Mice fecal microbiome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA928685 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23495326_1.fastq.gz | Fastqsanger.gz | |||
| SRR23495326_2.fastq.gz | Fastqsanger.gz | |||
| SRR23495327_1.fastq.gz | Fastqsanger.gz | |||
| SRR23495327_2.fastq.gz | Fastqsanger.gz | |||
| SRR23495328_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 64 |
Similar Datasets
Project description:Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals, reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease. In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles. RNA-Seq analysis of the human gut microbiome during consumption of a plant- or animal-based diet.
2013-12-05 | E-GEOD-46761 | biostudies-arrayexpress
Project description:We designed probes to understand bile salt hydrolase substrate specificity in the mousegut microbiome.
2024-06-04 | PXD052119 | Pride
Project description:E. coli DH5a expressing bile salt hydrolase variants in the presence of 1 mM glycocholate (GCA), taurocholate (TCA), or cholate (CA).
2023-06-09 | MSV000092138 | MassIVE
Project description:Engineered bacterial strains with bile salt hydrolase that changed in their expression levels with high diet and diurnal changes were synthesized. These synthetic strains were cultures in BHI media with bile acids spiked in.
2024-04-20 | MSV000094578 | MassIVE
Project description:Bifidobacterium are considered to be beneficial for human health and are classified as probiotic bacterium. They must resist many environmental stress factors in order to survive in the gastrointestinal environment including; pH, oxygen availability, bile and nutrient starvation (eg: iron or carbon). This study investigates Bifidobacterium breve UCC2003 global genome response to growth under ferrous and/or ferric iron limiting conditions. Revealing that growth under iron limitation effects many processes in the cell including carbon and nitrogen metabolism and induces/reduces the expression of numerous genes; including multiple iron uptake systems, DPS proteins (which are predicted to be involved in iron storage/DNA protection), Fe-S cluster associated proteins and a bile salt hydrolase (bshB). Insertional mutagenesis and survival assays were employed and demonstrated that iron starvation imposed on B. breve UCC2003 results in an increased resistance to bile stress due to in part the iron-inducible transcription of the bshB gene. Furthermore, this study links BSH activity in B. breve UCC2003 to its ability to survive the deleterious effects of bile salt and suggest that B. breve UCC2003 may be use iron as a signal to adapt to the constantly changing environment within the small intestine.
2018-03-31 | GSE110080 | GEO
Project description:The microorganisms colonizing the gastrointestinal tract of animals, collectively referred to as the gut microbiome, affect numerous host behaviors dependent on the central nervous system (CNS). Studies comparing germ-free mice to normally colonized mice have demonstrated influences of the microbiome on anxiety-related behaviors, voluntary activity, and gene expression in the CNS. Additionally, there is epidemiologic evidence supporting an intergenerational influence of the maternal microbiome on neurodevelopment of offspring and behavior later in life. There is limited experimental evidence however directly linking the maternal microbiome to long-term neurodevelopmental outcomes, or knowledge regarding mechanisms responsible for such effects. Here we show that that the maternal microbiome has a dominant influence on several offspring phenotypes including anxiety-related behavior, voluntary activity, and body weight. Adverse outcomes in offspring were associated with features of the maternal microbiome including bile salt hydrolase (Bsh) expression, abundance of certain bile acids, and hepatic expression of S1pr2. In cross-foster experiments, offspring resembled their birth dam phenotypically, despite faithful colonization in the postnatal period with the surrogate dam microbiome. Genome-wide methylation analysis of hippocampal DNA identified microbiome-associated differences in methylation of 196 loci in total, 176 of which were imprinted by the maternal microbiome. Further, single-cell transcriptional analysis revealed accompanying differences in expression of several differentially methylated genes within certain hippocampal cell clusters, and vascular expression of genes associated with bile acid transport. Inferred cell-to-cell communication in the hippocampus based on coordinated ligand-receptor expression revealed differences in expression of neuropeptides associated with satiety. Collectively, these data provide proof-of-principle that the maternal gut microbiome has a dominant influence on the neurodevelopment underlying certain offspring behaviors and activities, and selectively affects genome methylation and gene expression in the offspring CNS in conjunction with that neurodevelopment.
2024-11-01 | GSE239371 | GEO
Project description:Microbial transformation of bile acids affects intestinal immune homeostasis but its impact on inflammatory pathologies remains largely unknown. Using a mouse model of graft-versus-host disease (GVHD), we found that T cell-driven inflammation decreased the abundance of microbiome-encoded bile salt hydrolase (BSH) genes and reduced the levels of unconjugated and microbe-derived bile acids. Several microbe-derived bile acids attenuated farnesoid X receptor (FXR) activation, suggesting that loss of these metabolites during inflammation may increase FXR activity and exacerbate the course of disease. Indeed, mortality increased with pharmacological activation of FXR and decreased with its genetic ablation in donor T cells during mouse GVHD. Furthermore, patients with GVHD after allogeneic hematopoietic cell transplantation showed similar loss of BSH and the associated reduction in unconjugated and microbe-derived bile acids. Additionally, the FXR antagonist ursodeoxycholic acid reduced the proliferation of human T cells and was associated with a lower risk of GVHD-related mortality in patients. We propose that dysbiosis and loss of microbe-derived bile acids during inflammation may be an important mechanism to amplify T cell-mediated diseases.
2024-02-09 | GSE253360 | GEO
Project description:A selective gut bacterial bile salt hydrolase alters host metabolism
| PRJNA448196 | ENA
Project description:Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals, reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease. In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles.
2013-12-05 | GSE46761 | GEO