Dataset Information

Potential Functions of the Gastrointestinal Microbiome Inhabiting the Length of the Rat Digest Tract.

ABSTRACT: The rat is an important model animal used frequently in biological researches exploring the correlations between gut microbiome and a wide array of diseases. In this study, we used an extended ancestral-state reconstruction algorithm to predict the functional capabilities of the rat gastrointestinal microbiome. Our results indicate an apparent tendency toward metabolic heterogeneity along the longitudinal and transverse axes of the rat gastrointestinal tract (GIT). This heterogeneity was suggested by the enriched small-molecule transport activity and amino acid metabolism in the upper GIT, the aerobic energy metabolism in the stomach and the mucolysis-related metabolism in the lower GIT mucus layer. In contrast to prior results, many functional overlaps were observed when the gastrointestinal microbiomes of different hosts were compared. These overlaps implied that although both the biogeographic location and host genotype were prominent driving forces in shaping the gastrointestinal microbiota, the microbiome functions were similar across hosts when observed under similar physicochemical conditions at identical anatomical sites. Our work effectively complements the rat microbial biogeography dataset we released in 2017 and, thus, contributes to a better understanding and prediction of disease-related alterations in microbial community function.

SUBMITTER: Li D

PROVIDER: S-EPMC6429386 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

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Potential Functions of the Gastrointestinal Microbiome Inhabiting the Length of the Rat Digest Tract.

Li Dongyao D Chen Haiqin H Zhao Jianxin J Zhang Hao H Chen Wei W

International journal of molecular sciences 20190312 5

The rat is an important model animal used frequently in biological researches exploring the correlations between gut microbiome and a wide array of diseases. In this study, we used an extended ancestral-state reconstruction algorithm to predict the functional capabilities of the rat gastrointestinal microbiome. Our results indicate an apparent tendency toward metabolic heterogeneity along the longitudinal and transverse axes of the rat gastrointestinal tract (GIT). This heterogeneity was suggest ...[more]

PMID: 30870968

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Project description:Background: The molecular basis of segment specific epithelial functions of the stomach and bowel has not been established. Regionally unique molecular properties of epithelial cells can be identified using cell-specific gene expression in each epithelial region by comparative mRNA analysis. Aim: To describe segment-specific epithelial mRNA content by comparative mRNA analysis of purified epithelial cell suspensions of stomach, small and large bowel. Results: 12% of all annotated genes show segment specific enrichment. The gastric (>3000 genes) and ileal (519 genes) mucosa show the most diverse expression profile. (a) Stomach: The gastric mucosa expresses the machinery for acid secretion, digestive enzyme release, and hormone release by gastric enteroendocrine cells. Associated with acid secretion is a specific set of K+, Cl-, and bicarbonate channels. Novel is a pathway for glucose and fatty acid sensing, iodine and glutamate uptake, and taurine synthesis. Specific sets of transcription factors control epithelial (Barx1, Runx) and enteroendocrine (FoxA2/N4) cell differentiation. (b) Small Bowel: This epithelium expresses genes coding for a unique fructose/glucose uptake and utilization mechanism. Enteroendocrine signalling to the gastric function is present. The upper portion expresses genes for iron uptake, bicarbonate secretion, and detoxification of food contents. Epithelial differentiation is transcriptionally controlled by Meis2/Pdx1 and Onecut 2. Expression of digestive enzymes, lipid/bile acid uptake and utilization increases distally. The ileal epithelium is also involved in innate and acquired immune defence, regulation of motility, and electrolyte and water re-absorption. Transcriptional regulation of enterocyte and goblet cell differentiation is mainly controlled by increasing expression of Cdx1 and 2. (c) Colon: This epithelium is mainly involved in Ca++-, K+, and water re-absorption, fatty acid uptake and sensing, and innate and acquired immune defence. Epithelial differentiation is controlled by Hox transcription factors in addition to Cdx1/2. Conclusion: This regional survey of gene expression by the GI tract epithelium reveals unique epithelial properties, raising several important questions as to the role of the proteins encoded in gut physiology.

Project description:BackgroundAlterations in gastrointestinal (GI) microbial composition have been reported in patients with systemic sclerosis (SSc). However, it is unclear to what degree these alterations and/or dietary changes contribute to the SSc-GI phenotype.ObjectivesOur study aimed to 1) evaluate the relationship between GI microbial composition and SSc-GI symptoms, and 2) compare GI symptoms and GI microbial composition between SSc patients adhering to a low versus non-low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP) diet.MethodsAdult SSc patients were consecutively recruited to provide stool specimens for bacterial 16S rRNA gene sequencing. Patients completed the UCLA Scleroderma Clinical Trial Consortium Gastrointestinal Tract Instrument (GIT 2.0) and the Diet History Questionnaire (DHQ) II and were classified as adhering to a low or non-low FODMAP diet. GI microbial differences were assessed using three metrics of alpha diversity (species richness, evenness, and phylogenetic diversity), as well as beta diversity (overall microbial composition). Differential abundance analysis was performed to identify specific genera associated with SSc-GI phenotype and low versus non-low FODMAP diet.ResultsOf the 66 total SSc patients included, the majority were women (n = 56) with a mean disease duration of 9.6 years. Thirty-five participants completed the DHQ II. Increased severity of GI symptoms (total GIT 2.0 score) was associated with decreased species diversity and differences in GI microbial composition. Specifically, pathobiont genera (e.g., Klebsiella and Enterococcus) were significantly more abundant in patients with increased GI symptom severity. When comparing low (N = 19) versus non-low (N = 16) FODMAP groups, there were no significant differences in GI symptom severity or in alpha and beta diversity. Compared with the low FODMAP group, the non-low FODMAP group had greater abundance of the pathobiont Enterococcus.ConclusionSSc patients reporting more severe GI symptoms exhibited GI microbial dysbiosis characterized by less species diversity and alterations in microbial composition. A low FODMAP diet was not associated with significant alterations in GI microbial composition or reduced SSc-GI symptoms; however, randomized controlled trials are needed to evaluate the impact of specific diets on GI symptoms in SSc.

Dataset Information

Potential Functions of the Gastrointestinal Microbiome Inhabiting the Length of the Rat Digest Tract.

Publications

Potential Functions of the Gastrointestinal Microbiome Inhabiting the Length of the Rat Digest Tract.

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