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Wu Z, Liu T, Chen Q, Chen T, Hu J, Sun L, Wang B, Li W, Ni J. Unveiling the unknown viral world in groundwater. Nat Commun 2024; 15:6788. [PMID: 39117653 PMCID: PMC11310336 DOI: 10.1038/s41467-024-51230-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 08/01/2024] [Indexed: 08/10/2024] Open
Abstract
Viruses as the prevailing biological entities are poorly understood in underground realms. Here, we establish the first metagenomic Groundwater Virome Catalogue (GWVC) comprising 280,420 viral species ( ≥ 5 kb) detected from 607 monitored wells in seven geo-environmental zones throughout China. In expanding ~10-fold the global portfolio of known groundwater viruses, we uncover over 99% novel viruses and about 95% novel viral clusters. By linking viruses to hosts from 119 prokaryotic phyla, we double the number of microbial phyla known to be virus-infected in groundwater. As keystone ultrasmall symbionts in aquifers, CPR bacteria and DPANN archaea are susceptible to virulent viruses. Certain complete CPR viruses even likely infect non-CPR bacteria, while partial CPR/DPANN viruses harbor cell-surface modification genes that assist symbiont cell adhesion to free-living microbes. This study reveals the unknown viral world and auxiliary metabolism associated with methane, nitrogen, sulfur, and phosphorus cycling in groundwater, and highlights the importance of subsurface virosphere in viral ecology.
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Affiliation(s)
- Zongzhi Wu
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, PR China
- Environmental Microbiome and Innovative Genomics Laboratory, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, PR China
| | - Tang Liu
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, PR China
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, PR China
| | - Qian Chen
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, PR China
- Environmental Microbiome and Innovative Genomics Laboratory, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, PR China
| | - Tianyi Chen
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, PR China
| | - Jinyun Hu
- Environmental Microbiome and Innovative Genomics Laboratory, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, PR China
| | - Liyu Sun
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, PR China
| | - Bingxue Wang
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, PR China
| | - Wenpeng Li
- Center for Groundwater Monitoring, China Institute of Geo-environmental Monitoring, Beijing, 100081, PR China
| | - Jinren Ni
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, PR China.
- College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, 100871, PR China.
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Huang L, Guo R, Li S, Wu X, Zhang Y, Guo S, Lv Y, Xiao Z, Kang J, Meng J, Zhou P, Ma J, You W, Zhang Y, Yu H, Zhao J, Huang G, Duan Z, Yan Q, Sun W. A multi-kingdom collection of 33,804 reference genomes for the human vaginal microbiome. Nat Microbiol 2024; 9:2185-2200. [PMID: 38907008 PMCID: PMC11306104 DOI: 10.1038/s41564-024-01751-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 05/01/2024] [Indexed: 06/23/2024]
Abstract
The human vagina harbours diverse microorganisms-bacteria, viruses and fungi-with profound implications for women's health. Genome-level analysis of the vaginal microbiome across multiple kingdoms remains limited. Here we utilize metagenomic sequencing data and fungal cultivation to establish the Vaginal Microbial Genome Collection (VMGC), comprising 33,804 microbial genomes spanning 786 prokaryotic species, 11 fungal species and 4,263 viral operational taxonomic units. Notably, over 25% of prokaryotic species and 85% of viral operational taxonomic units remain uncultured. This collection significantly enriches genomic diversity, especially for prevalent vaginal pathogens such as BVAB1 (an uncultured bacterial vaginosis-associated bacterium) and Amygdalobacter spp. (BVAB2 and related species). Leveraging VMGC, we characterize functional traits of prokaryotes, notably Saccharofermentanales (an underexplored yet prevalent order), along with prokaryotic and eukaryotic viruses, offering insights into their niche adaptation and potential roles in the vagina. VMGC serves as a valuable resource for studying vaginal microbiota and its impact on vaginal health.
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Affiliation(s)
- Liansha Huang
- Department of Reproductive Health, Shenzhen Bao'an Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | | | - Shenghui Li
- Puensum Genetech Institute, Wuhan, China.
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China.
| | - Xiaoling Wu
- Department of Reproductive Health, Shenzhen Bao'an Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan, China
| | - Shumin Guo
- Department of Reproductive Health, Shenzhen Bao'an Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Ying Lv
- Department of Reproductive Health, Shenzhen Bao'an Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Zhen Xiao
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Jian Kang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | | | - Peng Zhou
- Department of Acupuncture, Shenzhen Bao'an Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Jie Ma
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Wei You
- Department of Acupuncture and Moxibustion, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Yan Zhang
- Department of Traditional Chinese Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Hailong Yu
- Puensum Genetech Institute, Wuhan, China
| | - Jixin Zhao
- Puensum Genetech Institute, Wuhan, China
| | - Guangrong Huang
- Department of Gynecology, Shenzhen Bao'an Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Zuzhen Duan
- Department of Gynecology, Shenzhen Bao'an Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Qiulong Yan
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China.
| | - Wen Sun
- Centre for Translational Medicine, Shenzhen Bao'an Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China.
- Key Laboratory of Health Cultivation of the Ministry of Education, Beijing University of Chinese Medicine, Beijing, China.
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3
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Cui S, Guo R, Chen C, Zhang Y, Meng J, Liu L, Li Y, Kang Z, Li S, Yan Q, Ma Y. Next-Generation Sequencing for Characterizing Respiratory Tract Virome and Improving Detection of Viral Pathogens in Children With Pneumonia. Influenza Other Respir Viruses 2024; 18:e13362. [PMID: 39118486 PMCID: PMC11310556 DOI: 10.1111/irv.13362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/05/2024] [Accepted: 07/26/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND Pneumonia is typically caused by a variety of pathogenic microorganisms. Traditional research often focuses on the infection of a few microorganisms, whereas metagenomic studies focus on the impact of the bacteriome and mycobiome on respiratory diseases. Reports on the virome characteristics of pediatric pneumonia remain relatively scarce. METHODS We employed de novo assembly and combined homology- and feature-based methods to characterize the respiratory virome in whole-genome DNA sequencing samples from oropharynx (OP) swabs, nasopharynx (NP) swabs, and bronchoalveolar lavage fluids (BALF) of children with pneumonia. RESULTS Significant differences were observed in the alpha and beta diversity indexes, as well as in the composition of the oropharyngeal virome, between pneumonia cases and controls. We identified 1137 viral operational taxonomic units (vOTUs) with significant differences, indicating a preference of pneumonia-reduced vOTUs for infecting Prevotella, Neisseria, and Veillonella, whereas pneumonia-enriched vOTUs included polyomavirus, human adenovirus, and phages targeting Staphylococcus, Streptococcus, Granulicatella, and Actinomyces. Comparative analysis revealed higher relative abundances and prevalence rates of pneumonia-enriched OP vOTUs in NP and BALF samples compared to pneumonia-reduced vOTUs. Additionally, virome analysis identified six pediatric patients with severe human adenovirus or polyomavirus infections, five of whom might have been undetected by targeted polymerase chain reaction (PCR)-based testing. CONCLUSIONS This study offers insights into pediatric pneumonia respiratory viromes, highlighting frequent transmission of potentially pathogenic viruses and demonstrating virome analysis as a valuable adjunct for pathogen detection.
