Identification of an Intestinal Microbiota Signature Associated With Severity of Irritable Bowel Syndrome

Fecal luminal factors from patients with irritable bowel syndrome induce distinct gene expression of colonoids

BACKGROUND

Alteration of the host-microbiota cross talk at the intestinal barrier may participate in the pathophysiology of irritable bowel syndrome (IBS). Therefore, we aimed to determine effects of fecal luminal factors from IBS patients on the colonic epithelium using colonoids.

METHODS

Colon-derived organoid monolayers, colonoids, generated from a healthy subject, underwent stimulation with fecal supernatants from healthy subjects and IBS patients with predominant diarrhea, phosphate-buffered saline (PBS), or lipopolysaccharide (LPS). Cytokines in cell cultures and fecal LPS were measured by ELISA and mRNA gene expression of monolayers was analyzed using Qiagen RT² Profiler PCR Arrays. The fecal microbiota profile was determined by the GA-map^™ dysbiosis test and the fecal metabolite profile was analyzed by untargeted liquid chromatography/mass spectrometry.

KEY RESULTS

Colonoid monolayers stimulated with fecal supernatants from healthy subjects (n = 7), PBS (n = 4) or LPS (n = 3) presented distinct gene expression profiles, with some overlap (R² Y = 0.70, Q²  = 0.43). Addition of fecal supernatants from healthy subjects and IBS patients (n = 9) gave rise to different gene expression profiles of the colonoid monolayers (R² Y = 0.79, Q²  = 0.64). Genes (n = 22) related to immune response (CD1D, TLR5) and barrier integrity (CLDN15, DSC2) contributed to the separation. Levels of proinflammatory cytokines in colonoid monolayer cultures were comparable when stimulated with fecal supernatants from either donor types. Fecal microbiota and metabolite profiles, but not LPS content, differed between the study groups.

CONCLUSIONS

Fecal luminal factors from IBS patients induce a distinct colonic epithelial gene expression, potentially reflecting the disease pathophysiology. The culture of colonoids from healthy subjects with fecal supernatants from IBS patients may facilitate the exploration of IBS related intestinal micro-environmental and barrier interactions.

Gut Non-Bacterial Microbiota: Emerging Link to Irritable Bowel Syndrome

As a common functional gastrointestinal disorder, irritable bowel syndrome (IBS) significantly affects personal health and imposes a substantial economic burden on society, but the current understanding of its occurrence and treatment is still inadequate. Emerging evidence suggests that IBS is associated with gut microbial dysbiosis, but most studies focus on the bacteria and neglect other communities of the microbiota, including fungi, viruses, archaea, and other parasitic microorganisms. This review summarizes the latest findings that link the nonbacterial microbiota with IBS. IBS patients show less fungal and viral diversity but some alterations in mycobiome, virome, and archaeome, such as an increased abundance of Candida albicans. Moreover, fungi and methanogens can aid in diagnosis. Fungi are related to distinct IBS symptoms and induce immune responses, intestinal barrier disruption, and visceral hypersensitivity via specific receptors, cells, and metabolites. Novel therapeutic methods for IBS include fungicides, inhibitors targeting fungal pathogenic pathways, probiotic fungi, prebiotics, and fecal microbiota transplantation. Additionally, viruses, methanogens, and parasitic microorganisms are also involved in the pathophysiology and treatment. Therefore, the gut nonbacterial microbiota is involved in the pathogenesis of IBS, which provides a novel perspective on the noninvasive diagnosis and precise treatment of this disease.

Modulating the gut microenvironment as a treatment strategy for irritable bowel syndrome: a narrative review

Irritable bowel syndrome (IBS) is a disorder of gut-brain interaction with a complex pathophysiology. Growing evidence suggests that alterations of the gut microenvironment, including microbiota composition and function, may be involved in symptom generation. Therefore, attempts to modulate the gut microenvironment have provided promising results as an indirect approach for IBS management. Antibiotics, probiotics, prebiotics, food and faecal microbiota transplantation are the main strategies for alleviating IBS symptom severity by modulating gut microbiota composition and function (eg. metabolism), gut barrier integrity and immune activity, although with varying efficacy. In this narrative review, we aim to provide an overview of the current approaches targeting the gut microenvironment in order to indirectly manage IBS symptoms.

The gut microbiota - a vehicle for the prevention and treatment of hepatocellular carcinoma

Hepatocellular carcinoma (HCC) arises principally against a background of cirrhosis and these two diseases are responsible globally for over 2 million deaths a year. There are few treatment options for liver cirrhosis and HCC, so it is vital to arrest these pathologies early in their development. To do so, we propose dietary and therapeutic solutions that involve the gut microbiota and its consequences. Integrated dietary, environmental and intrinsic signals result in a bidirectional connection between the liver and the gut with its microbiota, known as the gut-liver axis. Numerous lifestyle factors can result in dysbiosis with a change in the functional composition and metabolic activity of the microbiota. A panoply of metabolites can be produced by the microbiota, including ethanol, secondary bile acids, trimethylamine, indole, quinolone, phenazine and their derivatives and the quorum sensor acyl homoserine lactones that may contribute to HCC but have yet to be fully investigated. Gram-negative bacteria can activate the pattern recognition receptor toll-like receptor 4 (TLR4) in the liver leading to nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling, which can contribute to HCC initiation and progression. The goal in preventing HCC should be to ensure a healthy gut microbiota using probiotic supplements containing beneficial bacteria and prebiotic plant fibers such as oligosaccharides that stimulate their growth. The clinical development of TLR4 antagonists is urgently needed to counteract the pathological effects of dysbiosis on the liver and other organs. Further nutrigenomic studies are required to understand better how the diet influences the gut microbiota and its adverse effects on the liver.

The microbiome of patients with irritable bowel syndrome: pathophysiology and applied aspects

Irritable bowel syndrome is a clinically and socially significant disease. The pathophysiology, the clinical manifestations of this disease and the  prognosis for  the patient are closely related to dysbiotic disorders of  the intestine. This review summarizes the ideas about changes in the intestinal microbiome in patients with irritable bowel syndrome. The pathogenetically substantiated approaches to the correction of dysbiosis that improving treatment outcomes are also considered. The results of the FLORAVIE clinical trial, which were discussed at the Expert Council “Identification of indications for prescribing probiotics in patients with irritable bowel syndrome” on March 18, 2022, are presented. Members of the Expert Council, Russian and international clinical guidelines emphasize the relevance of targeted probiotics administration. It was noticed that only strain specificity allows predicting a positive clinical response and has a certain evidence base. In this regard, the FLORAVIE study, conducted in real clinical practice in patients with predominantly severe forms of irritable bowel syndrome, is clinically relevant. It has been demonstrated that 30-day administration of the B. longum 35624 probiotic has reduced the severity of irritable bowel syndrome and has improved the quality of life in all subgroups of patients, especially in those with the most severe form of the disease. The data presented indicate that the inclusion of probiotic strains with proven mechanism of action in the complex therapy of irritable bowel syndrome can lead to the transformation of the course of the disease and improve the quality of life of patients. The high level of evidence made it possible to introduce the probiotic strain Bifidobacterium longum 35624 into a number of domestic and foreign guidelines.

 

Involvement of toll-like receptor 5 in mouse model of colonic hypersensitivity induced by neonatal maternal separation

BACKGROUND

Chronic abdominal pain is the most common cause for gastroenterology consultation and is frequently associated with functional gastrointestinal disorders including irritable bowel syndrome and inflammatory bowel disease. These disorders present similar brain/gut/microbiota trialogue alterations, associated with abnormal intestinal permeability, intestinal dysbiosis and colonic hypersensitivity (CHS). Intestinal dysbiosis can alter colon homeostasis leading to abnormal activation of the innate immunity that promotes CHS, perhaps involving the toll-like receptors (TLRs), which play a central role in innate immunity.

AIM

To understand the mechanisms between early life event paradigm on intestinal permeability, fecal microbiota composition and CHS development in mice with TLRs expression in colonocytes.

