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PROVIDER: PRJNA306884 | ENA |
REPOSITORIES: ENA
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Project description:Resistant starches (RS) are dietary compounds processed by the gut microbiota into metabolites, such as butyrate, that are beneficial to the host. The production of butyrate by the microbiome appears to be affected by the plant source and type of RS as well as the individual’s microbiota. In this study, we used in vitro culture and metaproteomic methods to explore the consistency and variations in individual microbiome's functional responses to three types of RS - RS2(Hi Maize 260), RS3(Novelose 330) and RS4(Fibersym RW). Results showed that RS2 and RS3 significantly altered the levels of protein expression in the individual gut microbiomes, while RS4 did not result in significant protein changes. Significantly elevated protein groups were enriched in carbohydrate metabolism and transport functions of families Eubacteriaceae, Lachnospiraceae and Ruminococcaceae. In addition, Bifidobacteriaceae was significantly increased in response to RS3. We also observed taxon-specific enrichments of starch metabolism and pentose phosphate pathways corresponding to this family. Functions related to starch utilization, ABC transporters and pyruvate metabolism pathways were consistently increased in the individual microbiomes in response to RS2 and RS3; in contrast, the downstream butyrate producing pathway response varied. Our study confirm that different types of RS have markedly variable functional effects on the human gut microbiome, and also found considerable inter-individual differences in microbiome pathway responses.
2021-09-08 | PXD017907 | Pride
Project description:Background- Resistant starch is a prebiotic metabolized by the gut bacteria. It has been shown to attenuate chronic kidney disease (CKD) progression in rats. Previous studies employed taxonomic analysis using 16S rRNA sequencing and untargeted metabolomics profiling. Here we expand these studies by metaproteomics, gaining new insight into the host-microbiome interaction. Methods- Differences between cecum contents in CKD rats fed a diet containing resistant starch with those fed a diet containing digestible starch were examined by comparative metaproteomics analysis. Taxonomic information was obtained using unique protein sequences. Our methodology results in quantitative data covering both host and bacterial proteins. Results - 5,834 proteins were quantified, with 947 proteins originating from the host organism. Taxonomic information derived from metaproteomics data surpassed previous 16S RNA analysis, and reached species resolutions for moderately abundant taxonomic groups. In particular, the Ruminococcaceae family becomes well resolved – with butyrate producers and amylolytic species such as R. bromii clearly visible and significantly higher while fibrolytic species such as R. flavefaciens are significantly lower with resistant starch feeding. The observed changes in protein patterns are consistent with fiber-associated improvement in CKD phenotype. Several known host CKD-associated proteins and biomarkers of impaired kidney function were significantly reduced with resistant starch supplementation. Conclusions- Metaproteomics analysis of cecum contents of CKD rats with and without resistant starch supplementation reveals changes within gut microbiota at unprecedented resolution, providing both functional and taxonomic information. Proteins and organisms differentially abundant with RS supplementation point toward a shift from mucin degraders to butyrate producers.
2018-12-18 | PXD008845 | Pride
Project description:Consumption of diets rich in fibers has been associated with several beneficial effects on gastrointestinal health. However, detailed studies on the molecular effects of fibers in colon are limited. In this study we investigated and compared the influence of five different fibers on the mucosal transcriptome, and luminal microbiota and SCFA concentrations in murine colon. Mice were fed diets enriched with fibers that differed in carbohydrate composition, namely inulin (IN), oligofructose (FOS), arabinoxylan (AX), guar gum (GG), resistant starch (RS) or a control diet (corn starch) for 10 days. Gene expression profiling revealed the regulation of specific, but also overlapping sets of epithelial genes by each fiber, which on a functional level were mainly linked to cell cycle and various metabolic pathways including fatty acid oxidation, tricarboxylic acid cycle, and electron transport chain. In addition, the transcription factor PPAR was predicted to be a prominent upstream regulator of these processes. Microbiota profiles were distinct per dietary fiber, but the fibers IN, FOS, AX and GG induced a common change in microbial groups. All dietary fibers, except resistant starch, increased SCFA concentrations but to a different extent. Multivariate data integration revealed strong correlations between the expression of genes involved in energy metabolism and the relative abundance of bacteria belonging to the group of Clostridium cluster XIVa, that are known butyrate producers. These findings illustrate the potential of multivariate data analysis to unravel simple relationships in complex systems. Keywords: Expression profiling by array Mice received a control diet, or a diet supplemented with 10% dietary fibers for 10 days. After an overnight fast colon was removed, epithelial cells were scraped off, and subjected to gene expression profiling.
