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A novel phage from periodontal pockets associated with chronic periodontitis

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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.

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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.

Funding

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

Author information

Author notes

  1. Tong-Ling Shan and Xi-Ping Feng contributed equally to this study and share corresponding authorship.

Authors and Affiliations

  1. Department of Preventive Dentistry, Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhizaoju Road, Shanghai, China

    Yu Zhang, Fei Li, Tian Yu, Xi Chen & Xi-Ping Feng

  2. Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China

    Tong-Ling Shan

  3. Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai, China

    Yu Zhang, Fei Li, Tian Yu, Xi Chen & Xi-Ping Feng

  4. Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China

    Tong-Ling Shan

  5. Blood Systems Research Institute, San Francisco, CA, USA

    Xu-Tao Deng & Eric Delwart

  6. Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, USA

    Xu-Tao Deng & Eric Delwart

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  1. Yu Zhang
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  4. Tian Yu
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  6. Xu-Tao Deng
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  7. Eric Delwart
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  8. Xi-Ping Feng
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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.

Corresponding authors

Correspondence to Tong-Ling Shan or Xi-Ping Feng.

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The authors declare that they have no conflict of interest.

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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).

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Zhang, Y., Shan, TL., Li, F. et al. A novel phage from periodontal pockets associated with chronic periodontitis. Virus Genes 55, 381–393 (2019). https://doi.org/10.1007/s11262-019-01658-y

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