Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effect of Bifidobacterium infantis, Bacteroides thetaiotaomicron or heat-killed B. infantis on murine colonic transcriptome

ABSTRACT: To investigate bacteria-host interactions in vivo in a murine model. Mice were orally gavaged with bacteria at day 7 and 10 of life. The colonic transcriptome was analyzed at day 14 of life.

ORGANISM(S): Mus musculus

PROVIDER: GSE233864 | GEO | 2023/12/14

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Effect of Bifidobacterium infantis or its secreted byproducts, Bacteroides thetaiotaomicron or heat-killed B. infantis on human colonic epithelial cells transcriptome

Project description:To investigate bacteria-host interactions in vitro using human colonic epithelial cells. Mature colonic epithelial cells were stimulated with bacteria conditions for 6 hours. Cells were then lysed and RNA extracted. RNA sequencing was performed on cells stimulated under 6 different conditions (3 replicates per condition).

2023-12-14 | GSE233865 | GEO

Effect of Bifidobacterium infantis, Bacteroides thetaiotaomicron or heat-killed B. infantis on murine colonic transcriptome

Project description:Effect of Bifidobacterium infantis, Bacteroides thetaiotaomicron or heat-killed B. infantis on murine colonic transcriptome

| PRJNA978252 | ENA

Genome-wide RNA-seq of Bacteroides thetaiotaomicron VPI-5482 with Bacteroides phage challenge

Project description:Purpose: Examining the transcriptome of Bacteroides thetaiotaomicron VPI-5482 challenged with Bacteroides phage to assess surface molecule expression changes Methods: Bacteroides thetaiotaomicron was grown in BPRM in vitro or Germ-Free mice were monocolonized with Bacteroides thetaiotaomicron and gavaged with ARB25 phage. Fold change was calculated as live phage versus heat-killed phage treated samples with n=3 biological replicates. Once cells reached an optical density corresponding to mid-log phase growth (absorbance between 0.4-0.5), RNA was isolated and rRNA depleted. Samples were multiplexed for sequencing on the Illumina HiSeq platform at the University of Michigan Sequencing Core. Data was analyzed using Arraystar software (DNASTAR, Inc.) using DEseq2 normalization with default parameters. Genes with significant up- or down-regulation were determined by the following criteria: genes with an average fold-change >5-fold and with at least 2/3 biological replicates with a normalized expression level >1% of the overall average, and a p-value < 0.05 (t test with Benjamini-Hochberg correction) Results: Specific capsule expression was increased in wild-type B. thetaiotaomicron during phage infection in vitro and in vivo. Many corresponding in vivo genes were upregulated as well as other surface layer proteins.

2020-05-01 | GSE147071 | GEO

Genome-wide analysis of tumor-infiltrating dendritic cells comparing C57BL/6 mice obtained from Jackson laboratories or Taconic farms, untreated or treated with Bifidobacterium.

Project description:Comparison of gene expression in dendritic cells (DCs) isolated from tumors of C57BL/6 obtained from Taconic farms vs DCs isolated from tumor of C57BL/6 mice obtained from Jackson Labortaory vs DCs isolated from tumors of C57BL/6 obtained from Taconic farms and orally gavaged with Bifidobacterium prior to tumor implantation

2015-11-12 | GSE73475 | GEO

Bacteroides thetaiotaomicron

Project description:Depolymerization of plant cell wall glycans by symbiotic human gut bacteria (Bacteroides thetaiotaomicron)

| PRJNA142409 | ENA

Bacteroides thetaiotaomicron

Project description:Chronic colitis in Bacteroides Thetaiotaomicron-Monoassociated HLA-B27 Transgenic rats alters expression of receptor and metabolic genes in luminal bacteria.

| PRJNA150943 | ENA

Coculture fermentations of Bifidobacterium species and Bacteroides thetaiotaomicron reveal a mechanistic insight into the prebiotic effect of inulin-type fructans.

