Analysis of the fecal and oral microbiota in chronic recurrent multifocal osteomyelitis
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB22984 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2442390_1.fastq.gz | Fastqsanger.gz | |||
| ERR2442390_2.fastq.gz | Fastqsanger.gz | |||
| ERR2442400_1.fastq.gz | Fastqsanger.gz | |||
| ERR2442400_2.fastq.gz | Fastqsanger.gz | |||
| ERR2442410_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 178 |
Similar Datasets
Project description:Shisha smoking has been epidemiologically linked to development of oral lesions as well as various cancers. However, few molecular studies investigate the pathobiology of shisha induced cancer. In this study we investigate the effects of chronic shisha exposure in an in vitro model using normal, immortalized, non-transformed oral keratinocytes. Quantitative proteomic and phosphoproteomic analyses were performed on OKF6/TERT1 cells exposed to shisha for a period of 8 months. Gene Ontology and pathway analysis of dysregulated proteins and phosphoproteins were carried out to identify significantly enriched biological processes and pathways in shisha exposed cells compared to parental cells. Chronic shisha exposure resulted in increased cell scattering phenomenon in OKF6/TERT1 cells. Quantitative data analysis revealed differential phosphorylation of 164 phosphopeptides (fold change ≥1.5, p≤0.05) corresponding to 136 proteins. Kinases such as PRKCD were seen to be hyperphosphorylated. Pathway analysis revealed an enrichment of hyperphosphorylated and/or overexpressed proteins involved in the mTORC1 and EIF4F complexes. These complexes are associated with initiation of protein translation and are known to the affected in cancers. Network analysis also highlighted a downregulation of proteins associated with Type I interferon signaling in shisha exposed cells. High throughput phosphoproteomic analysis revealed global perturbations to the molecular milieu of oral keratinocytes upon shisha exposure. Further studies are needed to validate putative targets in oral cancer patients with shisha smoking history.
2019-07-23 | PXD011318 | Pride
Project description:The oral and fecal microbiome in chronic pancreatitis and pancreatic cancer.
| PRJEB38625 | ENA
Project description:Oral lichen planus (OLP) is a chronic inflammatory disease with various clinical subtypes. Recurrent erosion of OLP brings great physical and mental pain to patients without clear pathogenesis. Herein, this study is the first to utilize single-cell RNA sequencing combined with spatial transcriptome and bulk RNA-seq to explore the tissual microenvironments of patients within normal oral mucosa, non-erosive OLP (ENOLP) and erosive OLP (EOLP).
2022-08-24 | GSE211630 | GEO
Project description:Smoking is the leading cause of preventable death worldwide. It increases the risk for various diseases including respiratory diseases, vascular diseases and different cancers including lung, oral and bladder cancer. Despite being the leading cause of oral cancer, the molecular mechanisms resulting in malignancy upon cigarette smoke exposure are yet to be fully elucidated. It is crucial to note that disease development is observed upon chronic exposure to cigarette smoke, as opposed to a short-term exposure. Hence, we sought to investigate the effect of chronic smoke exposure on normal oral keratinocytes (OKF6/TERT1). We employed tandem mass tag-based quantitative proteomic and phosphoproteomic approaches to investigate the proteomic and signaling changes in OKF6/TERT1 cells chronically exposed to cigarette smoke compared to untreated cells. LC/MS2 analysis resulted in the quantification of 5,067 proteins among which expression of 360 proteins were found to be dysregulated in at least one replicate. Phosphoproteomic analysis revealed quantification of 3,647 phosphopeptides corresponding to 1,801 proteins. Majority of the dysregulated proteins were seen to be involved in cellular processes such as cell growth, cellular communication and energy metabolism. This study will aid in elucidating the effects of smoking in oral cancer and in the identification of potential candidates molecules which could serve as early detection biomarkers or therapeutic targets.
2018-03-05 | PXD007637 | Pride
Project description:Importance:Fecal microbiota transplantation (FMT) is effective in preventing recurrent Clostridium difficile infection (RCDI). However, it is not known whether clinical efficacy differs by route of delivery. Objective:To determine whether FMT by oral capsule is noninferior to colonoscopy delivery in efficacy. Design, Setting, and Participants:Noninferiority, unblinded, randomized trial conducted in 3 academic centers in Alberta, Canada. A total of 116 adult patients with RCDI were enrolled between October 2014 and September 2016, with follow-up to December 2016. The noninferiority margin was 15%. Interventions:Participants were randomly assigned to FMT by capsule or by colonoscopy at a 1:1 ratio. Main Outcomes and Measures:The primary outcome was the proportion of patients without RCDI 12 weeks after FMT. Secondary outcomes included (1) serious and minor adverse events, (2) changes in quality of life by the 36-Item Short Form Survey on a scale of 0 (worst possible quality of life) to 100 (best quality of life), and (3) patient perception on a scale of 1 (not at all unpleasant) to 10 (extremely unpleasant) and satisfaction on a scale of 1 (best) to 10 (worst). Results:Among 116 patients randomized (mean [SD] age, 58 [19] years; 79 women [68%]), 105 (91%) completed the trial, with 57 patients randomized to the capsule group and 59 to the colonoscopy group. In per-protocol analysis, prevention of RCDI after a single treatment was achieved in 96.2% in both the capsule group (51/53) and the colonoscopy group (50/52) (difference, 0%; 1-sided 95% CI, -6.1% to infinity; P < .001), meeting the criterion for noninferiority. One patient in each group died of underlying cardiopulmonary illness unrelated to FMT. Rates of minor adverse events were 5.4% for the capsule group vs 12.5% for the colonoscopy group. There was no significant between-group difference in improvement in quality of life. A significantly greater proportion of participants receiving capsules rated their experience as "not at all unpleasant" (66% vs 44%; difference, 22% [95% CI, 3%-40%]; P = .01). Conclusions and Relevance:Among adults with RCDI, FMT via oral capsules was not inferior to delivery by colonoscopy for preventing recurrent infection over 12 weeks. Treatment with oral capsules may be an effective approach to treating RCDI. Trial Registration:clinicaltrials.gov Identifier: NCT02254811.