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Affiliation(s)
- Song Cui
- Department of Biochemistry and Molecular Biology, College of Basic SciencesDalian Medical UniversityDalianChina
- Department of Critical Care MedicineDalian Municipal Central HospitalDalianChina
| | | | - Changming Chen
- Department of Rheumatology and ImmunologyThe Second Affiliated Hospital of Guizhou University of Traditional Chinese MedicineGuiyangChina
| | - Yue Zhang
- Puensum Genetech InstituteWuhanChina
| | | | - Lanxin Liu
- Department of Critical Care MedicineDalian Municipal Central HospitalDalianChina
| | - Yanxia Li
- Department of Critical Care MedicineDalian Municipal Central HospitalDalianChina
| | - Zhijie Kang
- Department of HematologyThe Second Hospital of Dalian Medical UniversityDalianChina
| | | | - Qiulong Yan
- Department of Microbiology, College of Basic SciencesDalian Medical UniversityDalianChina
| | - Yufang Ma
- Department of Biochemistry and Molecular Biology, College of Basic SciencesDalian Medical UniversityDalianChina
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4
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Tian X, Li S, Wang C, Zhang Y, Feng X, Yan Q, Guo R, Wu F, Wu C, Wang Y, Huo X, Ma X. Gut virome-wide association analysis identifies cross-population viral signatures for inflammatory bowel disease. MICROBIOME 2024; 12:130. [PMID: 39026313 PMCID: PMC11256409 DOI: 10.1186/s40168-024-01832-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 05/08/2024] [Indexed: 07/20/2024]
Abstract
BACKGROUND The gut virome has been implicated in inflammatory bowel disease (IBD), yet a full understanding of the gut virome in IBD patients, especially across diverse geographic populations, is lacking. RESULTS In this study, we conducted a comprehensive gut virome-wide association study in a Chinese cohort of 71 IBD patients (15 with Crohn's disease and 56 with ulcerative colitis) and 77 healthy controls via viral-like particle (VLP) and bulk virome sequencing of their feces. By utilizing an integrated gut virus catalog tailored to the IBD virome, we revealed fundamental alterations in the gut virome in IBD patients. These characterized 139 differentially abundant viral signatures, including elevated phages predicted to infect Escherichia, Klebsiella, Enterococcus_B, Streptococcus, and Veillonella species, as well as IBD-depleted phages targeting Prevotella, Ruminococcus_E, Bifidobacterium, and Blautia species. Remarkably, these viral signatures demonstrated high consistency across diverse populations such as those in Europe and the USA, emphasizing their significance and broad relevance in the disease context. Furthermore, fecal virome transplantation experiments verified that the colonization of these IBD-characterized viruses can modulate experimental colitis in mouse models. CONCLUSIONS Building upon these insights into the IBD gut virome, we identified potential biomarkers for prognosis and therapy in IBD patients, laying the foundation for further exploration of viromes in related conditions. Video Abstract.
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Affiliation(s)
- Xiangge Tian
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Shenghui Li
- Puensum Genetech Institute, Wuhan, 430076, China
| | - Chao Wang
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Yanyan Zhang
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Xiaoying Feng
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
| | - Qiulong Yan
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China.
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China.
| | - Ruochun Guo
- Puensum Genetech Institute, Wuhan, 430076, China
| | - Fan Wu
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
| | - Chunxue Wu
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
| | - Yan Wang
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
| | - Xiaokui Huo
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China.
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China.
| | - Xiaochi Ma
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China.
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China.
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5
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Zhang P, Shi H, Guo R, Li L, Guo X, Yang H, Chang D, Cheng Y, Zhao G, Li S, Zhong Q, Zhang H, Zhao P, Fu C, Song Y, Yang L, Wang Y, Zhang Y, Jiang J, Wang T, Zhao J, Li Y, Wang B, Chen F, Zhao H, Wang Y, Wang J, Ma S. Metagenomic analysis reveals altered gut virome and diagnostic potential in pancreatic cancer. J Med Virol 2024; 96:e29809. [PMID: 39016466 DOI: 10.1002/jmv.29809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 06/15/2024] [Accepted: 07/08/2024] [Indexed: 07/18/2024]
Abstract
Pancreatic cancer (PC) is a highly aggressive malignancy with a poor prognosis, making early diagnosis crucial for improving patient outcomes. While the gut microbiome, including bacteria and viruses, is believed to be essential in cancer pathogenicity, the potential contribution of the gut virome to PC remains largely unexplored. In this study, we conducted a comparative analysis of the gut viral compositional and functional profiles between PC patients and healthy controls, based on fecal metagenomes from two publicly available data sets comprising a total of 101 patients and 82 healthy controls. Our results revealed a decreasing trend in the gut virome diversity of PC patients with disease severity. We identified significant alterations in the overall viral structure of PC patients, with a meta-analysis revealing 219 viral operational taxonomic units (vOTUs) showing significant differences in relative abundance between patients and healthy controls. Among these, 65 vOTUs were enriched in PC patients, and 154 were reduced. Host prediction revealed that PC-enriched vOTUs preferentially infected bacterial members of Veillonellaceae, Enterobacteriaceae, Fusobacteriaceae, and Streptococcaceae, while PC-reduced vOTUs were more likely to infect Ruminococcaceae, Lachnospiraceae, Clostridiaceae, Oscillospiraceae, and Peptostreptococcaceae. Furthermore, we constructed random forest models based on the PC-associated vOTUs, achieving an optimal average area under the curve (AUC) of up to 0.879 for distinguishing patients from controls. Through additional 10 public cohorts, we demonstrated the reproducibility and high specificity of these viral signatures. Our study suggests that the gut virome may play a role in PC development and could serve as a promising target for PC diagnosis and therapeutic intervention. Future studies should further explore the underlying mechanisms of gut virus-bacteria interactions and validate the diagnostic models in larger and more diverse populations.
