Multivariate modelling of faecal bacterial profiles of patients with IBS predicts responsiveness to a diet low in FODMAPs

Pharmabiotic Manipulation of the Microbiota in Gastrointestinal Disorders: A Clinical Perspective

The advent and widespread availability of high-throughput technology has revolutionized the assessment of the communities of microorganisms that inhabit the gastrointestinal tract––the gut microbiota. As our understanding of the role of the microbiota in health and human disease increases, so also do efforts to prevent and treat disease through the modulation of the microbiota. Several strategies are available to us and range from time honored approaches, such as antibiotics and probiotics, to changes in diet, the administration of prebiotics as food supplements, and fecal microbiota transplantation. Of these, diet is perhaps the most pervasive but often ignored modulator of the microbiota, and a failure to recognize its impact complicates the interpretation of many microbiota studies. The impacts of antibiotics on the microbiota are more complex than originally thought and, though antibiotics can be life-saving, their effects on commensal bacterial populations can be clinically significant. Though there have been many studies of, and even more claims made for, probiotics, the majority of available studies suffer from significant deficits in study design and execution and many claims remain to be substantiated. Though holding much promise, the study of prebiotics in human disease is still in its infancy. Possibilities other than the administration of live organisms have been identified through efforts to mine the microbiota for novel therapeutics and include: dead organisms, bacterial components, small molecules elaborated by bacteria, and even bacterial DNA. Accordingly, the term pharmabiotic has been introduced to encompass the full range of therapeutic possibilities that the microbiota offers.

A low FODMAP diet is associated with changes in the microbiota and reduction in breath hydrogen but not colonic volume in healthy subjects

Background & aims

Ingestion of poorly digested, fermentable carbohydrates (fermentable oligo-, di-, mono-saccharides and polyols; FODMAPs) have been implicated in exacerbating intestinal symptoms and the reduction of intake with symptom alleviation. Restricting FODMAP intake is believed to relieve colonic distension by reducing colonic fermentation but this has not been previously directly assessed. We performed a randomised controlled trial comparing the effect of a low FODMAP diet combined with either maltodextrin or oligofructose on colonic contents, metabolites and microbiota.

Methods

A parallel randomised controlled trial in healthy adults (n = 37). All subjects followed a low FODMAP diet for a week and supplemented their diet with either maltodextrin (MD) or oligofructose (OF) 7g twice daily. Fasted assessments performed pre- and post-diet included MRI to assess colonic volume, breath testing for hydrogen and methane, and stool collection for microbiota analysis.

Results

The low FODMAP diet was associated with a reduction in Bifidobacterium and breath hydrogen, which was reversed by oligofructose supplementation. The difference in breath hydrogen between groups post-intervention was 27ppm (95% CI 7 to 50, P<0.01). Colonic volume increased significantly from baseline in both groups (OF increased 110ml (19.6%), 95% CI 30ml to 190ml, P = 0.01; MD increased 90ml (15.5%), 95% CI 6ml to 175ml, P = 0.04) with no significant difference between them. Colonic volumes correlated with total breath hydrogen + methane. A divergence in Clostridiales abundance was observed with increased abundance of Ruminococcaceae in the maltodextrin group, while in the oligofructose group, Lachnospiraceae decreased. Subjects in either group with high methane production also tended to have high microbial diversity, high colonic volume and greater abundance of methanogens.

Conclusion

A low FODMAP diet reduces total bacterial count and gas production with little effect on colonic volume.

Towards microbiome-informed dietary recommendations for promoting metabolic and mental health: Opinion papers of the MyNewGut project

The gut microbiota coexists in partnership with the human host through adaptations to environmental and physiological changes that help maintain dynamic homeostatic healthy states. Break-down of this delicate balance under sustained exposure to stressors (e.g. unhealthy diets) can, however, contribute to the onset of disease. Diet is a key modifiable environmental factor that modulates the gut microbiota and its metabolic capacities that, in turn, could impact human physiology. On this basis, the diet and the gut microbiota could act as synergistic forces that provide resilience against disease or that speed the progress from health to disease states. Associations between unhealthy dietary patterns, non-communicable diseases and intestinal dysbiosis can be explained by this hypothesis. Translational studies showing that dietary-induced alterations in microbial communities recapitulate some of the pathological features of the original host further support this notion. In this introductory paper by the European project MyNewGut, we briefly summarize the investigations conducted to better understand the role of dietary patterns and food components in metabolic and mental health and the specificities of the microbiome-mediating mechanisms. We also discuss how advances in the understanding of the microbiome's role in dietary health effects can help to provide acceptable scientific grounds on which to base dietary advice for promoting healthy living.

