Definition of species of Gram-negative anaerobic rods by multilocus sequence analysis

• Project/Area Number: 23580126
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Applied microbiology
• Research Institution: The Institute of Physical and Chemical Research
• Principal Investigator: SAKAMOTO Mitsuo 独立行政法人理化学研究所, バイオリソースセンター, 研究員 (50321766)
• Co-Investigator(Renkei-kenkyūsha): OHKUMA Moriya 独立行政法人理化学研究所, バイオリソースセンター, 室長 (10270597)
• Project Period (FY): 2011-04-28 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000); Fiscal Year 2013: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000); Fiscal Year 2012: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000); Fiscal Year 2011: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
• Keywords: Bacteroides / MLSA / dnaJ / gyrB / hsp60 / recA / rpoB / 16S rRNA

Outline of Final Research Achievements

Multilocus sequence analysis (MLSA) was performed on 107 species of Gram-negative anaerobic rods including the genus Bacteroides. The genes selected, dnaJ, gyrB, hsp60, recA, rpoB and 16S rRNA were amplified by direct PCR and then sequenced. For the genus Bacteroides, we defined species as a group of strains that share at least 97.5 % gene sequence similarity based on the fragments of five protein-coding housekeeping genes and 16S rRNA gene. Analyses of the concatenated sequences of all six genes revealed robust phylogenetic relationships among the species of Gram-negative anaerobic rods when compared with the single-gene trees.

