DOI QR코드

DOI QR Code

Draft genome sequence of Olsenella sp. KGMB 04489 isolated from healthy Korean human feces

건강한 한국인 분변으로부터 분리된 Olsenella sp. KGMB 04489 균주의 유전체 염기서열 초안

  • Han, Kook-Il (Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology) ;
  • Kang, Se Won (Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology) ;
  • Kim, Ji-Sun (Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology) ;
  • Lee, Keun Chul (Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology) ;
  • Eom, Mi Kyung (Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology) ;
  • Suh, Min Kuk (Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology) ;
  • Park, Seung-Hwan (Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology) ;
  • Lee, Ju Huck (Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology) ;
  • Park, Jam-Eon (Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology) ;
  • Oh, Byeong Seob (Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology) ;
  • Yu, Seung Yeob (Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology) ;
  • Choi, Seung-Hyeon (Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology) ;
  • Lee, Dong Ho (Seoul National University Bundang Hospital) ;
  • Yoon, Hyuk (Seoul National University Bundang Hospital) ;
  • Kim, Byung-Yong (ChunLab, Inc.) ;
  • Yang, Seung-Jo (ChunLab, Inc.) ;
  • Lee, Jung-Sook (Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology)
  • 한국일 (한국생명공학연구원 생물자원센터) ;
  • 강세원 (한국생명공학연구원 생물자원센터) ;
  • 김지선 (한국생명공학연구원 생물자원센터) ;
  • 이근철 (한국생명공학연구원 생물자원센터) ;
  • 엄미경 (한국생명공학연구원 생물자원센터) ;
  • 서민국 (한국생명공학연구원 생물자원센터) ;
  • 박승환 (한국생명공학연구원 생물자원센터) ;
  • 이주혁 (한국생명공학연구원 생물자원센터) ;
  • 박잠언 (한국생명공학연구원 생물자원센터) ;
  • 오병섭 (한국생명공학연구원 생물자원센터) ;
  • 유승엽 (한국생명공학연구원 생물자원센터) ;
  • 최승현 (한국생명공학연구원 생물자원센터) ;
  • 이동호 (분당서울대학교병원) ;
  • 윤혁 (분당서울대학교병원) ;
  • 김병용 (천랩) ;
  • 양승조 (천랩) ;
  • 이정숙 (한국생명공학연구원 생물자원센터)
  • Received : 2018.09.19
  • Accepted : 2018.11.07
  • Published : 2018.12.31

Abstract

The genus of Olsenella has been isolated from vertebrate animal mouth, rumen, and feces. Olsenella sp. KGMB 04489 was isolated from fecal samples obtained from a healthy Korean. The whole-genome sequence of Olsenella sp. KGMB 04489 was analyzed using the PacBio Sequel platform. The genome comprises a 2,108,034 bp chromosome with a G + C content of 65.50%, 1,838 total genes, 13 rRNA genes, and 52 tRNA genes. Also, we found that strain KGMB 04489 had some genes for hydrolysis enzymes, and antibiotic biosynthesis and resistance in its genome based on the result of genome analysis.

Olsenella 속 균주들은 척추동물의 구강, 반추위 및 분변 등에서 분리된 것으로 알려져 있다. 본 연구에서는 건강한 한국인 분변으로부터 Olsenella sp. KGMB 04489 균주를 분리하였으며 PacBio Sequel 플랫폼을 이용하여 Olsenella sp. KGMB 04489 균주의 유전체서열을 분석하였다. 유전체는 G + C 구성 비율이 65.5%이고, 1,838개의 유전자와 rRNA 13개, tRNA 52개로 구성되었으며, 염색체의 크기는 2,108,034 bp였다. 또한, 유전체 분석 결과를 통해 가수분해효소와 항생제 합성 및 내성과 관련된 다양한 유전자를 발견하였다.

Keywords

MSMHBQ_2018_v54n4_456_f0001.png 이미지

Fig. 1. Graphical circular map of Olsenella sp. KGMB 04489.

Table 1. General features of Olsenella sp. KGMB 04489

MSMHBQ_2018_v54n4_456_t0001.png 이미지

Acknowledgement

Supported by : National Research Foundation of Korea (NRF), Korea Research Institute of Bioscience & Biotechnology (KRIBB)

References

  1. Bolan S, Seshadri B, Talley NJ, and Naidu R. 2016. Bio-banking gut microbiome samples. EMBO Rep. 17, 929-930. https://doi.org/10.15252/embr.201642572
  2. Dewhirst FE, Paster BJ, Tzellas N, Coleman B, Downes J, Spratt DA, and Wade WG. 2001. Characterization of novel human oral isolates and cloned 16S rDNA sequences that fall in the family Coriobacteriaceae: description of Olsenella gen. nov., reclassification of Lactobacillus uli as Olsenella uli comb. nov. and description of Olsenella profusa sp. nov. Int. J. Syst. Evol. Microbiol. 51, 1797-1804. https://doi.org/10.1099/00207713-51-5-1797
  3. Dewhirst FE and Wade WG. 2015. Olsenella. Bergey's manual of systematics of archaea and bacteria. John Wiley & Sons, Ltd. Hoboken, N.J., USA.
  4. Gupta RS, Chen WJ, Adeolu M, and Chai Y. 2013. Molecular signatures for the class Coriobacteriia and its different clades; proposal for division of the class Coriobacteriia into the emended order Coriobacteriales, containing the emended family Coriobacteriaceae and Atopobiaceae fam. nov., and Eggerthellales ord. nov., containing the family Eggerthellaceae fam. nov. Int. J. Syst. Evol. Microbiol. 63, 3379-3397. https://doi.org/10.1099/ijs.0.048371-0
  5. Kau AL, Ahern PP, Griffin NW, Goodman AL, and Gordon JI. 2011. Human nutrition, the gut microbiome and the immune system. Nature 474, 327-336. https://doi.org/10.1038/nature10213
  6. Kraatz M, Wallace RJ, and Svensson L. 2011. Olsenella umbonata sp. nov., a microaerotolerant anaerobic lactic acid bacterium from the sheep rumen and pig jejunum, and emended descriptions of Olsenella, Olsenella uli and Olsenella profusa. Int. J. Syst. Evol. Microbiol. 61, 795-803. https://doi.org/10.1099/ijs.0.022954-0
  7. Lee I, Chalita M, Ha SM, Na SI, Yoon SH, and Chun J. 2017. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int. J. Syst. Evol. Microbiol. 67, 2053-2057. https://doi.org/10.1099/ijsem.0.001872
  8. Li X, Jensen RL, Hojberg O, Canibe N, and Jensen BB. 2015. Olsenella scatoligenes sp. nov., a 3-methylindole- (skatole) and 4-methylphenol- (p-cresol) producing bacterium isolated from pig faeces. Int. J. Syst. Evol. Microbiol. 65, 1227-1233. https://doi.org/10.1099/ijs.0.000083
  9. Olsen I, Johnson JL, Moore LV, and Moore WE. 1991. Lactobacillus uli sp. nov. and Lactobacillus rimae sp. nov. from the human gingival crevice and emended descriptions of Lactobacillus minutus and Streptococcus parvulus. Int. J. Syst. Bacteriol. 41, 261-266. https://doi.org/10.1099/00207713-41-2-261
  10. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, and Tyson GW. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043-1055. https://doi.org/10.1101/gr.186072.114