scholarly journals Leveraging 16S rRNA Microbiome Sequencing Data to Identify Bacterial Signatures for Irritable Bowel Syndrome

2021 ◽  
Vol 11 ◽  
Author(s):  
Yuxia Liu ◽  
Wenhui Li ◽  
Hongxia Yang ◽  
Xiaoying Zhang ◽  
Wenxiu Wang ◽  
...  
Keyword(s):  
Irritable Bowel Syndrome ◽  
16S Rrna ◽  
Statistical Significance ◽  
Critical Role ◽  
Gastrointestinal Disorder ◽  
Rrna Gene ◽  
Healthy Controls ◽  
Sequencing Data ◽  
Linear Discriminant ◽  
Irritable Bowel

Irritable bowel syndrome (IBS) is a chronic gastrointestinal disorder characterized by abdominal pain or discomfort. Previous studies have illustrated that the gut microbiota might play a critical role in IBS, but the conclusions of these studies, based on various methods, were almost impossible to compare, and reproducible microorganism signatures were still in question. To cope with this problem, previously published 16S rRNA gene sequencing data from 439 fecal samples, including 253 IBS samples and 186 control samples, were collected and processed with a uniform bioinformatic pipeline. Although we found no significant differences in community structures between IBS and healthy controls at the amplicon sequence variants (ASV) level, machine learning (ML) approaches enabled us to discriminate IBS from healthy controls at genus level. Linear discriminant analysis effect size (LEfSe) analysis was subsequently used to seek out 97 biomarkers across all studies. Then, we quantified the standardized mean difference (SMDs) for all significant genera identified by LEfSe and ML approaches. Pooled results showed that the SMDs of nine genera had statistical significance, in which the abundance of Lachnoclostridium, Dorea, Erysipelatoclostridium, Prevotella 9, and Clostridium sensu stricto 1 in IBS were higher, while the dominant abundance genera of healthy controls were Ruminococcaceae UCG-005, Holdemanella, Coprococcus 2, and Eubacterium coprostanoligenes group. In summary, based on six published studies, this study identified nine new microbiome biomarkers of IBS, which might be a basis for understanding the key gut microbes associated with IBS, and could be used as potential targets for microbiome-based diagnostics and therapeutics.

scholarly journals Mass spectrometry-based metabolomics for irritable bowel syndrome biomarkers

2019 ◽  
Vol 12 ◽  
pp. 175628481988642 ◽  
Author(s):  
Qihong Yu ◽  
Xinru Liu ◽  
Haojie Huang ◽  
Xingfeng Zheng ◽  
Xue Pan ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Irritable Bowel Syndrome ◽  
Gastrointestinal Disorder ◽  
Ultra Performance Liquid Chromatography ◽  
Healthy Controls ◽  
Multivariate Statistical ◽  
Clinical Trial Registration ◽  
Flight Mass Spectrometry ◽  
Hormone Biosynthesis ◽  
Irritable Bowel

Background: Irritable bowel syndrome (IBS) is a common gastrointestinal disorder without obvious structural abnormalities or consistent associated biomarkers, making its diagnosis difficult. In the present study, we used a urine-based metabolomics approach to identify IBS biomarkers. Methods: We used an ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) on urine samples from patients suffering from IBS and healthy controls. Data were coupled for multivariate statistical analysis methods. Results: We selected 30 differential metabolites associated with IBS and found steroid hormone biosynthesis and histidine metabolism alterations in patients with IBS that may be involved in the pathogenesis of the disease. In addition, we identified a panel of five metabolite markers composed of cortisone, citric acid, tiglylcarnitine, N6,-N6,-N6-trimethyl-L-lysine and L-histidine that could be used to discriminate between patients and healthy controls and may be appropriate as IBS diagnosis biomarkers. Conclusion: Our findings indicate that metabolomics combined with pattern recognition can be useful to identify disease diagnostic IBS markers. Clinical trial registration: ChiCTR1800020072

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

Digestion ◽  
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

<b><i>Background:</i></b> Most studies on gut microbiome of irritable bowel syndrome (IBS) have focused on fecal microbiota, instead of mucosa-associated microbiota (MAM). <b><i>Aims:</i></b> 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). <b><i>Methods:</i></b> 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. <b><i>Results:</i></b> There were no differences <i>in MAM composition between terminal</i> 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 <i>Ruminococcus</i>, <i>Akkermansia</i>, <i>Butyrivibrio</i>, <i>Methylobacterium</i>, and <i>Microbacterium</i> and the family Erysipelotrichaceae were significantly higher in the IBS-C group, and the abundance of the genera <i>Streptococcus</i>, <i>Acidaminococcus</i>, <i>Butyricicoccus</i>, and <i>Parvimonas</i> 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. <b><i>Conclusion:</i></b> 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.

