Intestinal microbiota from STEC-infected patients
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB23207 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2182603.fastq.gz | Fastqsanger.gz | |||
| ERR2182604.fastq.gz | Fastqsanger.gz | |||
| ERR2182505.fastq.gz | Fastqsanger.gz | |||
| ERR2270940_1.fastq.gz | Fastqsanger.gz | |||
| ERR2270940_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 25 |
Similar Datasets
Project description:The human intestinal microbiota is a homeostatic ecosystem with a remarkable impact on human health and the disruption of this equilibrium leads to an increased susceptibility to infection by numerous pathogens. In this study, we used shotgun metagenomic sequencing and two different bioinformatic approaches, based on mapping of the reads onto databases and on the reconstruction of putative draft genomes, to investigate possible changes in the composition of the intestinal microbiota in samples from patients with Shiga Toxin-producing E. coli (STEC) infection compared to healthy and healed controls, collected during an outbreak caused by a STEC O26:H11 infection. Both the bioinformatic procedures used, produced similar result with a good resolution of the taxonomic profiles of the specimens. The stool samples collected from the STEC infected patients showed a lower abundance of the members of Bifidobacteriales and Clostridiales orders in comparison to controls where those microorganisms predominated. These differences seemed to correlate with the STEC infection although a flexion in the relative abundance of the Bifidobacterium genus, part of the Bifidobacteriales order, was observed also in samples from Crohn's disease patients, displaying a STEC-unrelated dysbiosis. The metagenomics also allowed to identify in the STEC positive samples, all the virulence traits present in the genomes of the STEC O26 that caused the outbreak as assessed through isolation of the epidemic strain and whole genome sequencing. The results shown represent a first evidence of the changes occurring in the intestinal microbiota of children in the course of STEC infection and indicate that metagenomics may be a promising tool for the culture-independent clinical diagnosis of the infection.
| S-EPMC5808120 | biostudies-literature
Project description:The search for factors beyond the radiotherapy dose that could identify patients more at risk of developing radio-induced toxicity is essential to establish personalised treatment protocols for improving the quality-of-life of survivors. To investigate the role of the intestinal microbiota in the development of radiotherapy-induced gastrointestinal toxicity, the MicroLearner observational cohort study characterised the intestinal microbiota of 136 (discovery) and 79 (validation) consecutive prostate cancer patients at baseline radiotherapy. Gastrointestinal toxicity was assessed weekly during RT using CTCAE. An average grade >1.3 over time points was used to identify patients suffering from persistent acute toxicity (endpoint). The intestinal microbiota of patients was quantified from the baseline faecal samples using 16S rRNA gene sequencing technology.
2024-07-25 | GSE268869 | GEO
Project description:Purpose: In this work, we evaluated the role of two indicative species, Citrobacter werkmanii (CW) and Escherichia albertii (EA), in the virulence of two DEC pathotypes, Shiga toxin-producing (STEC) and enteroaggregative (EAEC) Escherichia coli. Methods: To determine the effect of supernatant obtained from CW and EA cultures in STEC strain 86-24 and EAEC strain 042 gene expression, a RNA-seq analysis was performed. T84 cells were infected with DEC strains in the presence or absence of supernatant from EA and IL-8 secretion was evaluated. The effect of supernatant from EA on the growth and adherence of STEC and EAEC to T84 cells was also evaluated. Finally, we studied the participation of long polar fimbriae (Lpf) in STEC and plasmid-encoded toxin (Pet) in EAEC during DEC infection in the presence of supernatant from EA. Results: RNA-seq analysis revealed that several virulence factors in STEC and EAEC were up-regulated in the presence of supernatants from CW and EA. Interestingly, an increase in the secretion of IL-8 was observed in T84 cells infected with STEC or EAEC in the presence of a supernatant from EA. Similar results were observed with the supernatants obtained from clinical strains of E. albertii. Supernatant from EA had no effect on the growth of STEC and EAEC, or on the ability of these DEC strains to adhere to intestinal epithelial cells. Finally, we found that Pet toxin in EAEC was up-regulated in the presence of a supernatant from EA. In STEC, using mutant strains for Lpf fimbriae, our data suggested that these fimbriae might be participating in the increase of IL-8 induced by STEC on intestinal epithelial cells in the presence of a supernatant from EA. Conclusion:Supernatant obtained from an indicative species of DEC-positive diarrhea could modulate gene expression in STEC and EAEC, and IL-8 secretion induced by these bacteria. These data provide new insights into the effect of gut microbiota species in the pathogenicity of STEC and EAEC.
