Ontology highlight
ABSTRACT:
PROVIDER: PRJEB88459 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Shotgun metagenomics to explore specific taxa associated with chronic bacterial osteomyelitis in the saliva microbiome
| PRJDB16210 | ENA
Project description:To explore new aspects of Chronic non-bacterial osteomyelitis (CNO) based on whole blood RNA sequencing (> 6Gb per sample)
2021-11-05 | GSE187429 | GEO
Project description:Atherosclerosis is a disease of mid-to-large arteries characterized by lipid accumulation, chronic inflammation, and pathologic remodeling of the vessel wall. Rupture of atherosclerotic plaques can generate thrombi that occlude blood flow and cause acute myocardial infarction (AMI) and acute ischemic stroke (AIS) that are leading causes of death and disability. Patients that develop severe bacterial infections are at increased risk of AMI and AIS, but the mechanisms underlying this association have not been well-characterized. Previous studies have reported that low-density lipoprotein (LDL) carries bacterial small (s)RNAs that can influence macrophage polarization within plaques, but whether infection alters LDL-associated sRNA or atherosclerotic plaque characteristics to promote AMI/AIS is unclear. Here, we tested whether chronic infection by the Gram-positive pathobiont Staphylococcus aureus was sufficient to alter LDL-associated bacterial sRNA and promote pathogenic changes in atheromatous plaques. Using a mouse model of injury-associated S. aureus osteomyelitis, we report minimal changes in the bacterial sRNA composition of LDL with no obvious changes in pathogen-derived sRNA on LDL of either normolipidemic or hyperlipidemic mice. Unexpectedly, hyperlipidemic mice with chronic osteomyelitis showed a reduction in plaque area within the aortic root relative to sham mice. Although these results do not explain increased risk of AMI/AIS in patients, we observed that hyperlipidemic mice had reduced bacterial burden and reduced bone disease relative to normolipidemic mice infected with S. aureus. Together, these findings highlight unresolved questions regarding the origin of bacterial sRNA associated with LDL and suggests that hyperlipidemia contributes to host protection against invasive S. aureus infection.
2026-08-13 | GSE343653 | GEO
Project description:Background: Saliva is an attractive body fluid for non-invasive biomarker discovery, containing both human and microbial components, associated with various chronic diseases. Type-2 diabetes (T2D) imposes a significant health and socio-economic burden. Prior research on T2D salivary microbiome utilised methods such as metagenomics, metatranscriptomics, 16S rRNA sequencing, and low-throughput proteomics. Results: We conducted ultra-fast, in-depth MS-based profiling of saliva from 15 T2D individuals and 15 age/BMI-matched healthy controls (HC). Using state-of-the-art proteomics, over 4500 proteins were identified in 21 minutes of analysis, including both human and bacterial proteins. Analysis revealed signatures of altered immune, lipid- and glucose-metabolism regulatory systems, increased oxidative stress, and possible precancerous changes in T2D saliva. Bacterial genera Neisseria and Corynebacterium showed biomarker potential, offering insights into disease pathophysiology and microbial applications for T2D management. Conclusions: This study provides a comprehensive map of salivary proteins and microbial communities, serving as a resource for better understanding of T2D pathophysiology. The identified biomarkers offer potential for improved diagnostics and therapeutic strategies in T2D and associated long-term complications.
2025-05-06 | PXD051453 | Pride
Project description:To explore how APOE functions in the mechanism of regulation of cholesterol metabolism during S. aureus osteomyelitis, we established S. aureus osteomyelitis models in WT mice and APOE knockout mice. We then performed gene expression profiling analysis using data obtained from RNA-seq of bone marrow from mice mentioned above at day 7 after operation.