Update on the Gastrointestinal Microbiome in Systemic Sclerosis

PURPOSE OF REVIEW

Accumulating evidence suggests that gut microbiota affect the development and function of the immune system and may play a role in the pathogenesis of autoimmune diseases. The purpose of this review is to summarize recent studies reporting gastrointestinal microbiota aberrations associated with the systemic sclerosis disease state.

RECENT FINDINGS

The studies described herein have identified common changes in gut microbial composition. Specifically, patients with SSc have decreased abundance of beneficial commensal genera (e.g., Faecalibacterium, Clostridium, and Bacteroides) and increased abundance of pathobiont genera (e.g., Fusobacterium, Prevotella, Erwinia). In addition, some studies have linked specific genera with the severity of gastrointestinal symptoms in systemic sclerosis. More research is needed to further characterize the gastrointestinal microbiota in systemic sclerosis and understand how microbiota perturbations can affect inflammation, fibrosis, and clinical outcomes. Interventional studies aimed at addressing/correcting these perturbations, either through dietary modification, pro/pre-biotic supplementation, or fecal transplantation, may lead to improved outcomes for patients with systemic sclerosis.

Role of the gut microbiota in nutrition and health

Ana M Valdes and colleagues discuss strategies for modulating the gut microbiota through diet and probiotics

The role of diet in the management of irritable bowel syndrome: a focus on FODMAPs

Irritable bowel syndrome is a common condition that negatively impacts quality of life and results in significant health care expenditures. The vast majority of IBS patients associate their symptoms with eating. Numerous randomized, controlled trials suggest that restriction of dietary FODMAPs improves overall symptoms, abdominal pain, bloating and quality of life in more than half of IBS sufferers. There is emerging data which suggests that other diets (gluten free, guided elimination diets) might also be of benefit to IBS patients. Areas covered: Comprehensive literature review on dietary therapies available for IBS to date and exploration into individualized dietary therapy development based on diagnostic testing. Expert commentary: FODMAP elimination identifies IBS patients who are sensitive to FODMAPs. Responders should undergo a structured reintroduction of foods containing FODMAPs to determine a patient's sensitivities. This information can then be used to create a personalized, less restrictive low FODMAP diet. Future research should focus on the identification of other effective diet therapies focusing on supplementation of functional foods in addition to elimination and the development of biomarker-based diet treatment plans which identify the right treatment for the right patient.

Fecal microbiota transplantation for managing irritable bowel syndrome

Irritable bowel syndrome (IBS) is a widespread gastrointestinal disorder affecting 11.2% of the world adult population. The intestinal microbiome is thought to play a pivotal role in the pathophysiology of IBS. The composition of the fecal microbiome in IBS patients differs from that in healthy individuals, but the exact bacteria species involved in the development of IBS remain to be determined. There is also an imbalance between useful and harmful bacteria (dysbiosis) in the intestinal microbiome in patients with IBS. Consuming prebiotics, probiotics, or synbiotics has a limited effect on IBS symptoms. In contrast, fecal microbiome transplantation (FMT) in IBS patients reverses the dysbiosis to normobiosis and reduces the IBS symptoms in about 70% of patients, and is not associated with any serious adverse events. Area covered: The available data on the microbiome and FMT in IBS regarding the efficacy of FMT in managing IBS were found using a PubMed search of these topics. Expert commentary: FMT is a promising tool for managing irritable syndrome. It appears to be effective, easy, and inexpensive procedure. However, more controlled studies involving larger cohorts of IBS are needed before FMT can be used as a routine procedure in the clinic.

Dysbiosis in Functional Bowel Disorders

Functional bowel disorders (FBD) resemble a group of diseases of the gastrointestinal (GI) tract that are without a clear pathogenesis; the best known is probably the "irritable bowel syndrome" (IBS). Only recently we have been able to explore the role of the gut microbiota in FBD due to progress in microbiological analytic techniques. There are different ways to explore the role of the gut microbiota and its dysbiosis in FBD. Comparison of the microbial composition in a group of patients with FBD, for example, with IBS to a group of healthy volunteers is one way. Studies have shown that the microbiota in FBD is different from that of healthy controls, but the recorded differences are not necessarily specific for FBD, they may also occur in other diseases. Another approach to explore the role of the gut microbiota in FBD is to challenge the existing "flora" with novel bacteria (probiotics) or with nutritional substrates that stimulate bacterial growth (prebiotics). More than 60 such trials including several thousand patients have been performed in IBS. These studies have produced mixed outcome: some probiotics appear to be better than others, and some appear to work only for a part of the IBS symptoms and not for all. An extreme form of this approach is the transfer of an entire microbiota from 1 healthy person to another, called fecal microbiota transplantation. This has rarely been tested in FBD but is not without risk in benign disorders.

