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Genome sequence of Bifidobacterium dentium strain ATCC 15424 originally isolated from pleural fluid of an empyema patient
Korean J. Microbiol 2019;55(3):280-282
Published online September 30, 2019
© 2019 The Microbiological Society of Korea.

Ji-Hoi Moon1, Suegene Kim1, Seok Bin Yang1, Eun-Young Jang1, Seung-Yun Shin2, Jin-Yong Lee1*, and Jae-Hyung Lee1,3*

1Department of Maxillofacial Biomedical Engineering, School of Dentistry, Kyung Hee University, Seoul 02447, Republic of Korea
2Department of Periodontology, School of Dentistry, Kyung Hee University, Seoul 02447, Republic of Korea
3Kyung Hee Medical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
Correspondence to: *(J.Y. Lee) E-mail: ljinyong@khu.ac.kr; Tel.: +82-2-961-9544 /
(J.H. Lee) E-mail: jaehlee@khu.ac.kr; Tel.: +82-2-961-9290
Received July 11, 2019; Revised August 8, 2019; Accepted August 8, 2019.
Abstract
We present here a draft genome sequence of Bifidobacterium dentium strain ATCC 15424, originally isolated from pleural fluid of an empyema patient. The genome is 2,625,535 bp in length and has a GC content of 58.5%. The genome includes 2,154 protein-coding genes, 4 rRNAs, and 55 tRNAs. Unlike other B. dentium strains isolated from human dental caries, ATCC 15424 carries 247 strain-specific genes, including prophage remnants and type III/IV secretion system proteins, N-acetylmuramoyl-L-alanine amidase, and PRTRC system protein E. The sequence information will contribute to understanding of the natural variation of B. dentium as well as the genome diversity within the bacterial species.
Keywords : Bifidobacterium dentium, genome, pleural fluid isolate
Body

The genus Bifidobacterium is mainly found in the gastrointestinal tract of human and known to have beneficial effects, such as reducing the number of harmful bacteria via the host and enhancing intestinal immunity (Gibson and Wang, 1994; Gill et al., 2001; Manome et al., 2019). Bifidobacterium dentium is predominant among Bifidobacterium species that are found in the intestine as well as in the mouth, and it has been recognized to be related to dental caries (Munson et al., 2004; Manome et al., 2019). The type strain of B. dentium (JCM 1195T) isolated from human dental caries was first reported by Scardovi and Crociani (1974) and the complete genome of this organism has recently been sequenced (Toh et al., 2015). Currently, the genome sequences of B. dentium strains, which were isolated from the human mouth, vagina, and infant and adult feces, are available in GenBank. Meanwhile, B. dentium ATCC 15424 was isolated from an empyema patient (Geroge et al., 1965) and initially described as “Actinomyces eriksonii”, but later found to be B. dentium (Biavati et al., 1982). As bacterial strains isolated from different environments can exhibit different phenotypic and genomic features, strain ATCC 15424 originated from pleural fluid drew our attention. Here we first report a draft genome sequence of B. dentium ATCC 15424. The sequence information will contribute to understanding of the natural variation of B. dentium as well as the genome diversity within the bacterial species.

B. dentium ATCC 15424 was grown at 37°C in tryptone-yeast extract-glucose (TYG) anaerobically (85% N2, 10% H2, and 5% CO2). The bacterial genomic DNA was extracted, and the sequencing library was constructed as described previously (Moon et al., 2019). In total, 6,923,297 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, resulting in 21 scaffolds (> 500-bp length). Gene annotation of the draft genome was performed by the NCBI Prokaryotic Genome Annotation Pipeline (Tatusova et al., 2016).

The genome of B. dentium ATCC 15424 is 2,625,535 bp long and has a GC content of 58.5%. A total of 2,154 protein-coding genes, 4 rRNAs, and 55 tRNAs were annotated (Table 1). We calculated Average Amino acid Identity (AAI) and Average Nucleotide Identity (ANI) between ATCC 15424 and other two strains isolated from dental caries (JCM 1195T and Bd1) using Enveomics collection (http://enve-omics.ce.gatech.edu/enveomics/). The sequence data of B. dentium strains were obtained from NCBI B. dentium genome site (https://www.ncbi.nlm.nih.gov/genome/?term=Bifidobacterium+dentium). The results showed that ATCC 15424 shares 98.29% AAI (two-way) and 98.88% ANI (two-way) with the other strains JCM and Bd1, respectively. Meanwhile, 247 genes specific for strain ATCC 15424 were identified, such as prophage remnants, and genes encoding type III and IV secretion system proteins, N-acetylmuramoyl-L-alanine amidase and PRTRC (ParB-Related, ThiF-Related Cassette) system protein E (Fig. 1).

