search for




 

Complete genome sequence of Parvimonas micra KCOM 1037 isolated from human postoperative maxillary cyst lesion
Korean J. Microbiol. 2019;55(2):149-151
Published online June 30, 2019
© 2019 The Microbiological Society of Korea.

Soon-Nang Park1,†, Yun Kyong Lim1,†, Ja Young Shin2, Hanseong Roh2, Kwanju Lim3, and Joong-Ki Kook1,*

1Korean Collection for Oral Microbiology and Department of Oral Biochemistry, College of Dentistry, Chosun University, Gwangju 61452, Republic of Korea,
2Macrogen Inc., Seoul 08511, Republic of Korea,
3School of Dentistry, Chosun University, Gwangju 61452, Republic of Korea
Correspondence to: E-mail: jkkook@chosun.ac.kr; Tel.: +82-62-230-6877; Fax: +82-62-236-2734
Received December 24, 2018; Revised December 30, 2018; Accepted January 16, 2019.
Abstract

Parvimonas micra is Gram-positive, strict anaerobic, non-motile, and non-spore forming coccus. It is a member of oral flora and is related to oral infectious diseases as well as systemic diseases. P. micra KCOM 1037 (= ChDC B276) was isolated from human postoperative maxillary cyst lesion. Here, we present the complete genome sequence of P. micra KCOM 1037.

Keywords : Parvimonas micra, genome sequence, postoperative maxillary cyst
Body

Parvimonas micra (formerly Peptostreptococcus micros) is a Gram-positive, strict anaerobic, non-motile, and non-spore forming coccus (Murdoch and Shah, 1999; Tindall and Euzéby, 2006). It is a member of oral flora and is related to oral infectious diseases (Haffajee and Socransky, 1994; de Sousa et al., 2003) as well as systemic diseases (Murdoch et al., 1988; Civen et al., 1995; Bartz et al., 2005; Endo et al., 2015; Gomez et al., 2015). Parvimonas micra KCOM 1037 (= ChDC B276) was isolated from human postoperative maxillary cyst lesion. In this report, we presented the complete genome sequence of P. micra KCOM 1037.

The P. micra KCOM 1037 was grown in a tryptic soy broth (TSB, Difco Laboratories) medium supplemented with 0.5% yeast extract, 0.05% cysteine HCl-H2O, 0.5 mg/ml of hemin, 2 μg/ml of vitamin K1, and 5% sheep blood in an anaerobic chamber (Model Bactron I) maintained using a gas mixture of 10% H2, 5% CO2, and 85% N2 (Park and Kook, 2013).

The bacterial genomic DNA was prepared as previously described (Cho et al., 2015). Genomic DNA of P. micra KCOM 1037 was sequenced using PacBio RSII SMRT sequencing platform using a 20 kb SMRTbell template library and Illumina HiSeq platform with 100 × 2 bp reads using 350 bp insert size library by Macrogen Inc. Approximately 777.3 Mb (457.7 ×) with 153,365 filtered subreads (mean subreads length: 5,068 bp) were generated and assembled into a single contig by HGAP (version: 3.0, default setting) in PacBio’s SMRT portal (http://www.pacb.com/products-and-services/analytical-software/smrt-analysis). The initial assembly was polished by Pilon (version: 1.21) with 1,561.6 Mb paired-end reads (939.7 ×, trimmed by trimmomatic 0.36) from Illumina Hiseq 2500 (Walker et al., 2014). Genome annotation was conducted by the NCBI Prokaryotic Genome Annotation Pipeline (Tatusova et al., 2016).

The complete genome of P. micra KCOM 1037 was composed of 1 contig, 1,661,863 bp in length. The average G+C content of the genome was 28.9% (Table 1). A total of 1,540 protein-coding sequences, 10 rRNAs, and 41 tRNAs were annotated (Table 1).

Genome features of Parvimonas micra KCOM 1037

AttributeValue
Genome size (bp)1,661,863
GC content (%)28.9
No. of contig1
Total genes1,854
Protein-coding genes1,540
tRNA41
Complete rRNA (5S, 16S, 23S)10 (4, 3, 3)
ncRNA3
Pseudogene44
CRISPR arrays1

The genome sequence contained several proteinase; putative protease YdcP, putative zinc metalloprotease, putative cysteine protease YraA, carboxy-terminal processing protease CtpA, serine protease Do-like HtrA, and ATP-dependent zinc metalloprotease FtsH. It contained biofilm formation-related gene, glycosyltransferase EpsH. It also contained antibiotic-resistance-related genes; putative multidrug resistance ABC transporter ATP-binding/permease protein YheI, multiple antibiotic resistance protein MarA, multidrug resistance protein NorM/MdtK, tetracycline resistance protein TetM, vancomycin B-type resistance protein VanW, and daunorubicin/doxorubicin resistance ATP-binding protein DrrA. It also contains type II secretion system protein F epsF, ESX secretion system protein EccC, and protein translocase subunit SecA/SecY/SecE. The genome also contained the oxidative stress-response gene, thioredoxin reductase.

