Ontology highlight
ABSTRACT:
PROVIDER: PRJNA663916 | ENA |
REPOSITORIES: ENA
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Project description:Analysis of gingival crevicular fluid (GCF) samples may give information of the identity of unattached (planktonic) subgingival bacteria, the 35 forefront candidates for systemic dispersal via ulcerated periodontal pocket epithelium. Our study represents the first one targeting the identity of bacteria in gingival crevicular fluid. Methodology/Principal findings: We determined bacterial species diversity in GCF samples of a group of periodontitis patients and delineated contributing bacterial and host-associated factors. Subgingival paper point (PP) samples from the same sites were taken for comparison. After DNA extraction, 16S rRNA genes were PCR amplified and DNA-DNA hybridization was performed using a microarray for over 300 bacterial species or groups. Altogether 133 species from 41 genera and 8 phyla 45 were detected with 9 to 62 and 18 to 64 species in GCF and PP samples, respectively, 46 per patient. Projection to latent structures by means of partial least squares (PLS) was applied to the multivariate data analysis. PLS regression analysis showed that species of genera including Campylobacter, Selenomonas, Porphyromonas, Catonella, Tannerella, Dialister, Peptostreptococcus, Streptococcus and Eubacterium had significant positive correlations and the number of teeth with low-grade attachment loss a significant negative correlation to species diversity in GCF samples. OPLS/O2PLS discriminant analysis revealed significant positive correlations to GCF sample group membership for species of genera Campylobacter, Leptotrichia, Prevotella, Dialister, Tannerella, Haemophilus, Fusobacterium, Eubacterium, and Actinomyces. Conclusions/Significance: Among a variety of detected species those traditionally classified as Gram-negative anaerobes growing in mature subgingival biofilms were the main predictors for species diversity in GCF samples as well as responsible for distinguishing GCF samples from PP samples. GCF bacteria may provide new prospects for studying dynamic properties of subgingival biofilms. The microbial profiles of GCF and subgingival plaque were analyzed from 17 subjects with periodontal disease.
2010-05-21 | E-GEOD-21929 | biostudies-arrayexpress
Project description:Analysis of gingival crevicular fluid (GCF) samples may give information of the identity of unattached (planktonic) subgingival bacteria, the 35 forefront candidates for systemic dispersal via ulcerated periodontal pocket epithelium. Our study represents the first one targeting the identity of bacteria in gingival crevicular fluid. Methodology/Principal findings: We determined bacterial species diversity in GCF samples of a group of periodontitis patients and delineated contributing bacterial and host-associated factors. Subgingival paper point (PP) samples from the same sites were taken for comparison. After DNA extraction, 16S rRNA genes were PCR amplified and DNA-DNA hybridization was performed using a microarray for over 300 bacterial species or groups. Altogether 133 species from 41 genera and 8 phyla 45 were detected with 9 to 62 and 18 to 64 species in GCF and PP samples, respectively, 46 per patient. Projection to latent structures by means of partial least squares (PLS) was applied to the multivariate data analysis. PLS regression analysis showed that species of genera including Campylobacter, Selenomonas, Porphyromonas, Catonella, Tannerella, Dialister, Peptostreptococcus, Streptococcus and Eubacterium had significant positive correlations and the number of teeth with low-grade attachment loss a significant negative correlation to species diversity in GCF samples. OPLS/O2PLS discriminant analysis revealed significant positive correlations to GCF sample group membership for species of genera Campylobacter, Leptotrichia, Prevotella, Dialister, Tannerella, Haemophilus, Fusobacterium, Eubacterium, and Actinomyces. Conclusions/Significance: Among a variety of detected species those traditionally classified as Gram-negative anaerobes growing in mature subgingival biofilms were the main predictors for species diversity in GCF samples as well as responsible for distinguishing GCF samples from PP samples. GCF bacteria may provide new prospects for studying dynamic properties of subgingival biofilms.
2010-05-21 | GSE21929 | GEO
Project description:Streptococcus pneumoniae is opportunistic bacteria cause’s acute otitis media (AOM) in children. It colonizes the nasopharynx in the form of biofilms, and these biofilms act as reservoir, and are vital for pneumococcal infections. The pneumococcal biofilms are regulated by LuxS/AI-2 media quorum sensing. In this study, we confirmed the role of LuxS/AI-2 for in vitro formation of biofilms, assessed the effects of the absence of LuxS/AI-2 signaling, for pneumococcal middle ear infection and identified global genes regulated by LuxS/AI-2 during formation of pneumococcal biofilms. In the cDNA-microarray analysis, 117 genes were differentially expressed in D39 luxS mutant when compared with D39 wild type. Among the 66 genes encoding putative proteins and previously characterized proteins, 60 were significantly down-regulated and 6 were significantly up-regulated. The functional annotation revealed that genes involve in DNA replication and repair, ATP synthesis, capsule biosynthesis, cell division and cell cycle, signal transduction, transcription regulation, competence, virulence, and carbohydrate metabolism were down-regulated in the absence of LuxS/AI-2.
2018-05-17 | GSE109347 | GEO
Project description:Investigation of whole genome gene expression differences between a full (four-gene) SlrV locus 1 deletion compared to the WT PittII strain. Removal of the four SlrV genes (aka macrophage survival factors : Δmsf) results in a competetive defect with the WT strain in in vitro biofilms and in the otitis media chinchilla model. It also results in an inability to persist within macrophages long-term in vitro and to escape from the middle-ear space and infect other sites in the chinchilla model.
2015-06-23 | GSE70172 | GEO
Project description:This study compared the subgingival microbiota of subjects with periodontitis to those with periodontal health using the Human Oral Microbe Identification Microarray (HOMIM).
2011-09-17 | GSE32159 | GEO
Project description:Glycine max cultivar:Shi-shi Raw sequence reads
| PRJNA302826 | ENA
Project description:We investigated the association between subgingival bacterial profiles and gene expression patterns in gingival tissues of patients with periodontitis.
2009-12-22 | GSE16134 | GEO
Project description:We investigated the association between subgingival bacterial profiles and gene expression patterns in gingival tissues of patients with periodontitis. A total of 120 patients undergoing periodontal surgery contributed with a minimum of two interproximal gingival papillae (range 2-4) from a maxillary posterior. Prior to tissue harvesting, subgingival plaque samples were collected from the mesial and distal aspects of each papilla. Gingival tissue RNA was extracted, reverse-transcribed, labeled, and hybridized with whole-genome microarrays (310 in total)
2009-12-21 | E-GEOD-16134 | biostudies-arrayexpress