A novel stepwise integrative analysis pipeline reveals distinct microbiota-host interactions and link to symptoms in irritable bowel syndrome

AbstractAlthough incompletely understood, microbiota-host interactions are assumed to be altered in irritable bowel syndrome (IBS). We, therefore, aimed to develop a novel analysis pipeline tailored for the integrative analysis of microbiota-host interactions and association to symptoms and prove its utility in a pilot cohort. A multilayer stepwise integrative analysis pipeline was developed to visualize complex variable associations. Application of the pipeline was demonstrated on a dataset of IBS patients and healthy controls (HC), using the R software package to analyze colonic host mRNA and mucosal microbiota (16S rRNA gene sequencing), as well as gastrointestinal (GI) and psychological symptoms. In total, 42 IBS patients (57% female, mean age 33.6 (range 18–58)) and 20 HC (60% female, mean age 26.8 (range 23–41)) were included. Only in IBS patients, mRNA expression of Toll-like receptor 4 and genes associated with barrier function (PAR2, OCLN, TJP1) intercorrelated closely, suggesting potential functional relationships. This host genes-based “permeability cluster” was associated to mucosa-adjacent Chlamydiae and Lentisphaerae, and furthermore associated to satiety as well as to anxiety, depression and fatigue. In both IBS patients and HC, chromogranins, secretogranins and TLRs clustered together. In IBS patients, this host genes-based “immune-enteroendocrine cluster” was associated to specific members of Firmicutes, and to depression and fatigue, whereas in HC no significant association to microbiota was identified. We have developed a stepwise integrative analysis pipeline that allowed identification of unique host-microbiota intercorrelation patterns and association to symptoms in IBS patients. This analysis pipeline may aid in advancing the understanding of complex variable associations in health and disease.

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Integrative analysis of the gut microbiome and metabolome in a rat model with stress induced irritable bowel syndrome

Scientific Reports ◽

10.1038/s41598-021-97083-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Yue Hu ◽

Fang Chen ◽

Haiyong Ye ◽

Bin Lu

Keyword(s):

Irritable Bowel Syndrome ◽

Gut Microbiota ◽

Rat Model ◽

Gut Microbiome ◽

16S Rrna Gene Sequencing ◽

Metabolic Phenotype ◽

Control Group ◽

Rrna Gene ◽

Microbial Dysbiosis ◽

Irritable Bowel

AbstractStress is one of the major causes of irritable bowel syndrome (IBS), which is well-known for perturbing the microbiome and exacerbating IBS-associated symptoms. However, changes in the gut microbiome and metabolome in response to colorectal distention (CRD), combined with restraint stress (RS) administration, remains unclear. In this study, CRD and RS stress were used to construct an IBS rat model. The 16S rRNA gene sequencing was used to characterize the microbiota in ileocecal contents. UHPLC-QTOF-MS/MS assay was used to characterize the metabolome of gut microbiota. As a result, significant gut microbial dysbiosis was observed in stress-induced IBS rats, with the obvious enrichment of three and depletion of 11 bacterial taxa in IBS rats, when compared with those in the control group (q < 0.05). Meanwhile, distinct changes in the fecal metabolic phenotype of stress-induced IBS rats were also found, including five increased and 19 decreased metabolites. Furthermore, phenylalanine, tyrosine and tryptophan biosynthesis were the main metabolic pathways induced by IBS stress. Moreover, the altered gut microbiota had a strong correlation with the changes in metabolism of stress-induced IBS rats. Prevotella bacteria are correlated with the metabolism of 1-Naphthol and Arg.Thr. In conclusion, the gut microbiome, metabolome and their interaction were altered. This may be critical for the development of stress-induced IBS.

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No distinct microbiome signature of irritable bowel syndrome found in a Swedish random population

Gut ◽

10.1136/gutjnl-2019-318717 ◽

2019 ◽

Vol 69 (6) ◽

pp. 1076-1084 ◽

Cited By ~ 13

Author(s):

Luisa W Hugerth ◽

Anna Andreasson ◽

Nicholas J Talley ◽

Anna M Forsberg ◽

Lars Kjellström ◽

...

