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Complete genome sequence of Granulicatella adiacens KHUD_009 isolated from subgingival biofilm
Korean J. Microbiol. 2023;59(2):142-144
Published online June 30, 2023
© 2023 The Microbiological Society of Korea.

Won Young Hong1, Cheul Kim2, Ji-Hoi Moon1*, and Jae-Hyung Lee1*

1Department of Oral Microbiology, College of Dentistry, Kyung Hee University, Seoul 02447, Republic of Korea
2Research Institute of Oral Science, College of Dentistry, Gangneung-Wonju National University, Gangneung 25457, Republic of Korea
Correspondence to: *(J. H. Moon) E-mail: prudence75@khu.ac.kr; Tel.: +82-2-961-0795; Fax: +82-2-962-0598 (J. H. Lee) E-mail: jaehlee@khu.ac.kr; Tel.: +82-2-961-9290; Fax: +82-2-962-0598
Received January 31, 2023; Revised April 5, 2023; Accepted April 20, 2023.
Abstract
Granulicatella adiacens is known to participate in several oral diseases including periodontitis, caries and endodontic infection. However, complete reference genome sequences for G. adiacens have only been analyzed for non-oral isolates. We sequenced the complete genome of G. adiacens KHUD_009 originated from the subgingival biofilm of a Korean with periodontitis, using the PacBio Sequel II platform. The genome is 1,949,834 bp with a GC content of 37.81% and includes 1,830 protein-coding genes, 15 rRNAs, and 58 tRNA. We identified that KHUD_009 carries several genes encoding virulence-associated proteins such as phosphocarrier and acyl carrier proteins and type VII secretion proteins.
Keywords : Granulicatella adiacens, genome, subgingival biofilm
Body

Granulicatella adiacens is a Gram-positive, non-motile, non-spore forming, oxidase- and catalase-negative, facultatively anaerobic coccus (Karched et al., 2019). The bacterium was previously known as a member of nutritionally variant streptococci (NVS) and transferred to a separate genus, Abiotrophia (Karched et al., 2019). Later on, this genus was divided into the genera Abiotrophia and Granulicatella (species G. adiacens, G. elegans, and G. balaenopterae) on the basis of 16S rRNA gene sequencing (Collins and Lawson, 2000; Gupta et al., 2018).

G. adiacens commonly resides in the oral cavity, urogenital tract, and intestinal tract (Ruoff, 1991; Karched et al., 2019). It can occasionally cause serious infections such as infective endocarditis (Lin and Hsu, 2007; Seo et al., 2010), and also participate in several oral diseases including periodontitis (Belstrøm et al., 2014), caries (Kanasi et al., 2010), and root canal infection (Siqueira and Rôças, 2006). However, at present, complete reference genomes for G. adiacens have been analyzed for only two strains: the type strain ATCC 49175, isolated from the throat, urine and blood of patients with endocarditis, and FDAARGOS_1477, a strain of unknown origin. Here, we report the complete genome sequence of G. adiacens KHUD_009 originated from the subgingival biofilm of a Korean patient with periodontitis (KHD IRB 1606-5).

The bacterial genomic DNA was extracted using Wizard HMW DNA Extraction Kit (promega). For the whole genome sequencing of G. adiacens KHUD_009, a Single-Molecule Real-Time (SMRT) bell library was prepared according to the manufacturer’s instructions (Pacific Biosciences). We obtained 82,073 raw sequencing subreads (average read length 8,526 bp) using Pacific Biosciences Sequel II with 2.0 sequencing chemistry. De novo genome of strain KHUD_009 was assembled by the Microbial Genome Analysis pipeline in the SMRT Analysis version 11.0 (https://www.pacb.com/support/software-downloads/) using default parameters. The NCBI Prokaryotic Genome Annotation Pipeline was used for gene annotation of the genomes.

G. adiacens KHUD_009 genome is 1,949,834 bp with G + C content of 37.81% (Table 1). A total of 1,830 protein-coding genes, 15 rRNAs (5S, 16S, 23S), and 58 tRNAs were identified. Although little is known about the virulence factors of G. adiacens, Karched et al. (2019) performed in silico prediction using the secretome of strain CCUG 27809. More than 20% of the secretome proteins were putative virulence proteins, including superoxide dismutase, thioredoxin, phosphocarrier, and acyl carrier proteins (Karched et al., 2019). As shown in Table 2, strain KHUD_009 also carries several genes encoding virulence-associated proteins. In addition, KHUD_009 genome contains genes encoding type VII secretion system, which has been implicated in interbacterial competition, nutrient acquisition, and virulence (Spencer and Doran, 2022). The strain has been deposited in the Korean Collection for Type Cultures (KCTC 25584) for future reference and research.

Genome features of Granulicatella adiacens KHUD_009
Attribute KHUD_009
Genome size (bp) 1,949,834
GC content (%) 37.81
Total genes 1,933
Protein-coding genes 1,830
tRNAs 58
Complete rRNAs (5S, 16S, 23S) 5, 5, 5
ncRNAs 4
Pseudogenes 26
Genome coverage 22.51x


Genes encoding putative virulence-associated proteins
ID NCBI annotation
UXY40975 superoxide dismutase
UXY42341, UXY41447, UXY40952 thioredoxin
UXY41002 phosphocarrier protein HPr
UXY42202, UXY41835 acyl carrier protein
UXY41531 type VII secretion protein EsaA
UXY41534 type VII secretion protein EssB
UXY41535 type VII secretion protein EssC
UXY41533 type VII secretion protein


Nucleotide sequence accession number

This Whole Genome Shotgun sequencing project for Granulicatella adiacens KHUD_009 is available at NCBI GenBank under BioProject ID PRJNA883546 (BioSample SAMN30968860, GenBank CP106751).

적 요

Granulicatella adiacens는 치주염, 치아 우식 및 근관 감염과 같은 구강 질환에 관여하는 것으로 알려져 있다. 그러나 G. adiacens에 대한 완전한 참조 유전체 서열은 비 경구 분리주에 대해서만 분석되었다. 본 연구는 PacBio Sequel II플랫폼을 이용하여 한국인 치주염환자 치은연하 세균막에서 분리한 G. adiacens KHUD_009의 전장 유전체 서열을 분석하였다. 균주 KHUD_009의 유전체는 1,949,834 bp (G + C 함량: 37.81%)이고, 1,830개의 단백질 암호화 유전자와 15개의 rRNA, 그리고 58개의 tRNA를 포함하고 있다. 또한, phosphocarrier 및 acyl carrier와 같은 운반체 단백질과 type VII 분비 시스템과 같은 병독성 관련 단백질을 암호화하는 여러 유전자가 확인되었다.

Acknowledgments

This research was supported by the National Research Foundation of Korea (NRF) funded by the Ministry of Science & ICT (NRF-2021R1A2C2008180, NRF-2022R1F1A1071248).

Conflict of Interest

The authors have no conflict of interest to report.

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