2022-07-22 | GSE197797 | GEO
Project description:Comparison of RNA expression profiles from STEC strain FHI96 expressing methyltransferase mod (ON; 52reps) or not (OFF; 51reps).
2024-06-30 | GSE129787 | GEO
Project description:Application of a mass spectrometry -based approach to assess the gut microbiota composition and the associated metaproteomic functionality in patients with intestinal COVID-19 infection
2022-09-01 | PXD024990 | Pride
Project description:The GeneChip Porcine Genome Array was used to identify the transcriptional response upon Salmonella typhimurium infection in three porcine intestinal sections (jejumun, ileum and colon) along a time course of 1,2 and 6 days post infection. The objetives in this study were i) characterize transcriptional changes upon S. typhimurium infection in the intestinal mucosa; ii) identify differences among porcine intestinal sections in inmune resposes against S. typhimurium; iii) identify change that could be associated to salmonellosis pathogenesis and symtomatology; and finally, iv) identify transcriptional changes that could be induced by S. typhimurium in order to get bacterial survival and successful colonization. Sixteen male and female crossbreeds weaned piglets, approximately 4 weeks of age, were used in this study. Before infection, faecal samples from each animal were analyzed to confirm that piglets were free of Salmonella. Pigs were housed in an environmentally controlled isolation facility at 25ºC and under constant light with ad libitum access to feed and water. After an acclimation period of 5 days, pigs were challenged orally with 108 cfu of Salmonella enterica serovar Typhimurium phagetype DT104 (n=12), whereas the control group (n=4) received sterile medium orally. The four non-infected control pigs were necropsied two hours prior to experimental infection. Four randomly chosen infected pigs were necropsied at 1 day post infection (dpi), 2 dpi and 6 dpi, respectively. Faecal swabs, blood and tissues samples were aseptically collected. Ileum was collected, sectioned in pieces of around 10 cm and immediately frozen in liquid nitrogen for mucosa isolation and RNA purification. To ensure the inoculated pigs were infected, faecal samples were cultured and checked for positive Salmonellae organism Four reps per treatment and tissue group except 'Ileum 1dpi' has only 3 replicates.
2012-06-19 | E-GEOD-22596 | biostudies-arrayexpress
Project description:The Salmonella effector SteC is the only protein kinase encoded by Salmonella pathogenicity island 2 that is secreted through the type III secretion system. SteC is known to trigger actin rearrangement via the phosphorylated MEK pathway, and our previous experiments demonstrated that the migration process of macrophages found during Salmonella infection is dependent on the rearrangement of the host cell actin backbone and the action of SteC.To further investigate the target of SteC in the host, we constructed a SteC-RAW264.7 cell line and performed phosphomics analysis using 4D-FastDIA to identify the direct substrates of SteC that trigger macrophage migration and lead to cytoskeletal rearrangement.
2024-02-22 | PXD042038 | Pride
Project description:Background: Prior analyses of mRNA expression in intestinal tissue as related to HIV cohorts has been on whole biopsies. More targeted isolation and enrichment of intestinal epithelial cells is needed to identify pathways specifically altered in the epithelium that may not be picked up at a global tissue scale. Results: Analysis of intestinal epithelial cells isolated from primary human tissues taken from HIV-infected cohorts as well as uninfected controls. Results demonstrate key genes differentially expressed in HIV in the absence or presence of ART-therapy.
2018-01-02 | GSE81198 | GEO
Project description:In this randomised placebo-controlled trial, irritable bowel syndrome (IBS) patients were treated with faecal material from a healthy donor (n=8, allogenic FMT) or with their own faecal microbiota (n=8, autologous FMT). The faecal transplant was administered by whole colonoscopy into the caecum (30 g of stool in 150 ml sterile saline). Two weeks before the FMT (baseline) as well as two and eight weeks after the FMT, the participants underwent a sigmoidoscopy, and biopsies were collected at a standardised location (20-25 cm from the anal verge at the crossing with the arteria iliaca communis) from an uncleansed sigmoid. In patients treated with allogenic FMT, predominantly immune response-related genes sets were induced, with the strongest response two weeks after FMT. In patients treated with autologous FMT, predominantly metabolism-related gene sets were affected.
2019-10-14 | GSE138297 | GEO
Project description:Routine surveillance of STEC at the Belgian NRC STEC
| PRJEB54005 | ENA