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"type": "studies",
"id": "MGYS00002215",
"attributes": {
"accession": "MGYS00002215",
"bioproject": "PRJNA84223",
"samples-count": 23,
"is-private": false,
"last-update": "2018-02-14T13:02:27",
"secondary-accession": "SRP010933",
"centre-name": "PHSA Labs",
"public-release-date": null,
"study-abstract": "Background: Endodontic infections are a leading cause of oro-facial pain and tooth loss in western countries, and may lead to severe life-threatening infections. These infections are polymicrobial with high bacterial diversity. Understanding the spatial transition of microbiota from normal oral cavities through the infected root canal to the acute periapical abscess can improve our knowledge of the pathogenesis of endodontic infections and lead to more effective treatment. We obtained samples from the oral cavity, infected root canal and periapical abscess of 8 patients (5 with localized and 3 with systemic infections). Microbial populations in these samples were analyzed using next-generation sequencing of 16S rRNA amplicons. Bioinformatics tools and statistical tests with rigorous criteria were used to elucidate the spatial transition of the microbiota from normal to diseased sites. Results: On average, 10,000 partial 16S rRNA gene sequences were obtained from each sample. All sequences fell into 11 different bacterial phyla. The microbial diversity in root canal and abscess samples was significantly lower than in the oral samples. Streptococcus was the most abundant genus in oral cavities while Prevotella and Fusobacterium were most abundant in diseased samples. Root canal and periapical abscess microbiota were more similar to each other than to the oral cavity microbiota. Using rigorous criteria and novel bioinformatics tools, we found that Granulicatella adiacens, Eubacterium yurii, Prevotella melaninogenica, Prevotella salivae, Streptococcus mitis, and Atopobium rimae were over-represented in diseased samples. Conclusions: We used a novel approach and high-throughput methodologies to describe microbial transition from normal to diseased oral sites in the same individuals Eight patients with root canal infections (5 with systemic infections and 3 with localized infection) undergone treatment. Samples were obtained from three sampling sites in each patient. Oral (OS): samples collected from the subjects by rubbing 3 fine paper points against patient''s cheek mucosa, lateral boarder of the tongue and supragingival plaque at the contra lateral side away from the affected tooth. Root Canal (RC): samples collected from the root canal space of the diseased tooth using 3 fine paper points. Abscess Aspiration (AS): the area of the swelling was aspirated with a syringe that has a 16 gauge needle, and expressed into a sterile vial.",
"study-name": "Human oral microbiome (root canal, apical abscess, and oral cavity) Targeted Locus",
"data-origination": "HARVESTED"
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