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Development of Novel Clinical Bacterial Tests with Innovative Implications through Metagenomic Approaches and the Application of DNA Methylation Analysis

Research Project

Project/Area Number 18K07408
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Review Section Basic Section 52010:General internal medicine-related
Research InstitutionChiba University

Principal Investigator

Nishimura Motoi  千葉大学, 医学部附属病院, 講師 (80400969)

Co-Investigator(Kenkyū-buntansha) 佐藤 守  千葉大学, 医学部附属病院, 特任准教授 (20401002)
田中 知明  千葉大学, 大学院医学研究院, 教授 (50447299)
別府 美奈子  千葉大学, 大学院医学研究院, 助教 (70623669)
松下 一之  千葉大学, 医学部附属病院, 准教授 (90344994)
土田 祥央  日本大学, 医学部, 助手 (90410422)
Project Period (FY) 2018-04-01 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2020: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2019: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2018: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
Keywords臨床検査 / microbiome / bacterial epigenetics / 細菌検査 / 薬剤耐性 / DNAメチル化 / エピゲノム / メタゲノム / メチル化解析 / 新型コロナウイルス感染症 / COVID-19 / SARS-CoV-2
Outline of Final Research Achievements

We have successfully achieved selective amplification of denatured DNA targeted for DNA methylation analysis using the bisulfite method, enabling the simultaneous integration of DNA methylation analysis with metagenomic analysis of bacterial communities across species using next-generation sequencing of 16S rRNA genes.
Upon analysis using the newly developed method, we have found evidence suggesting the presence of unreported DNA methylation and novel DNA-modifying enzymes in drug-resistant strains and bacterial communities. Additionally, we have successfully conducted microbiome analysis of clinical bacterial specimens, revealing diverse DNA methylation patterns in Enterococcus faecalis and suggesting the coexistence of multiple strains.

Academic Significance and Societal Importance of the Research Achievements

次世代シーケンシングの普及に伴って、検体中の核酸断片を網羅的に解析することによるバイオーム解析、いわゆるメタゲノム解析が可能となり、もっとも先進的な解析では1分子シーケンサーなどによるDNAメチル化解析と並行的に行われるようになっている。しかしながらこれら核酸断片に由来する配列情報は、多く由来する菌種が不明で、細菌種同定を柱とする感染症臨床検査としては非効率的で相性が悪かった。
本研究成果は臨床検査と相性が良くその延長として可能な従来なかった"16S rDNA meta-epigenetics"とでも呼ぶべき分野の登場を示している。

Report

(5 results)
  • 2021 Annual Research Report   Final Research Report ( PDF )
  • 2020 Research-status Report
  • 2019 Research-status Report
  • 2018 Research-status Report
  • Research Products

    (31 results)

All 2022 2021 2020 2019 2018

All Journal Article (18 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 18 results,  Open Access: 16 results) Presentation (13 results)

  • [Journal Article] Tracking SARS-CoV-2 variants by entire S-gene analysis using long-range RT-PCR and Sanger sequencing2022

    • Author(s)
      Matsubara Mirai、Imaizumi Yuri、Fujikawa Tatsuki、Ishige Takayuki、Nishimura Motoi、Miyabe Akiko、Murata Shota、Kawasaki Kenji、Taniguchi Toshibumi、Igari Hidetoshi、Matsushita Kazuyuki
    • Journal Title

      Clinica Chimica Acta

      Volume: 530 Pages: 94-98

    • DOI

      10.1016/j.cca.2022.03.014

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] DRD2 Taq1A Polymorphism-Related Brain Volume Changes in Parkinson’s Disease: Voxel-Based Morphometry2022

    • Author(s)
      Ohira K, Yokota H, Hirano S, Nishimura M, Mukai H, Horikoshi T, Sawai S, Yamanaka Y, Yamamoto T, Kakeda S, Kuwabara S, Tanaka T, Uno T.
    • Journal Title

      Parkinson's Disease

      Volume: - Pages: 1-7

    • DOI

      10.1155/2022/8649195

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Comprehensive mutational analysis of background mucosa in patients with Lugol‐voiding lesions2021

    • Author(s)
      Akizue Naoki、Okimoto Kenichiro、Arai Makoto、Hirotsu Yosuke、Amemiya Kenji、Oura Hirotaka、Kaneko Tatsuya et al
    • Journal Title

      Cancer Medicine

      Volume: 10 Issue: 11 Pages: 3545-3555

    • DOI

      10.1002/cam4.3905

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Genetic profiles of Barrett’s esophagus and esophageal adenocarcinoma in Japanese patients2021

