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Virus Genes

, Volume 55, Issue 3, pp 381–393 | Cite as

A novel phage from periodontal pockets associated with chronic periodontitis

  • Yu Zhang
  • Tong-Ling ShanEmail author
  • Fei Li
  • Tian Yu
  • Xi Chen
  • Xu-Tao Deng
  • Eric Delwart
  • Xi-Ping FengEmail author
Article

Abstract

Bacteriophages often constitute the majority of periodontal viral communities, but phages that infect oral bacteria remain uncharacterized. Here, we present the genetic analysis of the genome of a novel siphovirus, named Siphoviridae_29632, which was isolated from a patient with periodontitis using a viral metagenomics-based approach. Among 43 predicted open reading frames (ORFs) in the genome, the viral genes encoding structural proteins were distinct from the counterparts of other viruses, although a distant homology is shared among viral morphogenesis proteins. A total of 28 predicted coding sequences had significant homology to other known phage ORF sequences. In addition, the prevalence of Siphoviridae_29632 in a cohort of patients with chronic periodontitis was 41.67%, which was significantly higher than that in the healthy group (4.55%, P < 0.001), suggesting that this virus as well as its hosts may contribute to the ecological environment favored for chronic periodontitis.

Keywords

Bacteriophage Siphovirus Periodontitis Viral metagenomics Case–control study 

Notes

Acknowledgments

The authors are grateful to all participates in the research and appreciate the efforts of teams in the Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China.

Author contributions

XPF and TLS designed the study. XTD and ED completed the data analysis and statistics. YZ and FL completed the sample collection and the amplifications of the newly discovered full-length human anellovirus. YZ, TY, and XC completed the epidemiological investigation. All of the authors have read and approved the final manuscript.

Funding

The study was funded by the National Natural Science Foundation of China (Nos. 81800967 and 81470737).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards. Ethics Committee of the Ninth People’s Hospital, School of Medicine, Shanghai Jiao Tong University approved this study (No. 201406).

Informed consent

Informed consent was obtained from all individual participants included in the study.

Supplementary material

11262_2019_1658_MOESM1_ESM.docx (1.6 mb)
Supplementary material 1 (DOCX 1612 kb)
11262_2019_1658_MOESM2_ESM.docx (18 kb)
Supplementary material 2 (DOCX 17 kb)

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Yu Zhang
    • 1
    • 3
  • Tong-Ling Shan
    • 2
    • 4
    Email author
  • Fei Li
    • 1
    • 3
  • Tian Yu
    • 1
    • 3
  • Xi Chen
    • 1
    • 3
  • Xu-Tao Deng
    • 5
    • 6
  • Eric Delwart
    • 5
    • 6
  • Xi-Ping Feng
    • 1
    • 3
    Email author
  1. 1.Department of Preventive Dentistry, Ninth People’s HospitalShanghai JiaoTong University School of MedicineShanghaiChina
  2. 2.Department of Swine Infectious Disease, Shanghai Veterinary Research InstituteChinese Academy of Agricultural SciencesShanghaiChina
  3. 3.Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of StomatologyNational Clinical Research Center of StomatologyShanghaiChina
  4. 4.Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesYangzhouChina
  5. 5.Blood Systems Research InstituteSan FranciscoUSA
  6. 6.Department of Laboratory MedicineUniversity of California at San FranciscoSan FranciscoUSA

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