Research Products

• [Journal Article] Draft genome sequences of three strains of Bacteroides pyogenes isolated from feline and swine (2014)
  • Author(s): Sakamoto, M., Oshima, K., Suda, W., Kitamura, K., Iida, T., Hattori, M. and Ohkuma, M
  • Journal Title: Genome Announc. Volume: 2 Issue: 1
  • DOI: 10.1128/genomea.01242-13
  • Peer Reviewed
• [Journal Article] Draft genome sequences of Porphyromonas crevioricanis JCM 15906T and Porphyromonas cansulci JCM 13913T isolated from canine oral cavity (2013)
  • Author(s): Sakamoto, M., Tanaka, N., Shiwa, Y., Yoshikawa, H. and Ohkuma, M
  • Journal Title: Genome Announc. Volume: 1 Issue: 4
  • DOI: 10.1128/genomea.00483-13
  • Peer Reviewed
• [Journal Article] Parabacteroides chinchillae sp. nov., isolated from chinchilla (Chinchilla lanigera) faeces (2013)
  • Author(s): Kitahara, M., Sakamoto, M., Tsuchida, S., Kawasumi, K., Amao, H., Benno, Y. and Ohkuma, M
  • Journal Title: Int. J. Syst. Evol. Microbiol. Volume: 63 Issue: Pt_9 Pages: 3470-3474
  • DOI: 10.1099/ijs.0.050146-0
  • Peer Reviewed
• [Journal Article] Porphyromonas crevioricanis is an earlier heterotypic synonym of Porphyromonas cansulci and has priority (2013)
  • Author(s): Sakamoto, M. and Ohkuma, M.
  • Journal Title: Int. J. Syst. Evol. Microbiol. Volume: 63 Issue: Pt_2 Pages: 454-457
  • DOI: 10.1099/ijs.0.042531-0
  • Peer Reviewed
• [Journal Article] Bacteroides reticulotermitis sp. nov., isolated from the gut of the subterranean termite (Reticulitermes speratus) (2013)
  • Author(s): Sakamoto M, Ohkuma M
  • Journal Title: Int. J. Syst. Evol. Microbiol. Volume: 63 Issue: Pt_2 Pages: 691-695
  • DOI: 10.1099/ijs.0.040931-0
  • Peer Reviewed
• [Journal Article] Bacteroides sartorii is an earlier heterotypic synonym of Bacteroides chinchillae and has priority (2012)
  • Author(s): Sakamoto, M. and Ohkuma, M.
  • Journal Title: Int. J. Syst. Evol. Microbiol. Volume: 62 Issue: Pt_6 Pages: 1241-1244
  • DOI: 10.1099/ijs.0.035659-0
  • Peer Reviewed
• [Journal Article] Reclassification of Xylanibacter oryzae Ueki et al. 2006 as Prevotella oryzae comb. nov., with an emended description of the genus Prevotella (2012)
  • Author(s): Sakamoto, M. and Ohkuma, M
  • Journal Title: Int. J. Syst. Evol. Microbiol. Volume: 62 Issue: Pt_11 Pages: 2637-2643
  • DOI: 10.1099/ijs.0.038638-0
  • Peer Reviewed
• [Journal Article] Identification and classification of the genus Bacteroides by multilocus sequence analysis (2011)
  • Author(s): Sakamoto, M. and Ohkuma, M.
  • Journal Title: Microbiology Volume: 157 Issue: 12 Pages: 3388-3397
  • DOI: 10.1099/mic.0.052332-0
  • Peer Reviewed
• [Presentation] 多遺伝子座配列解析による嫌気性グラム陰性桿菌の分子系統 (2014)
  • Author(s): 坂本光央，大熊盛也
  • Organizer: 日本微生物資源学会第21回大会
  • Place of Presentation: 東京農業大学世田谷キャンパス
  • Year and Date: 2014-09-03 – 2014-09-04
• [Presentation] Multilocus sequence analysis (MLSA) of the genus Bacteroides and related taxa by using the dnaJ, gyrB, hsp60, recA, rpoB, and 16S rRNA genes (2014)
  • Author(s): Sakamoto, M. and Ohkuma, M.
  • Organizer: 14th International Congress of Bacteriology and Applied Microbiology
  • Place of Presentation: モントリオールコンベンションセンター
  • Year and Date: 2014-07-30
• [Presentation] Identification and classification of the genus Bacteroides by multilocus sequence analysis (2012)
  • Author(s): Sakamoto, M.
  • Organizer: 第85回日本細菌学会総会
  • Place of Presentation: 長崎ブリックホールおよび長崎新聞文化ホール（長崎）
• [Presentation] Multilocus sequence analysis (MLSA) of the genus Bacteroides by using the dnaJ, gyrB, hsp60, recA, rpoB, and 16S rRNA genes (2011)
  • Author(s): Sakamoto, M. and Ohkuma, M.
  • Organizer: 13th International Congress of Bacteriology and Applied Microbiology
  • Place of Presentation: 札幌コンベンションセンター（札幌）
• [Presentation] Porphyromonas cansulciはPorphyromonas crevioricanisのシノニムである
  • Author(s): 坂本光央、大熊盛也
  • Organizer: 日本微生物資源学会第20回大会
  • Place of Presentation: つくば国際会議場（つくば）
• [Presentation] Porphyromonas crevioricanis is an earlier heterotypic synonym of Porphyromonas cansulci and has priority
  • Author(s): Sakamoto, M. and Ohkuma, M
  • Organizer: The 5th ANRRC International Meeting
  • Place of Presentation: 湘南国際村センター（葉山）
• [Presentation] 嫌気性グラム陰性桿菌の系統分類学的研究
  • Author(s): 坂本 光央
  • Organizer: 公益財団法人発酵研究所第6回助成研究報告会
  • Place of Presentation: 千里ライフサイエンスセンター（大阪）
  • Invited
• [Presentation] キシラン分解性細菌Xylanibacter oryzaeの再分類
  • Author(s): 坂本 光央、大熊 盛也
  • Organizer: 日本微生物資源学会第19回大会
  • Place of Presentation: かずさアカデミアホール（木更津）
• [Presentation] チンチラの糞便から分離されたParabacteroides属の新種提唱
  • Author(s): 北原 真樹、坂本 光央、土田 さやか、川角 浩、天尾 弘実、辨野 義己、大熊 盛也
  • Organizer: 日本微生物資源学会第19回大会
  • Place of Presentation: かずさアカデミアホール（木更津）