    • Author(s)
      Tokunaga Mamoru、Okimoto Kenichiro、Akizue Naoki、Ishikawa Kentaro、Hirotsu Yosuke、Amemiya Kenji、Ota Masayuki、Matsusaka Keisuke、et al.
    • Journal Title

      Scientific Reports

      Volume: 11 Issue: 1 Pages: 17671-17671

    • DOI

      10.1038/s41598-021-97249-9

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] TAS4464, a NEDD8-activating enzyme inhibitor, activates both intrinsic and extrinsic apoptotic pathways via c-Myc-mediated regulation in acute myeloid leukemia.2021

    • Author(s)
      Ochiiwa H, Ailiken G, Yokoyama M, Yamagata K, Nagano H, Yoshimura C, Muraoka H, Ishida K, Haruma T, Nakayama A, Hashimoto N, Murata K, Nishimura M, Kawashima, Y, Ohara O, Okubo S, Tanaka T
    • Journal Title

      Oncogene

      Volume: 40 Issue: 7 Pages: 1217-1230

    • DOI

      10.1038/s41388-020-01586-4

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Comprehensive mutational analysis of background mucosa in patients with Lugol-voiding lesions2021

    • Author(s)
      Akizue, N; Okimoto, K; Arai, M; Hirotsu, Y; Amemiya, K; Oura, H; Kaneko, T; Tokunaga, M; Ishikawa, K; Ohta, Y Taida, T; Saito, K; Maruoka, D; Matsumura, T; Nakagawa, T; Nishimura, M ; Chiba, T; Matsushita, K; Mochizuki, H; Yokosuka, O; Omata, M; Kato, N
    • Journal Title

      Cancer Medicine

      Volume: in press

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Comprehensive Analysis of Barrett's Esophagus: Focused on Carcinogenic Potential for Barrett's Cancer in Japanese Patients2020

    • Author(s)
      Kentaro Ishikawa , Kenichiro Okimoto, et al.
    • Journal Title

      Dig Dis Sci .

      Volume: epub ahead of printing Issue: 8 Pages: 2674-2681

    • DOI

      10.1007/s10620-020-06563-1

    • Related Report
      2021 Annual Research Report 2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Highly sensitive detection of SARS-CoV-2 RNA by multiplex rRT-PCR for molecular diagnosis of COVID-19 by clinical laboratories2020

    • Author(s)
      Ishige Takayuki、Murata Shota、Taniguchi Toshibumi、Miyabe Akiko、Kitamura Kouichi、Kawasaki Kenji、Nishimura Motoi、Igari Hidetoshi、Matsushita Kazuyuki
    • Journal Title

      Clinica Chimica Acta

      Volume: 507 Pages: 139-142

    • DOI

      10.1016/j.cca.2020.04.023

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Monoamine Oxidase B rs1799836 G Allele Polymorphism Is a Risk Factor for Early Development of Levodopa-Induced Dyskinesia in Parkinson's Disease.2020

    • Author(s)
      Kakinuma S, Beppu M, Sawai S, Nakayama A, Hirano S, Yamanaka Y, Yamamoto T, Chigusa M, Aisihaer X, Aersilan A, Gao Y, Sato K, Itoga S, Ishige T, Nishimura M, Matsushita K, Satoh M, Nomura F, Kuwabara S, Tanaka T
    • Journal Title

      eNeurologicalSci.

      Volume: 19 Pages: 100239-100239

    • DOI

      10.1016/j.ensci.2020.100239

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Monoamine oxidase B rs1799836 G allele polymorphism is a risk factor for early development of levodopa-induced dyskinesia in Parkinson's disease.2020

    • Author(s)
      Kakinuma S, BeppuM, Sawai S, Akitoshi Nakayama A, Hirano S, Yamanaka Y, Yamamoto T, Chigusa M, Aisihaer X, Aersilan, A,Y Gao Y, Sato K, Itoga S, Ishige T, Nishimura M, Matsushita K, Satoh M, Nomura F, Kuwabara S, Tanaka T.
    • Journal Title

      eNeurologicalSci.