A Review of Microbiota and Irritable Bowel Syndrome: Future in Therapies

Irritable bowel syndrome (IBS), one of the most frequent digestive disorders, is characterized by chronic and recurrent abdominal pain and altered bowel habit. The origin seems to be multifactorial and is still not well defined for the different subtypes. Genetic, epigenetic and sex-related modifications of the functioning of the nervous and immune-endocrine supersystems and regulation of brain-gut physiology and bile acid production and absorption are certainly involved. Acquired predisposition may act in conjunction with infectious, toxic, dietary and life event-related factors to enhance epithelial permeability and elicit mucosal microinflammation, immune activation and dysbiosis. Notably, strong evidence supports the role of bacterial, viral and parasitic infections in triggering IBS, and targeting microbiota seems promising in view of the positive response to microbiota-related therapies in some patients. However, the lack of highly predictive diagnostic biomarkers and the complexity and heterogeneity of IBS patients make management difficult and unsatisfactory in many cases, reducing patient health-related quality of life and increasing the sanitary burden. This article reviews specific alterations and interventions targeting the gut microbiota in IBS, including prebiotics, probiotics, synbiotics, non-absorbable antibiotics, diets, fecal transplantation and other potential future approaches useful for the diagnosis, prevention and treatment of IBS.

Exploring Gut Microbiota Composition as an Indicator of Clinical Response to Dietary FODMAP Restriction in Patients with Irritable Bowel Syndrome

BACKGROUND

A diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) may relieve symptoms of irritable bowel syndrome (IBS). However, nutritional counseling is resource-demanding and not all patients will benefit.

AIMS

To explore whether gut microbial composition may identify symptom response to a low-FODMAP diet in patients with IBS.

METHODS

Patients were recruited consecutively to participate in a 4-week FODMAP-restricted diet. Response to diet was defined as ≥ 50% decrease in IBS symptom severity scores (IBS-SSS) compared to baseline. Fecal microbiota were analyzed by a commercially available method (the GA-map™ Dysbiosis Test), assessing 54 bacterial markers targeting more than 300 bacteria at different taxonomic levels.

RESULTS

Sixty-one patients (54 F; 7 M) were included: 32 (29 F; 3 M) classified as responders and 29 (25 F; 4 M) as non-responders. Ten of the 54 bacterial markers differed significantly between responders and non-responders. Based on median values (used as cutoff) of responders for these 10 bacterial markers, we constructed a Response Index (RI): Each patient was given a point when the value for each selected bacterial marker differed from the cutoff. These points were summed up, giving an RI from 0 to 10. Patients with RI > 3 were 5 times more likely to respond (OR = 5.05, 95% CI [1.58; 16.10]), and the probability to respond was 83.4%, 95% CI [61.2-94%].

CONCLUSIONS

Gut microbial composition, assessed by using a new RI, may constitute a tool to identify patients that are likely to respond to dietary FODMAP restriction.

The Gut-Brain Axis and the Microbiome: Clues to Pathophysiology and Opportunities for Novel Management Strategies in Irritable Bowel Syndrome (IBS)

Irritable bowel syndrome (IBS) is one of the most common of all medical disorders worldwide and, while for some it represents no more than a nuisance, for others it imposes significant negative impacts on daily life and activities. IBS is a heterogeneous disorder and may well have a number of causes which may lie anywhere from the external environment to the contents of the gut lumen and from the enteric neuromuscular apparatus and the gut immune system to the central nervous system. Consequently, the paradigm of the gut-brain axis, which includes the participation of these various factors, has proven a useful model to assist clinicians and patients alike in understanding the genesis of symptoms in IBS. Now, given the widespread interest in the gut microbiome in health and disease, in general, reports of disordered enteric bacterial communities in IBS, and experimental data to indicate that components of the gut microbiota can influence brain morphology and function, as well as behavior and cognition, this concept has been extended to encompass the microbiota-gut-brain axis. The implications of this novel concept to the assessment and management of IBS will be explored in this review.