METHODS

Maternal separation model (NMS) CHS model, which mimics deleterious events in childhood that can induce a wide range of chronic disorders during adulthood were used. Colonic sensitivity of NMS mice was evaluated by colorectal distension (CRD) coupled with intracolonic pressure variation (IPV) measurement. Fecal microbiota composition was analyzed by 16S rRNA sequencing from weaning to CRD periods. TLR mRNA expression was evaluated in colonocytes. Additionally, the effect of acute intrarectal instillation of the TLR5 agonist flagellin (FliC) on CHS in adult naive wildtype mice was analyzed.

RESULTS

Around 50% of NMS mice exhibited increased intestinal permeability and CHS associated with intestinal dysbiosis, characterized by a significant decrease of species richness, an alteration of the core fecal microbiota and a specific increased relative abundance of flagellated bacteria. Only TLR5 mRNA expression was increased in colonocytes of NMS mice with CHS. Acute intrarectal instillation of FliC induced transient increase of IPV, reflecting transient CHS appearance.

CONCLUSION

Altogether, these data suggest a pathophysiological continuum between intestinal dysbiosis and CHS, with a role for TLR5.

Role of gut microbiota-derived signals in the regulation of gastrointestinal motility

The gastrointestinal (GI) tract harbors trillions of commensal microbes, called the gut microbiota, which plays a significant role in the regulation of GI physiology, particularly GI motility. The GI tract expresses an array of receptors, such as toll-like receptors (TLRs), G-protein coupled receptors, aryl hydrocarbon receptor (AhR), and ligand-gated ion channels, that sense different gut microbiota-derived bioactive substances. Specifically, microbial cell wall components and metabolites, including lipopeptides, peptidoglycan, lipopolysaccharides (LPS), bile acids (BAs), short-chain fatty acids (SCFAs), and tryptophan metabolites, mediate the effect of gut microbiota on GI motility through their close interactions with the enteroendocrine system, enteric nervous system, intestinal smooth muscle, and immune system. In turn, GI motility affects the colonization within the gut microbiota. However, the mechanisms by which gut microbiota interacts with GI motility remain to be elucidated. Deciphering the underlying mechanisms is greatly important for the prevention or treatment of GI dysmotility, which is a complication associated with many GI diseases, such as irritable bowel syndrome (IBS) and constipation. In this perspective, we overview the current knowledge on the role of gut microbiota and its metabolites in the regulation of GI motility, highlighting the potential mechanisms, in an attempt to provide valuable clues for the development of gut microbiota-dependent therapy to improve GI motility.

The role of gut microbiota in the development of colorectal cancer: a review

PURPOSE

Colorectal cancer (CRC) is the cancer of the colon and rectum. Recent research has found a link between CRC and human gut microbiota. This review explores the effect of gut microbiota on colorectal carcinogenesis and the development of chemoresistance.

METHODS

A literature overview was performed to identify the gut microbiota species that showed altered abundance in CRC patients and the mechanisms by which some of them aid in the development of chemoresistance.

RESULTS

Types of gut microbiota present and methods of analyzing them were discussed. We observed that numerous microbiota showed altered abundance in CRC patients and could act as a biomarker for CRC diagnosis and treatment. Further, it was demonstrated that microbes also have a role in the development of chemoresistance by mechanisms like immune system activation, drug modification, and autophagy modulation. Finally, the key issue of the growing global problem of antimicrobial resistance and its relationship with CRC was highlighted.

CONCLUSION

This review discussed the role of gut microbiota dysbiosis on colorectal cancer progression and the development of chemoresistance.

Functional bowel disorders with diarrhoea: Clinical guidelines of the United European Gastroenterology and European Society for Neurogastroenterology and Motility

Irritable bowel syndrome with diarrhoea (IBS-D) and functional diarrhoea (FDr) are the two major functional bowel disorders characterized by diarrhoea. In spite of their high prevalence, IBS-D and FDr are associated with major uncertainties, especially regarding their optimal diagnostic work-up and management. A Delphi consensus was performed with experts from 10 European countries who conducted a literature summary and voting process on 31 statements. Quality of evidence was evaluated using the grading of recommendations, assessment, development, and evaluation criteria. Consensus (defined as >80% agreement) was reached for all the statements. The panel agreed with the potential overlapping of IBS-D and FDr. In terms of diagnosis, the consensus supports a symptom-based approach also with the exclusion of alarm symptoms, recommending the evaluation of full blood count, C-reactive protein, serology for coeliac disease, and faecal calprotectin, and consideration of diagnosing bile acid diarrhoea. Colonoscopy with random biopsies in both the right and left colon is recommended in patients older than 50 years and in presence of alarm features. Regarding treatment, a strong consensus was achieved for the use of a diet low fermentable oligo-, di-, monosaccharides and polyols, gut-directed psychological therapies, rifaximin, loperamide, and eluxadoline. A weak or conditional recommendation was achieved for antispasmodics, probiotics, tryciclic antidepressants, bile acid sequestrants, 5-hydroxytryptamine-3 antagonists (i.e. alosetron, ondansetron, or ramosetron). A multinational group of European experts summarized the current state of consensus on the definition, diagnosis, and management of IBS-D and FDr.

Hypnobiome: A New, Potential Frontier of Hypnotherapy in the Treatment of Irritable Bowel Syndrome-A Narrative Review of the Literature

Increasing evidence suggests that the gut-brain axis may play a key role in health and disease via a bidirectional communication network involving neural and immunoendocrine pathways. This complex interplay deeply influences both gut microbiota and brain behavior. Pathobiome or gut dysbiosis is relevant for the pathogenesis of functional gastrointestinal disorders, such as IBS, chronic pain syndromes, and neurological and mental disorders. As a consequence, targeting the gut microbiota is emerging as a novel, effective therapeutic perspective. Among many treatment options, psychological interventions, including hypnosis, have been used to target the so-called psychobiome and its hypnotic analogue, i.e., hypnobiome, referring to their potential efficacy to modulate the mind-gut axis in IBS patients. A narrative review of the recent literature is provided and circumstantial evidence suggests that hypnobiome may represent a new promising frontier of hypnotherapy.

Gut Microbiota Manipulation in Irritable Bowel Syndrome

Increased knowledge suggests that disturbed gut microbiota, termed dysbiosis, might promote the development of irritable bowel syndrome (IBS) symptoms. Accordingly, gut microbiota manipulation has evolved in the last decade as a novel treatment strategy in order to improve IBS symptoms. In using different approaches, dietary management stands first in line, including dietary fiber supplements, prebiotics, and probiotics that are shown to change the composition of gut microbiota, fecal short-chain fatty acids and enteroendocrine cells densities and improve IBS symptoms. However, the exact mixture of beneficial bacteria for each individual remains to be identified. Prescribing nonabsorbable antibiotics still needs confirmation, although using rifaximin has been approved for diarrhea-predominant IBS. Fecal microbiota transplantation (FMT) has recently gained a lot of attention, and five out of seven placebo-controlled trials investigating FMT in IBS obtain promising results regarding symptom reduction and gut microbiota manipulation. However, more data, including larger cohorts and studying long-term effects, are needed before FMT can be regarded as a treatment for IBS in clinical practice.

Global Research Trends in Irritable Bowel Syndrome: A Bibliometric and Visualized Study

Background

There are about 10–23% of adults worldwide suffering from irritable bowel syndrome (IBS). Over the past few decades, there are many aspects of uncertainty regarding IBS leading to an ongoing interest in the topic as reflected by a vast number of publications, whose heterogeneity and variable quality may challenge researchers to measure their scientific impact, to identify collaborative networks, and to grasp actively researched themes. Accordingly, with help from bibliometric approaches, our goal is to assess the structure, evolution, and trends of IBS research between 2007 and 2022.

Methods

The documents exclusively focusing on IBS from 2007 to 2022 were retrieved from the Science Citation Index Expanded of the Web of Science Core Collection. The annual productivity of IBS research, and the most prolific countries or regions, authors, journals and resource-, intellectual- and knowledge-sharing in IBS research, as well as co-citation analysis of references and keywords were analyzed through Microsoft Office Excel 2019, CiteSpace, and VOSviewer.

