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Enteric pathogen growth in pure culture and relative abundances in fecal communities grown on glycans. Six strains of a Klebsiella pneumoniae, b Escherichia coli, or c Enterococcus faecium were cultured with 5 g l −1 of a single SG (n = 148) or reference glycan (n = 32) in CM3 medium. Data is the mean maximum growth (OD 600 ) of triplicate cultures; strain names are shown above each plot. Fecal communities from a healthy donor were OD 600 -normalized to contain 8% of d K. pneumoniae CDC 003, e E. coli CDC 001, or f E. faecium ATCC 700221 and cultured in triplicate with 5 g l −1 of an SG (n = 45) or reference glycan (n = 17) for 45 h in MM29 medium. The relative abundances of the pathogens were quantified by 16S rRNA gene sequencing. Data points show FOS (indigo circle), BRF (yellow circle), or BQM (orange triangle) cultures. Box plots show median and interquartile ranges. Asterisks show significance (*p < 0.05, **p < 0.01) by two-sided Wilcoxon rank-sum test. Source data are provided as a Source Data file. SGs Synthetic Glycans, OD 600 optical density at 600 nm, FOS fructo-oligosaccharides.
Source publication
Relative abundances of bacterial species in the gut microbiome have been linked to many diseases. Species of gut bacteria are ecologically differentiated by their abilities to metabolize different glycans, making glycan delivery a powerful way to alter the microbiome to promote health. Here, we study the properties and therapeutic potential of chem...
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... fermentation can result in divergent changes to microbiome composition, even differentially promoting closely related species 8 . Therefore, we applied shotgun metagenomic sequencing to examine fecal cultures fermenting a compositionally diverse set of 190 SGs and 40 reference glycans (Supplementary Data 3). While there is heterogeneity in the level of microbiome diversity resulting from fermentation of different SGs, SG fermentation generally resulted in higher taxonomic diversity (Fig. 2c) and species richness (Fig. 2d) relative to reference glycans, as shown by BQM and BRF promoting higher diversity relative to reference glycans (Fig. 2e). ...
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... is in glycan cluster 2 (Fig. 2g, Supplementary Fig. 3b) with elevated levels of other Clostridiaceae and Parabacteroides, taxa associated with remission in Crohn's disease 33 . Clusters enriched in reference glycan fermentations contained elevated levels of Lactobacillaceae (cluster 5) and Bifidobacterium (clusters 6-8) (Fig. 2g, Supplementary Fig. 3e-h), which are adapted to metabolize simple oligosaccharides such as FOS 34 ...
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... and MDR clinical Enterobacteriaceae and Enterococcus strains (Supplementary Table 2) to grow on each of a compositionally diverse set of 148 SGs including BRF and BQM and 32 reference glycans including FOS (Supplementary Data 4) as a sole carbohydrate source in defined medium. Most strains of the model enteric pathogens Klebsiella pneumoniae (Fig. 3a), Escherichia coli (Fig. 3b), and Enterococcus faecium ( Fig. 3c) exhibited limited growth on SGs with final cell densities significantly lower than when grown on reference glycans including ...
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... and Enterococcus strains (Supplementary Table 2) to grow on each of a compositionally diverse set of 148 SGs including BRF and BQM and 32 reference glycans including FOS (Supplementary Data 4) as a sole carbohydrate source in defined medium. Most strains of the model enteric pathogens Klebsiella pneumoniae (Fig. 3a), Escherichia coli (Fig. 3b), and Enterococcus faecium ( Fig. 3c) exhibited limited growth on SGs with final cell densities significantly lower than when grown on reference glycans including ...
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... (Supplementary Table 2) to grow on each of a compositionally diverse set of 148 SGs including BRF and BQM and 32 reference glycans including FOS (Supplementary Data 4) as a sole carbohydrate source in defined medium. Most strains of the model enteric pathogens Klebsiella pneumoniae (Fig. 3a), Escherichia coli (Fig. 3b), and Enterococcus faecium ( Fig. 3c) exhibited limited growth on SGs with final cell densities significantly lower than when grown on reference glycans including ...