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Affiliation(s)
- Pan Zhang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Haitao Shi
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Ruochun Guo
- Puensum Genetech Institute, Wuhan, Hubei, China
| | - Lu Li
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Xiaoyan Guo
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Hui Yang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Danyan Chang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Yan Cheng
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Gang Zhao
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Shenghui Li
- Puensum Genetech Institute, Wuhan, Hubei, China
| | - Qingling Zhong
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Huan Zhang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Ping Zhao
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Cui Fu
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Yahua Song
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Longbao Yang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Yan Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan, Hubei, China
| | - Jiong Jiang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Ting Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Juhui Zhao
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Yong Li
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Biyuan Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Fenrong Chen
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Hongli Zhao
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Yonghua Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Jinhai Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Shiyang Ma
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
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6
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Zhang P, Ma S, Guo R, Li L, Guo X, Chang D, Li S, Zhang H, Fu C, Yang L, Zhang Y, Jiang J, Wang T, Wang J, Shi H. Metagenomic analysis of the gut virome in patients with irritable bowel syndrome. J Med Virol 2024; 96:e29802. [PMID: 39023095 DOI: 10.1002/jmv.29802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 07/02/2024] [Accepted: 07/04/2024] [Indexed: 07/20/2024]
Abstract
Irritable bowel syndrome (IBS), a chronic functional gastrointestinal disorder, is recognized for its association with alterations in the gut microbiome and metabolome. This study delves into the largely unexplored domain of the gut virome in IBS patients. We conducted a comprehensive analysis of the fecal metagenomic data set from 277 IBS patients and 84 healthy controls to characterize the gut viral community. Our findings revealed a distinct gut virome in IBS patients compared to healthy individuals, marked by significant variances in between-sample diversity and altered abundances of 127 viral operational taxonomic units (vOTUs). Specifically, 111 vOTUs, predominantly belonging to crAss-like, Siphoviridae, Myoviridae, and Quimbyviridae families, were more abundant in IBS patients, whereas the healthy control group exhibited enrichment of 16 vOTUs from multiple families. We also investigated the interplay between the gut virome and bacteriome, identifying a correlation between IBS-enriched bacteria like Klebsiella pneumoniae, Fusobacterium varium, and Ruminococcus gnavus, and the IBS-associated vOTUs. Furthermore, we assessed the potential of gut viral signatures in predicting IBS, achieving a notable area under the receiver operator characteristic curve (AUC) of 0.834. These findings highlight significant shifts in the viral diversity, taxonomic distribution, and functional composition of the gut virome in IBS patients, suggesting the potential role of the gut virome in IBS pathogenesis and opening new avenues for diagnostic and therapeutic strategies targeting the gut virome in IBS management.
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Affiliation(s)
- Pan Zhang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, PR China
| | - Shiyang Ma
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, PR China
| | | | - Lu Li
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, PR China
| | - Xiaoyan Guo
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, PR China
| | - Danyan Chang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, PR China
| | | | - Huan Zhang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, PR China
| | - Cui Fu
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, PR China
| | - Longbao Yang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, PR China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan, China
| | - Jiong Jiang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, PR China
| | - Ting Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, PR China
| | - Jinhai Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, PR China
| | - Haitao Shi
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, PR China
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7
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Chen CM, Yan QL, Guo RC, Tang F, Wang MH, Yi HZ, Huang CX, Liu C, Wang QY, Lan WY, Jiang Z, Yang YZ, Wang GY, Zhang AQ, Ma J, Zhang Y, You W, Ullah H, Zhang Y, Li SH, Yao XM, Sun W, Ma WK. Distinct characteristics of the gut virome in patients with osteoarthritis and gouty arthritis. J Transl Med 2024; 22:564. [PMID: 38872164 PMCID: PMC11170907 DOI: 10.1186/s12967-024-05374-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024] Open
Abstract
BACKGROUND/PURPOSE(S) The gut microbiota and its metabolites play crucial roles in pathogenesis of arthritis, highlighting gut microbiota as a promising avenue for modulating autoimmunity. However, the characterization of the gut virome in arthritis patients, including osteoarthritis (OA) and gouty arthritis (GA), requires further investigation. METHODS We employed virus-like particle (VLP)-based metagenomic sequencing to analyze gut viral community in 20 OA patients, 26 GA patients, and 31 healthy controls, encompassing a total of 77 fecal samples. RESULTS Our analysis generated 6819 vOTUs, with a considerable proportion of viral genomes differing from existing catalogs. The gut virome in OA and GA patients differed significantly from healthy controls, showing variations in diversity and viral family abundances. We identified 157 OA-associated and 94 GA-associated vOTUs, achieving high accuracy in patient-control discrimination with random forest models. OA-associated viruses were predicted to infect pro-inflammatory bacteria or bacteria associated with immunoglobulin A production, while GA-associated viruses were linked to Bacteroidaceae or Lachnospiraceae phages. Furthermore, several viral functional orthologs displayed significant differences in frequency between OA-enriched and GA-enriched vOTUs, suggesting potential functional roles of these viruses. Additionally, we trained classification models based on gut viral signatures to effectively discriminate OA or GA patients from healthy controls, yielding AUC values up to 0.97, indicating the clinical utility of the gut virome in diagnosing OA or GA. CONCLUSION Our study highlights distinctive alterations in viral diversity and taxonomy within gut virome of OA and GA patients, offering insights into arthritis etiology and potential treatment and prevention strategies.
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Affiliation(s)
- Chang-Ming Chen
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Qiu-Long Yan
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | | | - Fang Tang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Min-Hui Wang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Han-Zhi Yi
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Chun-Xia Huang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Can Liu
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Qiu-Yi Wang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Wei-Ya Lan
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Zong Jiang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Yu-Zheng Yang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Guang-Yang Wang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | | | - Jie Ma
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Yan Zhang
- Department of Traditional Chinese Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Wei You
- Department of Acupuncture and Moxibustion, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Hayan Ullah
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan, China
| | | | - Xue-Ming Yao
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China.
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Wen Sun
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China.
- Key Laboratory of Health Cultivation of the Ministry of Education, Beijing University of Chinese Medicine, Beijing, China.
| | - Wu-Kai Ma
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China.
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8
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Tang J, Baker JL. The salivary virome during childhood dental caries. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595360. [PMID: 38826395 PMCID: PMC11142174 DOI: 10.1101/2024.05.22.595360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
While many studies have examined the bacterial taxa associated with dental caries, the most common chronic infectious disease globally, little is known about the caries-associated virome. In this study, the salivary viromes of 21 children with severe caries (>2 dentin lesions) and 23 children with healthy dentition were examined. 2,485 viral metagenome-assembled genomes (vMAGs) were identified, binned, and quantified from the metagenomic assemblies. These vMAGs were mostly phage, and represented 1,547 unique species-level vOTUs, 247 of which appear to be novel. The metagenomes were also queried for all 3,835 unique species-level vOTUs of DNA viruses with a human host on NCBI Virus, however all but Human betaherpesvirus 7 were at very low abundance in the saliva. The oral viromes of the children with caries exhibited significantly different beta diversity compared to the oral virome of the children with healthy dentition; several vOTUs predicted to infect Pauljensenia and Neisseria were strongly correlated with health, and two vOTUs predicted to infect Saccharibacteria and Prevotella histicola, respectively, were correlated with caries. Co-occurrence analysis indicated that phage typically co-occurred with both their predicted hosts and with bacteria that were themselves associated with the same disease status. Overall, this study provided the sequences of 53 complete or nearly complete novel oral phages and illustrated the significance of the oral virome in the context of dental caries, which has been largely overlooked. This work represents an important step towards the identification and study of phage therapy candidates which treat or prevent caries pathogenesis.