Results

In total, 4,092 publications were reviewed. The USA led the list of countries with the most publications (1,226, 29.96%). Mayo Clinic contributed more publications than any other institution (193, 4.71%). MAGNUS SIMREN stood out as the most active and impactful scholar with the highest number of publications and the greatest betweenness centrality value. The most high-yield journal in this field was Neurogastroenterology and motility: the official journal of the European Gastrointestinal Motility Society (275, 6.72%). Gastroenterology had the most co-citations (3,721, 3.60%). Keywords with the ongoing strong citation bursts were chromogranin A, rat model, peptide YY, gut microbiota, and low-FODMAP diet, etc.

Conclusion

Through bibliometric analysis, we gleaned deep insight into the current status of literature investigating IBS for the first time. These findings will be useful to scholars interested in understanding the key information in the field, as well as identifying possible research frontiers.

Lactococcus lactis NCDO2118 exerts visceral antinociceptive properties in rat via GABA production in the gastro-intestinal tract

Gut disorders associated to irritable bowel syndrome (IBS) are combined with anxiety and depression. Evidence suggests that microbially produced neuroactive molecules, like γ-aminobutyric acid (GABA), can modulate the gut-brain axis. Two natural strains of Lactococcus lactis and one mutant were characterized in vitro for their GABA production and tested in vivo in rat by oral gavage for their antinociceptive properties. L. lactis NCDO2118 significantly reduced visceral hypersensitivity induced by stress due to its glutamate decarboxylase (GAD) activity. L. lactis NCDO2727 with similar genes for GABA metabolism but no detectable GAD activity had no in vivo effect, as well as the NCDO2118 ΔgadB mutant. The antinociceptive effect observed for the NCDO2118 strain was mediated by the production of GABA in the gastro-intestinal tract and blocked by GABA_B receptor antagonist. Only minor changes in the faecal microbiota composition were observed after the L. lactis NCDO2118 treatment. These findings reveal the crucial role of the microbial GAD activity of L. lactis NCDO2118 to deliver GABA into the gastro-intestinal tract for exerting antinociceptive properties in vivo and open avenues for this GRAS (Generally Recognized As safe) bacterium in the management of visceral pain and anxious profile of IBS patients.

Gut Microbiota Shifting in Irritable Bowel Syndrome: The Mysterious Role of Blastocystis sp

Irritable bowel syndrome (IBS) is a chronic disorder, which its causative agent is not completely clear; however, the interaction between microorganisms and gastrointestinal (GI) epithelial cells plays a critical role in the development of IBS and presenting symptoms. During recent decades, many studies have highlighted the high prevalence of Blastocystis sp. in patients with IBS and suggested a probable role for this protist in this disease. Recent studies have documented changes in the gut microbiota composition in patients with IBS regarding the presence of Blastocystis sp., but it is not clear that either disturbance of the gut during GI disorders is a favorable condition for Blastocystis sp. colonization or the presence of this protist may lead to alteration in the gut microbiota in IBS patients. In this review, we comprehensively gather and discuss scientific findings covering the role of Blastocystis sp. in IBS via gut microbiota shifting.

Structure and function of non-digestible carbohydrates in the gut microbiome

Together with proteins and fats, carbohydrates are one of the macronutrients in the human diet. Digestible carbohydrates, such as starch, starch-based products, sucrose, lactose, glucose and some sugar alcohols and unusual (and fairly rare) α-linked glucans, directly provide us with energy while other carbohydrates including high molecular weight polysaccharides, mainly from plant cell walls, provide us with dietary fibre. Carbohydrates which are efficiently digested in the small intestine are not available in appreciable quantities to act as substrates for gut bacteria. Some oligo- and polysaccharides, many of which are also dietary fibres, are resistant to digestion in the small intestines and enter the colon where they provide substrates for the complex bacterial ecosystem that resides there. This review will focus on these non-digestible carbohydrates (NDC) and examine their impact on the gut microbiota and their physiological impact. Of particular focus will be the potential of non-digestible carbohydrates to act as prebiotics, but the review will also evaluate direct effects of NDC on human cells and systems.

Efficacy and safety of a food supplement with standardized menthol, limonene, and gingerol content in patients with irritable bowel syndrome: A double-blind, randomized, placebo-controlled trial

Background

Irritable bowel syndrome (IBS) affects 9,2% of the global population and places a considerable burden on healthcare systems. Most medications for treating IBS, including spasmolytics, laxatives, and antidiarrheals, have low efficacy. Effective and safe therapeutic treatments have yet to be developed for IBS.

Purpose

This study assessed the efficacy and safety of a food supplement containing standardized menthol, limonene, and gingerol in human participants with IBS or IBS/functional dyspepsia (FD).

Design

A double-blind, randomized, placebo-controlled trial.

Methods

We randomly assigned 56 patients with IBS or IBS/FD to an intervention group (Group 1) or control group (Group 2) that were given supplement or placebo, respectively, in addition to the standard treatment regimen for 30 d. Three outpatient visits were conducted during the study. Symptom severity was measured at each visit using a 7×7 questionnaire. Qualitative and quantitative composition of the intestinal microbiota were assessed at visits 1 and 3 based on 16S rRNA gene sequencing.

Results

At visit 1 (before treatment), the median total 7×7 questionnaire score was in the moderately ill range for both groups, with no difference between the groups (p = 0.1). At visit 2, the total 7×7 score decreased to mildly ill, with no difference between the groups (p = 0.4). At visit 3, the total score for group 1 indicated borderline illness and for group 2 remained indicated mild illness (p = 0.009). Even though we observed some variations in gut microbiota between the groups, we did not find any statistically significant changes.

Conclusion

The food supplement with standardized menthol, limonene, and gingerol content increased the efficacy of standard therapy in IBS and FD patients. The use of the supplement did not cause any obvious side effects.

Registration

ClinicalTrials.gov Identifier: NCT04484467

Risk for Post-Colonoscopy Irritable Bowel Syndrome in Patients With and Without Antibiotic Exposure: A Retrospective Cohort Study

BACKGROUND & AIMS

Laboratory studies have demonstrated that antibiotic use in conjunction with bowel purgatives causes alterations to the gut microbiota. Because gut microbiota changes may be a trigger for the development of irritable bowel syndrome (IBS), we sought to assess whether individuals who undergo bowel cleansing for colonoscopy and have concurrent antibiotic exposure develop IBS at higher rates than individuals who undergo colonoscopy without antibiotic exposure.

METHODS

We used data from Optum's de-identified Clinformatics Data Mart Database in the United States to study a cohort of 50- to 55-year-olds who underwent screening colonoscopy. Individuals exposed to antibiotics within 14 days of colonoscopy were propensity-score matched to individuals who were not exposed to antibiotics around colonoscopy. The primary outcome was a new IBS diagnosis, and the composite outcome was a new claim for IBS, IBS medications, or IBS symptoms. The association of antibiotic exposure and the outcomes was calculated using Cox proportional hazards regression.

RESULTS

There were 408,714 individuals who met criteria for the screening colonoscopy cohort. Of these, 24,617 (6.0%) were exposed to antibiotics around the time of colonoscopy, and they were propensity-score matched to 24,617 individuals not exposed to antibiotics. There was no statistically significant association between antibiotic use and IBS (hazard ratio, 1.11; 95% confidence interval, 0.89-1.39), but there was a weak association between antibiotic use and the composite outcome (hazard ratio, 1.12; 95% confidence interval, 1.02-1.24; number needed to harm, 94).

CONCLUSIONS

Individuals concurrently exposed to antibiotics and bowel purgative had slightly higher rates of surrogate IBS outcomes compared with matched controls who did not receive antibiotics concurrently with bowel purgative.