| S-EPMC5820695 | biostudies-other
Project description:The effect of oral microbiota on the intestinal microbiota has garnered growing attention as a mechanism linking periodontal diseases to systemic diseases. However, the salivary microbiota is diverse and comprises numerous bacteria with a largely similar composition in healthy individuals and periodontitis patients. Thus, the systemic effects of small differences in the oral microbiota are unclear. In this study, we explored how health-associated and periodontitis-associated salivary microbiota differently colonized the intestine and their subsequent systemic effects by analyzing the hepatic gene expression and serum metabolomic profiles. The salivary microbiota was collected from a healthy individual and a periodontitis patient and gavaged into C57BL/6NJcl[GF] mice. Samples were collected five weeks after administration. Gut microbial communities were analyzed by 16S ribosomal RNA gene sequencing. Hepatic gene expression profiles were analyzed using a DNA microarray and quantitative polymerase chain reaction. Serum metabolites were analyzed by capillary electrophoresis time-of-flight mass spectrometry. The gut microbial composition at the genus level was significantly different between periodontitis-associated microbiota-administered (PAO) and health-associated oral microbiota-administered (HAO) mice. The hepatic gene expression profile demonstrated a distinct pattern between the two groups, with higher expression of Neat1, Mt1, Mt2, and Spindlin1, which are involved in lipid and glucose metabolism. Disease-associated metabolites such as 2-hydroxyisobutyric acid and hydroxybenzoic acid were elevated in PAO mice. These metabolites were significantly correlated with Bifidobacterium, Atomobium, Campylobacter, and Haemophilus, which are characteristic taxa in PAO mice. Conversely, health-associated oral microbiota were associated with higher levels of beneficial serum metabolites in HAO mice. The multi-omics approach used in this study revealed that periodontitis-associated oral microbiota is associated with the induction of disease phenotype when they colonized the gut of germ-free mice.
2022-08-17 | GSE198570 | GEO
Project description:The interplay among different cells in a tissue is essential for maintaining homeostasis. Although, disease states have been traditionally attributed to individual cell types, increasing evidence and new therapeutic options have demonstrated the primary role of multicellular functions to understand health and disease, opening new avenues to understand pathogenesis and develop new treatment strategies. We recently described the cellular composition and dynamics of the human oral mucosa; however, the spatial arrangement of cells is needed to better understand a morphologically complex tissue. Here, we link single-cell RNA sequencing, spatial transcriptomics, and high-resolution multiplex fluorescence in situ hybridisation to characterise human oral mucosa in health and oral chronic inflammatory disease. We define highly specialised epithelial and stromal compartments and describe location-specific immune programs. Furthermore, we discovered fine regional fibroblast states, and spatially mapped a rare pathogenic population localised in a highly immunogenic region, responsible for lymphocyte recruitment through CXCL8 and CXCL10 and with a possible role in pathological angiogenesis through ALOX5AP. Collectively, our study provides a comprehensive reference for the study of oral chronic disease pathogenesis.
2023-02-01 | GSE206621 | GEO
Project description:Oral and fecal microbiota in a wild passerine bird, the great tit
| PRJEB19204 | ENA
Project description:The practice of using chewing tobacco is common in certain socio-economic sections of southern Asia particularly in the Indian subcontinent. The molecular mechanism of smokeless tobacco which leads to malignancy is unclear. Chewing tobacco demonstrates a carcinogenic effect through chronic and not acute exposures. Using a cell line model, we studied the chronic effects of chewing tobacco on the proteome in normal oral keratinocytes (OKF6/TERT1). We carried out iTRAQ-based quantitative proteomic analysis of the untreated and chewing tobacco treated oral keratinocytes. LC-MS/MS analysis of this cell line pair resulted in the identification of 3,638 proteins of which 408 were found to be differentially expressed.
2016-12-14 | PXD001554 | Pride
Project description:The role of microbiota in Lynch syndrome (LS) is still under debate. We compared oral and fecal microbiota of LS saliva and stool samples with normal healthy controls (NHC). Total DNA was purified from feces and saliva to amplify the V3-V4 region of the 16s rRNA gene. Sequences with a high-quality score and length >250 bp were used for taxonomic analysis with QIIME software. Compared to NHC, LS fecal samples demonstrated a statistically significant increase of Bacteroidetes and Proteobacteria and a significant decrease of Firmicutes at the phylum level and of Ruminococcaceae at the family level. Moreover, LS oral samples exhibited a statistically significant increase of Veillonellaceae and Leptotrichiaceae and a statistically significant decrease of Pasteurellaceae. A beta-diversity index allowed differentiation of the two groups. A peculiar microbial signature is associated with LS, similar to that of sporadic colorectal cancer and Crohn's disease. These data suggest a possible role of proinflammatory bacteria in tumor development in a condition of genetic predisposition, such as LS.
| S-EPMC7563889 | biostudies-literature