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Affiliation(s)
- Jonah Tang
- Department of Oral Rehabilitation & Biosciences, OHSU School of Dentistry, Portland, OR, USA
| | - Jonathon L Baker
- Department of Oral Rehabilitation & Biosciences, OHSU School of Dentistry, Portland, OR, USA
- Genomic Medicine Group, J. Craig Venter Institute, La Jolla, CA, USA
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9
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Conde‐Pérez K, Buetas E, Aja‐Macaya P, Martin‐De Arribas E, Iglesias‐Corrás I, Trigo‐Tasende N, Nasser‐Ali M, Estévez LS, Rumbo‐Feal S, Otero‐Alén B, Noguera JF, Concha Á, Pardiñas‐López S, Carda‐Diéguez M, Gómez‐Randulfe I, Martínez‐Lago N, Ladra S, Aparicio LA, Bou G, Mira A, Vallejo JA, Poza M. Parvimonas micra can translocate from the subgingival sulcus of the human oral cavity to colorectal adenocarcinoma. Mol Oncol 2024; 18:1143-1173. [PMID: 37558206 PMCID: PMC11076991 DOI: 10.1002/1878-0261.13506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/01/2023] [Accepted: 08/08/2023] [Indexed: 08/11/2023] Open
Abstract
Oral and intestinal samples from a cohort of 93 colorectal cancer (CRC) patients and 30 healthy controls (non-CRC) were collected for microbiome analysis. Saliva (28 non-CRC and 94 CRC), feces (30 non-CRC and 97 CRC), subgingival fluid (20 CRC), and tumor tissue samples (20 CRC) were used for 16S metabarcoding and/or RNA sequencing (RNAseq) approaches. A differential analysis of the abundance, performed with the ANCOM-BC package, adjusting the P-values by the Holm-Bonferroni method, revealed that Parvimonas was significantly over-represented in feces from CRC patients (P-value < 0.001) compared to healthy controls. A total of 11 Parvimonas micra isolates were obtained from the oral cavity and adenocarcinoma of CRC patients. Genome analysis identified a pair of isolates from the same patient that shared 99.2% identity, demonstrating that P. micra can translocate from the subgingival cavity to the gut. The data suggest that P. micra could migrate in a synergistic consortium with other periodontal bacteria. Metatranscriptomics confirmed that oral bacteria were more active in tumor than in non-neoplastic tissues. We suggest that P. micra could be considered as a CRC biomarker detected in non-invasive samples such as feces.
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Affiliation(s)
- Kelly Conde‐Pérez
- meiGAbiome, Microbiology Research Group, Servicio de MicrobiologíaCenter for Advanced Scientific Research (CICA), Institute of Biomedical Research (INIBIC), University Hospital of A Coruña (HUAC), University of A Coruña (UDC), CIBER of Infectious Diseases (CIBERINFEC‐ISCIII), Hospital UniversitarioSpain
| | - Elena Buetas
- Genomic and Health DepartmentFISABIO Foundation, Center for Advanced Research in Public HealthValenciaSpain
| | - Pablo Aja‐Macaya
- meiGAbiome, Microbiology Research Group, Servicio de MicrobiologíaCenter for Advanced Scientific Research (CICA), Institute of Biomedical Research (INIBIC), University Hospital of A Coruña (HUAC), University of A Coruña (UDC), CIBER of Infectious Diseases (CIBERINFEC‐ISCIII), Hospital UniversitarioSpain
| | - Elsa Martin‐De Arribas
- Database LaboratoryResearch Center for Information and Communication Technologies (CITIC), University of A Coruña (UDC), Campus de ElviñaSpain
| | - Iago Iglesias‐Corrás
- Database LaboratoryResearch Center for Information and Communication Technologies (CITIC), University of A Coruña (UDC), Campus de ElviñaSpain
| | - Noelia Trigo‐Tasende
- meiGAbiome, Microbiology Research Group, Servicio de MicrobiologíaCenter for Advanced Scientific Research (CICA), Institute of Biomedical Research (INIBIC), University Hospital of A Coruña (HUAC), University of A Coruña (UDC), CIBER of Infectious Diseases (CIBERINFEC‐ISCIII), Hospital UniversitarioSpain
| | - Mohammed Nasser‐Ali
- meiGAbiome, Microbiology Research Group, Servicio de MicrobiologíaCenter for Advanced Scientific Research (CICA), Institute of Biomedical Research (INIBIC), University Hospital of A Coruña (HUAC), University of A Coruña (UDC), CIBER of Infectious Diseases (CIBERINFEC‐ISCIII), Hospital UniversitarioSpain
| | - Lara S. Estévez
- Pathological Anatomy Service and BiobankUniversity Hospital of A Coruña (HUAC), Institute of Biomedical Research (INIBIC), Hospital UniversitarioSpain
| | - Soraya Rumbo‐Feal
- meiGAbiome, Microbiology Research Group, Servicio de MicrobiologíaCenter for Advanced Scientific Research (CICA), Institute of Biomedical Research (INIBIC), University Hospital of A Coruña (HUAC), University of A Coruña (UDC), CIBER of Infectious Diseases (CIBERINFEC‐ISCIII), Hospital UniversitarioSpain
| | - Begoña Otero‐Alén
- Pathological Anatomy Service and BiobankUniversity Hospital of A Coruña (HUAC), Institute of Biomedical Research (INIBIC), Hospital UniversitarioSpain
| | - Jose F. Noguera
- General and Digestive Surgery ServiceUniversity Hospital of A Coruña (HUAC), Hospital UniversitarioSpain
| | - Ángel Concha
- Pathological Anatomy Service and BiobankUniversity Hospital of A Coruña (HUAC), Institute of Biomedical Research (INIBIC), Hospital UniversitarioSpain
| | - Simón Pardiñas‐López
- Periodontology and Oral SurgeryPardiñas Medical Dental Clinic, Cell Therapy and Regenerative Medicine Group, Institute of Biomedical Research (INIBIC)A CoruñaSpain
| | - Miguel Carda‐Diéguez
- Genomic and Health DepartmentFISABIO Foundation, Center for Advanced Research in Public HealthValenciaSpain
| | - Igor Gómez‐Randulfe
- Medical Oncology DepartmentUniversity Hospital of A Coruña (HUAC), Maternal and Child HospitalSpain
| | - Nieves Martínez‐Lago
- Medical Oncology DepartmentUniversity Hospital of A Coruña (HUAC), Maternal and Child HospitalSpain
| | - Susana Ladra
- Database LaboratoryResearch Center for Information and Communication Technologies (CITIC), University of A Coruña (UDC), Campus de ElviñaSpain
| | - Luis A. Aparicio
- Medical Oncology DepartmentUniversity Hospital of A Coruña (HUAC), Maternal and Child HospitalSpain
| | - Germán Bou
- meiGAbiome, Microbiology Research Group, Servicio de MicrobiologíaCenter for Advanced Scientific Research (CICA), Institute of Biomedical Research (INIBIC), University Hospital of A Coruña (HUAC), University of A Coruña (UDC), CIBER of Infectious Diseases (CIBERINFEC‐ISCIII), Hospital UniversitarioSpain
| | - Alex Mira
- Genomic and Health DepartmentFISABIO Foundation, Center for Advanced Research in Public HealthValenciaSpain
| | - Juan A. Vallejo
- meiGAbiome, Microbiology Research Group, Servicio de MicrobiologíaCenter for Advanced Scientific Research (CICA), Institute of Biomedical Research (INIBIC), University Hospital of A Coruña (HUAC), University of A Coruña (UDC), CIBER of Infectious Diseases (CIBERINFEC‐ISCIII), Hospital UniversitarioSpain
| | - Margarita Poza
- meiGAbiome, Microbiology Research Group, Servicio de MicrobiologíaCenter for Advanced Scientific Research (CICA), Institute of Biomedical Research (INIBIC), University Hospital of A Coruña (HUAC), University of A Coruña (UDC), CIBER of Infectious Diseases (CIBERINFEC‐ISCIII), Hospital UniversitarioSpain
- Microbiome and Health Group, Faculty of SciencesUniversity of A Coruña (UDC), Campus da ZapateiraSpain
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10
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Lv LJ, Wen JY, Zhang Y, Guo RC, Li H, Yi ZT, He TW, Chen MC, Chen Y, Wu XY, Li SH, Kang J, Hou YP, Yan QL, Yin AH. Deep metagenomic characterization of the gut virome in pregnant women with preeclampsia. mSphere 2024; 9:e0067623. [PMID: 38506520 PMCID: PMC11036803 DOI: 10.1128/msphere.00676-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 12/21/2023] [Indexed: 03/21/2024] Open
