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
Affiliations
Shenghui Li
Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China; Puensum Genetech Institute, Wuhan 430076, China; Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China; Corresponding author
Ruochun Guo
Puensum Genetech Institute, Wuhan 430076, China
Yue Zhang
Puensum Genetech Institute, Wuhan 430076, China
Peng Li
Puensum Genetech Institute, Wuhan 430076, China
Fang Chen
Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
Xifan Wang
Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China; Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
Jing Li
Department of Rheumatology and Immunology, Peking University People’s Hospital, Beijing 100044, China
Zhuye Jie
Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
Qingbo Lv
Puensum Genetech Institute, Wuhan 430076, China
Hao Jin
Puensum Genetech Institute, Wuhan 430076, China; College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
Guangyang Wang
Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
Qiulong Yan
Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China; Corresponding author
Summary: 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.