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... during glycan fermentation, we spiked a healthy donor fecal community with either CRE K. pneumoniae, CRE E. coli, or VRE E. faecium, cultured it in a medium containing each SG or reference glycan (Supplementary Data 5), and measured changes in relative abundances of the pathogen by 16S rRNA gene sequencing. The relative abundances of K. pneumonia (Fig. 3d), E. coli (Fig. 3e), and E. faecium (Fig. 3f) were significantly lower after growth on SGs including BRF and BQM than on reference glycans, consistent with the SGs favoring growth of commensal ...
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... we spiked a healthy donor fecal community with either CRE K. pneumoniae, CRE E. coli, or VRE E. faecium, cultured it in a medium containing each SG or reference glycan (Supplementary Data 5), and measured changes in relative abundances of the pathogen by 16S rRNA gene sequencing. The relative abundances of K. pneumonia (Fig. 3d), E. coli (Fig. 3e), and E. faecium (Fig. 3f) were significantly lower after growth on SGs including BRF and BQM than on reference glycans, consistent with the SGs favoring growth of commensal ...
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... donor fecal community with either CRE K. pneumoniae, CRE E. coli, or VRE E. faecium, cultured it in a medium containing each SG or reference glycan (Supplementary Data 5), and measured changes in relative abundances of the pathogen by 16S rRNA gene sequencing. The relative abundances of K. pneumonia (Fig. 3d), E. coli (Fig. 3e), and E. faecium (Fig. 3f) were significantly lower after growth on SGs including BRF and BQM than on reference glycans, consistent with the SGs favoring growth of commensal ...
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... Parabacteroides along with Clostridia such as Ruminiclostridium and multiple genera of Lachnospiraceae. There were also differences in taxa promoted by each SG. For example, Roseburia and Prevotella abundance were specifically elevated in the BRF treatment (Fig. 4a), similar to metagenomics of the BRF-containing glycan cluster 1 (Supplementary Fig. 3a). In contrast, lactulose treatment increased the relative abundance of Bifidobacterium and Lactobacillus, similar to the metagenomics of glycan cluster 5 that includes lactulose ( Supplementary Fig. 3e). show significance (*p < 0.05, **p < 0.01) by two-sided Wilcoxon rank-sum test. Source data are provided as a Source Data file. SGs ...
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... example, Roseburia and Prevotella abundance were specifically elevated in the BRF treatment (Fig. 4a), similar to metagenomics of the BRF-containing glycan cluster 1 (Supplementary Fig. 3a). In contrast, lactulose treatment increased the relative abundance of Bifidobacterium and Lactobacillus, similar to the metagenomics of glycan cluster 5 that includes lactulose ( Supplementary Fig. 3e). show significance (*p < 0.05, **p < 0.01) by two-sided Wilcoxon rank-sum test. ...
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... fermentation can result in divergent changes to microbiome composition, even differentially promoting closely related species 8 . Therefore, we applied shotgun metagenomic sequencing to examine fecal cultures fermenting a compositionally diverse set of 190 SGs and 40 reference glycans (Supplementary Data 3). While there is heterogeneity in the level of microbiome diversity resulting from fermentation of different SGs, SG fermentation generally resulted in higher taxonomic diversity (Fig. 2c) and species richness (Fig. 2d) relative to reference glycans, as shown by BQM and BRF promoting higher diversity relative to reference glycans (Fig. 2e). ...
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... is in glycan cluster 2 (Fig. 2g, Supplementary Fig. 3b) with elevated levels of other Clostridiaceae and Parabacteroides, taxa associated with remission in Crohn's disease 33 . Clusters enriched in reference glycan fermentations contained elevated levels of Lactobacillaceae (cluster 5) and Bifidobacterium (clusters 6-8) (Fig. 2g, Supplementary Fig. 3e-h), which are adapted to metabolize simple oligosaccharides such as FOS 34 ...