Gut Microbiome and Its Role in the Pathophysiology of Irritable Bowel Syndrome

2021 ◽  
Vol 51 (4) ◽  
Author(s):  
Giada De Palma ◽  
Premysl Bercik
Keyword(s):  
Irritable Bowel Syndrome ◽  
Abdominal Pain ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Gastrointestinal Disorder ◽  
Healthy Controls ◽  
Fecal Microbiome ◽  
Targeted Treatments ◽  
Irritable Bowel ◽  
And Function

Irritable bowel syndrome is the most common functional gastrointestinal disorder, affecting up to 9% individuals globally. Although the etiology of this syndrome is likely heterogenous, it presents with its hallmark symptoms of abdominal pain and altered intestinal motility. Moreover, it is considered to be a disorder of the gut-brain interaction, and the microbiome has often been implicated as a central player in its pathophysiology. Patients with irritable bowel syndrome display altered composition and function of the gut microbiota compared to healthy controls. Microbiome directed therapies, such as probiotics, antibiotics and fecal microbiome transplantation, appear to be beneficial for both gut symptoms and psychiatric comorbidities. This review aims to recapitulate the available literature on the microbiome contribution to the pathophysiology and symptoms presentation of irritable bowel syndrome, as well as the current literature on microbiome-targeted treatments for this disease.

scholarly journals Molecular analysis of the luminal- and mucosal-associated intestinal microbiota in diarrhea-predominant irritable bowel syndrome

2011 ◽  
Vol 301 (5) ◽  
pp. G799-G807 ◽  
Author(s):  
Ian M. Carroll ◽  
Tamar Ringel-Kulka ◽  
Temitope O. Keku ◽  
Young-Hyo Chang ◽  
Christopher D. Packey ◽  
...  
Keyword(s):  
Irritable Bowel Syndrome ◽  
Intestinal Microbiota ◽  
Microbial Community Composition ◽  
Rrna Gene ◽  
Healthy Controls ◽  
Molecular Fingerprinting ◽  
Microbial Biodiversity ◽  
Fecal Samples ◽  
Irritable Bowel ◽  
Bacterial 16S Rrna Gene

Alterations in the intestinal microbiota have been suggested as an etiological factor in the pathogenesis of irritable bowel syndrome (IBS). This study used a molecular fingerprinting technique to compare the composition and biodiversity of the microbiota within fecal and mucosal niches between patients with diarrhea-predominant IBS (D-IBS) and healthy controls. Terminal-restriction fragment (T-RF) length polymorphism (T-RFLP) fingerprinting of the bacterial 16S rRNA gene was used to perform microbial community composition analyses on fecal and mucosal samples from patients with D-IBS ( n = 16) and healthy controls ( n = 21). Molecular fingerprinting of the microbiota from fecal and colonic mucosal samples revealed differences in the contribution of T-RFs to the microbiota between D-IBS patients and healthy controls. Further analysis revealed a significantly lower (1.2-fold) biodiversity of microbes within fecal samples from D-IBS patients than healthy controls ( P = 0.008). No difference in biodiversity in mucosal samples was detected between D-IBS patients and healthy controls. Multivariate analysis of T-RFLP profiles demonstrated distinct microbial communities between luminal and mucosal niches in all samples. Our findings of compositional differences in the luminal- and mucosal-associated microbiota between D-IBS patients and healthy controls and diminished microbial biodiversity in D-IBS fecal samples further support the hypothesis that alterations in the intestinal microbiota may have an etiological role in the pathogenesis of D-IBS and suggest that luminal and mucosal niches need to be investigated.

scholarly journals Bile Acids and Microbiome Among Individuals With Irritable Bowel Syndrome and Healthy Volunteers

2020 ◽  
Vol 23 (1) ◽  
pp. 65-74
Author(s):  
Kendra J. Kamp ◽  
Kevin C. Cain ◽  
Angelita Utleg ◽  
Robert L. Burr ◽  
Daniel Raftery ◽  
...  
Keyword(s):  
Irritable Bowel Syndrome ◽  
Healthcare Providers ◽  
Gastrointestinal Disorder ◽  
Mucosal Inflammation ◽  
Rrna Gene ◽  
Rrna Gene Sequencing ◽  
Irritable Bowel ◽  
Pain Symptoms ◽  
16 S Rrna