Metagenomics and artificial intelligence in the context of human health

Human microbiome is ubiquitous, dynamic, and site-specific consortia of microbial communities. The pathogenic nature of microorganisms within human tissues has led to an increase in microbial studies. Characterization of genera, like Streptococcus, Cutibacterium, Staphylococcus, Bifidobacterium, Lactococcus and Lactobacillus through culture-dependent and culture-independent techniques has been reported. However, due to the unique environment within human tissues, it is difficult to culture these microorganisms making their molecular studies strenuous. MGs offer a gateway to explore and characterize hidden microbial communities through a culture-independent mode by direct DNA isolation. By function and sequence-based MGs, Scientists can explore the mechanistic details of numerous microbes and their interaction with the niche. Since the data generated from MGs studies is highly complex and multi-dimensional, it requires accurate analytical tools to evaluate and interpret the data. Artificial intelligence (AI) provides the luxury to automatically learn the data dimensionality and ease its complexity that makes the disease diagnosis and disease response easy, accurate and timely. This review provides insight into the human microbiota and its exploration and expansion through MG studies. The review elucidates the significance of MGs in studying the changing microbiota during disease conditions besides highlighting the role of AI in computational analysis of MG data.

Concomitant Irritable Bowel Syndrome Does Not Influence the Response to Antimicrobial Therapy in Patients with Functional Dyspepsia

BACKGROUND AND AIMS

Antimicrobial therapy improves symptoms in patients with irritable bowel syndrome (IBS), but the efficacy in functional dyspepsia (FD) is largely unknown. While FD and IBS frequently overlap, it is unknown if concomitant IBS in FD alters the response to antimicrobial therapy in FD. Thus, we aimed to assess and compare the effect of antimicrobial therapy on visceral sensory function and symptom improvement in FD patients with and without IBS.

METHODS

Adult patients with FD with or without IBS received rifaximin 550 mg BD for 10 days, followed by a 6-week follow-up period. The total gastrointestinal symptom score as measured by the SAGIS (Structured Assessment of Gastrointestinal Symptoms) questionnaire and subscores (dyspepsia, diarrhea, and constipation), symptom response to a standardized nutrient challenge and normalization of the glucose breath tests were measured.

RESULTS

Twenty-one consecutive adult patients with FD and 14/21 with concomitant IBS were recruited. Treatment with rifaximin resulted in a significant (p = 0.017) improvement in the total SAGIS score from 34.7 (± 15.4) at baseline to 26.0 (± 16.8) at 2 weeks and 25.6 (± 17.8) at 6 weeks post-treatment. Similarly, compared to baseline there was a statistically significant improvement in SAGIS subscores for dyspepsia and diarrhea (all p < 0.05) and effects persisted for 6 weeks post-treatment. Similarly, the symptom score (and subscores) following a standardized nutrient challenge improved significantly (p < 0.001) 2 weeks post-treatment. The presence of concomitant IBS did not significantly influence the improvement of symptoms after antibiotic therapy (all p > 0.5).

CONCLUSIONS

In FD patients, the response to antimicrobial therapy with rifaximin is not influenced by concomitant IBS symptoms.

BiGAMi: Bi-Objective Genetic Algorithm Fitness Function for Feature Selection on Microbiome Datasets

The relationship between the host and the microbiome, or the assemblage of microorganisms (including bacteria, archaea, fungi, and viruses), has been proven crucial for its health and disease development. The high dimensionality of microbiome datasets has often been addressed as a major difficulty for data analysis, such as the use of machine-learning (ML) and deep-learning (DL) models. Here, we present BiGAMi, a bi-objective genetic algorithm fitness function for feature selection in microbial datasets to train high-performing phenotype classifiers. The proposed fitness function allowed us to build classifiers that outperformed the baseline performance estimated by the original studies by using as few as 0.04% to 2.32% features of the original dataset. In 35 out of 42 performance comparisons between BiGAMi and other feature selection methods evaluated here (sequential forward selection, SelectKBest, and GARS), BiGAMi achieved its results by selecting 6-93% fewer features. This study showed that the application of a bi-objective GA fitness function against microbiome datasets succeeded in selecting small subsets of bacteria whose contribution to understood diseases and the host state was already experimentally proven. Applying this feature selection approach to novel diseases is expected to quickly reveal the microbes most relevant to a specific condition.

Communication between the gut microbiota and peripheral nervous system in health and chronic disease

Trillions of bacteria reside within our gastrointestinal tract, ideally forming a mutually beneficial relationship between us. However, persistent changes in diet and lifestyle in the western diet and lifestyle contribute to a damaging of the gut microbiota-host symbiosis leading to diseases such as obesity and irritable bowel syndrome. Many symptoms and comorbidities associated with these diseases stem from dysfunctional signaling in peripheral neurons. Our peripheral nervous system (PNS) is comprised of a variety of sensory, autonomic, and enteric neurons which coordinate key homeostatic functions such as gastrointestinal motility, digestion, immunity, feeding behavior, glucose and lipid homeostasis, and more. The composition and signaling of bacteria in our gut dramatically influences how our peripheral neurons regulate these functions, and we are just beginning to uncover the molecular mechanisms mediating this communication. In this review, we cover the general anatomy and function of the PNS, and then we discuss how the molecules secreted or stimulated by gut microbes signal through the PNS to alter host development and physiology. Finally, we discuss how leveraging the power of our gut microbes on peripheral nervous system signaling may offer effective therapies to counteract the rise in chronic diseases crippling the western world.

Gut Microbiome in Anesthesiology and Pain Medicine

The gut microbiome plays critical roles in human health and disease. Recent studies suggest it may also be associated with chronic pain and postoperative pain outcomes. In animal models, the composition of the gut microbiome changes after general anesthesia and affects the host response to medications, including anesthetics and opioids. In humans, the gut microbiome is associated with the development of postoperative pain and neurocognitive disorders. Additionally, the composition of the gut microbiome has been associated with pain conditions including visceral pain, nociplastic pain, complex regional pain syndrome, and headaches, partly through altered concentration of circulating bacterial-derived metabolites. Furthermore, animal studies demonstrate the critical role of the gut microbiome in neuropathic pain via immunomodulatory mechanisms. This article reviews basic concepts of the human gut microbiome and its interactions with the host and provide a comprehensive overview of the evidence linking the gut microbiome to anesthesiology, critical care, and pain medicine.

Progress in application of probiotics, prebiotics, and synbiotics in irritable bowel syndrome

Irritable bowel syndrome (IBS) is a common functional bowel disorder characterized by recurrent abdominal pain accompanied by changes in defecation frequency and/or stool characteristics. The global incidence of IBS is increasing year by year. Intestinal symptoms caused by IBS (such as constipation, diarrhea, abdominal pain, and abdominal distension) and accompanying changes in general nervous system function can significantly reduce patients' quality of life and work efficiency, and lead to high medical costs. Therefore, finding safe, effective, and economical treatments has become a hot research topic in recent years. Studies have shown that the intestinal flora of patients with IBS is different from that of healthy subjects, and regulating the intestinal flora can treat IBS. The purpose of this review is to summarize the application and recent progress of probiotics, prebiotics, and synbiotics in the treatment of IBS by regulating the intestinal flora.

Environmental factors shaping the gut microbiome in a Dutch population

The gut microbiome is associated with diverse diseases^1-3, but a universal signature of a healthy or unhealthy microbiome has not been identified, and there is a need to understand how genetics, exposome, lifestyle and diet shape the microbiome in health and disease. Here we profiled bacterial composition, function, antibiotic resistance and virulence factors in the gut microbiomes of 8,208 Dutch individuals from a three-generational cohort comprising 2,756 families. We correlated these to 241 host and environmental factors, including physical and mental health, use of medication, diet, socioeconomic factors and childhood and current exposome. We identify that the microbiome is shaped primarily by the environment and cohabitation. Only around 6.6% of taxa are heritable, whereas the variance of around 48.6% of taxa is significantly explained by cohabitation. By identifying 2,856 associations between the microbiome and health, we find that seemingly unrelated diseases share a common microbiome signature that is independent of comorbidities. Furthermore, we identify 7,519 associations between microbiome features and diet, socioeconomics and early life and current exposome, with numerous early-life and current factors being significantly associated with microbiome function and composition. Overall, this study provides a comprehensive overview of gut microbiome and the underlying impact of heritability and exposures that will facilitate future development of microbiome-targeted therapies.