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... and MDR clinical Enterobacteriaceae and Enterococcus strains (Supplementary Table 2) to grow on each of a compositionally diverse set of 148 SGs including BRF and BQM and 32 reference glycans including FOS (Supplementary Data 4) as a sole carbohydrate source in defined medium. Most strains of the model enteric pathogens Klebsiella pneumoniae (Fig. 3a), Escherichia coli (Fig. 3b), and Enterococcus faecium ( Fig. 3c) exhibited limited growth on SGs with final cell densities significantly lower than when grown on reference glycans including ...
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... and Enterococcus strains (Supplementary Table 2) to grow on each of a compositionally diverse set of 148 SGs including BRF and BQM and 32 reference glycans including FOS (Supplementary Data 4) as a sole carbohydrate source in defined medium. Most strains of the model enteric pathogens Klebsiella pneumoniae (Fig. 3a), Escherichia coli (Fig. 3b), and Enterococcus faecium ( Fig. 3c) exhibited limited growth on SGs with final cell densities significantly lower than when grown on reference glycans including ...
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... (Supplementary Table 2) to grow on each of a compositionally diverse set of 148 SGs including BRF and BQM and 32 reference glycans including FOS (Supplementary Data 4) as a sole carbohydrate source in defined medium. Most strains of the model enteric pathogens Klebsiella pneumoniae (Fig. 3a), Escherichia coli (Fig. 3b), and Enterococcus faecium ( Fig. 3c) exhibited limited growth on SGs with final cell densities significantly lower than when grown on reference glycans including ...
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... during glycan fermentation, we spiked a healthy donor fecal community with either CRE K. pneumoniae, CRE E. coli, or VRE E. faecium, cultured it in a medium containing each SG or reference glycan (Supplementary Data 5), and measured changes in relative abundances of the pathogen by 16S rRNA gene sequencing. The relative abundances of K. pneumonia (Fig. 3d), E. coli (Fig. 3e), and E. faecium (Fig. 3f) were significantly lower after growth on SGs including BRF and BQM than on reference glycans, consistent with the SGs favoring growth of commensal ...
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... we spiked a healthy donor fecal community with either CRE K. pneumoniae, CRE E. coli, or VRE E. faecium, cultured it in a medium containing each SG or reference glycan (Supplementary Data 5), and measured changes in relative abundances of the pathogen by 16S rRNA gene sequencing. The relative abundances of K. pneumonia (Fig. 3d), E. coli (Fig. 3e), and E. faecium (Fig. 3f) were significantly lower after growth on SGs including BRF and BQM than on reference glycans, consistent with the SGs favoring growth of commensal ...
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... donor fecal community with either CRE K. pneumoniae, CRE E. coli, or VRE E. faecium, cultured it in a medium containing each SG or reference glycan (Supplementary Data 5), and measured changes in relative abundances of the pathogen by 16S rRNA gene sequencing. The relative abundances of K. pneumonia (Fig. 3d), E. coli (Fig. 3e), and E. faecium (Fig. 3f) were significantly lower after growth on SGs including BRF and BQM than on reference glycans, consistent with the SGs favoring growth of commensal ...
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... Parabacteroides along with Clostridia such as Ruminiclostridium and multiple genera of Lachnospiraceae. There were also differences in taxa promoted by each SG. For example, Roseburia and Prevotella abundance were specifically elevated in the BRF treatment (Fig. 4a), similar to metagenomics of the BRF-containing glycan cluster 1 (Supplementary Fig. 3a). In contrast, lactulose treatment increased the relative abundance of Bifidobacterium and Lactobacillus, similar to the metagenomics of glycan cluster 5 that includes lactulose ( Supplementary Fig. 3e). show significance (*p < 0.05, **p < 0.01) by two-sided Wilcoxon rank-sum test. Source data are provided as a Source Data file. SGs ...
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... example, Roseburia and Prevotella abundance were specifically elevated in the BRF treatment (Fig. 4a), similar to metagenomics of the BRF-containing glycan cluster 1 (Supplementary Fig. 3a). In contrast, lactulose treatment increased the relative abundance of Bifidobacterium and Lactobacillus, similar to the metagenomics of glycan cluster 5 that includes lactulose ( Supplementary Fig. 3e). show significance (*p < 0.05, **p < 0.01) by two-sided Wilcoxon rank-sum test. ...