Keyword(s):

Irritable Bowel Syndrome ◽

Gut Microbiome ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Self Rated Health ◽

Faecal Samples ◽

Rrna Gene Sequencing ◽

Irritable Bowel ◽

Taxonomic Groups ◽

Faecal Microbiome

ObjectiveThe ethiopathogenesis of irritable bowel syndrome (IBS) is unknown. While a link to the gut microbiome is postulated, the heterogeneity of the healthy gut makes it difficult to draw definitive conclusions. We aimed to describe the faecal and mucosa-associated microbiome (MAM) and health correlates on a community cohort of healthy and IBS individuals with no colonoscopic findings.DesignThe PopCol study recruited a random sample of 3556 adults; 745 underwent colonoscopy. IBS was defined by Rome IV criteria and organic disease excluded. 16S rRNA gene sequencing was conducted on sigmoid biopsy samples from 376 representative individuals (63 IBS cases) and faecal samples from 185 individuals (32 IBS cases).ResultsWhile sigmoid MAM was dominated by Lachnospiraceae, faeces presented a higher relative abundance of Ruminococcaceae. Microbial richness in MAM was linearly correlated to that in faeces from the same individual (R²=0.255, p<3E-11) as was diversity (R²=0.06, p=0.0022). MAM diversity decreased with increasing body mass index (BMI; Pearson’s r=−0.1, p=0.08) and poorer self-rated health (r=−0.15, p=0.007), but no other health correlates. Faecal microbiome diversity was correlated to stool consistency (r=−0.16, p=0.043). Several taxonomic groups were correlated to age, BMI, depression and self-reported health, including Coprococcus catus associated with lower levels of depression (r=−0.003, p=0.00017). The degree of heterogeneity observed between IBS patients is higher than that observed between healthy individuals.ConclusionsNo distinct microbial signature was observed in IBS. Individuals presenting with low self-rated health or high BMI have lower gut microbiome richness.

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Efficacy of faecal microbiota transplantation for patients with irritable bowel syndrome in a randomised, double-blind, placebo-controlled study

Gut ◽

10.1136/gutjnl-2019-319630 ◽

2019 ◽

Vol 69 (5) ◽

pp. 859-867 ◽

Cited By ~ 36

Author(s):

Magdy El-Salhy ◽

Jan Gunnar Hatlebakk ◽

Odd Helge Gilja ◽

Anja Bråthen Kristoffersen ◽

Trygve Hausken

Keyword(s):

Irritable Bowel Syndrome ◽

Secondary Outcome ◽

Controlled Study ◽

Rrna Gene ◽

Faecal Microbiota ◽

Double Blind ◽

Double Blind Placebo ◽

Faecal Microbiota Transplantation ◽

Link Type ◽

Irritable Bowel

ObjectiveFaecal microbiota transplantation (FMT) from healthy donors to patients with irritable bowel syndrome (IBS) has been attempted in two previous double-blind, placebo-controlled studies. While one of those studies found improvement of the IBS symptoms, the other found no effect. The present study was conducted to clarify these contradictory findings.DesignThis randomised, double-blind, placebo-controlled study randomised 165 patients with IBS to placebo (own faeces), 30 g FMT or 60 g FMT at a ratio of 1:1:1. The material for FMT was obtained from one healthy, well-characterised donor, frozen and administered via gastroscope. The primary outcome was a reduction in the IBS symptoms at 3 months after FMT (response). A response was defined as a decrease of 50 or more points in the total IBS symptom score. The secondary outcome was a reduction in the dysbiosis index (DI) and a change in the intestinal bacterial profile, analysed by 16S rRNA gene sequencing, at 1 month following FMT.ResultsResponses occurred in 23.6%, 76.9% (p<0.0001) and 89.1% (p<00.0001) of the patients who received placebo, 30 g FMT and 60 g FMT, respectively. These were accompanied by significant improvements in fatigue and the quality of life in patients who received FMT. The intestinal bacterial profiles changed also significantly in the groups received FMT. The FMT adverse events were mild self-limiting gastrointestinal symptoms.ConclusionsFMT is an effective treatment for patients with IBS. Utilising a well-defined donor with a normal DI and favourable specific microbial signature is essential for successful FMT. The response to FMT increases with the dose.Trial registrationwww.clinicaltrials.gov (NCT03822299) and www.cristin.no (ID657402).