      Volume: in press

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Central blood pressure and pulse wave velocity in young and middle-aged Japanese adults with isolated systolic hypertension2019

    • Author(s)
      Nakagomi Atsushi、Imazeki Fumio、Nishimura Motoi、Sawabe Yuji、Matsushita Kazuyuki、Murata Akitoshi、Watase Mariko、Okada Sho、Kobayashi Yoshio
    • Journal Title

      Hypertension Research

      Volume: 43 Issue: 3 Pages: 207-212

    • DOI

      10.1038/s41440-019-0364-x

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Multiplex PCR and multicolor probes melting for the simultaneous detection of five UGT1A1 variants2019

    • Author(s)
      Ishige Takayuki、Itoga Sakae、Kawasaki Kenji、Sawai Setsu、Nishimura Motoi、Nomura Fumio、Matsushita Kazuyuki
    • Journal Title

      Analytical Biochemistry

      Volume: 587 Pages: 113448-113448

    • DOI

      10.1016/j.ab.2019.113448

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] A simple method for sequencing the whole human mitochondrial genome directly from samples and its application to genetic testing2019

    • Author(s)
      Yao Yue、Nishimura Motoi、Murayama Kei、Kuranobu Naomi、Tojo Satomi、Beppu Minako、Ishige Takayuki、Itoga Sakae、Tsuchida Sachio、Mori Masato、Takayanagi Masaki、Yokoyama Masataka、Yamagata Kazuyuki、Kishita Yoshihito、Okazaki Yasushi、Nomura Fumio、Matsushita Kazuyuki、Tanaka Tomoaki
    • Journal Title

      Scientific Reports

      Volume: 9 Issue: 1 Pages: 17411-17421

    • DOI

      10.1038/s41598-019-53449-y

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Development and validation of the simultaneous measurement of estrone and 17-β estradiol in serum by LC-MS/MS for clinical laboratory applications.2019

    • Author(s)
      Mamoru Satoh, Yui Miyabayashi, Masanori Seimiya, Takahiro Kazami, Takayuki Ishige, Toshihiko Yoshida, Motoi Nishimura, Kazuyuki Matsushita, Makio Shozu, Fumio Nomura.
    • Journal Title

      Medical Mass Spectrometry

      Volume: 3 Pages: 19-30

    • NAID

      130007897964

    • Related Report
      2019 Research-status Report
    • Peer Reviewed
  • [Journal Article] High-throughput genotyping of GC (vitamin D-binding protein) by melting analysis with locked nucleic acid-incorporating dual hybridization probe for improving mismatch discrimination.2018

    • Author(s)
      Ishige T, Satoh M, Itoga S, Nishimura M, Matsushita K, Nomura F.
    • Journal Title

      Clin Chim Acta

      Volume: 487 Pages: 126-132

    • DOI

      10.1016/j.cca.2018.09.034

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Surveillance evaluation of the standardization of assay values for serum total 25-hydroxyvitamin D concentration in Japan.2018

    • Author(s)
      Ihara H, Kiuchi S, Ishige T, Nishimura M, Matsushita K, Satoh M, Nomura F, Yamashita M, Kitajima I, Tsugawa N, Okano T, Hirota K, Miura M, Totani M, Hashizume N; Nutrition Division, Japan Society of Clinical Chemistry.
    • Journal Title

      Ann Clin Biochem.

      Volume: Epub ahead of print Issue: 6 Pages: 0-0

    • DOI

      10.1177/0004563218765570

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Assessment by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry of the Effects of Preanalytical Variables on Serum Peptidome Profiles Following Long-Term Sample Storage.2018

    • Author(s)
      Tsuchida S, Satoh M, Umemura H, Sogawa K, Takiwaki M, Ishige T, Miyabayashi Y, Iwasawa Y, Kobayashi S, Beppu M, Nishimura M, Kodera Y, Matsushita K, Nomura F
    • Journal Title

      Proteomics. Clinical applications

      Volume: 15 Issue: 3 Pages: 47-53

    • DOI

      10.1002/prca.201700047

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Variant in C-terminal region of intestinal alkaline phosphatase associated with benign familial hyperphosphatasaemia.2018

    • Author(s)
      Ishige T, Itoga S, Utsuno E, Nishimura M, Yoshikawa M, Kato N, Matsushita K, Yokosuka O, Nomura F
    • Journal Title

      Journal of medical genetics

      Volume: 10 Issue: 10 Pages: 47-53

    • DOI

      10.1136/jmedgenet-2017-104964

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] 変異株同定のためのサンガー法によるSARS-CoV-2のS遺伝子の塩基配列解析2022

    • Author(s)
      松原未来、藤川樹、石毛崇之、西村基、村田正太、谷口俊文、猪狩英俊、川崎健治、松下一之
    • Organizer
      日本臨床微生物学会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 小児横紋筋肉腫に対するがん遺伝子パネル検査(NCCオンコパネル)でLi-Fraumeni症候群と診断された2例2021