Citations
... Wei, Xia, et al. 2022). A recent study demonstrated that in vitro fermentation of 653 synthetic glycans that varied in monosaccharide composition, chemical bond type, and degree of polymerization led to compound-specific changes in taxonomic and metabolite profiles (Tolonen et al. 2022). Therefore, the structure of dietary polysaccharides affects the bioactivity of the gut microbiota, thereby affecting human health. ...
Beta-glucan (BG), a polysaccharide comprised of interfacing glucose monomers joined via beta-glycosidic linkages, can be defined as a type of dietary fiber with high specificity based on its interaction with the gut microbiota. It can induce similar interindividual microbiota responses, thereby having beneficial effects on the human body. In this paper, we review the four main sources of BG (cereals, fungi, algae, and bacteria) and their differences in structure and content. The interaction of BG with gut microbiota and the resulting health effects have been highlighted, including immune enhancement, regulation of serum cholesterol and insulin levels, alleviation of obesity and improvement of cognitive disorders. Finally, the application of BG in food products and its beneficial effects on the gut microbiota of consumers were discussed. Although some of the mechanisms of action remain unclear, revealing the beneficial functions of BG from the perspective of gut microbiota can help provide theoretical support for the development of diets that target the regulation of microbiota.
... As an intricate ecosystem, the gut has a large and diverse microbial community known as the gut microbiota. 17,18 The human gut microbiota contains probiotics and pathogenic bacteria that coexist harmoniously in a healthy body. However, this balance can be disrupted by abnormal environmental factors and genetic variations. ...
Background
Inflammatory bowel disease (IBD) is a non-specific chronic inflammatory disease of the intestine. In addition to genetic susceptibility, environmental factors and dysregulated host immunity, the gut microbiota is implicated in the pathogenesis of Crohn's disease (CD) or ulcerative colitis (UC), the two primary types of IBD. The P2X4 receptor has been demonstrated to have a crucial role in preventing infection, inflammation, and organ damage. However, it remains unclear whether the P2X4 receptor affects IBD and the underlying mechanisms.
Methods
Colitis was induced in mice administrated with dextran sodium sulphate (DSS). 16S rDNA sequencing was used to analyze the gut microbiota in knockout and wild-type mice. Clinical and histopathological parameters were monitored throughout the disease progression.
Results
Gene Expression Omnibus analysis showed the downregulation of P2RX4 (P2rx4) expression in colonic tissues from patients or mice with IBD. However, its expression at the protein levels was upregulated on day 4 or 6 and then downregulated on day 7 in C57BL/6 mice treated with DSS. Gene ablation of P2rx4 aggravated DSS-induced colitis accompanying gut microbiota dysbiosis in mice. Moreover, P2X4 receptor-positive modulator ivermectin alleviated colitis and corrected dysregulated microbiota in wild-type C57BL/6 mice. Further antibiotic-treated gut microbiota depletion, cohousing experiment, and fecal microbiota transplantation proved that gut microbiota dysbiosis was associated with the aggravation of colitis in the mouse model initiated by P2rx4.
Conclusions
Our findings elaborate on an unrevealed etiopathophysiological mechanism by which microbiota dysbiosis induced by the P2X4 receptor influences the development of colitis, indicating that the P2X4 receptor represents a promising target for treating patients with CD and UC.
... Novel tools such as glycan utilization screens can identify groups of bacteria capable of digesting fiber components [108]. The use of synthetic fibers might provide the opportunity to more precisely shape the strains targeted and metabolites generated by non-digestible dietary components [109]. Finally, researchers rely on food records which are very limited as current nutritional databases do not have the capability to capture the broad classes of fiber accurately. ...
