A metagenome-wide study of the gut virome in chronic kidney disease
<b>Rationale:</b> Chronic kidney disease (CKD) is a progressively debilitating condition leading to kidney dysfunction and severe complications. While dysbiosis of the gut bacteriome has been linked to CKD, the alteration in the gut viral community and its role in CKD remain poorly understood. <b>Methods:</b> Here, we characterize the gut virome in CKD using metagenome-wide analyses of faecal samples from 425 patients and 290 healthy individuals. <b>Results:</b> CKD is associated with a remarkable shift in the gut viral profile that occurs regardless of host properties, disease stage, and underlying diseases. We identify 4,649 differentially abundant viral operational taxonomic units (vOTUs) and reveal that some CKD-enriched viruses are closely related to gut bacterial taxa such as <i>Bacteroides</i>, <i>[Ruminococcus]</i>, <i>Erysipelatoclostridium</i>, and <i>Enterocloster</i> spp. In contrast, CKD-depleted viruses include more <i>crAss-like</i> viruses and often target <i>Faecalibacterium</i>, <i>Ruminococcus</i>, and <i>Prevotella</i> species. Functional annotation of the vOTUs reveals numerous viral functional signatures associated with CKD, notably a marked reduction in nicotinamide adenine dinucleotide (NAD<sup>+</sup>) synthesis capacity within the CKD-associated virome. Furthermore, most CKD viral signatures are reproducible in the gut viromes of diabetic kidney disease and several other common diseases, highlighting the considerable universality of disease-associated viromes. <b>Conclusions:</b> This research provides comprehensive resources and novel insights into the CKD-associated gut virome, offering valuable guidance for future mechanistic and therapeutic investigations.
Authors
- Kairuo Wang
- Longbao Yang (ORCID: https://orcid.org/0000-0002-2823-1711)
- Guangyang Wang (ORCID: https://orcid.org/0000-0003-1751-1790)
- Lin Cheng (ORCID: https://orcid.org/0000-0001-8066-527X)
- Jiang Deng (ORCID: https://orcid.org/0000-0002-3122-0300)
- Lu Li (ORCID: https://orcid.org/0000-0001-5887-370X)
- Danni He (ORCID: https://orcid.org/0000-0002-2622-3574)
- Qiulong Yan
- Ruochun Guo (ORCID: https://orcid.org/0000-0002-0322-3264)
- Jinxin Meng (ORCID: https://orcid.org/0000-0001-5325-1178)
- Shuxin Liu (ORCID: https://orcid.org/0009-0009-2913-7434)
- Xiaoyan Guo (ORCID: https://orcid.org/0000-0002-9388-484X)
- Shanshan Sha (ORCID: https://orcid.org/0000-0001-9530-9008)
- Fenrong Chen
- Hongli Jiang (ORCID: https://orcid.org/0000-0001-9262-6112)
- Shiyang Ma (ORCID: https://orcid.org/0000-0002-4423-5798)
- Lei Chen (ORCID: https://orcid.org/0009-0008-8096-7401)
- Pan Zhang (ORCID: https://orcid.org/0000-0001-8279-4008)
- Yanli Zhang (ORCID: https://orcid.org/0000-0001-8173-2024)
- Jinhai Wang (ORCID: https://orcid.org/0000-0003-0562-3998)
- Yizhen Wang (ORCID: https://orcid.org/0000-0002-3908-7102)
- Yue Zhang (ORCID: https://orcid.org/0009-0004-5956-2275)
- Haitao Shi (ORCID: https://orcid.org/0000-0003-2354-5209)
- Jian Kang (ORCID: https://orcid.org/0000-0003-0002-9690)
- Shenghui Li
- Shao Fan
- Gang Zhao
- Hailong Yu
Institutions
- Dalian Medical University (CN)
- Shaanxi Provincial People's Hospital (CN)
- Dalian Municipal Central Hospital (CN)
- First Affiliated Hospital of Xi'an Jiaotong University (CN)
- Second Affiliated Hospital of Xi'an Jiaotong University (CN)
- Affiliated Zhongshan Hospital of Dalian University (CN)
Publication Details
- Journal
- Theranostics
- Published
- 2024-12-31
- DOI
- https://doi.org/10.7150/thno.101601
- Citations
- 5
- Primary Topic
- Adolescent and Pediatric Healthcare
- Type
- article
- Field-Weighted Citation Impact
- 4.36
Funders
- National Natural Science Foundation of China