Abstract
Preeclampsia (PE), a pregnancy-specific syndrome, has been associated with the gut bacteriome. Here, to investigate the impact of the gut virome on the development of PE, we identified over 8,000 nonredundant viruses from the fecal metagenomes of 40 early-onset PE and 37 healthy pregnant women and profiled their abundances. Comparison and correlation analysis showed that PE-enriched viruses frequently connected to Blautia species enriched in PE. By contrast, bacteria linked to PE-depleted viruses were often the Bacteroidaceae members such as Bacteroides spp., Phocaeicola spp., Parabacteroides spp., and Alistipes shahii. In terms of viral function, PE-depleted viruses had auxiliary metabolic genes that participated in the metabolism of simple and complex polysaccharides, sulfur metabolism, lipopolysaccharide biosynthesis, and peptidoglycan biosynthesis, while PE-enriched viruses had a gene encoding cyclic pyranopterin monophosphate synthase, which seemed to be special, that participates in the biosynthesis of the molybdenum cofactor. Furthermore, the classification model based on gut viral signatures was developed to discriminate PE patients from healthy controls and showed an area under the receiver operating characteristic curve of 0.922 that was better than that of the bacterium-based model. This study opens up new avenues for further research, providing valuable insights into the PE gut virome and offering potential directions for future mechanistic and therapeutic investigations, with the ultimate goal of improving the diagnosis and management of PE.IMPORTANCEThe importance of this study lies in its exploration of the previously overlooked but potentially critical role of the gut virome in preeclampsia (PE). While the association between PE and the gut bacteriome has been recognized, this research takes a pioneering step into understanding how the gut virome, represented by over 8,000 nonredundant viruses, contributes to this condition. The findings reveal intriguing connections between PE-enriched viruses and specific gut bacteria, such as the prevalence of Blautia species in individuals with PE, contrasting with bacteria linked to PE-depleted viruses, including members of the Bacteroidaceae family. These viral interactions and associations provide a deeper understanding of the complex dynamics at play in PE.
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Affiliation(s)
- Li-Juan Lv
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Ji-Ying Wen
- Department of Obstetrics, Guangdong Women and Children Hospital, Guangzhou, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan, China
| | | | - Hui Li
- Department of Obstetrics, Guangdong Women and Children Hospital, Guangzhou, China
| | - Zhou-Ting Yi
- Department of Obstetrics, Guangdong Women and Children Hospital, Guangzhou, China
| | - Tian-Wen He
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Min-Chai Chen
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Yang Chen
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Xiao-Yan Wu
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | | | - Jian Kang
- Department of Microbiology, College of Basic Medical Science, Dalian Medical University, Dalian, China
| | - Ya-Ping Hou
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Qiu-long Yan
- Department of Microbiology, College of Basic Medical Science, Dalian Medical University, Dalian, China
| | - Ai-Hua Yin
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
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11
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Banar M, Rokaya D, Azizian R, Khurshid Z, Banakar M. Oral bacteriophages: metagenomic clues to interpret microbiomes. PeerJ 2024; 12:e16947. [PMID: 38406289 PMCID: PMC10885796 DOI: 10.7717/peerj.16947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/24/2024] [Indexed: 02/27/2024] Open
Abstract
Bacteriophages are bacterial viruses that are distributed throughout the environment. Lytic phages and prophages in saliva, oral mucosa, and dental plaque interact with the oral microbiota and can change biofilm formation. The interactions between phages and bacteria can be considered a portion of oral metagenomics. The metagenomic profile of the oral microbiome indicates various bacteria. Indeed, there are various phages against these bacteria in the oral cavity. However, some other phages, like phages against Absconditabacteria, Chlamydiae, or Chloroflexi, have not been identified in the oral cavity. This review gives an overview of oral bacteriophage and used for metagenomics. Metagenomics of these phages deals with multi-drug-resistant bacterial plaques (biofilms) in oral cavities and oral infection. Hence, dentists and pharmacologists should know this metagenomic profile to cope with predental and dental infectious diseases.
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Affiliation(s)
- Maryam Banar
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Dinesh Rokaya
- Department of Basic Medical and Dental Sciences, Faculty of Dentistry, Zarqa University, Zarqa, Jordan
| | - Reza Azizian
- Biomedical Innovation and Start-up student association (Biomino), Tehran University of Medical Sciences, Tehran, Iran
- Pediatric Infectious Diseases Research Center (PIDRC), Tehran University of Medical Sciences, Tehran, Iran
| | - Zohaib Khurshid
- Department of Prosthodontics and Implantology, College of Dentistry, King Faisal University, Al-Hofuf, Al Ahsa, Saudi Arabia
- Center of Excellence for Regenerative Dentistry, Department of Anatomy, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Morteza Banakar
- Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran
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12
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Kienbeck K, Malfertheiner L, Zelger-Paulus S, Johannsen S, von Mering C, Sigel RKO. Identification of HDV-like theta ribozymes involved in tRNA-based recoding of gut bacteriophages. Nat Commun 2024; 15:1559. [PMID: 38378708 PMCID: PMC10879173 DOI: 10.1038/s41467-024-45653-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 01/29/2024] [Indexed: 02/22/2024] Open
Abstract
Trillions of microorganisms, collectively known as the microbiome, inhabit our bodies with the gut microbiome being of particular interest in biomedical research. Bacteriophages, the dominant virome constituents, can utilize suppressor tRNAs to switch to alternative genetic codes (e.g., the UAG stop-codon is reassigned to glutamine) while infecting hosts with the standard bacterial code. However, what triggers this switch and how the bacteriophage manipulates its host is poorly understood. Here, we report the discovery of a subgroup of minimal hepatitis delta virus (HDV)-like ribozymes - theta ribozymes - potentially involved in the code switch leading to the expression of recoded lysis and structural phage genes. We demonstrate their HDV-like self-scission behavior in vitro and find them in an unreported context often located with their cleavage site adjacent to tRNAs, indicating a role in viral tRNA maturation and/or regulation. Every fifth associated tRNA is a suppressor tRNA, further strengthening our hypothesis. The vast abundance of tRNA-associated theta ribozymes - we provide 1753 unique examples - highlights the importance of small ribozymes as an alternative to large enzymes that usually process tRNA 3'-ends. Our discovery expands the short list of biological functions of small HDV-like ribozymes and introduces a previously unknown player likely involved in the code switch of certain recoded gut bacteriophages.
