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Zeng C, Wan SR, Guo M, Tan XZ, Zeng Y, Wu Q, Xie JJ, Yan P, Long Y, Zheng L, Jiang ZZ, Teng FY, Xu Y. Fecal virome transplantation: A promising strategy for the treatment of metabolic diseases. Biomed Pharmacother 2024; 177:117065. [PMID: 38971010 DOI: 10.1016/j.biopha.2024.117065] [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: 04/06/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 07/08/2024] Open
Abstract
Metabolic diseases are a group of disorders caused by metabolic abnormalities, including obesity, diabetes, non-alcoholic fatty liver disease, and more. Increasing research indicates that, beyond inherent metabolic irregularities, the onset and progression of metabolic diseases are closely linked to alterations in the gut microbiota, particularly gut bacteria. Additionally, fecal microbiota transplantation (FMT) has demonstrated effectiveness in clinically treating metabolic diseases, notably diabetes. Recent attention has also focused on the role of gut viruses in disease onset. This review first introduces the characteristics and influencing factors of gut viruses, then summarizes their potential mechanisms in disease development, highlighting their impact on gut bacteria and regulation of host immunity. We also compare FMT, fecal filtrate transplantation (FFT), washed microbiota transplantation (WMT), and fecal virome transplantation (FVT). Finally, we review the current understanding of gut viruses in metabolic diseases and the application of FVT in treating these conditions. In conclusion, FVT may provide a novel and promising treatment approach for metabolic diseases, warranting further validation through basic and clinical research.
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Affiliation(s)
- Chen Zeng
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Sheng-Rong Wan
- Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Man Guo
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Xiao-Zhen Tan
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Yan Zeng
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Macao 999078, China
| | - Qi Wu
- Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Macao 999078, China; Department of Pathology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Jia-Jie Xie
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Pijun Yan
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Department of Pathology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Institute of Cardiovascular Research, Peking University, Beijing 100871, China
| | - Yang Long
- Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Lemin Zheng
- Institute of Cardiovascular Research, Peking University, Beijing 100871, China
| | - Zong-Zhe Jiang
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Fang-Yuan Teng
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China.
| | - Yong Xu
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China.
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2
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Hu F, Li X, Liu K, Li Y, Xie Y, Wei C, Liu S, Song J, Wang P, Shi L, Li C, Li J, Xu L, Xue J, Zheng X, Bai M, Fang X, Jin X, Cao L, Hao P, He J, Wang J, Zhang C, Li Z. Rheumatoid arthritis patients harbour aberrant enteric bacteriophages with autoimmunity-provoking potential: a paired sibling study. Ann Rheum Dis 2024:ard-2024-225564. [PMID: 39084885 DOI: 10.1136/ard-2024-225564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 07/15/2024] [Indexed: 08/02/2024]
Abstract
OBJECTIVES Viruses have been considered as important participants in the development of rheumatoid arthritis (RA). However, the profile of enteric virome and its role in RA remains elusive. This study aimed to investigate the atlas and involvement of virome in RA pathogenesis. METHODS Faecal samples from 30 pairs of RA and healthy siblings that minimise genetic interferences were collected for metagenomic sequencing. The α and β diversity of the virome and the virome-bacteriome interaction were analysed. The differential bacteriophages were identified, and their correlations with clinical and immunological features of RA were analysed. The potential involvement of these differential bacteriophages in RA pathogenesis was further investigated by auxiliary metabolic gene annotation and molecular mimicry study. The responses of CD4+ T cells and B cells to the mimotopes derived from the differential bacteriophages were systemically studied. RESULTS The composition of the enteric bacteriophageome was distorted in RA. The differentially presented bacteriophages correlated with the immunological features of RA, including anti-CCP autoantibody and HLA-DR shared epitope. Intriguingly, the glycerolipid and purine metabolic genes were highly active in the bacteriophages from RA. Moreover, peptides of RA-enriched phages, in particular Prevotella phage and Oscillibacter phage could provoke the autoimmune responses in CD4+ T cells and plasma cells via molecular mimicry of the disease-associated autoantigen epitopes, especially those of Bip. CONCLUSIONS This study provides new insights into enteric bacteriophageome in RA development. In particular, the aberrant bacteriophages demonstrated autoimmunity-provoking potential that would promote the occurrence of the disease.
