Korean Journal of Microbiology (미생물학회지)

The Microbiological Society of Korea (한국미생물학회)
권호 표지
DOI QR코드

DOI QR Code

Genome sequence of Bifidobacterium dentium strain ATCC 15424 originally isolated from pleural fluid of an empyema patient

농흉 환자의 흉막액에서 분리된 Bifidobacterium dentium strain ATCC 15424의 유전체 염기서열 해독

  • Moon, Ji-Hoi (Department of Maxillofacial Biomedical Engineering, School of Dentistry, Kyung Hee University) ;
  • Kim, Suegene (Department of Maxillofacial Biomedical Engineering, School of Dentistry, Kyung Hee University) ;
  • Yang, Seok Bin (Department of Maxillofacial Biomedical Engineering, School of Dentistry, Kyung Hee University) ;
  • Jang, Eun-Young (Department of Maxillofacial Biomedical Engineering, School of Dentistry, Kyung Hee University) ;
  • Shin, Seung-Yun (Department of Periodontology, School of Dentistry, Kyung Hee University) ;
  • Lee, Jin-Yong (Department of Maxillofacial Biomedical Engineering, School of Dentistry, Kyung Hee University) ;
  • Lee, Jae-Hyung (Department of Maxillofacial Biomedical Engineering, School of Dentistry, Kyung Hee University)
  • 문지회 (경희대학교 치과대학 악안면생체공학교실) ;
  • 김수진 (경희대학교 치과대학 악안면생체공학교실) ;
  • 양석빈 (경희대학교 치과대학 악안면생체공학교실) ;
  • 장은영 (경희대학교 치과대학 악안면생체공학교실) ;
  • 신승윤 (경희대학교 치과대학 치주과학교실) ;
  • 이진용 (경희대학교 치과대학 악안면생체공학교실) ;
  • 이재형 (경희대학교 치과대학 악안면생체공학교실)
  • Received : 2019.07.11
  • Accepted : 2019.08.08
  • Published : 2019.09.30
Download PDF
⟨ Previous Next ⟩

Abstract

We present here a draft genome sequence of Bifidobacterium dentium strain ATCC 15424, originally isolated from pleural fluid of an empyema patient. The genome is 2,625,535 bp in length and has a GC content of 58.5%. The genome includes 2,154 protein-coding genes, 4 rRNAs, and 55 tRNAs. Unlike other B. dentium strains isolated from human dental caries, ATCC 15424 carries 247 strain-specific genes, including prophage remnants and type III/IV secretion system proteins, N-acetylmuramoyl-L-alanine amidase, and PRTRC system protein E. The sequence information will contribute to understanding of the natural variation of B. dentium as well as the genome diversity within the bacterial species.

본 논문에서는 농흉 환자의 흉막액에서분리된 Bifidobacterium dentium ATCC 15424균주의 유전체 염기서열을 분석하여 보고한다. 이 균주의 유전체는 구강에서 분리된 다른 B. dentium 균주에 존재하지 않는 type III 및 IV secretion system proteins, N-acetylmuramoyl-L-alanine amidase 그리고 PRTRC system protein E를 암호화하는 유전자 등 247개의 ATCC 15424균주 특이적인 유전자들을 포함한다. 이 유전체의 서열 정보는 B. dentium의 자연적 변이와 세균 종 내의 유전체 다양성을 이해하는 데 유용할 것이다.

Keywords

References

  1. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455-477. https://doi.org/10.1089/cmb.2012.0021
  2. Biavati B, Scardovi V, and Moore, WEC. 1982. Electrophoretic patterns of proteins in the genus Bifidobacterium and proposal of four new species. Int. J. Syst. Bacteriol. 32, 358-373. https://doi.org/10.1099/00207713-32-3-358
  3. George LK, Robertstad GW, Brinkman SA, and Hicklin MD. 1965. A new pathogenic anaerobic Actinomyces species. J. Infect. Dis. 115, 88-99. https://doi.org/10.1093/infdis/115.1.88
  4. Gibson GR and Wang X. 1994. Regulatory effects of bifidobacteria on the growth of other colonic bacteria. J. Appl. Bacteriol. 77, 412-420. https://doi.org/10.1111/j.1365-2672.1994.tb03443.x
  5. Gill HS, Rutherfurd KJ, Cross ML, and Gopal PK. 2001. Enhancement of immunity in the elderly by dietary supplementation with the probiotic Bifidobacterium lactis HN019. Am. J. Clin. Nutr. 74, 833-839. https://doi.org/10.1093/ajcn/74.6.833
  6. Manome A, Abiko Y, Kawashima J, Washio J, Fukumoto S, and Takahashi N. 2019. Acidogenic potential of oral Bifidobacterium and its high fluoride tolerance. Front. Microbiol. 10, 1099. https://doi.org/10.3389/fmicb.2019.01099
  7. Moon JH, Jang EY, Yang SB, Shin SY, Ryu JI, Lee JY, and Lee JH. 2019. Genome sequence of Prevotella intermedia strain originally isolated from cervicofacial actinomycosis. Korean J. Microbiol. 55, 58-60. https://doi.org/10.7845/kjm.2019.8097
  8. Munson MA, Banerjee A, Watson TF, and Wade WG. 2004. Molecular analysis of the microflora associated with dental caries. J. Clin. Microbiol. 42, 3023-3029. https://doi.org/10.1128/JCM.42.7.3023-3029.2004
  9. Scardovi V and Crociani F. 1974. Bifidobacterium catenulatum, Bifidobacterium dentium, and Bifidobacterium angulatum: three new species and their deoxyribonucleic acid homology relationships. Int. J. Syst. Bacteriol. 24, 6-20. https://doi.org/10.1099/00207713-24-1-6
  10. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, and Ostell J. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 44, 6614-6624. https://doi.org/10.1093/nar/gkw569
  11. Toh H, Hayashi J, Oshima K, Nakano A, Takayama Y, Takanashi K, Morita H, and Hattori M. 2015. Complete genome sequence of Bifidobacterium dentium strain JCM $1195^{T}$, isolated from human dental caries. Genome Announc. 3, pii: e00284-15.