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Primer, Pipelines, Parameters: Issues in 16S rRNA Gene Sequencing

mSphere ◽

10.1128/msphere.01202-20 ◽

2021 ◽

Vol 6 (1) ◽

Author(s):

Isabel Abellan-Schneyder ◽

Monica S. Matchado ◽

Sandra Reitmeier ◽

Alina Sommer ◽

Zeno Sewald ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Analysis Pipeline ◽

Reference Databases ◽

Clustering Approach ◽

Rrna Gene Sequencing

In 16S rRNA gene sequencing, certain bacterial genera were found to be underrepresented or even missing in taxonomic profiles when using unsuitable primer combinations, outdated reference databases, or inadequate pipeline settings. Concerning the last, quality thresholds as well as bioinformatic settings (i.e., clustering approach, analysis pipeline, and specific adjustments such as truncation) are responsible for a number of observed differences between studies.

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Mucosa-Associated Microbiota in Patients with Irritable Bowel Syndrome: A Comparison of Subtypes

Digestion ◽

10.1159/000512167 ◽

2020 ◽

pp. 1-8

Author(s):

Hiroshi Matsumoto ◽

Akiko Shiotani ◽

Ryo Katsumata ◽

Shinya Fukushima ◽

Yukiko Handa ◽

...

Keyword(s):

Irritable Bowel Syndrome ◽

Sigmoid Colon ◽

Terminal Ileum ◽

Lysine Biosynthesis ◽

Control Group ◽

Rrna Gene ◽

Unifrac Distance ◽

Linear Discriminant ◽

Α Diversity ◽

Irritable Bowel

Background: Most studies on gut microbiome of irritable bowel syndrome (IBS) have focused on fecal microbiota, instead of mucosa-associated microbiota (MAM). Aims: The aim of this study wasto investigate the MAM in IBS patients including the difference in subtypes of IBS, namely, diarrhea-predominant IBS (IBS-D) and constipation-predominant IBS (IBS-C). Methods: Endoscopic brush samples were taken from terminal ileum and sigmoid colon of patients with IBS (17 IBS-D patients and 7 IBS-C patients) and 10 healthy controls. The MAM of samples was profiled by 16S rRNA gene amplicon sequencing. Potential changes in the MAM at the functional level were evaluated using PICRUSt software and the KEGG database. Results: There were no differences in MAM composition between terminal ileum and sigmoid colon according to β-diversity based on the UniFrac distance. In view of α-diversity, Shannon (evenness) but not Chao1 (richness) or observed operational taxonomic units tended to be lower in sigmoid colon MAM of IBS-C and IBS-D than the control group. The abundance of 4 genera in the sigmoid colon and 7 genera in the terminal ileum was significantly different among the 3 groups. Linear discriminant analysis effect size (LEfSe) showed that the genera of Ruminococcus, Akkermansia, Butyrivibrio, Methylobacterium, and Microbacterium and the family Erysipelotrichaceae were significantly higher in the IBS-C group, and the abundance of the genera Streptococcus, Acidaminococcus, Butyricicoccus, and Parvimonas was significantly higher in the IBS-D group. In addition, the proportion of genes responsible for the secretion system and LPS biosynthesis was significantly higher and that for methane metabolism, lysine biosynthesis, and enzyme families was significantly lower in the IBS-D group than in the IBS-C group. Conclusion: Dysbiosis pattern and the function of the microbiome seem to be different among subtypes of IBS, and MAM may play a crucial role in IBS symptom generation.

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FODMAPs, but Not Gluten, Affect Symptoms and the Fecal Environment in Subjects With Irritable Bowel Syndrome. A Double Blinded-Randomized Three-Way Crossover Study

Current Developments in Nutrition ◽

10.1093/cdn/nzab044_032 ◽

2021 ◽

Vol 5 (Supplement_2) ◽

pp. 601-601

Author(s):

Elise Nordin ◽

Carl Brunius ◽

Johan Dicksved ◽

Erik Pelve ◽

Rikard Landberg ◽

...

Keyword(s):

