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Draft genome sequence of Dialister pneumosintes KCOM 1685 isolated from a human postoperative maxillary cyst lesion
Korean J. Microbiol 2019;55(1):52-54
Published online March 31, 2019
© 2019 The Microbiological Society of Korea.

Soon-Nang Park1,†, Chang-Won Lee2,†, Yun Kyong Lim1, Ja Young Shin3, Hanseong Roh3, and Joong-Ki Kook1,*

1Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School 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: +82-62-224-3706
Received November 13, 2018; Revised December 9, 2018; Accepted December 10, 2018.
Abstract

Dialister pneumosintes is a Gram-staining-negative, anaerobic, non-fermenting, and rod-shaped bacterium. D. pneumosintes is considered to be a periodontal pathogen. D. pneumosintes KCOM 1685 (= ChDC B414) was isolated from a human postoperative maxillary cyst lesion. In this report, we present the draft genome sequence of D. pneumosintes KCOM 1685.

Keywords : Dialister pneumosintes, human, postoperative maxillary cyst
Body

Dialister pneumosintes is a Gram-stain-negative, anaerobic, non-fermenting, nonsporulating, non-motile, and rod-shaped bacterium. It forms transparent, entire, circular, smooth, clear, shiny, and convex colonies on blood agar (Doan et al., 2000). The bacterium is considered to be a periodontal pathogen (Ghayoumi et al., 2002). D. pneumosintes KCOM 1685 (= ChDC B414) was isolated from a human periodontitis lesion. In this report, we present the draft genome sequence of D. pneumosintes KCOM 1685.

D. pneumosintes KCOM 1685 was grown in brain heart infusion (BHI, 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 et al., 2013). Genomic DNA of D. pneumosintes KCOM 1685 was prepared as previously described (Cho et al., 2015). DNA concentration was determined by the Epoch™ Microplate Spectrophotometer (BioTek Instruments Inc.) at wavelengths of 260 and 280 nm (Cho et al., 2015).

The genomic DNA of D. pneumosintes KCOM 1685 was sequenced using the Illumina Hiseq 2000 platform by Macrogen Inc. Tree libraries of 350 bp paired-end, 5 kb mate-pair, and 8 kb mate-pair were sequenced which reached coverage of 1,466,7 ×, 1,752.7 ×, and 1,407.3 ×, respectively. The de novo assembly was performed by SPAdes (http://bioinf.spbau.ru/spades) (Bankevich et al., 2012). All gaps among the scaffolds were filled by GapCloser (http://soap.genomics.org.cn/soapdenovo.html) (Luo et al., 2012). Error correction was performed by Pilon (https://github.com/broadinstitute/pilon/wiki) (Walker et al., 2014). Genome annotation was conducted by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (https://www. ncbi.nlm.nih.gov/genome/annotation_prok/) (Tatusova et al., 2016).

The draft genome of D. pneumosintes KCOM 1685 was composed of 3 contigs; 1,244,600 bp, 1,438 bp, and 1,369 bp in length. The average G+C content of the draft genome was 35.2%. A total of 1,154 protein-coding sequences (CDSs), 13 rRNAs, and 50 tRNAs were annotated (Table 1).

Genome features of Dialister pneumosintes KCOM 1685

Attribute Value
Genome size (bp) 1,247,407
GC content (%) 35.2
No. of contig 3
Total genes 1,230
Protein-coding genes 1,154
tRNA 50
Complete rRNA (5S, 16S, 23S) 13 (5,4,4)
ncRNA 3
Pseudogene 9
CRISPR arrays 1


The genome sequence contained antibiotic-resistance-related genes; multidrug export ATP-binding/permease protein, multidrug resistance protein MdtC/MdtN/NorM, multidrug export protein MepA, macrolide export ATP-binding/permease protein MacB, and macrolide export protein MacA. It contained several proteinase genes; protease HtpX/YdcP/CtpB, lon protease 1/2, modulator of FtsH protease HflK, putative protease YdcP, ATP-dependent zinc metalloprotease FtsH, and metalloprotease MmpA. Biofilm formation-related genes toxin PezT, toxin- antitoxin biofilm protein TabA, putative glycosyltransferase EpsJ, putative peptidoglycan glycosyltransferase FtsW, and peptidoglycan glycosyltransferase MrdB were also found in the genome sequence. It contained type II secretion system protein G, putative type II secretion system protein E/F, and protein translocase subunit SecA/SecY/SecE. The genome also contained the oxidative stress-response gene, thioredoxin reductase. The genome contained the one two-component system, pdtaS/ pdtaR.

The D. pneumosintes KCOM 1685 strain was deposited into the Korean Collection for Oral Microbiology.

Nucleotide sequence accession number

This whole genome sequence has been deposited at DDBJ/ ENA/GenBank under the accession QWKU00000000. The version described in this paper is version QWKU01000000.

적 요

Dialister pneumosintes는 그람 음성이면서, 혐기성, 비발효성 및 막대 모양의 세균이다. D. pneumosintes는 치주질환병원성세균으로 알려져 있다. D. pneumosintes KCOM 1685 (= ChDC B414) 균주가 수술후상악동낭종 병소에서 분리되었다. D. pneumosintes KCOM 1685 균주 유전체 염기서열을 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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March 2019, 55 (1)