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Complete genome sequence of Eikenella corrodens KCOM 3110 isolated from human subgingival dental plaque of periodontitis lesion
Korean J. Microbiol. 2019;55(2):154-156
Published online June 30, 2019
© 2019 The Microbiological Society of Korea.

Yun Kyong Lim1,†, Soon-Nang Park1,†, Ja Young Shin2, Hanseong Roh2, Suk Ji3, 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
3Department of Periodontics, Institute of Oral Health Science, Ajou University School of Medicine, Suwon 16499, Republic of Korea
Correspondence to: E-mail: jkkook@chosun.ac.kr; Tel.: +82-62-230-6877; Fax: +82-62-236-2734
Received January 18, 2019; Revised January 27, 2019; Accepted January 28, 2019.
Abstract

Eikenella corrodens is Gram-negative, facultatively anaerobic, and rod-shaped bacterium. It is a part of the normal human mucosal flora that can cause several systemic diseases such as endocarditis, liver abscess, and intracranial bacterial infection. E. corrodens KCOM 3110 (= JS217) was isolated from human subgingival dental plaque of periodontitis lesion. Here, we present the complete genome sequence of E. corrodens KCOM 3110.

Keywords : Eikenella corrodens, genome sequence, periodontitis
Body

Eikenella corrodens is Gram-negative, facultatively anaerobic, and rod-shaped bacterium (Jackson and Goodman, 1972). It is a part of the normal human mucosal flora, predominantly of the oropharynx (Perez Trallero et al., 1988) and is related to endocarditis, liver abscess, and intracranial bacterial infection (Das et al., 1997; Moazzam et al., 2015; Nordholm et al., 2018).

E. corrodens KCOM 3110 (= JS217) was isolated from the human subgingival dental plaque of periodontitis lesion. Herein, we presented the complete genome sequence of E. corrodens KCOM 3110.

E. corrodens KCOM 3110 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 et al., 2013).

The bacterial genomic DNA was prepared as previously described (Cho et al., 2015). Genomic DNA of E. corrodens KCOM 3110 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 587.5 Mb (239.0 × of coverage) with 65,227 filtered subreads (9,007 bp of mean subreads length and 14,371 bp of N50) 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 1,386.2 Mb paired-end reads (563.9 × of coverage, 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 genome of E. corrodens KCOM 3110 was composed of one contig, 2,458,478 bp in length. The G+C content of the genome was 56.0%. A total of 2,306 protein-coding sequences, 12 ribosomal RNAs (rRNAs) and 51 transfer RNAs (tRNAs) were annotated (Table 1).

Genome features of Eikenella corrodens KCOM 3110

Attribute Value
Genome size (bp) 2,458,478
GC content (%) 56.0
No. of contig 1
Total genes 2,477
Protein-coding genes 2,306
tRNA 51
rRNA (5S, 16S, 23S) 12 (4, 4, 4)
ncRNA 4
Pseudogene 104


The genome of E. corrodens KCOM 3110 contained antibiotic-resistance-related genes; multidrug resistance protein Stp/NorM, bifunctional polymyxin resistance protein ArnA, bicyclomycin resistance protein Bcr, multidrug efflux pump subunit AcrA/AcrB, peptide antibiotic transporter SbmA, and beta-lactamase hydrolase-like protein Blh. The E. corrodens KCOM 3110 genome also contained stress-related genes; TRAP-T-associated universal stress protein TeaD, acid stress protein IbaG, general stress protein 14 YwrO, ATP-dependent Clp protease ClpX/ClpP, persistence and stress-resistance toxin PasT, and persistence, and stress-resistance antitoxin PasI. It also contained ferrienterobactin receptor FepA, ferri-bacillibactin esterase BesA, ferric enterobactin PfeA, hemolysin secretion protein D plasmid HlyD, hemolysin A HlyA, hemolysin transporter protein ShlB, leukotoxin-activating lysine-acyltransferase LtxC, autotransporter adhesion NhhA, adhesin MafA, lipopolysaccharide (LPS)-assembly lipoprotein LptD/LptE, ADP-heptose-LPS heptosyltransferase 2 RfaF, tellurite-resistance protein TehA, putative glycosyltransferase EpsJ, toxin FitB, and antitoxin FitA/vapB1.

E. corrodens KCOM 3110 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 CP034670.

적 요

Eikenella corrodens는 그람 음성, 통성 혐기성이며 막대 모양의 세균이다. 이 세균 종은 사람의 심내막염, 간농양 및 두개내 세균감염 등과 같은 전신질환과 연관이 있을 뿐만 아니라 점막의 정상 세균총에 속한다. E. corrodens KCOM 3110 (= JS217) 균주가 사람 치주질환 병소의 치은연하치면세균막에서 분리되었다. 여기에서 E. corrodens KCOM 3110 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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September 2019, 55 (3)