Irritable Bowel Syndrome ◽

Gut Microbiota ◽

Rrna Gene ◽

Microbiota Composition ◽

Double Blind ◽

Funding Sources ◽

Irritable Bowel ◽

Double Blinded ◽

Gut Microbiota Composition ◽

Modest Effect

Abstract Objectives Irritable bowel syndrome (IBS) symptoms have been associated with fermentable oligo-, di-, monosaccharides and polyols (FODMAPs) as well as gluten. We aimed to evaluate the effects of provocations with diets rich in such components on IBS symptoms. We further aimed to study effects of FODMAPs and gluten on microbiota and if the microbiota composition was related to the severity of IBS symptoms. Methods A double-blind, placebo-controlled, randomised three-way crossover design (n = 110) was conducted. From run-in and throughout the study, IBS subjects maintained a diet with minimal FODMAP content and no gluten. Participants were block-randomised to one-week interventions with FODMAPs (50 g/day), gluten (17.3 g/day) or placebo, separated by one week of wash-out. Fecal samples were collected after each study week and analyzed for gut microbiota composition by sequencing of 16S rRNA gene amplicons. IBS symptoms were monitored by the IBS severity scoring system (IBS-SSS). Results In subjects with moderate to severe IBS (n = 103), FODMAPs caused higher total IBS-SSS (mean [SE] = 240 [9]) than placebo (208 [9]; p = 0.00056) or gluten (198 [9]; p = 0.013), but with no difference between gluten and placebo (p = 1.0). Relative abundance of Anaerostipes, Bifidobacterium and Faecalibacterium were higher after FODMAP compared to placebo. We found no difference in gut microbiota composition between gluten and placebo and no significant correlations between genera and severity of IBS-SSS. Conclusions In subjects with IBS, FODMAPs had an adverse but modest effect on typical IBS symptoms, whereas gluten had no effect. The microbiota composition was affected by the FODMAP but not the gluten intervention, in comparison to placebo. None of these differences were correlated to the severity of symptoms reflected in IBS-SSS, suggesting no apparent link between gut microbiota composition and IBS symptoms following intervention. Funding Sources Formas and the Swedish Research Council.

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Redefining Lactose as a Conditional Prebiotic

Canadian Journal of Gastroenterology ◽

10.1155/2004/350732 ◽

2004 ◽

Vol 18 (3) ◽

pp. 163-167 ◽

Cited By ~ 27

Author(s):

Andrew Szilagyi

Keyword(s):

Irritable Bowel Syndrome ◽

Present Article ◽

Exponential Growth ◽

Dairy Products ◽

Clinical Knowledge ◽

Host Interactions ◽

Lactose Tolerance ◽

Irritable Bowel

Lactose in dairy products is maldigested by up to 70% to 75% of the world's population and many people may therefore suffer symptoms reminiscent of irritable bowel syndrome. As a result, most research to date has concentrated on ways of improving lactose tolerance to enhance dairy as a source of nutrition. However, research on other possible benefits of lactose and its maldigestion has lagged. In view of an exponential growth in the understanding of intestinal microfloral host interactions and the expanding therapeutical potential of probiotics, a reassessment of the role of lactose as a potential prebiotic in lactase nonpersistent subjects is required. Gibson and Roberfroid introduced the concept of prebiotics and outlined definitive requirements for such a compound. The present article examines scientific and clinical knowledge about the properties of lactose and argues that in lactase nonpersistent subjects, lactose qualifies as a prebiotic.

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Probiotics, Symptoms, and Gut Microbiota: What Are the Relations? A Randomized Controlled Trial in Subjects with Irritable Bowel Syndrome

Gastroenterology Research and Practice ◽

10.1155/2012/214102 ◽

2012 ◽

Vol 2012 ◽

pp. 1-6 ◽

Cited By ~ 12

Author(s):

Per G. Farup ◽

Morten Jacobsen ◽

Solveig C. Ligaarden ◽

Knut Rudi

Keyword(s):

Irritable Bowel Syndrome ◽

Gut Microbiota ◽

Direct Effect ◽

Controlled Trial ◽

Fecal Microbiota ◽

Rrna Gene ◽

Double Blind ◽

Once Daily ◽

Randomized Controlled ◽

Irritable Bowel

Introduction. Knowledge of the mechanism of action of probiotics in subjects with irritable bowel syndrome (IBS) is imperfect. Objective. This trial aimed at discriminating between a direct effect on the gut wall and an indirect effect caused by modulation of the fecal microbiota. Design. Randomized, double-blind, crossover trial. Material and Methods. Patients with IBS were given one capsule of 1010 CFU L. plantarum MF 1298 or placebo once daily. Symptoms were registered (score 0–15) and feces collected at the end of each period. The gut microbiota was analyzed with 16S rRNA gene analyses and results reported as proportions of Bacteroides, Faecalibacterium, and Lachnospiraceae and Simpson’s D diversity score. Results. Sixteen participants (11 women) with a mean age of 50 years (SD 11) were available for the analyses. Intake of L. plantarum MF 1298 was associated with a significant aggravation of symptoms, but neither intake of L. plantarum MF 1298 nor symptoms were associated with the composition of the fecal microbiota (P values >0.10). Conclusions. The trial indicates that the symptomatic aggravation related to intake of L. plantarum MF 1298 was a direct effect of the microbe on the gut wall and not caused by changes in the fecal microbiota.

