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Complete genome sequence of Prevotella denticola KCOM 1525 isolated from human periapical abscess
Korean J. Microbiol. 2019;55(2):152-153
Published online June 30, 2019
© 2019 The Microbiological Society of Korea.

Yun Kyong Lim1,†, Soon-Nang Park1,†, Se Ho Park2, Ja Young Shin3, Hanseong Roh3, and Joong-Ki Kook1,*

1Korean Collection for Oral Microbiology and Department of Oral Biochemistry, College of Dentistry, Chosun University, Gwangju 61452, Republic of Korea,
2School of Dentistry, Chosun University, Gwangju 61452, Republic of Korea,
3Macrogen Inc., Seoul 08511, Republic of Korea
Correspondence to: E-mail: jkkook@chosun.ac.kr; Tel.: +82-62-230-6877; Fax: +82-62-236-2734
Received December 21, 2018; Revised January 18, 2019; Accepted January 18, 2019.
Abstract

Prevotella denticola is Gram-negative, obligately anaerobic, non-motile, non-spore forming, and rod-shaped bacterium. P. denticola is associated with periodontal disease and is a risk indicator of periodontal disease. P. denticola KCOM 1525 (= ChDC B698) was isolated from human periapical abscess. Herein, we present the complete genome sequence of P. denticola KCOM 1525.

Keywords : Prevotella denticola, genome sequence, periapical abscess
Body

Prevotella denticola is Gram-negative, obligately anaerobic, non-motile, non-spore forming, and rod-shaped bacterium (Shah and Collins, 1990). P. denticola is associated with periodontal disease and is a risk indicator of periodontal disease (Lourenco et al., 2014). P. denticola KCOM 1525 (= ChDC B698) was isolated from human periapical abscess. In this report, we presented the complete genome sequence of P. denticola KCOM 1525.

P. denticola KCOM 1525 was cultured on tryptic soy agar (TSA; BD Difco Laboratories) plate 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 et al., 2013). Genomic DNA of P. denticola KCOM 1525 was prepared as previously described (Cho et al., 2015).

The genomic DNA of P. denticola KCOM 1525 was sequenced using PacBio RSII SMRT sequencing platform using a 20 kb SMRTbell template library and Illumina HiSeq 2500 by Macrogen Inc. Approximately 1,473.1 Mb (509.1 × of coverage) with 157,270 filtered subreads (9,366 bp of mean subreads length and 14,006 bp of N50) were generated and assembled 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 13,629,778 paired-end reads (475.7 × of coverage, trimmed by trimmomatic 0.36) from Illumina Hiseq 2500 (https://github.com/broadinstitute/pilon/wiki) (Walker et al., 2014). The pilon fixed 33 INDELs and most of errors were A/T insertions or G/C deletions. Genome annotation was conducted using the NCBI Prokaryotic Genome Annotation Pipeline (Tatusova et al., 2016).

The complete genome of P. denticola KCOM 1525 was composed of two chromosomes; 1,846,186 bp and 1,047,661 bp in length. The average G+C content of the genome was 50.13% (Table 1). A total of 2,238 protein-coding sequences, 12 rRNAs, and 49 tRNAs were annotated (Table 1).

Genome features of Prevotella denticola KCOM 1525

AttributeValue
Genome size (bp)2,893,847
GC content (%)50.13
No. of chromosome2
Total genes2.383
Protein-coding genes2,238
tRNA49
rRNA (5S, 16S, 23S)12 (4, 4, 4)
ncRNA3
Pseudogene81

The genome sequence contained antibiotic-resistance-related genes; multidrug resistance protein MdtN/NorM/LmrA and multidrug export protein MepA. It contained toxin-related genes; actin cross-linking toxin VgrG1, toxin Doc, and toxin RTX-I translocation ApxIB. It also contained stress-related genes; general stress protein Ctc, ATP-dependent Clp protease ClpC/ClpP, peptide methionine sulfoxide reductase MsrA/ MsrB and thioredoxin reductase TrxA/TrxB. Hemolysin TlyC, conserved virulence factor CvfB, ferric aerobactin IutA, putative glycosyltransferase EpsJ, toxin-antitoxin biofilm protein TabA, and type IV secretion system VirB4 were also found in the genome sequence.

The P. denticola KCOM 1525 strain was deposited into the Korean Collection for Oral Microbiology.

Nucleotide sequence accession number

This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession CP032056/CP032057. The version described in this paper is version CP032056.1/CP032057.1.

적 요

Prevotella denticola는 그람 음성, 절대 혐기성, 비운동성이면서 아포를 형성하지 않는 막대 모양의 세균이다. P. denticola는 치주질환과 관련이 있으며, 치주질환의 위험 인자 중 하나이다. P. denticola KCOM 1525 (= ChDC B698) 균주가 사람 치근단 농양에서 분리되었다. P. denticola KCOM 1525 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).

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June 2019, 55 (2)