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Draft genome sequence of Streptococcus sp. strain NM isolated from head and neck cancer patients
Korean J. Microbiol 2019;55(1):61-63
Published online March 31, 2019
© 2019 The Microbiological Society of Korea.

Young Suk Kim1, Kyoung-Tag Do2, and Soo-Je Park3,*

1Department of Radiation Oncology, Jeju National University Hospital, School of Medicine, Jeju National University, Jeju 63243, Republic of Korea
2Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 63243, Republic of Korea
3Department of Biology, Jeju National University, Jeju 63243, Republic of Korea
Correspondence to: E-mail: sjpark@jejunu.ac.kr;
Tel.: +82-64-754-3524; Fax: +82-64-756-3541
Received November 23, 2018; Revised December 17, 2018; Accepted December 17, 2018.
Abstract

Streptococcus sp. strain NM belonging to Firmicutes was isolated from head and neck cancer patients. Here, we report the draft genome sequence of strain NM with a size of approximately 1.90 Mbp and a mean G+C content of 39.3%. The draft genome included 1,845 coding sequences, and 12 ribosomal RNA and 58 transfer RNA genes. In the draft genome, genes involved in the antimicrobial resistance, hemolysis and defense system have been identified.

Keywords : Streptococcus, genome, oral
Body

Many members of the genus Streptococcus classified into a member of the Firmicutes have been known as a major colonizer in humans or animals. To date, there are validated 129 species isolated from various environments including human specimens (http://www.bacterio.net/streptococcus.html). Normally, the streptococcal members are found as an opportunistic pathogen of the oral cavity and upper respiratory tract (Mitchell, 2003; Doern and Burnham, 2010). They are Gram-staining positive, aerobic or facultative anaerobic, coccus-shaped. Here, we describe the draft genome sequence and annotation of Streptococcus sp. strain NM isolated from oral microflora of head and neck cancer patient.

To isolate, the sample was swabbed using sterilized cotton, rinsed into phosphate buffered saline (PBS, pH 7.0), immediately. Then, the PBS was serially diluted to five-folds with fresh PBS. Then 100 µl of the aliquot from the diluted sample was spread on Blood agar plates (BAPs, Hanil KOMED) and incubated at 37°C for one week under a microaerobic condition generated by BD GasPak EZ CampyPouch system (BD). Under naked eyes, we selected some strains with hemolysis activity, and repetitively transferred to new BAPs in order to get purified colony, which designed as strain NM. The purified strain NM has been deposited at Korean Culture Center for Microorganisms (KCCM) as KCCM 43307. To extract genomic DNA (gDNA) of strain NM, we used a commercial DNA extraction kit (GeneAll Biotechnology, Co. Ltd.) according to the manufacturer’s instructions. Before whole-genome sequencing, the phylogenetic relationship for the strain NM was determined using the sequence of the 16S ribosomal RNA gene (Koh et al., 2015) and used EzBioCloud server (https://www.ezbiocloud.net/). Then, we confirmed that strain NM was most closely related to Streptococcus pseudopneumoniae ATCC BAA-960T (99.7% 16S rRNA gene sequence similarity) isolated from lower respiratory tract (Arbique et al., 2004). Whole-genome sequencing was performed on the PacBio RS II sequencing platform (Pacific Biosciences of California) at Macrogen. A reads passed filtering a total of about 1.54 Gb in sequenced reads used into contig assembly. The trimming of the resulting nucleotide sequences and assembling de novo were accomplished by Falcon (v.0.2.1) (Chin et al., 2016). Finally, 10 contigs (a mean of 260 depth) were obtained in this study. To estimate genome completeness and quality, we used checkM (Parks et al., 2015). The resulting assembled sequences were annotated by NCBI Prokaryotic Genome Annotation Pipeline with GeneMarkS + version 4.5, using the best-placed reference protein method (Angiuoli et al., 2008). Finally, the draft genome size of the strain NM is ca. 1.90 Mb with 39.9% G+C content. The results of CheckM estimation indicated that genome completeness at 93.8% with 0.76% contamination and 75% strain heterogeneity.

The genome includes 1,918 predicted genes, and 12 ribosomal RNA and 58 transfer RNA genes (Table 1). Among coding sequences (n = 1,776), only 938 CDSs were matched in KEGG database (52.8% of total CDSs), in which most of them were affiliated into protein families: genetic information processing category. Despite the similarity for 16S rRNA gene sequence was high, the result (92.0%) of average nucleotide identify calculation indicated that strain NM might be new species of the genus Streptococcus, against Streptococcus pseudopneumoniae ATCC BAA-960T (Figueras et al., 2014).

Streptococcus sp. strain NM genome assembly and its general features

Item Description
Genome Assembly Data
 Assembly Method FALCON v. 0.2.1
 Genome Coverage 260X
 Sequencing Technology PacBio RSII
 No. of contigs 10
Genome features
 Size (Mbp) 1.90
 GC content (%) 39.9
 No. of total predicted genes 1,918
 No. of total coding sequences 1,845
 No. of hypothetical proteins 244
 rRNA (23S, 16S, 5S) 12 (4, 4, 4)
 tRNA 58


Genome analysis revealed that there were hyaluronidase/ collagenases and hemolysin genes, both of which have been reported to play a damaging toxin for membrane or extracellular matrix in staphylococci. Also, we identified some genes involved in two-component regulatory systems (TCRS, e.g. ciaRH and vicRK) in Streptococcus pneumoniae (AlonsoDeVelasco et al., 1995). These TCRS have been known as an essential for growth (Wagner et al., 2002). The genome also contained the antimicrobial resistance genes such as aminoglycoside resistance gene (aadK), accessory gene for vancomycin resistance (vanWY), and cationic antimicrobial peptide resistance operon (dltABCD).

Accession number

This Whole Genome Shotgun project of the strain NM (= KCCM 43307) has been deposited at DDBJ/ENA/GenBank under the accession QUOS00000000. The version described in this paper is version QUOS01000000.

적 요

Firmicutes에 속하는 Streptococcus sp. strain NM을 두경부암 환자로부터 분리하였다. 본 연구에서는 약1.90 Mb의 크기와 39.3%의 평균 G+C 함량을 가진 NM 균주의 비완전한 유전체를 보고한다. 유전체는 1,845개의 코딩서열, 12개의 리보솜 RNA 및 58개의 전사 RNA유전자를 포함하였다. 본 유전체로부터, 항생제내성, 용혈 및 방어시스템과 관련된 유전자들이 확인되었다.

Acknowledgements

This work was supported by a research grant from Jeju National University Hospital in 2018.

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March 2019, 55 (1)