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Covariation of the gut microbiome with diet in Aves

10.21203/rs.3.rs-19604/v1 ◽

2020 ◽

Author(s):

Kangpeng Xiao ◽

Yutan Fan ◽

Zhipeng Zhang ◽

Xuejuan Shen ◽

Xiaobing Li ◽

...

Keyword(s):

Gut Microbiome ◽

Dietary Diversity ◽

Basal Diet ◽

16S Rrna Gene Sequencing ◽

Vital Role ◽

Rrna Gene ◽

Host Interactions ◽

Multiple Factors ◽

The Past ◽

Rrna Gene Sequencing

Abstract Background:Research over the past few decades has revealed a vital role for the gut microbiome in the health of various animals including birds. Multiple factors can influence the gut microbiome. Opportunistic feeding and multiple other environment factors can influence the results, and bias the conclusions, when wild animals are used to study the influence of phylogeny and diet on their gut microbiomes. Therefore, to study this question in this study, we collected fecal samples from 43 species of Aves at one time to avoid influences such as geography, weather, and season. Results:Approaches based on both 16S rRNA gene sequencing (135 samples) and whole metagenome shotgun sequencing (17 samples) were used. Our data show that diets containing native starch will increase the abundance of Lactobacillus in gut microbiome, while those containing plant-derived fiber will mainly enrich the levels of Clostridium. Greater numbers of Fusobacteria and Proteobacteria are detected in carnivorous birds, while in birds fed a commercial corn-soybean basal diet, a stronger inner-connected microbial community containing Clostridia and Bacteroidia was enriched. Furthermore, a microbial functional analysis based on the metagenomic sequences showed that the function of microbes was adapted to different food types to achieve the most beneficial state for the hosts. Conclusions:The covariation of diet and gut microbiome identified in our study demonstrates modulation of the gut microbiome by dietary diversity and expands our knowledge of diet-microbiome-host interactions in birds.

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Molecular analysis of faecal and duodenal samples reveals significantly higher prevalence and numbers of Pseudomonas aeruginosa in irritable bowel syndrome

Journal of Medical Microbiology ◽

10.1099/jmm.0.022848-0 ◽

2011 ◽

Vol 60 (2) ◽

pp. 236-245 ◽

Cited By ~ 74

Author(s):

Angèle P. M. Kerckhoffs ◽

Kaouther Ben-Amor ◽

Melvin Samsom ◽

Michel E. van der Rest ◽

Joris de Vogel ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Irritable Bowel Syndrome ◽

Small Intestine ◽

Healthy Subjects ◽

Denaturing Gradient Gel Electrophoresis ◽

Pcr Analysis ◽

Rrna Gene ◽

Faecal Samples ◽

Small Intestinal ◽

Irritable Bowel

Intestinal microbiota may play a role in the pathophysiology of irritable bowel syndrome (IBS). In this case–control study, mucosa-associated small intestinal and faecal microbiota of IBS patients and healthy subjects were analysed using molecular-based methods. Duodenal mucosal brush and faecal samples were collected from 37 IBS patients and 20 healthy subjects. The bacterial 16S rRNA gene was amplified and analysed using PCR denaturing gradient gel electrophoresis (DGGE). Pooled average DGGE profiles of all IBS patients and all healthy subjects from both sampling sites were generated and fingerprints of both groups were compared. The DGGE band fragments which were confined to one group were further characterized by sequence analysis. Quantitative real-time PCR (q-PCR) was used to quantify the disease-associated microbiota. Averaged DGGE profiles of both groups were identical for 78.2 % in the small intestinal samples and for 86.25 % in the faecal samples. Cloning and sequencing of the specific bands isolated from small intestinal and faecal DGGE patterns of IBS patients showed that 45.8 % of the clones belonged to the genus Pseudomonas, of which Pseudomonas aeruginosa was the predominant species. q-PCR analysis revealed higher levels (P<0.001) of P. aeruginosa in the small intestine of IBS patients (8.3 %±0.950) than in the small intestine of healthy subjects (0.1 %±0.069). P. aeruginosa was also significantly (P<0.001) more abundant (2.34 %±0.31) in faeces of IBS patients than in faeces of healthy subjects (0.003 %±0.0027). This study shows that P. aeruginosa is detected more frequently and at higher levels in IBS patients than in healthy subjects, suggesting its potential role in the pathophysiology of IBS.

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