Irritable bowel syndrome and microbiome; Switching from conventional diagnosis and therapies to personalized interventions

The human microbiome has been linked to several diseases. Gastrointestinal diseases are still one of the most prominent area of study in host-microbiome interactions however the underlying microbial mechanisms in these disorders are not fully established. Irritable bowel syndrome (IBS) remains as one of the prominent disorders with significant changes in the gut microbiome composition and without definitive treatment. IBS has a severe impact on socio-economic and patient’s lifestyle. The association studies between the IBS and microbiome have shed a light on relevance of microbial composition, and hence microbiome-based trials were designed. However, there are no clear evidence of potential treatment for IBS. This review summarizes the epidemiology and socioeconomic impact of IBS and then focus on microbiome observational and clinical trials. At the end, we propose a new perspective on using data-driven approach and applying computational modelling and machine learning to design microbiome-aware personalized treatment for IBS.

Long-term Outcomes Following Multiply Recurrent Clostridioides difficile Infection and Fecal Microbiota Transplantation

BACKGROUND AND AIMS

Fecal microbiota transplantation (FMT) is a commonly used therapy for multiply recurrent Clostridioides difficile (mrCDI). By altering the gut microbiota, there is the potential for FMT to impact the risk for cardiometabolic, intestinal or immune-mediated conditions. Likewise, the microbiota disturbance associated with mrCDI could potentially lead to these conditions. We aimed to assess the associations of mrCDI and FMT with cardiometabolic, immune-mediated diseases, and irritable bowel syndrome.

METHODS

This retrospective cohort study using a United States commercial claims database included persons diagnosed with CDI or undergoing FMT. We created 2 pairwise comparisons: mrCDI vs non-mrCDI, and non-mrCDI or mrCDI treated with FMT vs mrCDI without FMT.

RESULTS

We found no significant association between mrCDI (vs non-mrCDI) and inflammatory bowel disease (adjusted hazard ratio (aHR) = 1.65; 95% confidence interval, 0.67-4.04), rheumatoid arthritis (HR = 0.86; 0.47-1.56), psoriasis (HR = 0.72; 0.23-2.27), diabetes (aHR = 0.97; 0.67-1.40), hypertension (aHR = 1.05; 0.76-1.44), myocardial infarction (aHR = 0.82; 0.63-1.06), stroke (aHR = 0.83; 0.62-1.12), or irritable bowel syndrome (HR = 0.94; 0.61-1.45). Similarly, we found no association of CDI with FMT (vs mrCDI without FMT) and diabetes (aHR = 0.92; 0.27-3.11), hypertension (aHR = 1.41; 0.64-3.15), stroke (aHR = 1.27; 0.69-2.34) or inflammatory bowel syndrome (aHR = 0.80; 0.26-2.46). However, the incidence of myocardial infarction was increased following FMT (aHR = 1.68; 1.01-2.81).

CONCLUSION

Relative to those with CDI, persons with mrCDI do not appear to be intrinsically at higher risk of cardiometabolic, immune-mediated diseases, or irritable bowel syndrome. However, those who underwent FMT for CDI had a higher incidence of myocardial infarction. Future studies should assess this association to assess reproducibility.

Bacteria and Methanogens in the Human Microbiome: a Review of Syntrophic Interactions

Methanogens are microorganisms belonging to the Archaea domain and represent the primary source of biotic methane. Methanogens encode a series of enzymes which can convert secondary substrates into methane following three major methanogenesis pathways. Initially recognized as environmental microorganisms, methanogens have more recently been acknowledged as host-associated microorganisms after their detection and initial isolation in ruminants in the 1950s. Methanogens have also been co-detected with bacteria in various pathological situations, bringing their role as pathogens into question. Here, we review reported associations between methanogens and bacteria in physiological and pathological situations in order to understand the metabolic interactions explaining these associations. To do so, we describe the origin of the metabolites used for methanogenesis and highlight the central role of methanogens in the syntrophic process during carbon cycling. We then focus on the metabolic abilities of co-detected bacterial species described in the literature and infer from their genomes the probable mechanisms of their association with methanogens. The syntrophic interactions between bacteria and methanogens are paramount to gut homeostasis. Therefore, any dysbiosis affecting methanogens might impact human health. Thus, the monitoring of methanogens may be used as a bio-indicator of dysbiosis. Moreover, new therapeutic approaches can be developed based on their administration as probiotics. We thus insist on the importance of investigating methanogens in clinical microbiology.

Gut microbiota signatures and modulation in irritable bowel syndrome

Irritable bowel syndrome (IBS) affects approximately one tenth of the general population and is characterized by abdominal pain associated with abnormalities in bowel habits. Visceral hypersensitivity, abnormal intestinal motor function, mucosal immune activation, and increased intestinal permeability concur to its pathophysiology. Psychological factors can influence symptom perception at the central nervous system level. In addition, recent evidence suggests that dysbiosis may be a key pathophysiological factor in patients with IBS. Increasing understanding of the pathophysiological mechanisms translates into new and more effective therapeutic approaches. Indeed, in line with this evidence, IBS therapies nowadays include agents able to modulate gut microbiota function and composition, such as diet, prebiotics, probiotics, and antibiotics. In addition, in the last decade, an increasing interest in fecal microbiota transplantation has been paid. An in-depth understanding of the intestinal microenvironment through accurate faucal microbiota and metabolite analysis may provide valuable insights into the pathophysiology of IBS, finally shaping new tailored IBS therapies.

Efficacy of Fecal Microbiota Transplantation in Irritable Bowel Syndrome: A Meta-Analysis of Randomized Controlled Trials

Background

Randomized controlled trials (RCTs) have examined the efficacy of fecal microbiota transplantation (FMT) in irritable bowel syndrome (IBS) with inconsistent results. We performed a meta-analysis to assess both the short- and long-term efficacy of FMT in IBS.

Methods

MEDLINE, EMBASE, and the Cochrane Central Register were searched through September 2021. RCTs recruiting adult patients with IBS that compared FMT with placebo with dichotomous data of response to therapy were eligible. Dichotomous data were pooled to obtain a relative risk (RR) of symptom not improving after therapy. RR was also pooled for adverse events (AEs). Continuous data were calculated using a mean difference for IBS-Quality of Life (IBS-QoL). GRADE methodology was used to assess quality of evidence.

Results

The search strategy generated 658 citations. Seven RCTs comprising 472 patients with IBS were included. FMT was not associated with a significant improvement in global symptom in IBS at 12 weeks in comparison with placebo (RR 0.75, 95% CI 0.43–1.31) with high heterogeneity between studies (I² 87%). Subgroup analyses showed that FMT was superior to placebo when administered via colonoscopy or gastroscope (RR 0.70, 95% CI 0.51–0.96; RR 0.37, 95% CI 0.14–0.99, respectively, while FMT was inferior to placebo when administered via oral capsules (RR 1.88, 95% CI 1.06–3.35). FMT induced a significant improvement in IBS-QoL compared to placebo (mean difference 9.39, 95% CI 3.86–14.91) at 12 weeks. No significant difference in the total number of AEs was observed between FMT and placebo (RR 1.20, 95% CI 0.59–2.47). FMT did not significantly improve global symptom in IBS at 1-year follow-up compared with placebo (RR 0.90, 95% CI 0.72–1.12). The GRADE quality evidence to support recommending FMT in IBS was very low.

Conclusion

IBS patients may benefit from FMT when administered via colonoscopy or gastroscope. FMT may improve the quality of life of IBS. The long-term use of FMT in IBS warrants further investigation. There is very-low-quality evidence to support recommending FMT in IBS.

Bidirectional association between alopecia areata and irritable bowel syndrome: A nationwide population-based cohort study

BACKGROUND

Alopecia areata (AA) and irritable bowel syndrome (IBS) are two distinct diseases that share a similar pathophysiology; however, the relationship between these two diseases is unknown. This study aimed to investigate the bidirectional relationship between AA and IBS.

METHODS

Participants were recruited from the National Health Insurance Research Database in Taiwan. We included 5446 patients with AA and 21 784 matched controls to assess the risk of IBS, and 56 429 patients with IBS and 225 716 matched controls to assess the risk of AA. The Cox proportional-hazards regression model was used to calculate the adjusted hazard ratio (aHR).

