title: Highly diverse microbiota in dental root canals in cases of apical periodontitis (data of illumina sequencing).
abstract: BACKGROUND
  Chronic apical periodontitis (CAP) is a frequent condition that has a considerable effect on a patient's quality of life. We aimed to reveal root canal microbial communities in antibiotic-naive patients by applying Illumina sequencing (Illumina Inc, San Diego, CA).
  
  
  METHODS
  Samples were collected under strict aseptic conditions from 12 teeth (5 with primary CAP, 3 with secondary CAP, and 4 with a periapical abscess [PA]) and characterized by profiling the microbial community on the basis of the V6 hypervariable region of the 16S ribosomal RNA gene by using Illumina HiSeq2000 sequencing combinatorial sequence-tagged polymerase chain reaction products.
  
  
  RESULTS
  Root canal specimens displayed highly polymicrobial communities in all 3 patient groups. One sample contained 5-8 (mean = 6.5) phyla of bacteria. The most numerous were Firmicutes and Bacteroidetes, but Actinobacteria, Fusobacteria, Proteobacteria, Spirochaetes, Tenericutes, and Synergistetes were also present in most of the patients. One sample contained 30-70 different operational taxonomic units; the mean (± standard deviation) was lower in the primary CAP group (36 ± 4) than in the PA (45 ± 4) and secondary CAP (43 ± 13) groups (P < .05). The communities were individually different, but anaerobic bacteria predominated as the rule. Enterococcus faecalis was found only in patients with secondary CAP. One PA sample displayed a significantly high proportion (47%) of Proteobacteria, mainly at the expense of Janthinobacterium lividum.
  
  
  CONCLUSIONS
  This study provided an in-depth characterization of the microbiota of periapical tissues, revealing highly polymicrobial communities and minor differences between the study groups. A full understanding of the etiology of periodontal disease will only be possible through further in-depth systems-level analyses of the host-microbiome interaction.
authors.affiliation: Department of Stomatology, University of Tartu, Tartu, Estonia.
authors.forename: Veiko
authors.initials: V
authors.lastname: Vengerfeldt
authors.affiliation: Department of Microbiology, Faculty of Medicine, University of Tartu, Tartu, Estonia.
authors.forename: Katerina
authors.initials: K
authors.lastname: Špilka
authors.affiliation: Department of Stomatology, University of Tartu, Tartu, Estonia.
authors.forename: Mare
authors.initials: M
authors.lastname: Saag
authors.affiliation: Department of Geography, Faculty of Science and Technology, University of Tartu, Tartu, Estonia; Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia.
authors.forename: Jens-Konrad
authors.initials: JK
authors.lastname: Preem
authors.affiliation: Department of Geography, Faculty of Science and Technology, University of Tartu, Tartu, Estonia; Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia.
authors.forename: Kristjan
authors.initials: K
authors.lastname: Oopkaup
authors.affiliation: Department of Geography, Faculty of Science and Technology, University of Tartu, Tartu, Estonia; Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia.
authors.forename: Jaak
authors.initials: J
authors.lastname: Truu
authors.affiliation: Department of Microbiology, Faculty of Medicine, University of Tartu, Tartu, Estonia; Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia. Electronic address: reet.mandar@ut.ee.
authors.forename: Reet
authors.initials: R
authors.lastname: Mändar
mesh_terms: D039903:Actinobacteria / Q000302:isolation & purification; D000328:Adult; D000368:Aged; D041963:Bacteroidetes / Q000302:isolation & purification; D003786:Dental Pulp Cavity / Q000382:microbiology*; D013293:Enterococcus faecalis / Q000302:isolation & purification; D005260:Female; D000068536:Bacillota / Q000302:isolation & purification; D045182:Fusobacteria / Q000302:isolation & purification; D006089:Gram-Negative Anaerobic Bacteria / Q000302:isolation & purification; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008297:Male; D059013:Microbial Consortia / Q000235:genetics; D064307:Microbiota / Q000235:genetics; D008875:Middle Aged; D042802:Oxalobacteraceae / Q000302:isolation & purification; D010482:Periapical Abscess / Q000382:microbiology; D010485:Periapical Periodontitis / Q000382:microbiology*; D020560:Proteobacteria / Q000302:isolation & purification; D012336:RNA, Ribosomal, 16S / Q000032:analysis; D017423:Sequence Analysis, RNA / Q000379:methods*; D013144:Spirochaetales / Q000302:isolation & purification; D008973:Tenericutes / Q000302:isolation & purification; D055815:Young Adult
chemical_list: D012336:RNA, Ribosomal, 16S
keywords: Bacteria; Janthinobacterium lividum; next-generation sequencing; oral microbial ecology; periapical abscess; periodontal diseases