Irritable bowel syndrome (IBS) is a common functional gastrointestinal disorder. High bile acid (BA) profiles have been associated with abdominal pain symptoms, mucosal inflammation, and diarrhea in a subgroup of those with IBS. The purpose of this study was to compare: 1) fecal primary and secondary BAs in women with and without IBS; and 2) symptoms, gut microbiome, and diet between women with high and normal BAs (i.e., similar to healthy [HC] women). Women (ages 18–45) with IBS and HCs were recruited from healthcare providers or the community. Participants kept a 28-day symptom diary, completed a 3-day food journal, and collected a stool sample for microbiome analysis (16 S rRNA gene sequencing). Primary and secondary BA levels were determined by mass spectrometry. Primary BAs did not differ between IBS (n = 45) and HC (n = 28) groups; women with IBS had significantly increased conjugated secondary BAs (glycodeoxycholic acid [ p = 0.006], taurodeoxycholic acid [ p = 0.006], and glycolithocholic acid [ p = 0.01]). Sixty percent of women with IBS had normal BAs whereas 40% had high BAs. Women with high fecal BAs were predominantly IBS-Diarrhea or IBS-Mixed and consumed less fiber and vegetable protein and more animal protein compared to women with IBS whose fecal BAs levels were comparable to HCs. Those with high conjugated secondary fecal BAs also had a greater Firmicutes/Bacteroidetes ratio, less abundance of phylum Bacteroidetes and genus Gemmiger, and more abundance of family Erysipelotrichaceae compared to IBS women with normal BAs. Determination of fecal BA levels provides additional insights into pathophysiological links between diet and microbiome in IBS.

scholarly journals Mir-23a and mir-181b serum levels in irritable bowel syndrome and colorectal cancer – A pilot study

2019 ◽  
Author(s):  
Alexandra Chira ◽  
Mihai-Stefan Muresan ◽  
Cornelia Braicu ◽  
Liviuta Budisan ◽  
Lajos Raduly ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Irritable Bowel Syndrome ◽  
Statistical Significance ◽  
Serum Levels ◽  
Diagnostic Value ◽  
Healthy Controls ◽  
Phosphatase And Tensin Homolog ◽  
Reverse Transcription Pcr ◽  
Tensin Homolog ◽  
Irritable Bowel

An emerging evidence suggests that microRNAs (miRNAs) may be reliable biomarkers for inflammation or oncogenesis. The aim of this study was to investigate the diagnostic value of miR-23a and miR-181b in patients with irritable bowel syndrome (IBS) and patients with colorectal cancer (CRC) vs. healthy controls. Forty patients with IBS (29 females, 11 males), 33 patients with CRC (14 females, 19 males), and 33 healthy controls (17 females, 16 males) were prospectively included. Serum levels of miRNAs were evaluated by quantitative reverse transcription PCR. MiR-23a and miR-181b had significantly higher serum levels (p = 0.0009 and p = 0.004, respectively) in IBS patients than in controls. Serum levels of miR-23a and miR-181b in CRC patients were also significantly higher than in controls (p = 0.002 and p = 0.029, respectively). The levels of miR-23a and miR-181b in CRC vs. IBS patients suggested a trend of overexpression in patients with CRC, however, without statistical significance (p = 0.169 and p = 0.179, respectively). miRNet and Reactome database showed phosphatase and tensin homolog (PTEN) to be a major common pathway, suggesting inflammation as a central mechanism. MiRNAs may serve as reliable biomarkers in clinical practice, but further studies are necessary to establish a cut-off limit for specific miRNAs in different diseases.