2015-05-26 | E-GEOD-59494 | biostudies-arrayexpress
Project description:Consumption of diets rich in fibers has been associated with several beneficial effects on gastrointestinal health. However, detailed studies on the molecular effects of fibers in colon are limited. In this study we investigated and compared the influence of five different fibers on the mucosal transcriptome, and luminal microbiota and SCFA concentrations in murine colon. Mice were fed diets enriched with fibers that differed in carbohydrate composition, namely inulin (IN), oligofructose (FOS), arabinoxylan (AX), guar gum (GG), resistant starch (RS) or a control diet (corn starch) for 10 days. Gene expression profiling revealed the regulation of specific, but also overlapping sets of epithelial genes by each fiber, which on a functional level were mainly linked to cell cycle and various metabolic pathways including fatty acid oxidation, tricarboxylic acid cycle, and electron transport chain. In addition, the transcription factor PPAR was predicted to be a prominent upstream regulator of these processes. Microbiota profiles were distinct per dietary fiber, but the fibers IN, FOS, AX and GG induced a common change in microbial groups. All dietary fibers, except resistant starch, increased SCFA concentrations but to a different extent. Multivariate data integration revealed strong correlations between the expression of genes involved in energy metabolism and the relative abundance of bacteria belonging to the group of Clostridium cluster XIVa, that are known butyrate producers. These findings illustrate the potential of multivariate data analysis to unravel simple relationships in complex systems. Keywords: Expression profiling by array
2015-05-26 | GSE59494 | GEO
Project description:The understanding of the effects of compounds on the gut microbiome is limited and in particular we don’t know whether structurally similar compounds have similar or distinct effects on the gut microbiome. Here we selected berberine (BBR), an isoquinoline quaternary alkaloid, and sixteen structural analogues, and evaluated their effects on in vitro cultured individual gut microbiomes. The responses of the individual microbiomes were evaluated by metaproteomic profiles and by assessing butyrate production. BBR and eight analogues led to changes in proteins involved in microbial defense and stress responses, and enrichment of proteins from Verrumicrobia, Proteobacteria and Bacteroides phyla. It also led to a decrease in proteins from the Firmicutes phylum and its Clostridiales order which correlated to decrease proteins involved in the butyrate production pathway and butyrate concentration. Three of the compounds, Sanguinarine, Chelerythrine and Ethoxysanguinarine activated bacterial protective mechanisms, enriched Proteobacteria, increased opacity proteins and markedly reduced butyrate production. Dihydroberberine had a similar function to BBR in enriching the Akkermansia genus. In addition, it showed less overall adverse impacts on the functionality of the gut microbiome, including a better maintenance of the butyrate level. Our study shows that ex vivo microbiome assay can assess differential regulating effects of compounds with subtle differences and reveals that compound analogues can have distinct effects on the microbiome.
2020-07-21 | PXD015934 | Pride
Project description:Consumption of resistant starch (RS) has been associated with various intestinal health benefits, but knowledge on its effects on global gene expression in the colon is limited. The main objective of the current study was to identify genes affected by RS in the proximal colon to infer which biologic pathways were modulated. Ten 17-wk-old male pigs, fitted with a cannula in the proximal colon for repeated collection of tissue biopsy samples and luminal content, were fed a digestible starch (DS) diet or a diet high in RS (34%) for 2 consecutive periods of 14 d in a crossover design. Analysis of the colonic transcriptome profiles revealed that, upon RS feeding, oxidative metabolic pathways, such as the tricarboxylic acid cycle and β-oxidation, were induced, whereas many immune response pathways, including adaptive and innate immune system, as well as cell division were suppressed. The nuclear receptor peroxisome proliferator-activated receptor γ (PPARG) was identified as a potential key upstream regulator. RS significantly (P < 0.05) increased the relative abundance of several butyrate-producing microbial groups, including the butyrate producers Faecalibacterium prausnitzii and Megasphaera elsdenii, and reduced the abundance of potentially pathogenic members of the genus Leptospira and the phylum Proteobacteria. Concentrations in carotid plasma of the 3 main short-chain fatty acids acetate, propionate, and butyrate were significantly higher with RS consumption compared with DS consumption. Overall, this study provides novel insights on effects of RS in proximal colon and contributes to our understanding of a healthy diet. Ten pigs were fitted with a cannula in the proximal colon for repeated collection of tissue biopsies, and were fed a digestible starch or a resistant starch diet for two consecutive periods of 14 days in a crossover design. After each intervention period a colonic biopsy was taken and subjected to gene expression profiling.
