Intestine-adapted bacterial symbiont response to polysaccharide rich and polysaccharide deficient diets in mice lacking fucosyltransferase-2
Ontology highlight
ABSTRACT:
ORGANISM(S): Bacteroides thetaiotaomicron Bifidobacterium longum
PROVIDER: GSE45641 | GEO | 2014/04/21
SECONDARY ACCESSION(S): PRJNA195463
REPOSITORIES: GEO
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Project description:Analysis of Bacteroides thetaiotaomicron (BT) from the ceca of ex-germ free Fut2+ or Fut2- mice on polysaccharide rich or glucose rich polysaccharide deficient diet. BT is involved in the breakdown of plant polysaccharides and is also efficiently utilizes host glycans. BT-colonized mice represent a human gut ecosystem model. Results identify genes that may endow flexibility in adapting to dietary changes by mucosal foraging depending on host fucosylation status In vitro transcriptional profiles of Bacteroides thetaiotaomicron obtained from ceca of ex-germ free Fut2+ or Fut2- mice on polysaccharide rich or glucose rich polysaccharide deficient diet.
2014-04-21 | E-GEOD-45641 | biostudies-arrayexpress
Project description:Analysis of Clostridium difficile (Cd) from the cecal contents of germ-free mice or Bacteroides thetaiotaomicron (Bt)-monocolonized mice on a standard, polysaccharide rich diet or polysaccharide deficient diet 5 days after infection. Results identify genes that are involved in the Cd response to diet, in vivo colonization and in interactions with Bt. In vitro transcriptional profiles of Clostridium difficile obtained from cecal contents of germ-free or Bt-monocolonized mice on a standard, polysaccharide rich or polysaccharide deficient diet. 4 samples/group. 2 control genomic DNA samples for Clostridium difficile and 2 reference genomic DNA samples for Bacteroides thetaiotaomicron Please note that 4 control samples (genomic DNA) were used to determine whether the genomic DNA correctly bound to the probes and thus, were not included in data processing (i.e no processed/normalized data).
2015-08-13 | E-GEOD-60751 | biostudies-arrayexpress
Project description:Analysis of Clostridium difficile (Cd) from the cecal contents of germ-free mice or Bacteroides thetaiotaomicron (Bt)-monocolonized mice on a standard, polysaccharide rich diet or polysaccharide deficient diet 5 days after infection. Results identify genes that are involved in the Cd response to diet, in vivo colonization and in interactions with Bt.
2015-08-13 | GSE60751 | GEO
Project description:Transcriptional profiling of Bacteroides thetaiotaomicron was performed on samples taken from (i) chemostat cultures (in vitro) and (ii) from the ceca of gnotobiotic monoassociated NMRI mice (in vivo). In vitro profiles were obtained from biological duplicate cultures taken at five timepoints from log to stationary phase in three types of media: (i) minimal media glucose (MM-G), (ii) minimal media maltotriose (MM-M), and (iii) rich media (TYG). In vivo profiling was performed on 12 mice, each colonized with B. thetaiotaomicron for ten days. The in vivo profiling was conducted in two separate experiments: (i) 6 male NMRI mice fed standard polysaccharide rich mouse chow and (ii) 3 male NMRI mice fed standard polysaccharide rich mouse chow and 3 male NMRI mice fed a simple sugar diet containing glucose and sucrose but deficient in polysaccharides. Keywords: other
2005-03-30 | GSE2231 | GEO
Project description:Analysis of Pseudomonas aeruginosa PA01 (ATCC 15692) Psl polysaccharide deficient mutant. Psl polysaccharide deficient mutant is evaluated with microarray to understand the genes affected by this polysaccharide. Our results provide new vision on the roles played by Psl polysaccharide in P. aeruginosa. Exopolysaccharide Psl is a critical biofilm matrix component in Pseudomonas aeruginosa, which forms a fiber-like matrix to enmesh bacteria communities. Iron has been shown to serve as a signal in P. aeruginosa biofilm development, yet how iron controls biofilm formation is not clear. Here we perform a transcriptomic analysis to compare Psl negative strain versus its isogenic wild-type strain PAO1. The results indicate that the expression of genes involved in iron homeostasis and oxidative stress response increased drastically at transcriptional level in Psl negative strain, suggesting Psl deficiency induces iron limitation. Subsequent studies confirm that Psl can efficiently bind iron in vitro and Psl fibers functions as an iron storage channel in P. aeruginosa biofilms. We used two wild type (WT) replicates and two mutant (MT) replicates to compare the differential gene expression.
2016-01-26 | E-GEOD-77163 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE11944: Mucosal Glycan Foraging Enhances the Fitness and Transmission of a Saccharolytic Human Distal Gut Symbiont GSE11953: Mucosal Glycan Foraging Enhances the Fitness and Transmission of a Saccharolytic Human Distal Gut Symbiont: ECF mutant GSE11962: Growth of B. thetaiotaomicron on purified host mucosal glycans and glycan fragments Refer to individual Series
2008-11-20 | E-GEOD-11980 | biostudies-arrayexpress
Project description:Analysis of Pseudomonas aeruginosa PA01 (ATCC 15692) Psl polysaccharide deficient mutant. Psl polysaccharide deficient mutant is evaluated with microarray to understand the genes affected by this polysaccharide. Our results provide new vision on the roles played by Psl polysaccharide in P. aeruginosa. Exopolysaccharide Psl is a critical biofilm matrix component in Pseudomonas aeruginosa, which forms a fiber-like matrix to enmesh bacteria communities. Iron has been shown to serve as a signal in P. aeruginosa biofilm development, yet how iron controls biofilm formation is not clear. Here we perform a transcriptomic analysis to compare Psl negative strain versus its isogenic wild-type strain PAO1. The results indicate that the expression of genes involved in iron homeostasis and oxidative stress response increased drastically at transcriptional level in Psl negative strain, suggesting Psl deficiency induces iron limitation. Subsequent studies confirm that Psl can efficiently bind iron in vitro and Psl fibers functions as an iron storage channel in P. aeruginosa biofilms.