RESULTS

After adjustment for potential confounders, patients with AA had an aHR of 5.20 [95% confidence interval (CI) 3.97-6.82] for IBS in comparison with the controls. Furthermore, compared with the controls, IBS patients had an aHR of 5.38 (95% CI 3.95-7.34) for AA.

CONCLUSION

AA is bidirectionally associated with IBS. Further investigation is needed to elucidate the shared pathogenesis underlying these two diseases.

Pathophysiological Commonality Between Irritable Bowel Syndrome and Metabolic Syndrome: Role of Corticotropin-releasing Factor-Toll-like Receptor 4-Proinflammatory Cytokine Signaling

Irritable bowel syndrome (IBS) displays chronic abdominal pain with altered defecation. Most of the patients develop visceral hypersensitivity possibly resulting from impaired gut barrier and altered gut microbiota. We previously demonstrated that colonic hyperpermeability with visceral hypersensitivity in animal IBS models, which is mediated via corticotropin-releasing factor (CRF)-Toll-like receptor 4 (TLR4)-proinflammatory cytokine signaling. CRF impairs gut barrier via TLR4. Leaky gut induces bacterial translocation resulting in dysbiosis, and increases lipopolysaccharide (LPS). Activation of TLR4 by LPS increases the production of proinflammatory cytokines, which activate visceral sensory neurons to induce visceral hypersensitivity. LPS also activates CRF receptors to further increase gut permeability. Metabolic syndrome (MS) is a cluster of cardiovascular risk factors, including insulin resistance, obesity, dyslipidemia, and hypertension, and recently several researchers suggest the possibility that impaired gut barrier and dysbiosis with low-grade systemic inflammation are involved in MS. Moreover, TLR4-proinflammatory cytokine contributes to the development of insulin resistance and obesity. Thus, the existence of pathophysiological commonality between IBS and MS is expected. This review discusses the potential mechanisms of IBS and MS with reference to gut barrier and microbiota, and explores the possibility of existence of pathophysiological link between these diseases with a focus on CRF, TLR4, and proinflammatory cytokine signaling. We also review epidemiological data supporting this possibility, and discuss the potential of therapeutic application of the drugs used for MS to IBS treatment. This notion may pave the way for exploring novel therapeutic approaches for these disorders.

Effect of Bifidobacterium longum 35624 on disease severity and quality of life in patients with irritable bowel syndrome

BACKGROUND

Bifidobacterium longum 35624 has shown efficacy in improving irritable bowel syndrome (IBS) symptoms compared with placebo in double-blind randomized studies. However, few data are available from real-life clinical practice or from studies that used Rome IV criteria to diagnose IBS.

AIM

To assess the effect of B. longum 35624 on IBS severity and quality of life in a real-life setting.

METHODS

From November 2018 to January 2020, 278 patients with IBS (according to Rome IV criteria) were enrolled in a prospective, open-label, multicenter observational study by private practice gastroenterologists to received one capsule of B. longum 35624 (10⁹ colony-forming units) per day for 30 d. Participation in the study was independently proposed to patients during spontaneous consultations. Disease severity (assessed by the IBS severity scoring system) and patient quality of life (assessed by the IBS quality of life questionnaire) were compared between the inclusion visit (baseline) and the visit at the end of 30 d of treatment. The characteristics of patients were described at baseline. Continuous variables comparisons between inclusion and end-of-treatment visits were performed using the t-test and Kruskal-Wallis test. Categorical variables comparisons were performed using the χ2 test.

RESULTS

A total of 233 patients, with a mean age of 51.4 years and composed of 71.2% women, were included in the study. Of these patients, 48.1% had moderate IBS and 46.4% had severe IBS. After a 30-d treatment period with one B. longum 35624 capsule per day, a significant decrease in IBS severity was observed compared to baseline (mean ± SD, IBS severity scoring system scores: 208 ± 104 vs 303 ± 81, P < 0.001) and 57% of patients moved to lower severity categories or achieved remission. The quality of life of patients was also improved by the treatment (IBS Quality of Life questionnaire score: 68.8 ± 20.9 vs 60.2 ± 20.5; P < 0.001) and 63.8% of patients were satisfied with the treatment.

CONCLUSION

Thirty days of treatment with B. longum 35624 reduces disease severity and improves the quality of life of patients with IBS, particularly those with the most severe forms of IBS.

Maintaining work life under threat of symptoms: a grounded theory study of work life experiences in persons with Irritable Bowel Syndrome

Background

Irritable Bowel Syndrome (IBS) is a highly prevalent functional gastrointestinal disorder. Earlier studies have shown that IBS can limit the ability to perform at work and lead to absenteeism. However, few studies focus on work life experiences based on patients’ narratives. The purpose of this study was to construct a theory for how persons with IBS maintain their work life.

Methods

A qualitative study was performed using constructivist grounded theory. Semi-structured interviews with 15 women and 8 men with IBS (26–64 years of age) were conducted. Fourteen participants worked full-time, six worked part-time and three were on sick leave. The interviews were transcribed verbatim and coded line-by-line, incident-by-incident and thereafter focused coding was done. From the data and codes, categories were generated. Finally, a core category was constructed explaining the process of maintaining work life when living with IBS.

Results

Balancing work life while being under threat of symptoms constituted of four categories, being prepared, restricting impact, reconciling and adjusting. Persons with IBS restricted the impact of IBS on work by using strategies and upholding daily routines and strived to being prepared by exerting control over work life. These ongoing processes served to limit the influence of IBS on work by symptoms being less intense, perceived as less frequent, or not as bothersome. Reconciling IBS with work life was understood as a successful outcome from being prepared and restricting impact but was also influenced by the individual’s outlook on life. Adjusting to other people at work interfered with the strategies of being prepared, restricting impact, and reconciling, leaving persons with IBS more susceptible to symptoms.

Conclusions

This study deepens the understanding of the work situation for persons with IBS. Health care professionals can use the results of this study in the dialogue with the patient discussing work ability and sick leave. The results imply that although balancing work life under threat of symptoms can be a struggle, there are strategies that persons with IBS and employers together can initiate and use to reduce impact on work on several different levels.

The Impact of a Mediterranean Diet on the Gut Microbiome in Healthy Human Subjects: A Pilot Study

BACKGROUND AND AIMS

Despite the reported salutary benefits of a Mediterranean diet (MD) on a wide variety of health conditions, the specific microbial changes associated with an MD within the gastrointestinal (GI) tract are not well studied. Specifically, although population and survey-based studies have shown microbial changes, there are no published data on how an MD alters the gut flora in a controlled setting.

METHODS

We recruited 10 healthy subjects, each of whom gave a stool sample at baseline and then was provided with prepared meals of a "typical" American diet; after 2 weeks, a second stool sample was collected. All subjects were then provided with prepared meals based on the MD for another 2 weeks, followed by a final stool sample collection. Stool samples were batch analyzed with DNA extraction, and sequencing libraries were generated. Measures of bacterial diversity, species richness, and enterotypes were performed.

RESULTS

All ten subjects tolerated the diets well. Bacterial diversity increased with an MD, as measured by alpha diversity via the Simpson index. Furthermore, there were significant differences in 5 bacterial genera between the 2 diets.

CONCLUSION

This small pilot study of controlled diets demonstrates that the MD can rapidly alter the gut microbiome in healthy subjects at the level of global microbial diversity and individual genera. These data confirm the findings of previous observational studies and establish the feasibility of conducting longer term studies on the impact of the MD on the flora of the GI tract and its relationship to digestive diseases.