Evidence-based dietary guidance around dietary fiber in inflammatory bowel disease (IBD) has been limited owing to insufficient reproducibility in intervention trials. However, the pendulum has swung because of our increased understanding of the importance of fibers in maintaining a health-associated microbiome. Preliminary evidence suggests that dietary fiber can alter the gut microbiome, improve IBD symptoms, balance inflammation, and enhance health-related quality of life. Therefore, it is now more vital than ever to examine how fiber could be used as a therapeutic strategy to manage and prevent disease relapse. At present, there is limited knowledge about which fibers are optimal and in what form and quantity they should be consumed to benefit patients with IBD. Additionally, individual microbiomes play a strong role in determining the outcomes and necessitate a more personalized nutritional approach to implementing dietary changes, as dietary fiber may not be as benign as once thought in a dysbiotic microbiome. This review describes dietary fibers and their mechanism of action within the microbiome, details novel fiber sources, including resistant starches and polyphenols, and concludes with potential future directions in fiber research, including the move toward precision nutrition.
... Both bound and free glycans also originate from microbial flora, dietary sources, as well as normal metabolism of host glycoconjugates. Glyco-chemistry, encouraged by the diversity of the tumor glycome, has fueled research in identifying the immunological functions of these glycans in diseases such as cancers and autoimmune diseases [1][2][3][4] . Tumor cells have been found to incorporate non-human derived glycan modifications, such as N-glycolylneuraminic acid (NeuGc) onto glycoproteins 5 . ...
Type 1 diabetes (T1D) is an autoimmune disease, characterized by the presence of autoantibodies to protein and non-protein antigens. Here we report the identification of specific anti-carbohydrate antibodies (ACAs) that are associated with pathogenesis and progression to T1D. We compare circulatory levels of ACAs against 202 glycans in a cross-sectional cohort of T1D patients (n = 278) and healthy controls (n = 298), as well as in a longitudinal cohort (n = 112). We identify 11 clusters of ACAs associated with glycan function class. Clusters enriched for aminoglycosides, blood group A and B antigens, glycolipids, ganglio-series, and O-linked glycans are associated with progression to T1D. ACAs against gentamicin and its related structures, G418 and sisomicin, are also associated with islet autoimmunity. ACAs improve discrimination of T1D status of individuals over a model with only clinical variables and are potential biomarkers for T1D.
... In the future it will be relevant to use synthetic glycans spanning the chemical and structural diversity of dietary glycans that can be efficiently and consistently produced. Synthetic glycans enable a wide range of targeted changes to the microbiome and potentially open new avenues for the prevention and treatment of disease (83). HMO are other new interesting prebiotics to test in the context of IBD by their natural properties to support the immune system maturation, the cognitive function, the digestive health, and the development of gut microbiome (84). ...
Inflammatory bowel diseases (IBD), a heterogeneous group of inflammatory conditions that encompass both ulcerative colitis and Crohn's disease, represent a major public health concern. The etiology of IBD is not yet fully understood and no cure is available, with current treatments only showing long-term effectiveness in a minority of patients. A need to increase our knowledge on IBD pathophysiology is growing, in order to define preventive measures, to improve disease outcome, and to develop new effective and lasting treatments. IBD pathogenesis is sustained by aberrant immune responses, associated with alterations of the intestinal epithelial barrier (IEB), modifications of the enteric nervous system and changes in microbiota composition. Currently, most of the treatments target the inflammation and the immune system, but holistic approaches targeting lifestyle and diet improvements are emerging. As dysbiosis is involved in IBD pathogenesis, pre-, pro-, syn- and postbiotics are used/tested to reduce the inflammation or strengthen the IEB. The present review will resume these works, pointing out the stage of life, the duration and the environmental conditions that should go along with microbiota or microbiota-derived treatments.