2016-01-26 | GSE77163 | GEO
Project description:Bacteroides thetaiotaomicron, one of the most eminent representative gut commensal Bacteroides species, is able to use the L-fucose in host-derived and dietary polysaccharides to modify its capsular polysaccharides and glycoproteins through a mammalian-like salvage metabolic pathway. This process is essential for the colonization of the bacteria and for symbiosis with the host. However, despite the importance of fucosylated proteins (FGPs) in Bacteroide thetaiotaomicron, their types, distribution, and functions remain unclear. In this project, the effects of different saccharide (glucose, corn starch, mucin, and fucoidan) nutrition conditions on FGP expressions and fucosylation are investigated using a chemical biological method based on metabolic labeling and bioorthogonal reaction. According to the results of label-free quantification, 559 FGPs (205 downregulated and 354 upregulated) are affected by the dietary conditions. Of these differentially expressed proteins, 65 proteins show extremely sensitive fucosylation levels. Specifically, the fucosylation of the chondroitin sulfate ABC enzyme, Sus proteins, and cationic efflux system proteins varies significantly upon the addition of mucin, corn starch, or fucoidan. Moreover, these polysaccharides can trigger an appreciable increase in the fucosylation level of the two-component system and ammonium transport proteins. These results highlight the efficiency of the combined metabolic glycan labeling and bio-orthogonal reaction in enriching the intestinal Bacteroide glycoproteins. Moreover, it emphasize the sensitivity of Bacteroides fucosylation to polysaccharide nutrition conditions, which allows for the regulation of bacterial growth.
2022-02-08 | PXD023756 | Pride
Project description:Background. The regenerative and immunomodulatory properties of human mesenchymal stem cells (hMSC) have raised great hope for their use in cell therapy. However, when intravenously infused, hMSCs fail to reach sites of tissue injury. Fucose addition in α-(1,3)-linkage to terminal sialyllactosamines on CD44 creates the molecule known as hematopoietic cell E-/L-selectin ligand (HCELL), programming hMSC binding to E-selectin that is expressed on microvascular endothelial cells of bone marrow (BM), skin, and at all sites of inflammation. Here we describe how this modification on BM-derived hMSC (BM-hMSCs) can be adapted to good manufacturing practice (GMP) standards. Methods. BM-hMSC were expanded using xenogenic-free media and exofucosylated using α-(1,3)-fucosyltransferases VI (FTVI) or VII (FTVII). Enforced fucosylation converted CD44 into HCELL, and HCELL formation was assessed by western blot, flow cytometry, and cell binding assays. Untreated (unfucosylated), buffer-treated and exofucosylated BM-hMSC were each characterized by immunophenotype , differentiation potential and cell viability and fucosylation stability were assessed at room temperature and at 4°C. Safety was assessed by microbiological testing, karyotype, and c-Myc mRNA expression, and potential effects on genetic reprogramming and in cell signaling were analyzed by gene expression microarrays and receptor tyrosine kinase (RTK) phosphorylation arrays. Results. Our protocol efficiently generates HCELL on clinical-scale batches of BM-hMSC. Exofucosylation yields stable HCELL expression for 48 hours at 4°C. Exofucosylation preserved full cell viability and identity, without changing gene expression or RTK phosphorylation. Discussion. The described exofucosylation protocol using xenogenic-free reagents enforces HCELL expression on hMSC endowing potent E-selectin binding without affecting cell viability or native phenotype. This described protocol is readily scalable for GMP-compliant clinical production.
2018-09-05 | GSE90131 | GEO
Project description:Polysaccharides from macroalgae are important bacterial nutrient source and central biogeochemical component in the oceans. To illuminate the cellular mechanisms of polysaccharide degradation by marine bacteria, growth of Alteromonas macleodii 83-1 on a mix of laminarin, alginate and pectin was characterized using transcriptomics, proteomics and exometabolomics. A. macleodii 83-1 showed two distinct growth stages, with exponential growth during laminarin utilization followed by maintenance during simultaneous alginate/pectin utilization. The biphasic growth coincided with major temporal shifts in gene expression and metabolite secretion, enabling to define major/accessory polysaccharide utilization loci, reconstruct the complete degradation pathways for each polysaccharide, as well as identify temporal phenotypes in other relevant traits. FT-ICR-MS revealed a distinct suite of secreted metabolites for each growth phase, with pyrroloquinoline quinone exclusively produced with alginate/pectin. The finding of substrate-unique phenotypes indicates an exquisite adaptation to polysaccharide utilization with probable relevance for the degradation of macroalgal biomass, which comprises a complex mix of polysaccharides. Moreover, substrate-unique exometabolomes possibly influence metabolic interactions with other community members. Overall, the presence of fine-tuned genetic machineries for polysaccharide degradation and the widespread detection of related CAZymes in global locations indicate an ecological relevance of A. macleodii in marine polysaccharide cycling and bacteria-algae interactions.
2018-08-01 | GSE107306 | GEO