, which may be influenced by the sorts as well as dosages of probiotics and prebiotics included in various combinations. Nonetheless, synbiotic research is a new area of study that aims to understand their impact on the pathologic mechanisms of gut inflammation and develop a viable treatment for IBD and other gut-related illnesses [209]. Therefore, more research on humans and animals is needed to gather conclusive data and gain a better understanding of their immediate effects on health, particularly in IBD patients.

5.4. Fecal Microbiota Transplantation (FMT)

FMT is a new approach for treating patients with dysbiosis that involves restoring the normal balance of the patients’ aberrant gut microbiome by the transplanting of normal fecal microbiota from healthy individuals [210,211,212] (Figure 8). FMT’s different approaches include oral capsules, enemas, nasogastric or nasojejunal tubes, and other methods for restoring healthy gut flora [213]. According to reports, this approach showed promising results for treating recurrent C. difficile infections (CDIs) [214]. The key factors of the successful management of IBD patients employing FMT include early intervention, the content of the stool of healthy donors, and the use of several FMTs [215]. It is believed that FMT plays an important role in restoring gut microbiome balance in IBD patients and, so, prevents the proliferation and growth of pathogenic microorganisms like C. difficile [216]. This is accomplished by competition between pathogens and the restored microbiota for resources and colonization, by the regained microbiota producing antimicrobials that significantly affect pathogens, and by a bile acid-mediated process that inhibits vegetative development and spore germination [214]. It is essential to keep in mind that the viral as well as fungal content in donors’ feces may have an impact on how well IBD patients respond to FMT [217]. According to reports, utilizing C. albicans-rich feces greatly reduces the effectiveness of the therapy [217]. Sokol et al. conducted their trial to determine how FMT affects CD patients. They observed that certain patients’ donor and recipient microbiotas had a low similarity index, indicating that a single FMT would not be sufficient to cause these patients to experience substantial improvements [218]. In mild-to-severe UC patients, Costello et al. demonstrated that an 8-week therapy period with anaerobically processed fecal material increased the likelihood of remission [219]. Furthermore, Sood et al. observed a statistically significant effect on endoscopic and histological remission upon FMT on UC patients in clinical remission [220]. Furthermore, Li et al. investigated the optimal FMT scheduling for retaining the long-term therapeutic advantages in UC patients [221]. They provided proof that UC patients had to complete the second FMT course no later than four months following the completion of the first. They also demonstrated how the abundance of Lactobacillus, Ruminococcus, Eubacterium, and Eggerthella may serve as markers of the long-term effectiveness of FMT in UC patients [221]. Similar to this, the species Ruminococcus bromii, Roseburia inulivorans, and Eubacterium hallii were suggested to estimate the effectiveness of FMT treatment in UC patients [222]. On the other hand, FMT has a lot of drawbacks. Initially, the results will depend on the sample because various samples reflect diverse bacterial populations, which means varying effectiveness [223]. Additionally, the donated stool sample may contain unacceptable strains or features that pose a danger to patient safety, such as pathogenic strains of enteropathogenic E. coli, virulence factors, and transferrable antibiotic resistance elements [223]. A newly developed FMT method called washed microbiota transplantation (WMT) offers a particular amount of enriched microbiota and may eliminate certain toxic components of the donor’s feces, and it has shown promising results in the treatment of IBD [224]. For instance, recent research revealed that WMT effectively treated a recurrent invasive fungal infection in UC patients. Moreover, WMT may emphasize the significance of a particular gut microbiota component in IBD as a novel technique that might regulate the fecal microbiota transplanted into the patient’s digestive tract [225].

6. Conclusions and Future Perspectives

According to what has been said above, the gut microbiome has several beneficial functions for human wellness, and any long-term alteration of this community will possibly cause illness. IBD patients often have fewer Bacteroidetes and Firmicutes alongside more Proteobacteria and Actinobacteria. These alterations in the microbiome disrupt their activities, which are characterized by decreased formation of SCFAs, decreased bile acid hydrolysis, increased generation of H₂S, and increased redox potential. The host is thought to be adversely impacted by the interplay between the two sides of dysfunctionality, dysbiosis, and inflammation, which may also affect how chronic the illness becomes. There is currently a lack of understanding regarding the cause-and-effect link between this dysbiosis and inflammation. Consequently, new methods that influence gut microbiota are being developed to minimize inflammatory response in GIT and enhance the outcome. Among these are live biotherapeutics like probiotics and FMT, substances that boost the microbial communities in the gut like prebiotics or a combination of them like synbiotics.

Many barriers still lie in the way of the creation of successful microbiome-based therapeutics, despite recent improvements in our knowledge of the function of the microbiome in IBD. Firstly, scientists must investigate if microbial engraftment is required for long-term benefit and, if so, which bacteria are most appropriate for this use. Given the dramatic interindividual variations in the gut microbiome, microbiome-based therapies will probably need a highly individualized approach. Moreover, prospective studies are required to establish a real cause-and-effect relationship between the gut microbiome and IBD to pinpoint the precise causal bacterial species or key microbiome and clarify the destiny of the gut microbiome in IBD. Such research should involve colonizing wild-type, genetically altered, and germ-free mice with a particular bacterial species or a combination of bacteria.