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Affiliation(s)
- Kasimir Kienbeck
- Department of Chemistry, University of Zurich, Zurich, CH-8057, Switzerland
| | - Lukas Malfertheiner
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, CH-8057, Switzerland
| | | | - Silke Johannsen
- Department of Chemistry, University of Zurich, Zurich, CH-8057, Switzerland
| | - Christian von Mering
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, CH-8057, Switzerland.
| | - Roland K O Sigel
- Department of Chemistry, University of Zurich, Zurich, CH-8057, Switzerland.
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13
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Baker JL, Mark Welch JL, Kauffman KM, McLean JS, He X. The oral microbiome: diversity, biogeography and human health. Nat Rev Microbiol 2024; 22:89-104. [PMID: 37700024 PMCID: PMC11084736 DOI: 10.1038/s41579-023-00963-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2023] [Indexed: 09/14/2023]
Abstract
The human oral microbiota is highly diverse and has a complex ecology, comprising bacteria, microeukaryotes, archaea and viruses. These communities have elaborate and highly structured biogeography that shapes metabolic exchange on a local scale and results from the diverse microenvironments present in the oral cavity. The oral microbiota also interfaces with the immune system of the human host and has an important role in not only the health of the oral cavity but also systemic health. In this Review, we highlight recent advances including novel insights into the biogeography of several oral niches at the species level, as well as the ecological role of candidate phyla radiation bacteria and non-bacterial members of the oral microbiome. In addition, we summarize the relationship between the oral microbiota and the pathology of oral diseases and systemic diseases. Together, these advances move the field towards a more holistic understanding of the oral microbiota and its role in health, which in turn opens the door to the study of novel preventive and therapeutic strategies.
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Affiliation(s)
- Jonathon L Baker
- Oregon Health & Science University, Portland, OR, USA
- J. Craig Venter Institute, La Jolla, CA, USA
- UC San Diego School of Medicine, La Jolla, CA, USA
| | - Jessica L Mark Welch
- The Forsyth Institute, Cambridge, MA, USA
- Marine Biological Laboratory, Woods Hole, MA, USA
| | | | | | - Xuesong He
- The Forsyth Institute, Cambridge, MA, USA.
- Harvard School of Dental Medicine, Boston, MA, USA.
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14
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Rozwalak P, Barylski J, Wijesekara Y, Dutilh BE, Zielezinski A. Ultraconserved bacteriophage genome sequence identified in 1300-year-old human palaeofaeces. Nat Commun 2024; 15:495. [PMID: 38263397 PMCID: PMC10805732 DOI: 10.1038/s41467-023-44370-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 12/11/2023] [Indexed: 01/25/2024] Open
Abstract
Bacteriophages are widely recognised as rapidly evolving biological entities. However, knowledge about ancient bacteriophages is limited. Here, we analyse DNA sequence datasets previously generated from ancient palaeofaeces and human gut-content samples, and identify an ancient phage genome nearly identical to present-day Mushuvirus mushu, a virus that infects gut commensal bacteria. The DNA damage patterns of the genome are consistent with its ancient origin and, despite 1300 years of evolution, the ancient Mushuvirus genome shares 97.7% nucleotide identity with its modern counterpart, indicating a long-term relationship between the prophage and its host. In addition, we reconstruct and authenticate 297 other phage genomes from the last 5300 years, including those belonging to unknown families. Our findings demonstrate the feasibility of reconstructing ancient phage genome sequences, thus expanding the known virosphere and offering insights into phage-bacteria interactions spanning several millennia.
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Affiliation(s)
- Piotr Rozwalak
- Department of Computational Biology, Faculty of Biology, Adam Mickiewicz University, Poznan, 61-614, Poland
| | - Jakub Barylski
- Department of Molecular Virology, Faculty of Biology, Adam Mickiewicz University, Poznan, 61-614, Poland
| | - Yasas Wijesekara
- Institute of Bioinformatics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475, Greifswald, Germany
| | - Bas E Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743, Jena, Germany.
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands.
| | - Andrzej Zielezinski
- Department of Computational Biology, Faculty of Biology, Adam Mickiewicz University, Poznan, 61-614, Poland.
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15
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Liu J, Jaffe AL, Chen L, Bor B, Banfield JF. Host translation machinery is not a barrier to phages that interact with both CPR and non-CPR bacteria. mBio 2023; 14:e0176623. [PMID: 38009957 PMCID: PMC10746230 DOI: 10.1128/mbio.01766-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/12/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE Here, we profiled putative phages of Saccharibacteria, which are of particular importance as Saccharibacteria influence some human oral diseases. We additionally profiled putative phages of Gracilibacteria and Absconditabacteria, two Candidate Phyla Radiation (CPR) lineages of interest given their use of an alternative genetic code. Among the phages identified in this study, some are targeted by spacers from both CPR and non-CPR bacteria and others by both bacteria that use the standard genetic code as well as bacteria that use an alternative genetic code. These findings represent new insights into possible phage replication strategies and have relevance for phage therapies that seek to manipulate microbiomes containing CPR bacteria.