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

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Annikka Polster ◽  
Lena Öhman ◽  
Julien Tap ◽  
Muriel Derrien ◽  
Boris Le Nevé ◽  
...  
Keyword(s):  
Irritable Bowel Syndrome ◽  
Complex Variable ◽  
16S Rrna Gene Sequencing ◽  
Integrative Analysis ◽  
Rrna Gene ◽  
Analysis Pipeline ◽  
Host Interactions ◽  
Functional Relationships ◽  
Irritable Bowel ◽  
Host Genes

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.

scholarly journals Intestinal barrier dysfunction in irritable bowel syndrome: a systematic review

2021 ◽  
Vol 14 ◽  
pp. 175628482199358
Author(s):  
Nikita Hanning ◽  
Adam L. Edwinson ◽  
Hannah Ceuleers ◽  
Stephanie A. Peters ◽  
Joris G. De Man ◽  
...  
Keyword(s):  
Quality Of Life ◽  
Systematic Review ◽  
Irritable Bowel Syndrome ◽  
Abdominal Pain ◽  
Barrier Function ◽  
Significant Proportion ◽  
Healthy Controls ◽  
Barrier Dysfunction ◽  
Irritable Bowel

Background and Aim: Irritable bowel syndrome (IBS) is a complex and heterogeneous disorder. Sensory, motor and barrier dysfunctions are the key physiological endophenotypes of IBS. Our aim is to review studies evaluating barrier dysfunction in adults and children with IBS, as well as to link those changes with IBS symptomatology and quality of life. Methods: A comprehensive and systematic review of multiple databases was performed up to March 2020 to identify studies comparing intestinal permeability in IBS patients with healthy controls. Both in vivo and in vitro studies were considered. Results: We identified 66 studies, of which 27 used intestinal probes to quantify barrier function. The prevalence of barrier dysfunction differed between PI-IBS (17–50%), IBS-D (37–62%) and IBS-C (4–25%). At a group level, permeability was increased compared with healthy controls in IBS-D (9/13 studies) and PI-IBS (4/4 studies), but only a minority of IBS-C (2/7 studies) and not in the only IBS-M study. All four studies in children with IBS demonstrated loss of barrier function. A heterogeneous set of tight junction genes were found to be altered in small and large intestines of adults with IBS, but these have not been evaluated in children. Positive associations were identified between barrier dysfunction and bowel disturbances (6/9 studies), abdominal pain (9/13 studies), overall symptom severity (1/6 studies), depression and anxiety (1/1 study) and quality of life (1/4 studies). Fecal slurry or supernatants of IBS patients were found to induce barrier disruption in animal models (5/6 studies). Conclusions: Barrier dysfunction is present in a significant proportion of adult and all pediatric IBS studies, especially in the IBS-D and PI-IBS subtype. The majority of studies indicated a positive association between loss of barrier function and symptoms such as abdominal pain and changes in the bowel function.

scholarly journals The Prevalence of Anti-Zein Antibodies: A Comparative Study between Celiac Disease and Irritable Bowel Syndrome

Nutrients ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 649
Author(s):  
Luis Alberto Sánchez-Vargas ◽  
Karina Guadalupe Hernández-Flores ◽  
Francisco Javier Cabrera-Jorge ◽  
José María Remes-Troche ◽  
Job Reyes-Huerta ◽  
...  
Keyword(s):  
Irritable Bowel Syndrome ◽  
Celiac Disease ◽  
Gastrointestinal Disorder ◽  
Newly Diagnosed ◽  
Disease Group ◽  
Immune Mediated ◽  
Healthy Control ◽  
Gliadin Peptides ◽  
Irritable Bowel ◽  
First Time

Celiac disease (CD) is a chronic immune-mediated enteropathy triggered by exposure to dietary gluten in genetically predisposed individuals. In contrast, irritable bowel syndrome (IBS) is a common functional gastrointestinal disorder affecting the large intestine, without an autoimmune component. Here, we evaluated the prevalence of IgA and IgG antibodies to maize zeins (AZA) in patients with CD and IBS. Using an in-house ELISA assay, the IgA and IgG anti-zein antibodies in the serum of 37 newly diagnosed CD (16 biopsy proved and 21 serological diagnosis) and 375 IBS patients or 302 healthy control (HC) subjects were measured. Elevated levels of IgA AZA were found in CD patients compared with IBS patients (p < 0.01) and HC (p < 0.05). CD patients had the highest prevalence (35.1%), followed by IBS (4.3%) and HCs (2.3%) (p < 0.0001). IgG AZA antibodies were not found in any CD patients, IBS patients, or HC subjects. A significant positive correlation was found between IgA AZA with IgA anti-gliadin (AGA, r = 0.34, p < 0.01) and IgA anti-deaminated gliadin peptides (DGP, r = 0.42, p < 0.001) in the celiac disease group. Taken together, our results show for the first time a higher prevalence of AZA IgA antibodies in newly diagnosed CD patients than in IBS patients, confirming a biased immune response to other gliadin-related prolamins such as maize zeins in genetically susceptible individuals.

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