Structure and functional potential of intracanal microbiome: Bioinformatics for endodontic therapy

• Project/Area Number: 17K11698
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Conservative dentistry
• Research Institution: Tohoku University
• Principal Investigator: Yamaki Keiko 東北大学, 歯学研究科, 非常勤講師 (90182419)
• Co-Investigator(Kenkyū-buntansha): 佐藤 拓一 新潟大学, 医歯学系, 教授 (10303132) ; 鷲尾 純平 東北大学, 歯学研究科, 准教授 (20400260)
• Project Period (FY): 2017-04-01 – 2023-03-31
• Project Status: Completed (Fiscal Year 2022)
• Budget Amount: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000); Fiscal Year 2019: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2018: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000); Fiscal Year 2017: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
• Keywords: 根尖性歯周炎 / 根管内細菌叢 / 16S rRNA遺伝子 / メタ16S解析 / 根管内フローラ / 歯内疾患 / V3-V4領域 / パンゲノム / メタゲノム解析 / メタボローム解析

Outline of Final Research Achievements

Microbial composition of infected root canals varies consistently among reports. To determine the characteristics of the endodontic microbiome, the intracanal flora of apical periodontitis in 13 patients were profiled and compared with the profiles of their saliva and plaque. Infected root canal wall dentin was harvested from the involved teeth and their saliva and plaque were collected. Bacterial DNA was extracted from the samples and 16S rRNA gene analysis targeting the V3-V4 region was conducted on the Illumina MiSeq platform using QIIME2. The functional potential of the microbiomes was inferred using PICRUSt2. The endodontic microbiomes were more anaerobic, rich in Firmicutes, and scarce in Actinobacteriota and Proteobacteria, compared with saliva and plaque microbiomes. Despite their difference in structure and membership, the nine most abundant metabolic pathways were common among them. The intra-individual variance in endodontic microbiome was also found.

Academic Significance and Societal Importance of the Research Achievements

根尖性歯周炎は歯科臨床現場において高頻度で遭遇する歯内疾患であり、その原因は根管に侵入定着した口腔細菌である。約1000種とされるヒト口腔細菌のうち一人が保有するのは100-200種のため、感染根管から検出される細菌はレポートにより大きく異なる。現在、根尖性歯周炎の病因は特定の菌ではなく、細菌叢すなわち多種多様な細菌の集合体と考えられており、次世代シーケンサー（NGS）を利用した細菌叢の解析が進行中である。本研究を通じて明らかとなった感染根管内の細菌叢の特徴を踏まえ、従来の標準治療法より普遍的かつ効率的な根管治療法が開発され、国民の健康増進に資するることが期待される。

