A catalog of 48,425 nonredundant viruses from oral metagenomes expands the horizon of the human oral virome

Shenghui Li; Ruochun Guo; Yue Zhang; Peng Li; Fang Chen; Xifan Wang; Jing Li; Zhuye Jie; Qingbo Lv; Hao Jin; Guangyang Wang; Qiulong Yan

doi:10.1016/j.isci.2022.104418

A catalog of 48,425 nonredundant viruses from oral metagenomes expands the horizon of the human oral virome

iScience. 2022 May 18;25(6):104418. doi: 10.1016/j.isci.2022.104418. eCollection 2022 Jun 17.

Authors

Shenghui Li^{1

2

3}, Ruochun Guo², Yue Zhang², Peng Li², Fang Chen¹, Xifan Wang^{3

4}, Jing Li⁵, Zhuye Jie⁶, Qingbo Lv², Hao Jin^{2

7}, Guangyang Wang¹, Qiulong Yan¹

Affiliations

¹ Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China.
² Puensum Genetech Institute, Wuhan 430076, China.
³ Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China.
⁴ Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA.
⁵ Department of Rheumatology and Immunology, Peking University People's Hospital, Beijing 100044, China.
⁶ Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark.
⁷ College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China.

Abstract

The human oral cavity is a hotspot of numerous, mostly unexplored, viruses that are important for maintaining oral health and microbiome homeostasis. Here, we analyzed 2,792 publicly available oral metagenomes and proposed the Oral Virus Database (OVD) comprising 48,425 nonredundant viral genomes (≥5 kbp). The OVD catalog substantially expanded the known phylogenetic diversity and host specificity of oral viruses, allowing for enhanced delineation of some underrepresented groups such as the predicted Saccharibacteria phages and jumbo viruses. Comparisons of the viral diversity and abundance of different oral cavity habitats suggested strong niche specialization of viromes within individuals. The virome variations in relation to host geography and properties were further uncovered, especially the age-dependent viral compositional signatures in saliva. Overall, the viral genome catalog describes the architecture and variability of the human oral virome, while offering new resources and insights for current and future studies.

Keywords: Microbiome; Virology.