Dietary therapies for functional bowel symptoms: Recent advances, challenges, and future directions

BACKGROUND

Functional gastrointestinal symptoms in irritable bowel syndrome (IBS) and quiescent inflammatory bowel disease (IBD) cause significant morbidity and a reduction in quality of life. Multiple dietary therapies are now available to treat these symptoms, but supporting evidence for many is limited. In addition to a further need for studies demonstrating efficacy and mechanism of action of dietary therapies, the risk of nutritional inadequacy, alterations to the microbiome and changes in quality of life are key concerns requiring elucidation. Identifying predictors of response to dietary therapy is an important goal as management could be tailored to the individual to target specific dietary components, and thereby reduce the level of dietary restriction necessary.

PURPOSE

This review discusses the available dietary therapies to treat symptoms in patients with IBS and patients with quiescent IBD suffering from IBS symptoms, with the aim to understand where current dietary evidence lies and how to move forward in dietary research in this field.

Evaluation of a faecal dysbiosis test for irritable bowel syndrome in subjects with and without obesity

Biomarkers for irritable bowel syndrome (IBS) are demanded. An altered faecal microbiome has been reported in subjects with IBS and could be a valuable biomarker. This study evaluated the diagnostic properties of a new test for faecal dysbiosis, designed to distinguish IBS from healthy volunteers and compared the prevalence rates of dysbiosis related to IBS and morbid obesity. Subjects with and without morbid obesity and IBS were included. The faecal microbiota was assessed with GA-map^TM Dysbiosis Test (Genetic Analysis AS, Oslo, Norway). The test result was given as dysbiosis (yes/no). Comparisons were made between four groups: subjects with IBS and morbid obesity (IBS+/MO+); subjects without IBS and with morbid obesity (IBS-/MO+); subjects with IBS and without morbid obesity (IBS+/MO-); and healthy volunteers (IBS-/MO-).The prevalence rates of dysbiosis in the groups IBS+/MO+, IBS-/MO+, IBS+/MO- and IBS-/MO- were 18/28 (64%), 45/71 (63%), 31/63 (49%) and 38/91 (42%). Dysbiosis was more prevalent in subjects with morbid obesity, both in those with and without IBS, than in healthy volunteers (p values .04 and .006). Used as a diagnostic test for IBS in subjects without morbid obesity, the positive and negative likelihood ratios (LR) were 1.18 (0.83-1.67) and 0.87 (0.65-1.18), respectively, and in subjects with morbid obesity the LR were 1.01 (95% CI: 0.73-1.41) and 0.98 (0.54-1.75) respectively. The dysbiosis test was unsuitable as a diagnostic test for IBS. Dysbiosis was statistically significantly associated with morbid obesity, but not with IBS.

Microbiome at the Frontier of Personalized Medicine

The genomic revolution promises to transform our approach to treat patients by individualizing treatments, reducing adverse events, and decreasing health care costs. The early advances using this have been realized primarily by optimizing preventive and therapeutic approaches in cancer using human genome sequencing. The ability to characterize the microbiome, which includes all the microbes that reside within and upon us and all their genetic elements, using next-generation sequencing allows us to now incorporate this important contributor to human disease into developing new preventive and therapeutic strategies. In this review we highlight the importance of the microbiome in all aspects of human disease, including pathogenesis, phenotype, prognosis, and response to treatment, as well as their role as diagnostic and therapeutic biomarkers. We provide a role for next-generation sequencing in both precise microbial identification of infectious diseases and characterization of microbial communities and their function. Taken together, the microbiome is emerging as an integral part of precision medicine approach as it not only contributes to interindividual variability in all aspects of a disease but also represents a potentially modifiable factor that is amenable to targeting by therapeutics.

Nutrition in the management of gastrointestinal diseases and disorders: the evidence for the low FODMAP diet

A growing interest from both physicians and patients is fueling research in the interaction of symptoms related to irritable bowel syndrome (IBS) and diet, particularly the low FODMAP diet. Recent studies further define the role of these short-chain fermentable carbohydrates on IBS symptoms and their effects in different parts of the gastrointestinal tract. Mounting evidence supports the use of a low FODMAP diet in the clinical setting, but this dietary approach is not without potential drawbacks. This review illustrates the mechanisms by which the low FODMAP diet leads to improvement in IBS symptoms, summarizes the available clinical evidence, and offers practical advice regarding implementation of this dietary strategy.

Severe intestinal dysbiosis is prevalent in primary Sjögren's syndrome and is associated with systemic disease activity

Background

Altered microbial composition of the intestine, commonly referred to as dysbiosis, has been associated with several autoimmune diseases including primary Sjögren’s syndrome (pSS). The aims of the current study were to study the intestinal microbial balance in pSS and to identify clinical features associated with dysbiosis.

