Bacteria
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB11989 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Prostate of SD rats was injected with 0.1 ml 1% carrageenan to induce chronic nonbacterial prostatitis, and the control rats injected with sterile saline. Then, the cecal contents were collected for 16S rDNA sequencing.
2021-07-07 | GSE179639 | GEO
Project description:Transcriptome analysis of oral tissue samples taken from peri-implantitis and healthy control patients Peri-implantitis is a condition resulting in destructive inflammation in the peri-implant soft tissue barrier. Clinically, it demonstrates vast clinical differences to periodontitis that suggests distinct inflammatory mechanisms. Implant-derived Titanium particles (i-TiPs) frequently found around diseased implants appear to alter the microenvironment and confer resistance to antibiotic treatments. Studies in orthopedic implants have demonstrated a strong inflammatory response to i-TiPs, involving a variety of cell types, in aseptic conditions. Nonetheless, the genetic programs of cells surveilling and supporting the peri-implant soft tissue barrier in response to the combined challenges of biomaterial degradation products and oral bacteria are poorly defined. Thus, we studied gene expression specific to oral peri-implant inflammatory disease. We found that certain cellular pathways were highly upregulated in diseased tissues. Upregulated pathways provided insight into important physiological pathways that might play a role in peri-implant pathology. These findings could potentially contribute to the production of more targeted and effective therapeutics for the disease.
2021-06-17 | GSE178351 | GEO
Project description:16S rDNA amplicon sequencing of 196 human fecal samples of an Inulin cross-over trial in healthy, mildly constipated individuals.
| EGAD00001004956 | EGA
Project description:RA_Normal_Relatives 16S rDNA microbiome analysis
| PRJNA317370 | ENA
Project description:Firs 1106 16S rDNA data for the Flemish Gut Flora Project
| EGAD00001001936 | EGA
Project description:We used phylogenetic low-density microarrays targeting the 16S rRNA gene to characterize the gingival flora of acute noma and acute necrotizing gingivitis lesions, and compared them to healthy control subjects of the same geographical and social background. Various types of samples were collected (column characteristics); patients from the same hospital without mouth infection (H), matched control populations (T), patients suffering gengivitis (Gengivitis), patient suffering NOMA (noma), patient suffering NOMA receiving antimicrobials (N-ATB). Sampled from patients were retrieved from both sides (column Description); healthy- or lesion-side of the mouth. All controls are matched with specific patients (see column patient category and number) We designed low-density 16S rDNA arrays representing 339 different phylotypes. We used an arbitrary cutoff of 1% of overall abundance to select from this dataset the most abundant sequences for probe design. Using this cutoff, the 132 most abundant 16S rRNA gene sequences were scanned for probes respecting defined physico-chemical properties (Tm = 65M-BM-15M-BM-0C; probe length = 23M-bM-^@M-^S50 nt; < -5.0 kcal/mol for hairpins; < -8.0 kcal/mol for self-dimers; and dinucleotide repeats shorter than 5 bp) using a commercial software (Array Designer TM 2.0 by Premier Biosoft). The 335 oligonucleotide probes were synthesized with a C6-linker with free primary amine (Sigma-Aldrich) and spotted on ArrayStrips microarrays (Clondiag GmbH, Jena, Germany).
2013-12-27 | E-GEOD-43612 | biostudies-arrayexpress
Project description:Background and aims. The etiopathology of inflammatory bowel diseases is still poorly understood. To date, only few little data are available on the microbiota composition in ulcerative colitis (UC), representing a major subform of inflammatory bowel diseases. Currently, one of the main challenges is to unravel the interactions between genetics and environmental factors in the onset or during the progression and maintenance of the disease. The aim of the present study was to analyse twin pairs discordant for UC for both gut microbiota dysbiosis and host expression profiles at a mucosal level and to get insight into the functional genomic crosstalk between microbiota and mucosal epithelium in vivo. Methods. Biopsies were sampled from the sigmoid colon of both healthy and diseased siblings from UC discordant twin pairs but also from healthy twins. Microbiota profiles were assessed by 16S rDNA libraries while mRNA expression profiles were analysed from the same volunteers using Affymetrix microarrays. Results. UC patients showed a dysbiotic microbiota with lower diversity and more species belonging to Actinobacteria and Proteobacteria phyla. On the contrary, their healthy siblingsM-bM-^@M-^Y microbiota contained more bacteria from the Lachnospiracea and Ruminococcaceae family than did healthy individuals . Sixty-three host transcripts significantly correlated with bacterial genera in healthy individuals whereas only 43 and 32 correlated with bacteria in healthy and UC siblings from discordant pairs, respectively. Several transcripts related to oxidative and immune responses were differentially expressed between unaffected and UC siblings. Conclusion. A loss of crosstalk between gut microbiota and host was highlighted in UC patients. This defect was also striking in healthy siblings from discordant pairs, as was the lower biodiversity within the microbiota. Our results suggest disease-relevant interactions between host transcriptome and microbiota. Moreover, unusual aerobic bacteria were noticed in UC mucosal microbiota, whereas healthy siblings from discordant pairs had higher percentages of potentially beneficialusual commensal bacterial species. Paired samples (twins) were analyzed to obtain data independent of genetic variation
2012-01-18 | E-GEOD-22619 | biostudies-arrayexpress
Project description:In a prior report, we observed two distinct lung microbiomes in healthy subjects that we termed â??pneumotypesâ??: pneumotypeSPT, characterized by high bacterial load and supraglottic predominant taxa (SPT) such as the anaerobes Prevotella and Veillonella; and pneumotypeBPT, with low bacterial burden and background predominant taxa (BPT) found in the saline lavage and bronchoscope. Here, we determined the prevalence of these two contrasting lung microbiome types, in a multi-center study of healthy subjects. We confirmed that a lower airway microbiome enriched with upper airway microbes (pneumotypeSPT) was present in ~45% of healthy individuals. Cross-sectional Multicenter cohort. BAL of 49 healthy subjects from three cohort had their lower airway microbiome assessed by 16S rDNA sequencing and microbial gene content (metagenome) was computationally inferred from taxonomic assignments. The amplicons from total 100 samples are barcoded; the barcode and other clinical characteristics (e.g. inflammatory biomarkers and metabolome data) for each sample are provided in the 'Pneumotype.sep.Map.A1.txt' file.
2016-03-29 | E-GEOD-74395 | biostudies-arrayexpress