Predictors of Symptom-Specific Treatment Response to Dietary Interventions in Irritable Bowel Syndrome

(1) Background: Predictors of dietary treatment response in irritable bowel syndrome (IBS) remain understudied. We aimed to investigate predictors of symptom improvement during the low FODMAP and the traditional IBS diet for four weeks. (2) Methods: Baseline measures included faecal Dysbiosis Index, food diaries with daily energy and FODMAP intake, non-gastrointestinal (GI) somatic symptoms, GI-specific anxiety, and psychological distress. Outcomes were bloating, constipation, diarrhea, and pain symptom scores treated as continuous variables in linear mixed models. (3) Results: We included 33 and 34 patients on the low FODMAP and traditional IBS diet, respectively. Less severe dysbiosis and higher energy intake predicted better pain response to both diets. Less severe dysbiosis also predicted better constipation response to both diets. More severe psychological distress predicted worse bloating response to both diets. For the different outcomes, several differential predictors were identified, indicating that baseline factors could predict better improvement in one treatment arm, but worse improvement in the other treatment arm. (4) Conclusions: Psychological, nutritional, and microbial factors predict symptom improvement when following the low FODMAP and traditional IBS diet. Findings may help individualize dietary treatment in IBS.

Integrated fecal microbiome-metabolome signatures reflect stress and serotonin metabolism in irritable bowel syndrome

To gain insight into the complex microbiome-gut-brain axis in irritable bowel syndrome (IBS), several modalities of biological and clinical data must be combined. We aimed to identify profiles of fecal microbiota and metabolites associated with IBS and to delineate specific phenotypes of IBS that represent potential pathophysiological mechanisms. Fecal metabolites were measured using proton nuclear magnetic resonance (¹H-NMR) spectroscopy and gut microbiome using shotgun metagenomic sequencing (MGS) in a combined dataset of 142 IBS patients and 120 healthy controls (HCs) with extensive clinical, biological and phenotype information. Data were analyzed using support vector classification and regression and kernel t-SNE. Microbiome and metabolome profiles could distinguish IBS and HC with an area-under-the-receiver-operator-curve of 77.3% and 79.5%, respectively, but this could be improved by combining microbiota and metabolites to 83.6%. No significant differences in predictive ability of the microbiome-metabolome data were observed between the three classical, stool pattern-based, IBS subtypes. However, unsupervised clustering showed distinct subsets of IBS patients based on fecal microbiome-metabolome data. These clusters could be related plasma levels of serotonin and its metabolite 5-hydroxyindoleacetate, effects of psychological stress on gastrointestinal (GI) symptoms, onset of IBS after stressful events, medical history of previous abdominal surgery, dietary caloric intake and IBS symptom duration. Furthermore, pathways in metabolic reaction networks were integrated with microbiota data, that reflect the host-microbiome interactions in IBS. The identified microbiome-metabolome signatures for IBS, associated with altered serotonin metabolism and unfavorable stress response related to GI symptoms, support the microbiota-gut-brain link in the pathogenesis of IBS.

Charting a path forward for clinical research in artificial intelligence and gastroenterology

Gastroenterology has been an early leader in bridging the gap between artificial intelligence (AI) model development and clinical trial validation, and in recent years we have seen the publication of several randomized clinical trials examining the role of AI in gastroenterology. As AI applications for clinical medicine advance rapidly, there is a clear need for guidance surrounding AI-specific study design, evaluation, comparison, analysis and reporting of results. Several initiatives are in the publication or pre-publication phase including AI-specific amendments to minimum reporting guidelines for clinical trials, society task force initiatives aimed at priority use cases and research priorities, and minimum reporting guidelines that guide the reporting of clinical prediction models. In this paper, we examine applications of AI in clinical trials and discuss elements of newly published AI-specific extensions to the Consolidated Standards of Reporting Trials and Standard Protocol Items: Recommendations for Interventional Trials statements that guide clinical trial reporting and development. We then review AI applications at the pre-trial level in both endoscopy and other subfields of gastroenterology and explore areas where further guidance is needed to supplement the current guidance available at the pre-trial level.

Taxonomic composition and biodiversity of the gut microbiome from patients with irritable bowel syndrome, ulcerative colitis, and asthma

To date, the association of an imbalance of the intestinal microbiota with various human diseases, including both diseases of the gastrointestinal tract and disorders of the immune system, has been shown. However, despite the huge amount of accumulated data, many key questions still remain unanswered. Given limited data on the composition of the gut microbiota in patients with ulcerative colitis (UC) and irritable bowel syndrome (IBS) from different parts of Siberia, as well as the lack of data on the gut microbiota of patients with bronchial asthma (BA), the aim of the study was to assess the biodiversity of the gut microbiota of patients with IBS, UC and BA in comparison with those of healthy volunteers (HV). In this study, a comparative assessment of the biodiversity and taxonomic structure of gut microbiome was conducted based on the sequencing of 16S rRNA genes obtained from fecal samples of patients with IBS, UC, BA and volunteers. Sequences of the Firmicutes and Bacteroidetes types dominated in all samples studied. The third most common in all samples were sequences of the Proteobacteria type, which contains pathogenic and opportunistic bacteria. Sequences of the Actinobacteria type were, on average, the fourth most common. The results showed the presence of dysbiosis in the samples from patients compared to the sample from HVs. The ratio of Firmicutes/Bacteroidetes was lower in the IBS and UC samples than in HV and higher the BA samples. In the samples from patients with intestinal diseases (IBS and UC), an increase in the proportion of sequences of the Bacteroidetes type and a decrease in the proportion of sequences of the Clostridia class, as well as the Ruminococcaceae, but not Erysipelotrichaceae family, were found. The IBS, UC, and BA samples had signif icantly more Proteobacteria sequences, including Methylobacterium, Sphingomonas, Parasutterella, Halomonas, Vibrio, as well as Escherichia spp. and Shigella spp. In the gut microbiota of adults with BA, a decrease in the proportion of Roseburia, Lachnospira, Veillonella sequences was detected, but the share of Faecalibacterium and Lactobacillus sequences was the same as in healthy individuals. A signif icant increase in the proportion of Halomonas and Vibrio sequences in the gut microbiota in patients with BA has been described for the f irst time.

Gut microbiota modulation by prednisolone in a rat kindling model of pentylenetetrazol (PTZ)-induced seizure

The gut microbiota is a complex community composed by several microorganisms that interact in the maintenance of homeostasis and contribute to physiological processes, including brain function. The relationship of the taxonomic composition of the gut microbiota with neurological diseases such as autism, Parkinson's, Alzheimer's, anxiety, and depression is widely recognized. The immune system is an important intermediary between the gut microbiota and the central nervous system, being one of the communication routes of the gut-brain axis. Although the complexity of the relationship between inflammation and epilepsy has not yet been elucidated, inflammatory processes are similar in many ways to the consequences of dysbiosis and contribute to disease progression. This study aimed to analyze the taxonomic composition of the gut microbiota of rats treated with prednisolone in a kindling model of epilepsy. Male Wistar rats (90 days, n = 24) divided into four experimental groups: sodium chloride solution 0.9 g%, diazepam 2 mg/kg, prednisolone 1 mg/kg, and prednisolone 5 mg/kg administered intraperitoneally (i.p.) for 14 days. The kindling model was induced by pentylenetetrazole (PTZ) 25 mg/kg i.p. on alternate days. The taxonomic profile was established by applying metagenomic DNA sequencing. There was no change in alpha diversity, and the composition of the gut microbiota between prednisolone and diazepam was similar. The significant increase in Verrucomicrobia, Saccharibacteria, and Actinobacteria may be related to the protective activity against seizures and inflammatory processes that cause some cases of epilepsy. Further studies are needed to investigate the functional influence that these species have on epilepsy and the inflammatory processes that trigger it.

