Transcriptome analysis of Bifidobacterium adolescentis P2P3 cultivated with resistant starch
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ABSTRACT:
ORGANISM(S): Bifidobacterium adolescentis
PROVIDER: GSE138588 | GEO | 2022/10/08
REPOSITORIES: GEO
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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 goal was to assess the impact of carbon source and cross-feeding on transcription profile of both bacteria. R. gnavus was grown in monoculture with glucose (Glc). R. bromii was grown in monoculture with soluble (SS) or resistant (RS) starch. R. bromii and R. gnavus were co-cultured with SS or RS. Total RNA was extracted from a culture sample taken at mid- to late exponential phase of growth. rRNA was depleted and mRNA sequenced. 3 biological replicates were prepared for each condition.
2019-07-31 | E-MTAB-7138 | biostudies-arrayexpress
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.
2013-10-18 | GSE45554 | GEO
Project description:Background. Resistant Starch (RS) improves CKD outcomes. In this report we study how RS modulates host-microbiome interactions in CKD by measuring changes in abundance of proteins and bacteria in the gut. In addition, we demonstrate RS-mediated reduction in CKD-induced kidney damage. Methods. Eight mice underwent 5/6 nephrectomy to induce CKD and 8 served as healthy controls. CKD and Healthy (H) groups were further split into those receiving RS (CKDRS, n=4; HRS, n=4) and those on normal diet (CKD, n=4, H, n=4). Kidney injury was evaluated by measuring BUN/creatinine and by most-mortem histopathological evaluation. Cecal contents were analyzed mass spectrometry-based metaproteomics. PEAKS Studio was used to identify peptides via de novo sequencing. A set of R/Bioconductor packages and in house written scripts was further used to infer bacteria present, to evaluate changes in proteins and bacterial abundances, and to perform statistical analysis and hierarchical clustering. Results. The 5/6 nephrectomy compromised kidney function as seen by an increase in creatinine and BUN. Representative photomicrographs of trichrome-stained kidney sections showed reduced tubulointerstitial injury in CKD mice fed HAM-RS2 diet comparing to CKD mice fed normal diet. Identified organisms and proteins point toward a higher population of butyrate-producing bacteria, and reduced abundance of mucin-degrading bacteria. Conclusion. Resistant starch slows the progression of chronic kidney disease. Gut barrier function through maintenance of the mucin barrier plays a role in RS-associated improvements in CKD phenotype. Resistant starch supplementation leads to the active bacterial proliferation and the reduction of harmful bacterial metabolites.
2020-10-19 | PXD019623 | Pride
Project description:Purpose: The ∆col-26 mutant cannot utilize starch components and many other simple sugars efficiently. We employed RNA-seq based transcriptome profiling to reveal genes under the control of col-26. Method: We first obtained transcriptional data of Neurospora crassa WT on Vogel's minimal medium (VMM) without carbon source, on VMM with 2% sucrose, and on VMM with starch component, and transcriptional data of the ∆col-26 mutant on VMM with maltose or amylose. Results: We identified a starch-regulon of 322 genes and found that 255 of the starch-regulon were down regulated in in absence of col-26. We also found that genes with functions in primary carbon and nitrogen metabolism and amino acid biosynthesis were also down regulated in the mutant. Conclusion: Our data represents a systematic transcriptome profiling of filamentous fungi on different starch components and identify COL-26 as a critical regulator in both starch degradation and primary carbon and nitrogen regulation.
2017-04-09 | GSE92848 | GEO
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:Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and Metabolome
| PRJEB22786 | ENA
Project description:Ruminococcus bromii is a keystone species in the human gut that has the rare ability to degrade dietary resistant starch (RS). This bacterium secretes a suite of starch-active proteins that work together within larger complexes called amylosomes that allow R. bromii to adhere to and degrade RS. Sas20 is one of the more abundant proteins assembled within amylosomes, but little could be predicted about its molecular features based upon amino acid sequence. Here, we perform a structure-function analysis of Sas20 which features two discrete starch-binding domains separated by a flexible linker. Sas20 domain 1 has an N-terminal β-sandwich followed by a cluster of α-helices and captures the non-reducing end of maltooligosaccharides between these structural features. The crystal structure of a close homolog of Sas20 domain 2 revealed a unique bilobed starch-binding groove that targets the helical 1,4-linked glycan chains found in amorphous regions of amylopectin and crystalline regions of amylose within starch granules. Affinity PAGE and isothermal titration calorimetry demonstrate both domains bind maltoheptaose and soluble starch with relatively high affinity (Kd 20 M) but exhibit limited or no binding to cyclodextrins. Small angle x-ray scattering analysis of the individual and combined domains support that these structures are highly flexible, which may allow the protein to adopt conformations that enhance its starch-targeting efficiency.
2022-06-09 | PXD032013 | Pride
Project description:This phase II, randomized pilot trial studies the effect of the consumption of foods made with resistant starch compared to foods made with corn starch on biomarkers that may be related to colorectal cancer progression in stage I-III colorectal cancer survivors. Foods made with resistant starch may beneficially influence markers of inflammation, insulin resistance, and the composition of gut bacteria in colorectal cancer survivors.
| 2292640 | ecrin-mdr-crc
Project description:Thermophilic fungus Myceliophthora thermophila with great capacity for polysaccharides degradation is attractive to be engineered into a cell factory to produce chemicals and biofuels directly from renewable polysaccharides such as starch. Understanding the molecular mechanism of starch degradation of the fungi would be helpful. To date, there has been no transcriptome analysis on starch in thermophilic fungi. In this study, we performed the transcriptomic profile of M. thermophila responding to soluble starch, and a 342-gene set was identified as “starch regulon”, including the major amylolytic enzyme (Mycth_72393), which was verified thereafter as the most important such hydrolase for starch degradation in this fungus. Moreover, the function of key amylolytic enzyme regulator AmyR in M. thermophila was evaluated by analyzing the performance of its deletion mutant using our CRISPR/Cas9 system, which showed significantly decreased amylase activity and poor growth on starch. Additionally, deletion of amyR led to resistance to carbon catabolite repression (CCR) and enhanced cellulases production. Our study provides an insight into understanding the molecular basis of starch degradation in this thermophilic fungus, and will accelerate the fungal strain rational engineering for starch-based biochemical production.
2021-02-02 | GSE110062 | GEO