Genome features of Bifidobacterium dentium ATCC 15424

Attribute Value
Genome size (Mb) 2.62554
GC content (%) 58.5
No. of scaffolds 21
Total genes 2,258
Protein-coding genes 2,154
tRNAs 55
Complete rRNAs (5S, 16S, 23S) 2, 1, 1
Partial rRNAs 0
ncRNAs 3
Pseudogenes 42
N50 383,661
Overall estimated genome coverage 782.3x

Fig. 1.

Genomic comparison of B. dentium ATCC 15424 with other strains from dental caries. Venn diagram illustrates the number of shared and strain-specific genes found in the genome of each B. dentium strain.



Nucleotide sequence accession number

This Whole Genome Shotgun sequencing project for B. dentium ATCC 15424 is available at GenBank under the accession SQQK00000000.1. The BioProject ID in GenBank is PRJNA529663.

적 요

본 논문에서는 농흉 환자의 흉막액에서 분리된 Bifidobacterium dentium ATCC 15424균주의 유전체 염기서열을 분석하여 보고한다. 이 균주의 유전체는 구강에서 분리된 다른 B. dentium 균주에 존재하지 않는 type III 및 IV secretion system proteins, N-acetylmuramoyl-L-alanine amidase 그리고 PRTRC system protein E를 암호화하는 유전자 등 247개의 ATCC 15424균주 특이적인 유전자들을 포함한다. 이 유전체의 서열 정보는 B. dentium의 자연적 변이와 세균 종 내의 유전체 다양성을 이해하는 데 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-2017M3A9B6062027 and NRF-2018R1A2B6002173).

References
  1. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, and Prjibelski AD, et al. 2012. SPAdes:a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol 19, 455-477.
    Pubmed CrossRef
  2. Biavati B, Scardovi V, and Moore WEC. 1982. Electrophoretic patterns of proteins in the genus Bifidobacterium and proposal of four new species. Int. J. Syst. Bacteriol 32, 358-373.
    CrossRef
  3. George LK, Robertstad GW, Brinkman SA, and Hicklin MD. 1965. A new pathogenic anaerobic Actinomyces species. J. Infect. Dis 115, 88-99.
    Pubmed CrossRef
  4. Gibson GR, and Wang X. 1994. Regulatory effects of bifidobacteria on the growth of other colonic bacteria. J. Appl. Bacteriol 77, 412-420.
    Pubmed CrossRef
  5. Gill HS, Rutherfurd KJ, Cross ML, and Gopal PK. 2001. Enhancement of immunity in the elderly by dietary supplementation with the probiotic Bifidobacterium lactis HN019. Am. J. Clin. Nutr 74, 833-839.
    Pubmed CrossRef
  6. Manome A, Abiko Y, Kawashima J, Washio J, Fukumoto S, and Takahashi N. 2019. Acidogenic potential of oral Bifidobacterium and its high fluoride tolerance. Front. Microbiol 10, 1099.
    Pubmed CrossRef
  7. Moon JH, Jang EY, Yang SB, Shin SY, Ryu JI, Lee JY, and Lee JH. 2019. Genome sequence of Prevotella intermedia strain originally isolated from cervicofacial actinomycosis. Korean J. Microbiol 55, 58-60.
  8. Munson MA, Banerjee A, Watson TF, and Wade WG. 2004. Molecular analysis of the microflora associated with dental caries. J. Clin. Microbiol 42, 3023-3029.
    Pubmed CrossRef
  9. Scardovi V, and Crociani F. 1974. Bifidobacterium catenulatum Bifidobacterium dentium Bifidobacterium angulatum:three new species and their deoxyribonucleic acid homology relationships. Int. J. Syst. Bacteriol 24, 6-20.
    CrossRef
  10. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, and Ostell J. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44, 6614-6624.
    Pubmed CrossRef
  11. Toh H, Hayashi J, Oshima K, Nakano A, Takayama Y, Takanashi K, Morita H, and Hattori M. 2015. Complete genome sequence of Bifidobacterium dentium strain JCM 1195Tisolated from human dental caries. Genome Announc 3, e00284-15.
    Pubmed CrossRef


September 2019, 55 (3)