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Affiliation(s)
- Jett Liu
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Department of Microbiology, Forsyth Institute, Cambridge, Massachusetts, USA
| | - Alexander L. Jaffe
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Department of Earth System Science, Stanford University, Stanford, California, USA
| | - LinXing Chen
- Innovative Genomics Institute, University of California, Berkeley, California, USA
- Department of Earth and Planetary Science, University of California, Berkeley, California, USA
| | - Batbileg Bor
- Department of Microbiology, Forsyth Institute, Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Jillian F. Banfield
- Innovative Genomics Institute, University of California, Berkeley, California, USA
- Department of Earth and Planetary Science, University of California, Berkeley, California, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
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16
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Chen C, Zhang Y, Yao X, Yan Q, Li S, Zhong Q, Liu Z, Tang F, Liu C, Li H, Zhu D, Lan W, Ling Y, Lu D, Xu H, Ning Q, Wang Y, Jiang Z, Zhang Q, Gu G, Sun L, Wang N, Wang G, Zhang A, Ullah H, Sun W, Ma W. Characterizations of the multi-kingdom gut microbiota in Chinese patients with gouty arthritis. BMC Microbiol 2023; 23:363. [PMID: 38001408 PMCID: PMC10668524 DOI: 10.1186/s12866-023-03097-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
OBJECTIVE The gut microbial composition has been linked to metabolic and autoimmune diseases, including arthritis. However, there is a dearth of knowledge on the gut bacteriome, mycobiome, and virome in patients with gouty arthritis (GA). METHODS We conducted a comprehensive analysis of the multi-kingdom gut microbiome of 26 GA patients and 28 healthy controls, using whole-metagenome shotgun sequencing of their stool samples. RESULTS Profound alterations were observed in the gut bacteriome, mycobiome, and virome of GA patients. We identified 1,117 differentially abundant bacterial species, 23 fungal species, and 4,115 viral operational taxonomic units (vOTUs). GA-enriched bacteria included Escherichia coli_D GENOME144544, Bifidobacterium infantis GENOME095938, Blautia_A wexlerae GENOME096067, and Klebsiella pneumoniae GENOME147598, while control-enriched bacteria comprised Faecalibacterium prausnitzii_G GENOME147678, Agathobacter rectalis GENOME143712, and Bacteroides_A plebeius_A GENOME239725. GA-enriched fungi included opportunistic pathogens like Cryptococcus neoformans GCA_011057565, Candida parapsilosis GCA_000182765, and Malassezia spp., while control-enriched fungi featured several Hortaea werneckii subclades and Aspergillus fumigatus GCA_000002655. GA-enriched vOTUs mainly attributed to Siphoviridae, Myoviridae, Podoviridae, and Microviridae, whereas control-enriched vOTUs spanned 13 families, including Siphoviridae, Myoviridae, Podoviridae, Quimbyviridae, Phycodnaviridae, and crAss-like. A co-abundance network revealed intricate interactions among these multi-kingdom signatures, signifying their collective influence on the disease. Furthermore, these microbial signatures demonstrated the potential to effectively discriminate between patients and controls, highlighting their diagnostic utility. CONCLUSIONS This study yields crucial insights into the characteristics of the GA microbiota that may inform future mechanistic and therapeutic investigations.
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Affiliation(s)
- Changming Chen
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan, China
| | - Xueming Yao
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Qiulong Yan
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | | | - Qin Zhong
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Zhengqi Liu
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Fang Tang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Can Liu
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Hufan Li
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Dan Zhu
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Weiya Lan
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Yi Ling
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Daomin Lu
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Hui Xu
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Qiaoyi Ning
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Ying Wang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Zong Jiang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Qiongyu Zhang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Guangzhao Gu
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Liping Sun
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Nan Wang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Guangyang Wang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | | | - Hayan Ullah
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Wen Sun
- Key Laboratory of Health Cultivation of the Ministry of Education, Beijing University of Chinese Medicine, Beijing, China.
| | - Wukai Ma
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China.
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17
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Zuber P, Kreth J. Aspects of oral streptococcal metabolic diversity: Imagining the landscape beneath the fog. Mol Microbiol 2023; 120:508-524. [PMID: 37329112 DOI: 10.1111/mmi.15106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 06/18/2023]
Abstract
It is widely acknowledged that the human-associated microbial community influences host physiology, systemic health, disease progression, and even behavior. There is currently an increased interest in the oral microbiome, which occupies the entryway to much of what the human initially encounters from the environment. In addition to the dental pathology that results from a dysbiotic microbiome, microbial activity within the oral cavity exerts significant systemic effects. The composition and activity of the oral microbiome is influenced by (1) host-microbial interactions, (2) the emergence of niche-specific microbial "ecotypes," and (3) numerous microbe-microbe interactions, shaping the underlying microbial metabolic landscape. The oral streptococci are central players in the microbial activity ongoing in the oral cavity, due to their abundance and prevalence in the oral environment and the many interspecies interactions in which they participate. Streptococci are major determinants of a healthy homeostatic oral environment. The metabolic activities of oral Streptococci, particularly the metabolism involved in energy generation and regeneration of oxidative resources vary among the species and are important factors in niche-specific adaptations and intra-microbiome interactions. Here we summarize key differences among streptococcal central metabolic networks and species-specific differences in how the key glycolytic intermediates are utilized.
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Affiliation(s)
- Peter Zuber
- Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, Oregon, USA
| | - Jens Kreth
- School of Dentistry, Oregon Health & Science University, Portland, Oregon, USA
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18
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Paietta EN, Kraberger S, Custer JM, Vargas KL, Espy C, Ehmke E, Yoder AD, Varsani A. Characterization of Diverse Anelloviruses, Cressdnaviruses, and Bacteriophages in the Human Oral DNA Virome from North Carolina (USA). Viruses 2023; 15:1821. [PMID: 37766228 PMCID: PMC10537320 DOI: 10.3390/v15091821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
The diversity of viruses identified from the various niches of the human oral cavity-from saliva to dental plaques to the surface of the tongue-has accelerated in the age of metagenomics. This rapid expansion demonstrates that our understanding of oral viral diversity is incomplete, with only a few studies utilizing passive drool collection in conjunction with metagenomic sequencing methods. For this pilot study, we obtained 14 samples from healthy staff members working at the Duke Lemur Center (Durham, NC, USA) to determine the viral diversity that can be identified in passive drool samples from humans. The complete genomes of 3 anelloviruses, 9 cressdnaviruses, 4 Caudoviricetes large bacteriophages, 29 microviruses, and 19 inoviruses were identified in this study using high-throughput sequencing and viral metagenomic workflows. The results presented here expand our understanding of the vertebrate-infecting and microbe-infecting viral diversity of the human oral virome in North Carolina (USA).
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Affiliation(s)
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Joy M. Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Karla L. Vargas
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Claudia Espy
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Erin Ehmke
- Duke Lemur Center, Duke University, Durham, NC 27705, USA;
| | - Anne D. Yoder
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7925, South Africa
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19
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Ettinger CL, Saunders M, Selbmann L, Delgado-Baquerizo M, Donati C, Albanese D, Roux S, Tringe S, Pennacchio C, Del Rio TG, Stajich JE, Coleine C. Highly diverse and unknown viruses may enhance Antarctic endoliths' adaptability. MICROBIOME 2023; 11:103. [PMID: 37158954 PMCID: PMC10165816 DOI: 10.1186/s40168-023-01554-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/19/2023] [Indexed: 05/10/2023]
Abstract
BACKGROUND Rock-dwelling microorganisms are key players in ecosystem functioning of Antarctic ice free-areas. Yet, little is known about their diversity and ecology, and further still, viruses in these communities have been largely unexplored despite important roles related to host metabolism and nutrient cycling. To begin to address this, we present a large-scale viral catalog from Antarctic rock microbial communities. RESULTS We performed metagenomic analyses on rocks from across Antarctica representing a broad range of environmental and spatial conditions, and which resulted in a predicted viral catalog comprising > 75,000 viral operational taxonomic units (vOTUS). We found largely undescribed, highly diverse and spatially structured virus communities which had predicted auxiliary metabolic genes (AMGs) with functions indicating that they may be potentially influencing bacterial adaptation and biogeochemistry. CONCLUSION This catalog lays the foundation for expanding knowledge of virosphere diversity, function, spatial ecology, and dynamics in extreme environments. This work serves as a step towards exploring adaptability of microbial communities in the face of a changing climate. Video Abstract.
