Comparison of gut microbiotal compositional analysis of patients with irritable bowel syndrome through different bioinformatics pipelines / 北京大学学报(医学版)

OBJECTIVE@#To assess whether the same biological conclusion, diagnostic or curative effects regarding microbial composition of irritable bowel syndrome (IBS) patients could be reached through different bioinformatics pipelines, we used two common bioinformatics pipelines (Uparse V2.0 and Mothur V1.39.5)to analyze the same fecal microbial 16S rRNA high-throughput sequencing data.@*METHODS@#The two pipelines were used to analyze the diversity and richness of fecal microbial 16S rRNA high-throughput sequencing data of 27 samples, including 9 healthy controls (HC group), 9 diarrhea IBS patients before (IBS group) and after Rifaximin treatment (IBS-treatment, IBSt group). Analyses such as microbial diversity, principal co-ordinates analysis (PCoA), nonmetric multidimensional scaling (NMDS) and linear discriminant analysis effect size (LEfSe) were used to find out the microbial differences among HC group vs. IBS group and IBS group vs. IBSt group.@*RESULTS@#(1) Microbial composition comparison of the 27 samples in the two pipelines showed significant variations at both family and genera levels while no significant variations at phylum level; (2) There was no significant difference in the comparison of HC vs. IBS or IBS vs. IBSt (Uparse: HC vs. IBS, F=0.98, P=0.445; IBS vs. IBSt, F=0.47,P=0.926; Mothur: HC vs.IBS, F=0.82, P=0.646; IBS vs. IBSt, F=0.37, P=0.961). The Shannon index was significantly decreased in IBSt; (3) Both workshops distinguished the significantly enriched genera between HC and IBS groups. For example, Nitrosomonas and Paraprevotella increased while Pseudoalteromonadaceae and Anaerotruncus decreased in HC group through Uparse pipeline, nevertheless Roseburia 62 increased while Butyricicoccus and Moraxellaceae decreased in HC group through Mothur pipeline.Only Uparse pipeline could pick out significant genera between IBS and IBSt, such as Pseudobutyricibrio, Clostridiaceae 1 and Clostridiumsensustricto 1.@*CONCLUSION@#There were taxonomic and phylogenetic diversity differences between the two pipelines, Mothur can get more taxonomic details because the count number of each taxonomic level is higher. Both pipelines could distinguish the significantly enriched genera between HC and IBS groups, but Uparse was more capable to identity the difference between IBS and IBSt groups. To increase the reproducibility and reliability and to retain the consistency among similar studies, it is very important to consider the impact on different pipelines.

Gut Microbiota as Potential Orchestrators of Irritable Bowel Syndrome

Irritable bowel syndrome (IBS) is a multifactorial functional disorder with no clearly defined etiology or pathophysiology. Modern culture-independent techniques have improved the understanding of the gut microbiota's composition and demonstrated that an altered gut microbiota profile might be found in at least some subgroups of IBS patients. Research on IBS from a microbial perspective is gaining momentum and advancing. This review will therefore highlight potential links between the gut microbiota and IBS by discussing the current knowledge of the gut microbiota; it will also illustrate bacterial-host interactions and how alterations to these interactions could exacerbate, induce or even help alleviate IBS.

Sindrome de intestino irritable: ¿Un trastorno funcional? / [Irritable bowel syndrome: a functional disorder?].

Irritable bowel syndrome is a highly prevalent condition responsible for almost one third of visits to the gastroenterologist and huge expenses for diagnosis, treatment and loss of working days. A unique pathophysiologic mechanism has not been elucidated yet and several possibilities have been proposed such as senso-perception and motor disturbances, the effect of stress and anxiety, serotonin receptor failures, activation of abnormal brain areas and pain modulation differences, among others. The absence of a biological marker has led the investigators to consider this syndrome as an exclusion diagnostic condition, once the organic diseases have been discarded The changes in gut microbiota have recently raised great interest among gastroenterologists. The study of the small intestinal bowel overgrowth syndrome, the effect of antibiotics upon the flora, the recognition of post-infectious irritable bowel syndrome and the action of probiotics, together with the effect of malabsortion of diet carbohydrates have brought some new light in our knowledge. The present update will focus on the published evidence about the subject, bearing in mind that the mechanisms elicited here are only suitable for a subgroup of patients.

Sobrecrecimiento bacteriano en trastornos funcionales del intestino / Small intestinal bacterial overgrowth in patients with functional gastrointestinal diseases[

Background: Recent studies have described a high percentage of small intestinal bacterial overgrowth (SIBO) in patients with irritable bowel syndrome (IBS). However, the prevalence of SIBO has not been well established in other functional disorders. Aim: To evaluate the prevalence of SIBO in patients with different functional gastrointestinal disorders (FGID). Material and methods: Patients with FGID completed a self-administered questionnaire providing information to diagnose functional disorders on the basis of Rome II criteria. SIBO was assessed using a standardized lactulose breath test. A basal value of breath hydrogen (H2) >20 ppm and/or two lectures of HZ values >20 ppm during the first 60 minutes were considered suggestive of SIBO. Results: We studied 367 patients with a mean age of 50 years (87 percent females). Of these, 225 had IBS (45 constipation predominant, 121 diarrhea predominant and 59 alternating type), 33 had functional constipation, 83 had functional bloating and 26 had functional diarrhea. SIBO was found in 76 percent of patients with IBS, 73 percent of those with functional constipation, 69 percent of those with functional diarrhea and 68 percent of those with functional bloating. Conclusions: This study confirms a high percentage of SIBO in patients with IBS and other FGID. The eradication of SIBO should be considered as a therapeutic tool in these patients.

Sobrecrecimiento bacteriano intestinal / Small intestinal bacterial overgrowth. An update

Small intestinal bacterial overgrowth (SIBO) is characterized by nutrient malabsorption, associated with an excessive number of bacteria in the proximal small intestine. Unfortunately, the diagnosis of bacterial overgrowth presents several difficulties and limitations, and as yet there is not a widespread agreement on the best diagnostic test. SIBO occurs when there are alterations in intestinal anatomy, gastrointestinal motility, or a lack of gastric acid secretion. The true association between SIBO and irritable bowel syndrome and celiac disease remains uncertain. The treatment usually consists in the eradication of bacterial overgrowth with repeated courses of antimicrobials, nutritional support and when it is possible, the correction of underlying predisposing conditions.