P. micra KCOM 1037 strain was deposited into the Korean Collection for Oral Microbiology.

Nucleotide sequence accession number

This whole genome sequence was deposited in GenBank under the accession number CP031971.

적 요

Parvimonas micra는 그람 양성, 절대 혐기성, 비운동성 및 아포를 생성하지 않는 구균이다. 이 세균 종은 구강의 정상 세균 총 하나이며, 구강 감염성질환 및 전신질환고도 연관이 있다. P. micra KCOM 1037 (= ChDC B276) 균주가 수술후상악낭종 병소에서 분리되었다. 여기에서 P. micra KCOM 1037 균주의 유전체 염기서열을 완전 해독하여 보고한다.

Acknowledgements

This research was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (No. 2018R1A2B5002239).

References
  1. Bartz H, Nonnenmacher CB, Bollmann C, Kuhl M, Zimmermann S, Heeg K, and Mutters R. 2005. Micromonas (Peptostreptococcus) micros: unusual case of prosthetic joint infection associated with dental procedures. Int. J. Med. Microbiol. 294, 465-470.
    Pubmed CrossRef
  2. Cho E, Park SN, Lim YK, Shin Y, Paek J, Hwang CH, Chang YH, and Kook JK. 2015. Fusobacterium hwasookii sp. nov., isolated from a human periodontitis lesion. Curr. Microbiol. 70, 169-175.
    Pubmed CrossRef
  3. Civen R, Jousimies-Somer H, Marina M, Borenstein L, Shah H, and Finegold SM. 1995. A retrospective review of cases of anaerobic empyema and update of bacteriology. Clin. Infect. Dis. 20, S224-S229.
    Pubmed CrossRef
  4. de Sousa EL, Ferraz CC, Gomes BP, Pinheiro ET, Teixeira FB, and de Souza-Filho FJ. 2003. Bacteriological study of root canals associated with periapical abscesses. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod. 96, 332-339.
    Pubmed CrossRef
  5. Endo S, Nemoto T, Yano H, Kakuta R, Kanamori H, Inomata S, Ishibashi N, Aoyagi T, Hatta M, and Gu Y, et al. 2015. First confirmed case of spondylodiscitis with epidural abscess caused by Parvimonas micra. J. Infect. Chemother. 21, 828-830.
    Pubmed CrossRef
  6. Gomez CA, Gerber DA, Zambrano E, Banaei N, Deresinski S, and Blackburn BG. 2015. First case of infectious endocarditis caused by Parvimonas micra. Anaerobe. 36, 53-55.
    Pubmed CrossRef
  7. Haffajee AD, and Socransky SS. 1994. Microbial etiological agents of destructive periodontal diseases. Periodontology 2000. 5, 78-111.
    Pubmed CrossRef
  8. Murdoch DA, Mitchelmore IJ, and Tabaqchali S. 1988. Peptostreptococcus micros in polymicrobial abscesses. Lancet. 1, 594.
    CrossRef
  9. Murdoch DA, and Shah HN. 1999. Reclassification of Peptostreptococcus magnus (Prevot 1933) Holdeman and Moore 1972 as Finegoldia magna comb. nov. and Peptostreptococcus micros 2712 International Journal of Systematic and Evolutionary Microbiology 56 B. J. Tindall and J. P. Euze´by (Prevot 1933) Smith 1957 as Micromonas micros comb. nov. Anaerobe. 5, 555-559.
    CrossRef
  10. Park SN, and Kook JK. 2013. Development of Streptococcus gordonii-specific quantitative real-time polymerase chain reaction primers based on the nucleotide sequence of rpoB. Microbiol. Immunol. 57, 583-588.
    Pubmed CrossRef
  11. 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.
    Pubmed KoreaMed CrossRef
  12. Tindall B, and Euzéby J. 2006. Proposal of Parvimonas gen. nov. and Quatrionicoccus gen. nov. as replacements for the illegitimate, prokaryotic, generic names Micromonas Murdoch and Shah 2000 and Quadricoccus Maszenan et al 2002, respectively. Int. J. Syst. Evol. Microbiol. 56, 2711-2713.
    Pubmed CrossRef
  13. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, and Young SK, et al. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One. 9, e112963.
    Pubmed KoreaMed CrossRef


June 2019, 55 (2)