2023-07-09 | GSE227521 | GEO
Project description:Microbiota assembly in the infant gut is influenced by time and duration of dietary exposure to breast-milk, infant formula and solid foods. In this randomized controlled intervention study, longitudinal sampling of infant stools (n=998) showed similar development of fecal bacterial communities between formula- and breast-fed infants during the first year of life (N=210). Infant formula supplemented with galacto-oligosaccharides (GOS) was most efficient to sustain high levels of bifidobacteria compared to formula containing B. longum and B. breve or placebo. Metabolite (untargeted) and bacterial profiling (16S rRNA/shallow metagenomics sequencing) revealed 24-hour oscillations and integrated data analysis identified circadian networks. Rhythmicity in bacterial diversity, specific taxa and functional pathways increased with age and was most pronounced following breast-feeding and GOS-supplementation. Circadian rhythms in dominant taxa were discovered ex-vivo in a chemostat model. Hence microbiota rhythmicity develops early in life, likely due to bacterial intrinsic clock mechanism and is affected by diet.
2024-01-10 | MSV000093802 | MassIVE
Project description:Purpose The role of intestinal flora in carcinogenesis and chemotherapy efficacy has been increasingly studied; however, comparisons between oral and intestinal flora remain limited. This study aimed to identify the microbial changes in urothelial carcinoma (UC) by analyzing oral saliva and stool samples from healthy individuals and patients. We also examined the association between microbial composition and immune checkpoint inhibitor (ICI) response. Methods A total of 20 healthy individuals and 38 patients with UC were analyzed. Among them, 27 patients with UC underwent ICI treatment. Oral saliva and stool samples were analyzed for 16S rRNA sequences to assess bacterial composition. Operational taxonomic units were generated, and phylogenetic analysis was performed using the 16S Metagenomics app whithin the Illumina BaseSpace Sequence Hub. Results Patients with UC showed higher Veillonellaceae and Prevotellaceae levels in saliva and stool, with lower levels of these bacteria associated with more prolonged overall survival and progression-free survival, particularly Veillonellaceae in stool. A higher neutrophil-to-lymphocyte ratio correlated with increased levels of these bacteria. Conclusion Veillonellaceae and Prevotellaceae are potential microbial biomarkers of survival outcomes and ICI efficacy in patients with UC. Non-invasive oral microbial sampling may facilitate personalized cancer treatment strategies.
2025-05-28 | GSE293354 | GEO
Project description:A metaproteomics analysis was conducted on the infant fecal microbiome to characterize global protein expression in 8 samples obtained from infants with a range of early-life experiences. Samples included breast-, formula- or mixed-fed, mode of delivery, and antibiotic treatment and one set of monozygotic twins. Although label-free mass spectrometry-based proteomics is routinely used for the identification and quantification of thousands of proteins in complex samples, the metaproteomic analysis of the gut microbiome presents particular technical challenges. Among them: the extreme complexity and dynamic range of member taxa/species, the need for matched, well-annotated metagenomics databases, and the high inter-protein sequence redundancy/similarity between related members. In this study, a metaproteomic approach was developed for assessment of the biological phenotype and functioning, as a complement to 16S rRNA sequencing analysis to identify constituent taxa. A sample preparation method was developed for recovery and lysis of bacterial cells, followed by trypsin digestion, and pre-fractionation using Strong Cation Exchange chromatography. Samples were then subjected to high performance LC-MS/MS. Data was searched against the Human Microbiome Project database, and a homology-based meta-clustering strategy was used to combine peptides from multiple species into representative proteins. Bacterial taxonomies were also identified, based on species-specific protein sequences, and protein metaclusters were assigned to pathways and functional groups. The results obtained demonstrate the applicability of this approach for performing qualitative comparisons of human fecal microbiome composition, physiology and metabolism, and also provided a more detailed assessment of microbial composition in comparison to 16S rRNA.
2019-03-29 | PXD006033 | Pride
Project description:Monitoring microbial communities can aid in understanding the state of these habitats. Environmental DNA (eDNA) techniques provide efficient and comprehensive monitoring by capturing broader diversity. Besides structural profiling, eDNA methods allow the study of functional profiles, encompassing the genes within the microbial community. In this study, three methodologies were compared for functional profiling of microbial communities in estuarine and coastal sites in the Bay of Biscay. The methodologies included inference from 16S metabarcoding data using Tax4Fun, GeoChip microarrays, and shotgun metagenomics.
2024-04-14 | E-MTAB-13075 | biostudies-arrayexpress