2013-10-18 | E-GEOD-45554 | biostudies-arrayexpress
Project description:The starch, acting as the major energy-producing component of the daily diet, is the main carbohydrate in mammal nutrition. However, the nutritional value of starch can vary widely depending upon its source and site of digestion. The distinct physiological responses were previously observed both in human and other mammals, but still little is known about the underlying mechanisms regarding the metabolic shifts due to the intake of various dietary starches. Here, we assessed the overall metabolic changes in weaned pigs induced by different dietary starch sources at the transcriptome level. Sixteen weaned pigs (DurocÃLandraceÃYorkshire) were selected and randomly allotted to diets containing either wheat (WH) or cassava (CA) starch as the energy source (n=8). We measured serum metabolites and hormones and generated transcriptional profiles of liver. 648 genes in liver were differentially expressed in response to dietary starch sources. Pathway analysis indicated that dietary starch sources altered both carbohydrate and lipid metabolism in liver. In contrast, CA may be more healthful as dietary energy source than WH by down-regulating lipogenesis and steroidogenesis in liver. Sixteen weaned pigs (DurocÃLandraceÃYorkshire) with an average initial body weight of 7.37±0.25 kg were selected and randomly allotted to two dietary treatments (either wheat or cassava starch as the energy source) for 21 d. At the end of the trial, the liver tissue were collected for transcriptome analysis using Agilent porcine microarrays.
2010-09-09 | E-GEOD-20721 | biostudies-arrayexpress
Project description:Previous works in the framework of EU ARRAINA Project evidenced a pro-inflammatory condition in gilthead sea bream (Sparus aurata) fed extremely low fish meal/fish oil diets, and this effect was mostly reversed by butyrate supplementation. The hypothesis of work is that these nutritionally-mediated changes can be extensive to intestinal mucus proteome and gut microbiota, which in turn could modify disease outcome.s If so, the prevalence and progression of the disease might be also modified by diet composition and feed additives. Gilthead sea bream fingerlings were fed with control and experimental diets formulated by BioMar until two year-old. FM was added at 25% in the control diet (D1) and at 5% in the other three diets (D2-D4). Added oil was either FO (D1 control diet) or a blend of vegetable oils, replacing the 58% (D2) and the 84% (D3-D4 diets) of FO. A commercial sodium butyrate preparation (NOREL, BP70) was added to the D4 diet at 0.4%. At month 20, 6 fish per each dietary treatment were sampled for iTRAQ profiling and fingerprinting of intestinal mucus proteome. Mucus collected from anterior and posterior intestine segments was trypsin digested, labelled with iTRAQ reagents, isoelectrofocused and resolved by LC-MS/MS. More than 1000 proteins were unequivocally annotated and principal component analysis clearly separated anterior and posterior segments. The diet effect with changes in the abundance of approximately 120 proteins was restricted to anterior section with a reversion of the pattern of the extreme diet (D3 fish) with dietary butyrate supplementation. Butyrate supplementation also reversed the decrease of microbiotay diversity associated with D3 feeding, and led to a improvement the disease outcomes in fish challenged with Photobacterium damselae and the intestinal parasite Enteromyxum leei.
2018-10-24 | PXD006183 | Pride
Project description:Resistant starches (RS), fed as high amylose maize starch (HAMS) or butyrylated HAMS (HAMSB), oppose dietary protein-induced colonocyte DNA damage in rats. In this study, rats were fed diets high in fat (19%) and protein (20%) with different forms of digestible starch (low amylose maize starch (LAMS) or low amylose whole wheat (LAW)) or RS (HAMS, HAMSB, or a whole high amylose wheat (HAW) generated by RNA interference (RNAi)) for 11 wk. A control diet contained 7% fat, 13% protein and LAMS. The aim of this study was to detect changes in the expression of DNA damage and repair genes in response to the above dietary treatments.
2012-12-01 | GSE32312 | GEO