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Genome sequence of Veillonella atypica KHUD-V1 isolated from a human subgingival dental plaque of periodontitis lesion
Korean J. Microbiol 2019;55(1):77-79
Published online March 31, 2019
© 2019 The Microbiological Society of Korea.

Jae-Hyung Lee1,2,3,†, Seung-Yun Shin4,†, Han Lee1, Seok Bin Yang1, Eun-Young Jang5, Jae-In Ryu6, Jin-Yong Lee1,*, and Ji-Hoi Moon1,2,*

1Department of Maxillofacial Biomedical Engineering, School of Dentistry, 2Department of Life and Nanopharmaceutical Sciences, 3Kyung Hee Medical Science Institute, 4Department of Periodontology, School of Dentistry, 5Department of Dentistry, Graduate School, 6Department of Preventive Dentistry, School of Dentistry, Kyung Hee University, Seoul 02447, Republic of Korea
Correspondence to: (J.Y. Lee) E-mail: ljinyong@khu.ac.kr;
Tel.: +82-2-961-9544; Fax: +82-2-962-0598 /
(J.H. Moon) E-mail: prudence75@khu.ac.kr;
Tel.: +82-2-961-0795; Fax: +82-2-962-0598
Received November 26, 2018; Revised January 10, 2019; Accepted January 22, 2019.
Abstract

Here we report the genome sequence of Veillonella atypica strain KHUD-V1 isolated from subgingival dental plaque of Korean chronic periodontitis patients. Unlike other V. atypica strains, KHUD-V1 carries two prophage regions and prophage remnants, as well as several genes homologous to prophage- associated virulence factors, such as virulence-associated protein E, a Clp protease, and a toxin-antitoxin system. The isolate and its genome sequence obtained here will aid to understand the diversity of the genome architecture of Veillonella within an evolutionary framework and the role of prophages that contribute to the genetic diversity as well as the virulence of V. atypica.

Keywords : Veillonella atypicau, genome, periodontitis, prophage
Body

Anaerobic, Gram-negative cocci Veillonella species are a part of the normal microflora of the oral cavity, gastrointestinal and urogenital tracts in humans (Pei et al., 2004; Keijser et al., 2008; van den Bogert et al., 2011). However, they can participate in mixed-species infections and have been isolated from patients with skin, dental, and respiratory infections. Rarely, Veillonella can cause serious infections like meningitis, endocarditis, and osteomyelitis (Saladi et al., 2017).

Bacteriophages are viruses that infect bacteria. Once the bacteriophage genome is integrated into the host cell genome, it is called a prophage. Prophages play an intricate role in the evolution of bacterial genome, contribute to the genetic diversity even within the same species, and act as regulators of the microbiota composition (Roodt et al., 2012; Lugli et al., 2016). Prophages are also known to be closely related to the adaptation of existing pathogens to new hosts and the emergence of new pathogens or epidemic clones.

So far, very little is known about the occurrence and genetic variability of prophages within the Veillonella. Here, we report a genome sequence of V. atypica strain KHUD-V1 isolated from subgingival dental plaque of Korean chronic periodontitis patients. Interestingly, the genome of this strain contains two prophage regions, which are not found in the currently registered V. atypica genomes. Several virulence factors that may be associated with the prophages were also found. V. atypica strain KHUD-V1 has been deposited in the Korean Collection for Type Cultures (KCTC) for future reference and research. The new clinical isolate and its genome sequence obtained here will aid to understand the diversity of the genome architecture of Veillonella within an evolutionary framework, and the role of prophages that contribute to the genetic diversity as well as the virulence of V. atypica.

The bacterial genomic DNA was extracted, and the sequencing library was constructed following the paired-end sequencing on the Illumina Hi-Seq X platform. In total, 15,818,696 paired- end read pairs (2 × 151 bp) were obtained. After filtering out low quality raw reads, SPAdes (version 3.12.0) (Bankevich et al., 2012) with default parameters was used to construct the genome, creating 54 scaffolds (> 500-bp length). Gene annotation of the genome was performed by the NCBI Prokaryotic Genome Annotation Pipeline (Tatusova et al., 2016). The genome of V. atypica KHUD-V1 was found to contain 2,189,293 bp with a G+C content of 38.99% (Table 1). A total of 1,969 protein- coding genes, 7 rRNAs, and 42 tRNAs were annotated (Table 1). Two clustered regularly interspaced short palindromic repeats (CRISPRs) arrays were also identified.

Genome features of Veillonella atypica KHUD-V1

Attribute Value
Genome size (bp) 2,189,293
GC content (%) 38.99
No. of scaffolds 54
Total genes 2,056
Protein-coding genes 1,969
tRNAs 42
Complete rRNAs (5S, 16S, 23S) 1, 1, 1
Partial rRNAs (16S, 23S) 1, 3
ncRNAs 4
Pseudogenes 34


Pan genome analysis was performed using the currently registered V. atypica genomes in NCBI GenBank by Pan Genome Analysis Pipeline (PGAP) tools (Zhao et al., 2012). PHASTER (PHAge Search Tool Enhanced Release) (Arndt et al., 2016) was used to identify and annotate prophage sequence regions (Fig. 1). We identified 247 KHUD-V1 strain-specific genes, including two prophage regions and prophage remnants, as well as several genes homologous to prophage-associated virulence factors, such as virulence associated protein E, a Clp protease, and a toxin-antitoxin system.

Fig. 1.

Prophages present in Veillonella atypica KHUD-V1. Location of the prophages on the host chromosome and characterization of the genes were imaged using PHASTER.



Nucleotide sequence accession number

This Whole Genome Shotgun sequencing project for V. atypica KHUD-V1 is available at GenBank under the accession no. QXZZ00000000. The version described in this paper is Version QXZZ01000000.

적 요

본 논문에서는 한국인 만성 치주염 환자의 치은연하치태에서 분리된 Veillonella atypica KHUD-V1의 유전체 서열을 보고한다. 다른 V. atypica 균주와 달리, KHUD-V1에서는 프로파지 및 이와 관련된 것으로 추정되는 여러 병독성 인자가 확인되었다. V. atypica KHUD-V1 균주 및 이 균주의 유전체 서열정보는 Veillonella의 유전체 다양성을 진화론적 관점에서 이해하고, V. atypica의 병독성 및 유전적 다양성에 기여하는 프로파지의 역할을 연구하는데 유용할 것이다.

Acknowledgements

This research was supported by the National Research Foundation of Korea (NRF) funded by the Ministry of Science & ICT (NRF-2016R1D1A1B03932450, NRF-2018R1A2B6002173, and NRF-2017M3A9B6062027).

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