Research Products

• [Journal Article] Bacterial amounts and compositions in liquid baby formula and a baby drink consumed with an artificial nipple. (2021)
  • Author(s): Wakui A, Sano H, Kawachi M, Aida A, Takenaka Y, Yonezawa A, Nakahata N, Moriyama S, Nishikata M, Washio J, Abiko Y, Mayanagi G, Yamaki K, Sakashita R, Tanaka K, Takahashi N, Sato T
  • Journal Title: J Oral Biosci. Volume: 印刷中 Issue: 2 Pages: 161-168
  • DOI: 10.1016/j.job.2021.03.001
  • Peer Reviewed / Open Access
• [Journal Article] Profiling of microbiota at the mouth of bottles and in remaining tea after drinking directly from plastic bottles of tea (2021)
  • Author(s): Wakui A*, Sano H*, Hirabuki Y*, Kawachi M, Aida A, Washio J, Abiko Y, Mayanagi G, Yamaki K, Tanaka K, Takahashi N, Sato T
  • Journal Title: Dentistry Journal Volume: 9 Issue: 6 Pages: 58-58
  • DOI: 10.3390/dj9060058
  • Peer Reviewed / Open Access
• [Journal Article] Profiling system of oral microbiota utilizing polymerase chain reaction-restriction fragment length polymorphism analysis (2021)
  • Author(s): Sano H, Wakui A, Kawachi M, Washio J, Abiko Y, Mayanagi G, Yamaki K, Tanaka K, Takahashi N, Sato T
  • Journal Title: Journal of Oral Biosciences Volume: 63 Issue: 3 Pages: 292-297
  • DOI: 10.1016/j.job.2021.05.003
  • Peer Reviewed / Open Access
• [Journal Article] Profiling of microbiota in liquid baby formula consumed with an artificial nipple (2019)
  • Author(s): SANO Hiroto、WAKUI Anna、KAWACHI Miho、KATO Rito、MORIYAMA Sachie、NISHIKATA Mayumi、WASHIO Jumpei、ABIKO Yuki、MAYANAGI Gen、YAMAKI Keiko、SAKASHITA Reiko、TOMIDA Junko、KAWAMURA Yoshiaki、TANAKA Kaori、TAKAHASHI Nobuhiro、SATO Takuichi
  • Journal Title: Biomedical Research Volume: 40 Issue: 4 Pages: 163-168
  • DOI: 10.2220/biomedres.40.163
  • NAID: 130007689885
  • Peer Reviewed / Open Access
• [Presentation] The composition and structure of oral microbiome: 16S rRNA gene analysis on saliva, plaque, infected root canals obtained from a patient. (2021)
  • Author(s): Keiko Yamaki, Jumpei Washio, Toru Tamahara, Takuichi Sato
  • Organizer: The 69th annual meeting of Japanese Association for Dental Research
• [Presentation] Profiling of microbiota of baby-drinks after drinking with artificial nipples. (2020)
  • Author(s): Wakui A, Sano H, Kawachi M, Maruyama S, Masuda N, Washio J, Abiko Y, Mayanagi G, Yamaki K, Takahashi N, Okada Y, Sato T.
  • Organizer: The Update Symposium 7 in the 62nd Anual Meeting of Japanese Association for Oral Biology
• [Presentation] Oral microbiota analyzing system: Profiling by PCR-RFLP method. (2020)
  • Author(s): Kawachi M, Maruyama S, Masuda N, Sano H, Wakui A, Yamaki K, Washio J, Takahashi N, Sato T.
  • Organizer: The 62nd Annual Meeting of Japanese Association for Oral Biology
• [Presentation] Profiling system of oral microbiota utilizing PCR-RFLP analysis. (2019)
  • Author(s): Sano H, Wakui A, Washio J, Yamaki K, Takahashi N, Sato T.
  • Organizer: The 4th Asia Pacific Regional Congress of the International Association for Dental Research
  • Int'l Joint Research
• [Presentation] Profiling of microbiota of liquid baby formula after drinking with artificial nipples. (2019)
  • Author(s): Wakui A, Sano H, Kawachi M, Kato R, Moriyama S, Nishikata M, Washio J, Yamaki K, Sakashita R, Takahashi N, Sato T.
  • Organizer: The 4th Asia Pacific Regional Congress of the International Association for Dental Research
  • Int'l Joint Research
• [Presentation] Profiling of microbiota in baby-drinks and liquid baby formula consumed with an artificial nipple. (2019)
  • Author(s): Wakui A, Sano H, Kawachi M, Kato R, Washio J, Abiko Y, Mayanagi G, Yamaki K, Takahashi N, Sato T.
  • Organizer: The Update Symposium 2 in the 61st Annual Meeting of Japanese Association for Oral Biology
• [Presentation] Profiling system of oral microbiota using PCR-RFLP method. (2019)
  • Author(s): Sano H, Wakui A, Washio J, Yamaki K, Takahashi N, Sato T.
  • Organizer: The 61st Annual Meeting of Japanese Association for Oral Biology
• [Presentation] Profiling of microbiota of baby-drinks after drinking with artificial nipples. (2018)
  • Author(s): Wakui A, Sano H, Aihara H, Kawachi M, Takahashi A, Washio J, Abiko Y, Mayanagi G, Ishiguro K, Yamaki K, N. Takahashi N, Sato T.
  • Organizer: 第66回国際歯科研究学会日本部会（JADR）学術大会
• [Presentation] Oral anaerobes in saliva and intraoperative bronchial fluids of elderly patients with pulmonary carcinoma. (2018)
  • Author(s): Wakui A, Sano H, Washio J, Yamaki K, Tomida J, Tanaka K, Kawamura Y, Sato T.
  • Organizer: The Inaugural Forsyth Symposium－The Uncultivable Bacteria
  • Int'l Joint Research
• [Presentation] ニプルを通して飲んだ際の、ベビー飲料内への口腔細菌の流入 (2018)
  • Author(s): 相原 瞳、涌井杏奈、佐野拓人、河内美帆、鷲尾純平、安彦友希、真柳 弦、八巻恵子、高橋信博、佐藤拓一.
  • Organizer: 第60回歯科基礎医学会学術大会
• [Presentation] Profiling of microbiota in plastic bottles after drinking straight from bottles. (2018)
  • Author(s): Sano H, Wakui A, Aida A, Takenaka Y, Yonezawa A, Nakahata N, Aihara H, Kawachi M, Vidanapathirana GU, Washio J, Abiko Y, Mayanagi G, Ishiguro K, Yamaki K, Takahashi N, Sato T.
  • Organizer: The 6th Conference on SLJCR (Sri Lanka-Japan Collaborative Research)
  • Int'l Joint Research
• [Presentation] Profiling of microbiota at the mouth of plastic bottles. (2018)
  • Author(s): Sano H, Wakui A, Aida A, Takenaka Y, Yonezawa A, Nakahata N, Aihara H, Kawachi M, Washio J, Abiko Y, Mayanagi G, Ishiguro K, Yamaki K, Takahashi N, Sato T.
  • Organizer: The 96th IADR
  • Int'l Joint Research
• [Presentation] Microbiota profiling at the mouth of plastic bottles after drinking straight from bottles. (2018)
  • Author(s): Sano H, Aida A, Vidanapathirana GU, Wakui A, Hirabuki Y, Takenaka Y, Kawachi M, Aihara H, Washio J, Abiko Y, Mayanagi G, Ishiguro K, Yamaki K, Takahashi N, Sato T.
  • Organizer: International Symposium for Multimodal Research and Education in IOHS-Liaison 2018
  • Int'l Joint Research
• [Presentation] A microbiological study on bacteria in the PET bottles after drinking. (2017)
  • Author(s): Aida A, Sano H, Wakui A, Hirabuki Y, Takenaka Y, Kawachi M, Vidanapathirana GU, Washio J, Abiko Y, Mayanagi G, Ishiguro K, Yamaki K, Takahashi N, Sato T.
  • Organizer: 第65回JADR総会・学術大会
• [Presentation] Quantification and composition of remaining bacteria in plastic bottles after drinking. (2017)
  • Author(s): Sano H, Hirabuki Y, Wakui A, Aida A, Abiko Y, Yamaki K, Mayanagi G, Washio J, Takahashi N, Sato T.
  • Organizer: 第59回歯科基礎医学会学術大会