Project description:Four bifidobacteria, each representing a cluster of strains with specific inulin-type-fructan degradation capacities, were grown in coculture fermentations with Bacteroides thetaiotaomicron LMG 11262, a strain able to metabolize both oligofructose and inulin. In a medium for colon bacteria with inulin as the sole added energy source, the ability of the bifidobacteria to compete for this substrate reflected phenotypical variation. Bifidobacterium breve Yakult, a strain that was not able to degrade oligofructose or inulin, was outcompeted by B. thetaiotaomicron LMG 11262. Bifidobacterium adolescentis LMG 10734, a strain that could degrade oligofructose (displaying a preferential breakdown mechanism) but that did not grow on inulin, managed to become competitive when oligofructose and short fractions of inulin started to accumulate in the fermentation medium. Bifidobacterium angulatum LMG 11039(T), a strain that was previously shown to degrade all oligofructose fractions simultaneously and to be able to partially break down inulin, was competitive from the beginning of the fermentation, consuming short fractions of inulin from the moment they appeared. Bifidobacterium longum LMG 11047, representing a cluster of bifidobacteria that shared both high fructose consumption and oligofructose degradation rates and were able to perform partial breakdown of inulin, was the dominating strain in a coculture with B. thetaiotaomicron LMG 11262. These observations indicate that distinct subgroups within the large-intestinal Bifidobacterium population will be stimulated by different groups of prebiotic inulin-type fructans, a variation that could be reflected in differences concerning their health-promoting effects.

| S-EPMC2675216 | biostudies-other

Bovine Glycomacropeptide promotes the growth of Bifidobacterium longum subsp. infantis and modulates its gene expression

Project description:Microarray analysis of gene transcription in B. infantis following exposure to Glycomacropeptide (GMP) revealed a substantial transcriptional response to GMP relative to untreated bacteria or bacteria treated with periodate denatured GMP-P, with a greater number of differentially expressed transcripts and larger fold changes versus the control. The pool of differentially expressed transcripts included two glycoside hydrolase (family 25) genes, which were substantially up-regulated following exposure to GMP but not GMP-P.

2018-05-31 | GSE75969 | GEO

Xenosiderophore Utilization Promotes Bacteroides thetaiotaomicron Resilience during Colitis.

Project description:During short-lived perturbations, such as inflammation, the gut microbiota exhibits resilience and reverts to its original configuration. Although microbial access to the micronutrient iron is decreased during colitis, pathogens can scavenge iron by using siderophores. How commensal bacteria acquire iron during gut inflammation is incompletely understood. Curiously, the human commensal Bacteroides thetaiotaomicron does not produce siderophores but grows under iron-limiting conditions using enterobacterial siderophores. Using RNA-seq, we identify B. thetaiotaomicron genes that were upregulated during Salmonella-induced gut inflammation and were predicted to be involved in iron uptake. Mutants in the xusABC locus (BT2063-2065) were defective for xenosiderophore-mediated iron uptake in vitro. In the normal mouse gut, the XusABC system was dispensable, while a xusA mutant colonized poorly during colitis. This work identifies xenosiderophore utilization as a critical mechanism for B. thetaiotaomicron to sustain colonization during inflammation and suggests a mechanism of how interphylum iron metabolism contributes to gut microbiota resilience.

| S-EPMC7439322 | biostudies-literature

Gene expression of Bacteroides thetaiotaomicron, in vivo with and without IgA 225.4

Project description:Rag1-/- C57BL/6 or Rag1-/- C57BL/6 injected with the IgA producing hybridoma producing 225.4 anti- Bacteroides thetaiotaomicron (Capsular polysaccharide 4 dependent carbohydrate epitope specific epitope) mice were colonized with B. thetaiotaomicron wildtype strain VPI-5482 for 10 days. Cecal bacteria were harvested and snap frozen and RNA isolated. Keywords: Single time point, experimental and control groups.

2007-12-27 | GSE9019 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data