Bacteria
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA407051 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The aim of this research was to isolate purple bacteria from waste that degrade plastics. Using metagenomic techniques, bacteria living in plastic debris were identified, and subsequently the metabolic pathways and proteins involved in them were studied using metaproteomics.
2026-04-13 | PXD068661 | Pride
Project description:The aim of this research was to isolate purple bacteria from waste that degrade plastics. Using metagenomic techniques, bacteria living in plastic debris were identified, and subsequently the metabolic pathways and proteins involved in them were studied using metaproteomics.
2026-04-13 | PXD068590 | Pride
Project description:gut bacteria of mice Metagenomic assembly
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Project description:The gut microbiome is a key regulator of intestinal homeostasis. Although dysbiosis is pervasively reported in inflammatory bowel diseases (IBD), its drivers and impact in disease pathophysiology are not yet fully understood. By integrating public metagenomic and metabolomic datasets from >5000 individuals across 12 ethnically diverse cohorts with independent validation cohorts and using neural-network based feature attribution, we identified epimerized bile acids (BAs) produced by microbial hydroxysteroid dehydrogenases (HSDHs) as a novel hallmark of IBD-associated dysbiosis. This shift occurs alongside previously reported changes including a depletion of microbe-derived C7-dehydroxylated BAs and an accumulation of host-derived C7-hydroxylated BAs. We show that increased levels of host-derived BA lead to epithelial remodelling during disease and are sufficient to recapitulate key features of IBD-related dysbiosis, including reduced microbial diversity and expansion of bile-resistant bacteria such as Mediterraneibacter gnavus and Escherichia coli. HSDHs found in IBD-enriched bacteria facilitate growth under high host-derived BA conditions by converting these molecules into urso- and iso-forms. While epimerized 7α-dehydroxylated BA have established immunoregulatory properties, the function of host-derived BA epimers remain poorly understood. We demonstrate that epimerized host-derived BAs exhibit reduced FXR agonist activity and that increased levels of these metabolites, or the bacteria that produce them, are associated with diminished ileal FXR signaling and altered circulating FGF19 and C4 levels in IBD patients. Our findings identify enhanced BA epimerization as a defining metabolic feature of IBD-associated dysbiosis and reveal a mechanism by which bile-resistant bacteria reshape BA signaling, linking microbial adaptation, impaired host-microbiome feedback regulation, and intestinal inflammation.
2026-08-08 | GSE335355 | GEO
Project description:The aim of this experiment was to determine if the development of resistance to antibiotics can be driven by the concentration and speciation of Cu. Experimental setup was designed to investigate two hypotheses for which two strains of Gram- bacteria have been selected: - Do TE enhance AR in resistant bacteria? Resistant strain: Bioluminescent Pseudomonas aeruginosa PAO1 (Xen41, Tetracycline resistant) - Do TE induce AR in sensitive bacteria? Sensitive strain: Pseudomonas aeruginosa PAO1 (Wild Type)
2020-10-28 | GSE160188 | GEO
Project description:Distal gut bacteria play a pivotal role in the digestion of dietary polysaccharides by producing a large number of carbohydrate-active enzymes (CAZymes) that the host otherwise does not produce. We report here the design of a high density custom microarray that we used to spot non-redundant DNA probes for more than 6,500 genes encoding glycoside hydrolases and lyases selected from 174 reference genomes from distal gut bacteria. The custom microarray was tested and validated by the hybridization of bacterial DNA extracted from the stool samples of lean, obese and anorexic individuals. Our results suggest that a microarray-based study can detect genes from low-abundance bacteria better than metagenomic-based studies. A striking example was the finding that a gene encoding a GH6-family cellulase was present in all subjects examined, whereas metagenomic studies have consistently failed to detect this gene in both human and animal gut microbiomes. In addition, an examination of eight stool samples allowed the identification of a corresponding CAZome core containing 46 families of glycoside hydrolases and polysaccharide lyases, which suggests the functional stability of the gut microbiota despite large taxonomical variations between individuals.
2013-10-28 | GSE51760 | GEO