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Affiliation(s)
- Cassandra L Ettinger
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA.
| | - Morgan Saunders
- Department of Biological Sciences, California State Polytechnic University, Pomona, CA, USA
- The University of Arizona, Tucson, AZ, USA
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad Y Funcionamiento Ecosistémico, Instituto de Recursos Naturales Y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, Seville, E-41012, Spain
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, Seville, 41013, Spain
| | - Claudio Donati
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele All'Adige, 38098, Italy
| | - Davide Albanese
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele All'Adige, 38098, Italy
| | - Simon Roux
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA
| | - Susannah Tringe
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA
| | - Christa Pennacchio
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA
| | - Tijana G Del Rio
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA
- Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Claudia Coleine
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA.
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy.
- Laboratorio de Biodiversidad Y Funcionamiento Ecosistémico, Instituto de Recursos Naturales Y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, Seville, E-41012, Spain.
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20
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Li C, Zhang Y, Yan Q, Guo R, Chen C, Li S, Zhang Y, Meng J, Ma J, You W, Wu Z, Sun W. Alterations in the gut virome in patients with ankylosing spondylitis. Front Immunol 2023; 14:1154380. [PMID: 37063855 PMCID: PMC10098016 DOI: 10.3389/fimmu.2023.1154380] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/20/2023] [Indexed: 04/03/2023] Open
Abstract
IntroductionAnkylosing spondylitis (AS), a chronic autoimmune disease, has been linked to the gut bacteriome.MethodsTo investigate the characteristics of the gut virome in AS, we profiled the gut viral community of 193 AS patients and 59 healthy subjects based on a metagenome-wide analysis of fecal metagenomes from two publicly available datasets.ResultsAS patients revealed a significant decrease in gut viral richness and a considerable alteration of the overall viral structure. At the family level, AS patients had an increased abundance of Gratiaviridae and Quimbyviridae and a decreased abundance of Drexlerviridae and Schitoviridae. We identified 1,004 differentially abundant viral operational taxonomic units (vOTUs) between patients and controls, including a higher proportion of AS-enriched Myoviridae viruses and control-enriched Siphoviridae viruses. Moreover, the AS-enriched vOTUs were more likely to infect bacteria such as Flavonifractor, Achromobacter, and Eggerthellaceae, whereas the control-enriched vOTUs were more likely to be Blautia, Ruminococcus, Collinsella, Prevotella, and Faecalibacterium bacteriophages. Additionally, some viral functional orthologs differed significantly in frequency between the AS-enriched and control-enriched vOTUs, suggesting the functional role of these AS-associated viruses. Moreover, we trained classification models based on gut viral signatures to discriminate AS patients from healthy controls, with an optimal area under the receiver operator characteristic curve (AUC) up to 0.936, suggesting the clinical potential of the gut virome for diagnosing AS.DiscussionThis work provides novel insight into the AS gut virome, and the findings may guide future mechanistic and therapeutic studies for other autoimmune diseases.
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Affiliation(s)
- Chen Li
- Department of Rheumatology, Fangshan Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Yan Zhang
- Department of Traditional Chinese Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Qiulong Yan
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | | | - Changming Chen
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | | | - Yue Zhang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | | | - Jie Ma
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Wei You
- Beijing Key Laboratory of Acupuncture Neuromodulation, Department of Acupuncture and Moxibustion, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Zhisong Wu
- Department of Intensive Care Medicine, Dongfang Hospital Beijing University of Chinese Medicine, Beijing, China
| | - Wen Sun
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
- Key Laboratory of Health Cultivation of the Ministry of Education, Beijing University of Chinese Medicine, Beijing, China
- Beijing Key Laboratory of Health Cultivation, Beijing University of Chinese Medicine, Beijing, China
- *Correspondence: Wen Sun,
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21
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Huang L, Wu X, Guo S, Lv Y, Zhou P, Huang G, Duan Z, Sun W. Metagenomic-based characterization of the gut virome in patients with polycystic ovary syndrome. Front Microbiol 2022; 13:951782. [PMID: 36051758 PMCID: PMC9424824 DOI: 10.3389/fmicb.2022.951782] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/27/2022] [Indexed: 11/18/2022] Open
Abstract
Background Polycystic ovary syndrome (PCOS) is a complex disease that afflicts women of reproductive age, and its pathological mechanism has not been well explained. The gut microbiota is believed to be closely related to the development of PCOS. Although an important component of the gut microbiome, the role of the gut virome in the development of PCOS is still unclear. Methods In this study, we profiled and compared the gut viral community of 50 patients with PCOS and 43 healthy women based on the analysis of their fecal whole-metagenome dataset. Results The gut virome of PCOS patients exhibited a significant decrease in within-sample viral diversity and a remarkable alteration of the overall virome composition compared with that of healthy controls. At the family level, Siphoviridae was significantly depleted in the gut virome of patients, while Quimbyviridae was enriched. We identified 1,089 viral operational taxonomic units (vOTUs) that differed in relative abundance between the two groups, of which 455 vOTUs were enriched in PCOS patients (including numerous Bacteroidaceae phages) and 634 were enriched in controls (including numerous viruses predicted to infect Oscillospiraceae, Prevotellaceae, and Ruminococcaceae). Functional comparison of the PCOS-enriched and control-enriched vOTUs uncovered the viral functional signatures associated with PCOS. Furthermore, we demonstrated gut viral signatures for disease discrimination and achieved an area under the receiver operator characteristic curve (AUC) of 0.938, demonstrating the potential of the gut virome in the prediction of PCOS. Conclusion Our findings reveal specific alterations in viral diversity and taxonomic and functional compositions of the gut virome of PCOS patients. Further studies on the etiology of PCOS and the gut viral community will offer new prospects for treating and preventing PCOS and its related diseases.
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Affiliation(s)
- Liansha Huang
- Department of Reproductive Health, Shenzhen Bao'an Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Xiaoling Wu
- Department of Reproductive Health, Shenzhen Bao'an Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Shumin Guo
- Department of Reproductive Health, Shenzhen Bao'an Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Ying Lv
- Department of Reproductive Health, Shenzhen Bao'an Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Peng Zhou
- Department of Acupuncture, Shenzhen Bao'an Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Guangrong Huang
- Department of Gynecology, Shenzhen Bao'an Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Zuzhen Duan
- Department of Gynecology, Shenzhen Bao'an Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Wen Sun
- Key Laboratory of Health Cultivation of the Ministry of Education, Beijing University of Chinese Medicine, Beijing, China
- Beijing key Laboratory of Health Cultivation, Beijing University of Chinese Medicine, Beijing, China
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
- *Correspondence: Wen Sun,
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