    • Author(s)
      力石浩志、日野もえ子、山下喜晴、奥主朋子、宇津野恵美、西村基、松下一之、服部真也、市川智彦、濱田洋通
    • Organizer
      日本人類遺伝学会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 当院で検出された新型コロナウイルス(SARS-CoV-2)のRNA配列の解析2021

    • Author(s)
      西村 基、村田 正太、石毛 崇之、松原 未来、藤川 樹、宮部 安規子、北村 浩一、根川 真実、古家 若葉、梅谷 友輔、堀田 恵海、吉田 俊彦、川崎 健治、松下 一之
    • Organizer
      日本遺伝子診療学会
    • Related Report
      2021 Annual Research Report
  • [Presentation] SARS-CoV-2 S-gene sequencing and its mutational dynamics at the Chiba University Hospital2021

    • Author(s)
      松原未来、藤川樹、石毛崇之、西村基、村田正太、谷口俊文、猪狩英俊、川崎健治、松下一之
    • Organizer
      日本遺伝子診療学会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 当院で検出された新型コロナウイルス(SARS-CoV-2)のRNA配列の解析2021

    • Author(s)
      西村 基、石毛 崇之、吉田 俊彦、川崎 健治、松下 一之
    • Organizer
      日本臨床化学会
    • Related Report
      2021 Annual Research Report
  • [Presentation] SARS-CoV-2抗原定性検査(イムノクロマト法)2021

    • Author(s)
      村田正太、宮部安規子、斎藤知子、瀬川俊介、堀田恵海、山下晃司、松原未来、鈴木眞、川崎健治、西村基、松下一之
    • Organizer
      日本感染症学会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 新型コロナウイルスの全ゲノム解析におけるMinIONの性能評価2021

    • Author(s)
      藤川樹、石毛崇之、西村基、松原未来、村田正太、谷口俊文、猪狩英俊、川崎健治、松下一之
    • Organizer
      日本医療検査科学会
    • Related Report
      2021 Annual Research Report
  • [Presentation] デヂエを用いた多職種連携のためのがん遺伝子プロファイリング検査管理システムの構築2021

    • Author(s)
      北村 浩一, 藤澤陽子, 川崎 健治, 西村 基, 松下 一之
    • Organizer
      日本医療検査科学会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 当院で検出された新型コロナウイルス(SARS-CoV-2)のRNA配列の解析2020

    • Author(s)
      西村基、村田正太、石毛崇之、宮部安規子、北村浩一、根川真実、藤川樹、古家若葉、梅谷友輔、堀田恵海、吉田俊彦、川崎健治、松下一之
    • Organizer
      第32回日本臨床微生物学会総会・学術集会
    • Related Report
      2020 Research-status Report
  • [Presentation] 腫瘍部組織のみを調べるがん遺伝子パネル検査で二次的所見が疑われた3症例の当院における取り扱い2020

    • Author(s)
      西村基、楯真一、錦見恭子、松岡歩、生水真紀夫、太和田暁之、新井誠人、滝口裕一、藤木亮次、金田篤志、宇津野恵美、市川 智彦、太田昌幸、松坂恵介、佐伯 宏美、藤澤陽子、石毛崇之、北村浩一、小林崇平、中津川智子、清水直美、松下一之
    • Organizer
      第44回日本遺伝カウンセリング学会学術集会
    • Related Report
      2020 Research-status Report
  • [Presentation] 千葉大学医学部附属病院検査部における教育業務の担当と、そこからバンキングされた検体の研究への活用2019

    • Author(s)
      西村基、土田祥央、石毛崇之、浅野はるな、吉田俊彦、川崎健治 、糸賀栄 、澤部祐司 、野村文夫 、松下一
    • Organizer
      日本臨床検査医学会
    • Related Report
      2019 Research-status Report
  • [Presentation] 遺伝学的にdefinitiveなQT延長症候群とてんかん様症状の合併症例の3例とそれらの考察2019

    • Author(s)
      西村 基, 江畑 亮太, 小林 弘信, 近藤 祐介, 仲野 美代,上田 希彦, 石川 亜貴, 水上 都, 澤井 摂,下条 直樹, 小林 欣夫, 野村 文夫, 松下 一之, 市川 智彦
    • Organizer
      日本遺伝カウンセリング学会
    • Related Report
      2019 Research-status Report
  • [Presentation] 血液培養陽性検体よりの複数菌由来の核酸検出2018

    • Author(s)
      西村 基, 村田 正太, 姚 躍, 土田 祥央, 田中 知明, 松下 一之
    • Organizer
      第25回日本遺伝子診療学会大会
    • Related Report
      2018 Research-status Report

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Published: 2018-04-23   Modified: 2025-03-27  

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