Integrating metagenomics and cultivation unveils oral phage diversity and potential impact on hosts
Bacteriophages play important roles in the regulation of bacterial communities and may thus impact human health. However, the scarcity of genomic data of oral microorganism has limited information on oral phages. We collected data on 5427 metagenomic samples and 2178 cultivated bacterial genomes across different geographical areas and populations, generating the Oral Phage Database (OPD), comprising 189,859 representative phage genome sequences, including 3416 huge phages (genome size > 200 kbp). OPD reveals that most oral viruses are unknown and encode an enormous variety of dark proteins. Numerous oral phages infecting a broad range of hosts carry anti-defense genes, auxiliary metabolic genes, and virulence factors that may affect bacterial metabolism and influence human health. The composition of oral phages varies among different populations, and several phages have the potential to act as biomarkers for disease. OPD expands our knowledge of phage-bacteria interactions, huge phages diversity, and potential impacts on human health.
Authors
- Huanming Yang (ORCID: https://orcid.org/0000-0002-0858-3410)
- Liang Xiao (ORCID: https://orcid.org/0000-0003-0836-4397)
- Karsten Kristiansen (ORCID: https://orcid.org/0000-0002-6024-0917)
- Tongyuan Hu (ORCID: https://orcid.org/0000-0003-4172-3136)
- Yanmei Ju (ORCID: https://orcid.org/0000-0002-1600-3164)
- Weiting Liang (ORCID: https://orcid.org/0000-0002-9573-5709)
- Zhuye Jie (ORCID: https://orcid.org/0000-0003-0833-6134)
- Yanzheng Meng (ORCID: https://orcid.org/0000-0002-1357-9635)
- Xin Tong (ORCID: https://orcid.org/0000-0002-4849-6522)
- Hewei Liang (ORCID: https://orcid.org/0000-0003-4639-6314)
- Xiaoqian Lin (ORCID: https://orcid.org/0009-0004-0999-7182)
- Mo Han (ORCID: https://orcid.org/0000-0002-4404-297X)
- Jian Wang (ORCID: https://orcid.org/0000-0003-4949-4753)
- Jiahao Zhang (ORCID: https://orcid.org/0000-0002-8780-1497)
- Xun Xu (ORCID: https://orcid.org/0000-0002-0504-362X)
- Xin Jin
- Wenwei Zhang
- Tao Zhang (ORCID: https://orcid.org/0000-0003-2765-2802)
- Wenxi Li (ORCID: https://orcid.org/0000-0002-7892-1737)
- Yuanqiang Zou (ORCID: https://orcid.org/0000-0003-3293-5858)
Institutions
- BGI Group (China) (CN)
- University of Copenhagen (DK)
- Peking University (CN)
- Bioscience (China) (CN)
- Center for Life Sciences (CN)
- BGI Research (CN)
- South China University of Technology (CN)
Publication Details
- Journal
- npj Biofilms and Microbiomes
- Published
- 2025-07-26
- DOI
- https://doi.org/10.1038/s41522-025-00773-z
- Citations
- 1
- Primary Topic
- Bacteriophages and microbial interactions
- Type
- article
- Field-Weighted Citation Impact
- 1.72
Funders
- Government of Jiangxi Province
- Natural Science Foundation of Guangdong Province
- National Key Research and Development Program of China