Methods

Forty-two consecutive pSS patients and 35 age-matched and sex-matched control subjects were included in the study in an open clinic setting. Stool samples were analyzed for intestinal dysbiosis using a validated 16S rRNA-based microbiota test (GA-map™ Dysbiosis Test; Genetic Analysis, Oslo, Norway). Dysbiosis and severe dysbiosis were defined in accordance with the manufacturer’s instructions. Patients were evaluated with regard to disease activity (European League Against Rheumatism (EULAR) Sjögren’s Syndrome Disease Activity Index (ESSDAI) and Clinical ESSDAI (ClinESSDAI)). In addition, patients were examined for laboratory and serological features of pSS as well as fecal calprotectin levels.

Furthermore, patients were investigated regarding patient-reported outcomes for pSS (EULAR Sjögren’s Syndrome Patient Reported Index (ESSPRI)) and irritable bowel syndrome (IBS)-like symptoms according to the Rome III criteria.

Results

Severe dysbiosis was more prevalent in pSS patients in comparison to controls (21 vs 3%; p = 0.018). Subjects with pSS and severe dysbiosis had higher disease activity as evaluated by the ESSDAI total score (13 vs 5; p = 0.049) and the ClinESSDAI total score (12 vs 5; p = 0.049), lower levels of complement component 4 (0.11 vs 0.17 g/L; p = 0.004), as well as higher levels of fecal calprotectin (110 vs 33 μg/g; p = 0.001) compared to the other pSS patients. In contrast, severe dysbiosis among pSS patients was not associated with disease duration, IBS-like symptoms, or the ESSPRI total score.

Conclusions

Severe intestinal dysbiosis is a prevalent finding in pSS and is associated both with clinical and laboratory markers of systemic disease activity as well as gastrointestinal inflammation. Further studies are warranted to elucidate a potential causative link between dysbiosis and pSS.

Modulation of the gut microbiota: a focus on treatments for irritable bowel syndrome

Irritable bowel syndrome (IBS), which is characterized by recurrent abdominal pain and disordered bowel habits, is one of the most common functional bowel disorders. IBS is a substantial burden on both patient health-related quality of life and healthcare costs. Several pathophysiologic mechanisms have been postulated for the occurrence of IBS, including altered gastrointestinal motility, visceral hypersensitivity, changes in gut permeability, immune activation, gut-brain dysregulation, central nervous system dysfunction, and changes in the gut microbiota. Of note, both qualitative and quantitative differences have been observed in the gut microbiota of a population with IBS versus a healthy population. Because of the substantial interest in the gut microbiota and its role as a therapeutic target in IBS, this article provides an overview of specific interventions with the potential to modulate the gut microbiota in IBS, including elimination diets, prebiotics, probiotics, synbiotics, and nonsystemic antibiotics. Although probiotics and synbiotics are generally well tolerated, differences in the composition and concentration of different bacterial species and inclusion or exclusion of prebiotic components varies widely across studies and has prevented strong recommendations on their use in IBS. For nonsystemic antibiotics, rifaximin is indicated in the United States for the treatment of IBS with diarrhea in adults and has been shown to be efficacious and well tolerated in well-designed clinical trials. Overall, more consistent evidence is needed regarding the efficacy and safety of elimination diets, prebiotics, probiotics, and synbiotics for the treatment of patients with IBS. Furthermore, additional well-designed studies are needed that examine alterations in the gut microbiota that occur with these interventions and their potential associations with clinical symptoms of IBS.

From clinical uncertainties to precision medicine: the emerging role of the gut barrier and microbiome in small bowel functional diseases

Over the last decade, remarkable progress has been made in the understanding of disease pathophysiology. Many new theories expound on the importance of emerging factors such as microbiome influences, genomics/omics, stem cells, innate intestinal immunity or mucosal barrier complexities. This has introduced a further dimension of uncertainty into clinical decision-making, but equally, may shed some light on less well-understood and difficult to manage conditions. Areas covered: Comprehensive review of the literature on gut barrier and microbiome relevant to small bowel pathology. A PubMed/Medline search from 1990 to April 2017 was undertaken and papers from this range were included. Expert commentary: The scenario of clinical uncertainty is well-illustrated by functional gastrointestinal disorders (FGIDs). The movement towards achieving a better understanding of FGIDs is expressed in the Rome IV guidelines. Novel diagnostic and therapeutic protocols focused on the GB and SB microbiome can facilitate diagnosis, management and improve our understanding of the underlying pathological mechanisms in FGIDs.