The genetic diversity and populational specificity of the human gut virome at single-nucleotide resolution
Here, we introduce the Chinese Gut Viral Reference (CGVR) set, consisting of 120,568 viral genomes from 3234 deeply sequenced fecal samples collected nationwide, covering 72,751 viral operational taxonomic units (vOTUs), nearly 90% of which are likely absent from current databases. Analysis of single-nucleotide variations (SNVs) in 233 globally prevalent vOTUs revealed that 18.9% showed significant genetic stratification between Chinese and non-Chinese populations, potentially linked to bacterial infection susceptibility. The predicted bacterial hosts of population-stratified viruses exhibit distinct genetic components associated with health-related functions, including multidrug resistance. Additionally, viral strain diversity at the SNV level correlated with human phenotypic traits, such as age and gastrointestinal issues like constipation. Our analysis also indicates that the human gut bacteriome is specifically shaped by the virome, which mediates associations with human phenotypic traits. Video Abstract CONCLUSIONS: Our analysis underscores the unique genetic makeup of the gut virome across populations and emphasizes the importance of recognizing gut viral genetic heterogeneity for deeper insights into regional health implications.
Authors
- Chengcheng Zhang (ORCID: https://orcid.org/0000-0001-9378-7655)
- M. Gao (ORCID: https://orcid.org/0009-0006-6002-1542)
- Yuwen Jiao (ORCID: https://orcid.org/0000-0001-9417-4279)
- Jing Shi (ORCID: https://orcid.org/0000-0002-9183-9631)
- Shuai Yang (ORCID: https://orcid.org/0000-0001-5782-4148)
- Shixian Hu (ORCID: https://orcid.org/0000-0002-1190-0325)
- Qixiao Zhai (ORCID: https://orcid.org/0000-0002-0605-2675)
- Huayiyang Zou
- Xiuchao Wang (ORCID: https://orcid.org/0000-0002-3205-8544)
- Pan Huang
- Yanwen Zhou (ORCID: https://orcid.org/0000-0003-3636-0123)
- Yanhui Sheng
- Yi Duan (ORCID: https://orcid.org/0000-0002-6229-9461)
- Lianmin Chen (ORCID: https://orcid.org/0000-0003-0660-3518)
- Liming Tang (ORCID: https://orcid.org/0000-0002-7970-7951)
- Beining Ma
- Wei Sun (ORCID: https://orcid.org/0000-0003-0504-3707)
- Yifeng Wang (ORCID: https://orcid.org/0000-0002-1815-3991)
- Chuan Zhang (ORCID: https://orcid.org/0000-0002-9311-0799)
- Tingting Wu (ORCID: https://orcid.org/0000-0003-3437-8899)
- Zijing Huang (ORCID: https://orcid.org/0000-0002-1065-760X)
- Kong Xiangqing (ORCID: https://orcid.org/0000-0003-0163-9650)
- Quanbin Dong (ORCID: https://orcid.org/0000-0002-0849-8136)
- Wei Chen (ORCID: https://orcid.org/0000-0003-3348-4710)
- Youpeng Deng
Institutions
- Jiangnan University (CN)
- University of Science and Technology of China (CN)
- Sun Yat-sen University (CN)
- The First Affiliated Hospital, Sun Yat-sen University (CN)
- Changzhou No.2 People's Hospital (CN)
- State Key Laboratory of Food Science and Technology (CN)
- Nanjing Medical University (CN)
Publication Details
- Journal
- Microbiome
- Published
- 2025-08-20
- DOI
- https://doi.org/10.1186/s40168-025-02185-9
- Citations
- 2
- Primary Topic
- Bacteriophages and microbial interactions
- Type
- article
- Field-Weighted Citation Impact
- 3.43
Funders
- National Natural Science Foundation of China
- Chinese Academy of Sciences
- Government of Jiangsu Province
- Nanjing Medical University
- Priority Academic Program Development of Jiangsu Higher Education Institutions
- Young Scientists Fund
- Fundamental Research Funds for the Central Universities