Most diets and medications enhance host health via microbiota-dependent ways, but it is in the present situation of untargeted regulation. Non-targeted regulation may lead to the ineffectiveness of dietary supplements or drug treatment. Microbiota-directed food, aiming to improve diseases by targeting specific microbes without affecting other bacteria, have been proposed to deal with this problem. However, there is currently no universally applicable method to explore such foods or drugs. In this review, thirty studies on recent efforts in microbiota directed diets and medications are summarized from various databases. The methods used to find new foods and medications are primarily divided into four groups depending on the experimental models: in vivo and in vitro, as well as predictions based on bioinformatics. We also discuss their implementation, interpretation, and respective limitations, and describe the present situation. We further put forward a framework for microbiota-directed foods and medicine according to above methods and other microbiome manipulation, which will spur precision medicine.
Ulcerative colitis (UC) has emerged as a global healthcare issue due to high prevalence and unsatisfying therapeutic measures. 20(S)- Protopanaxadiol saponins (PDS) from Panax notoginseng with anti-inflammatory properties is a potential anti-colitis agent. Herein, we explored the effects and mechanisms of PDS administration on experimental murine UC. Dextran sulfate sodium-induced murine UC model was employed to investigate anti-colitis effects of PDS, and associated mechanisms were further verified in HMGB1-exposed THP-1 macrophages. Results indicated that PDS administration exerted ameliorative effects against experimental UC. Moreover, PDS administration remarkably downregulated mRNA expressions and productions of related pro-inflammatory mediators, and reversed elevated expressions of proteins related to NLRP3 inflammasome after colitis induction. Furthermore, administration with PDS also suppressed the expression and translocation of HMGB1, interrupting the downstream TLR4/NF-κB pathway. In vitro, ginsenoside CK and 20(S)-protopanaxadiol, the metabolites of PDS, exhibited greater potential in anti-inflammation, and intervened with the TLR4-binding domain of HMGB1 predictably. Expectedly, ginsenoside CK and 20(S)-protopanaxadiol administrations inhibited the activation of TLR4/NF-κB/NLRP3 inflammasome pathway in HMGB1-exposed THP-1 macrophages. Summarily, PDS administration attenuated inflammatory injury in experimental colitis by blocking the binding of HMGB1 to TLR4, majorly attributed to the antagonistic efficacies of ginsenoside CK and 20(S)-protopanaxadiol.
Experimental evidence supports the fact that changes in the bowel microflora due to environmental or dietary factors have been investigated as implicating factors in the etiopathogenesis of inflammatory bowel disease (IBD). The amassing knowledge that the inhabited microbiome regulates the gut physiology and immune functions in IBD, has led researchers to explore the effectiveness of prebiotics, probiotics, and synbiotics in treating IBD. This therapeutic approach focuses on restoring the dynamic balance between the microflora and host defense mechanisms in the intestinal mucosa to prevent the onset and persistence of intestinal inflammation. Numerous microbial strains and carbohydrate blends, along with their combinations have been examined in experimental colitis models and clinical trials, and the results indicated that it can be an attractive therapeutic strategy for the suppression of inflammation, remission induction, and relapse prevention in IBD with minimal side effects. Several mechanisms of action of probiotics (for e.g., Lactobacillus species, and Bifidobacterium species) have been reported such as suppression of pathogen growth by releasing certain antimicrobial mediators (lactic and hydrogen peroxide, acetic acid, and bacteriocins), immunomodulation and initiation of an immune response, enhancement of barrier activity, and suppression of human T-cell proliferation. Prebiotics such as lactulose, lactosucrose, oligofructose, and inulin have been found to induce the growth of certain types of host microflora, resulting in an enriched enteric function. These non-digestible food dietary components have been reported to exert anti-inflammatory effects by inhibiting the expression of tumor necrosis factor-α-related cytokines while augmenting interleukin-10 levels. Although pro-and prebiotics has established their efficacy in healthy subjects, a better understanding of the luminal ecosystem is required to determine which specific bacterial strain or combination of probiotics and prebiotics would prove to be the ideal treatment for IBD. Clinical trials, however, have given some conflicting results, requiring the necessity to cite the more profound clinical effect of these treatments on IBD remission and prevention. The purpose of this review article is to provide the most comprehensive and updated review on the utility of prebiotics, probiotics, and synbiotics in the management of active Crohn's disease and ulcerative colitis/pouchitis.