Understanding of the Site-Specific Microbial Patterns towards Accurate Identification for Patients with Diarrhea-Predominant Irritable Bowel Syndrome

Fecal microbial community could not fully represent the intestinal microbial community. However, most studies analyzing diarrhea-dominant irritable bowel syndrome (IBS-D) were mainly based on fecal samples. We aimed to characterize the IBS-D microbial community patterns using samples at multiple intestinal sites. This study recruited 74 IBS-D patients and 20 healthy controls (HC). 22.34%, 8.51%, 14.89%, and 54.26% of them contributed to one, two, three, and four sites: duodenal mucosa (DM), duodenal lumen (DL), rectal mucosa (RM), and rectal lumen (RL) of intestinal samples, respectively. Then 16S rRNA gene analysis was performed on these 283 samples. The result showed that IBS-D microbial communities have specific patterns at each intestinal site differing from that of HC. Across hosts and sites, Bacillus, Burkholderia, and Faecalibacterium were the representative genera in duodenum of IBS-D, duodenum of HC, and rectum of HC, respectively. Samples from mucosa and lumen in rectum were highly distinguishable, regardless of IBS-D and HC. Additionally, IBS-D patients have lower microbial co-abundance network connectivity. Moreover, RM site-specific biomarker: Bacteroides used alone or together with Prevotella and Oscillospira in RM showed outstanding performance in IBS-D diagnosis. Furthermore, Bacteroides and Prevotella in RM were strongly related to the severity of abdominal pain, abdominal discomfort, and bloating in IBS-D patients. In summary, this study also confirmed fecal microbial community could not fully characterize intestinal microbial communities. Among these site-specific microbial communities, RM microbial community would be more applicable in the diagnosis of IBS-D. IMPORTANCE Microbial community varied from one site to another along the gastrointestinal tract, but current studies about intestinal microbial community in IBS-D were mainly based on fecal samples. Based on 283 intestinal samples collected from DM, DL, RM, and RL of HC and IBS-D, we found different intestinal sites had their site-specific microbial patterns in IBS-D. Notably, RM site-specific microbes Bacteroides, Prevotella, and Oscillospira could be used to discriminate IBS-D from HC accurately. Our findings could help clinicians realize the great potential of the intestinal microbial community in RM for better diagnosis of IBS-D patients.

Interplay between gut microbiota and bile acids in diarrhoea-predominant irritable bowel syndrome: a review

Irritable bowel syndrome (IBS) is a common functional gastrointestinal disease that disturbs the physiology and psychology of patients and increases the burden on families, the healthcare system, society, and economic development, affecting more and more people around the world. Despite the multiple factors that account for IBS remaining incompletely studied, emerging evidence demonstrated the abnormal changes in gut microbiota and bile acids (BAs) metabolism closely associated with IBS. Moreover, microbiota drives significant modifications for BAs, consisting of deconjugation, 7α-dehydroxylation, oxidation, epimerization, desulfation, esterification, and so on, while BAs, in turn, affect the microbiota directly or indirectly. In light of the complex connection among gut microbiota, BAs, and IBS, it is urgent to review the latest research progress in this field. In this review, we described the disorders of intestinal microecology and BAs profiles in IBS-D and also highlighted the cross-talk between gut microbiota and BAs in the context of IBS-D. Integrating these, we suggest that new therapeutic strategies targeting the microbiota-BAs axis for IBS-D, even for other related diseases caused by bacteria-bile acid dysbiosis should be expected.

GWAS of stool frequency provides insights into gastrointestinal motility and irritable bowel syndrome

Gut dysmotility is associated with constipation, diarrhea, and functional gastrointestinal disorders like irritable bowel syndrome (IBS), although its molecular underpinnings are poorly characterized. We studied stool frequency (defined by the number of bowel movements per day, based on questionnaire data) as a proxy for gut motility in a GWAS meta-analysis including 167,875 individuals from UK Biobank and four smaller population-based cohorts. We identify 14 loci associated with stool frequency (p ≤ 5.0 × 10-8). Gene set and pathway analyses detected enrichment for genes involved in neurotransmitter/neuropeptide signaling and preferentially expressed in enteric motor neurons controlling peristalsis. PheWAS identified pleiotropic associations with dysmotility syndromes and the response to their pharmacological treatment. The genetic architecture of stool frequency correlates with that of IBS, and UK Biobank participants from the top 1% of stool frequency polygenic score distribution were associated with 5× higher risk of IBS with diarrhea. These findings pave the way for the identification of actionable pathological mechanisms in IBS and the dysmotility syndromes.

Gut microbiota profiles and the role of anti-CdtB and anti-vinculin antibodies in patients with functional gastrointestinal disorders (FGID)

BACKGROUND

Distinct faecal microbiota profiles are reported to be associated with various subtypes of IBS. Circulating antibodies to cytolethal distending toxin B (CdtB) and vinculin are proposed as biomarkers to identify post-infectious IBS. The aim of our study was to analyse serum levels of anti-CdtB and anti-vinculin antibodies in patients with different functional gastrointestinal disorders (FGID) and their correlation with the composition of faecal microbiome.

METHODS

The study cohort comprised 65 prospectively recruited individuals: 15 with diarrhoea-type-IBS (IBS-D), 13 with constipation-type-IBS (IBS-C), 15 with functional dyspepsia (FD) and 22 healthy controls. FGID subgroups were defined according to Rome III criteria. Serum levels of anti-CdtB and anti-vinculin antibodies were measured by ELISA. Faecal microbiome composition analysis and assessment of dysbiosis were performed by GA-map® Dysbiosis Test.

RESULTS

Positivity rate either for anti-CdtB or anti-vinculin antibodies was higher in the IBS-C group (76.9%) compared to IBS-D (40.0%), FD (60%) and healthy (63.6%) groups. Dysbiosis was more frequent in subjects positive for anti-CdtB antibodies and in IBS-C patients, who showed an increased amount of opportunistic/pro-inflammatory bacteria and reduced gut protective bacteria. IBS-C patients showed a high inter-individual variation of bacterial communities compared to other FGID subgroups and healthy individuals, whereas microbial profiles of patients with IBS-D and FD were overlapping with those of healthy controls. No bacteria markers showed significant differences between FGID subgroups and healthy controls.

CONCLUSION

Neither anti-CdtB/anti-vinculin antibodies nor faecal microbial profiles allowed to discriminate between specific FGID subgroups. Dysbiosis was more frequent in patients presenting with anti-CdtB antibodies and in IBS-C patients.

Microbiota and the irritable bowel syndrome

Gut microbiota plays a vital role in human health. The number of microorganisms inhabiting the gastrointestinal (GI) tract has been estimated to exceed 1013. The dominant genera in the human intestine are Firmicutes (more than 180 species of Lactobacillus), Actinobacteria (among others the Bifidobacteriae), Bacteroidetes (the most important is B. fragilis) and Proteobacteria (E. coli, Salmonella, Yersinia, Shigella, Vibrio, Haemophilus, etc.), but the composition of the flora varies individually, as well as in relation to factors such as host genetics, stress, diet, antibiotics and early childhood experiences. Irritable bowel syndrome (IBS) is one of the most common functional gastrointestinal disorders (FGIDs), which has now been renamed disorders of gut-brain interaction, which affect a large number of people worldwide. It is characterized by abdominal pain and altered bowel habits in the absence of obvious anatomic or physiologic abnormalities. It poses a negative economic impact to the global health care system in addition to reducing the quality of life in patients. The pathophysiology of IBS is not fully understood. In IBS subjects gut microbiota relative to healthy controls was observed with an increase in Enterobacteriaceae, Ruminococcus, Clostridium, Dorea species and a decrease of Lactobacillus, Bifidobacterium, and Faecalibacterium species. IBS with diarrhea predominance (IBS-D) IBS with mixed bowel habits (IBS-M) share similarities in the microbial profile. Recent studies suggest that perturbations within "brain-gut-microbiota" axis may lead to IBS development. The aim of this review was to highlight the potential role of gut microbiota on pathophysiological mechanisms underlying IBS.

Nutritional Contributions and Health Associations of Traditional Fermented Foods

The growing interest in the consumption and study of traditionally fermented food worldwide has led to the development of numerous scientific investigations that have focused on analyzing the microbial and nutritional composition and the health effects derived from the consumption of these foods. Traditionally fermented foods and beverages are a significant source of nutrients, including proteins, essential fatty acids, soluble fiber, minerals, vitamins, and some essential amino acids. Additionally, fermented foods have been considered functional due to their prebiotic content, and the presence of specific lactic acid bacterial strains (LAB), which have shown positive effects on the balance of the intestinal microbiota, providing a beneficial impact in the treatment of diseases. This review presents a bibliographic compilation of scientific studies assessing the effect of the nutritional content and LAB profile of traditional fermented foods on different conditions such as obesity, diabetes, and gastrointestinal disorders.