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Affiliation(s)
- Fanlei Hu
- Department of Rheumatology and Immunology, Peking University People's Hospital & Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, China
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
- Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Xin Li
- Department of Rheumatology and Immunology, Peking University People's Hospital & Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Kai Liu
- Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, University of Chinese Academy of Sciences, shanghai, China
- Department of Clinical Laboratory, Qingpu Branch of Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yanpeng Li
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yang Xie
- Department of Rheumatology and Immunology, Peking University People's Hospital & Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, China
| | - Chaonan Wei
- Department of Rheumatology and Immunology, Peking University People's Hospital & Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, China
| | - Shuyan Liu
- Department of Rheumatology and Immunology, Peking University People's Hospital & Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, China
| | - Jing Song
- Department of Rheumatology and Immunology, Peking University People's Hospital & Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Ping Wang
- Department of Rheumatology and Immunology, Peking University People's Hospital & Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, China
| | - Lianjie Shi
- Department of Rheumatology and Immunology, Peking University Shougang Hospital, Beijing, China
| | - Chun Li
- Department of Rheumatology and Immunology, Peking University People's Hospital & Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, China
| | - Jing Li
- Department of Rheumatology and Immunology, Peking University People's Hospital & Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, China
| | - Liling Xu
- Department of Rheumatology and Immunology, Peking University People's Hospital & Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, China
| | - Jimeng Xue
- Department of Rheumatology and Immunology, Peking University People's Hospital & Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, China
| | - Xi Zheng
- Department of Rheumatology and Immunology, Peking University People's Hospital & Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Mingxin Bai
- Department of Rheumatology and Immunology, Peking University People's Hospital & Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, China
| | - Xiangyu Fang
- Department of Rheumatology and Immunology, Peking University People's Hospital & Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, China
| | - Xu Jin
- Department of Rheumatology and Immunology, Peking University People's Hospital & Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Lulu Cao
- Department of Rheumatology and Immunology, Peking University People's Hospital & Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, China
| | - Pei Hao
- Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, University of Chinese Academy of Sciences, shanghai, China
| | - Jing He
- Department of Rheumatology and Immunology, Peking University People's Hospital & Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, China
| | - Jun Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, China
| | - Chiyu Zhang
- Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, University of Chinese Academy of Sciences, shanghai, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Zhanguo Li
- Department of Rheumatology and Immunology, Peking University People's Hospital & Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, China
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
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3
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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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Gholamzad A, Khakpour N, Hashemi SMA, Goudarzi Y, Ahmadi P, Gholamzad M, Mohammadi M, Hashemi M. Exploring the virome: An integral part of human health and disease. Pathol Res Pract 2024; 260:155466. [PMID: 39053136 DOI: 10.1016/j.prp.2024.155466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/06/2024] [Accepted: 07/12/2024] [Indexed: 07/27/2024]
Abstract
The human microbiome is a complex network of microorganisms that includes viruses, bacteria, and fungi. The gut virome is an essential component of the immune system, which is responsible for regulating the growth and responses of the host's immune system. The virome maintains a crucial role in the development of numerous diseases, including inflammatory bowel disease (IBD), Crohn's disease, and neurodegenerative disorders. The human virome has emerged as a promising biomarker and therapeutic target. This comprehensive review summarizes the present understanding of the virome and its implications in matters of health and disease, with a focus on the Human Microbiome Project.
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Affiliation(s)
- Amir Gholamzad
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Niloofar Khakpour
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Mohammad Ali Hashemi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Yalda Goudarzi
- Department of Biology, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Parisa Ahmadi
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mehrdad Gholamzad
- Department of Microbiology and Immunology, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Mahya Mohammadi
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology ,Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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5
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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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6
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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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7
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Li YN, Chen T, Xue Y, Jia JY, Yan TK, Xu PC. Causal relationship between gut microbiota and Behçet's disease: a Mendelian randomization study. Front Microbiol 2024; 15:1416614. [PMID: 38933023 PMCID: PMC11201155 DOI: 10.3389/fmicb.2024.1416614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
Background While observational epidemiological studies have suggested an association between gut microbiota and Behçet's disease (BD), the causal relationship between the two remains uncertain. Methods Statistical data were obtained from gut microbiome Genome-Wide Association Studies (GWAS) published by the MiBioGen consortium, and genetic variation points were screened as instrumental variables (IV). Mendelian randomization (MR) study was performed using inverse variance weighted (IVW), weighted median, MR-Egger regression, simple mode, and weighted mode methods to evaluate the causal relationship between gut microbiota (18,340 individuals) and BD (317,252 individuals). IVW was the main method of analysis. The stability and reliability of the results were verified using the leave-one-out method, heterogeneity test, and horizontal genetic pleiotropy test. Finally, a reverse MR analysis was performed to explore reverse causality. Results Inverse variance weighted (IVW) results showed that the genus Parasutterella (OR = 0.203, 95%CI 0.055-0.747, p = 0.016), Lachnospiraceae NC2004 group (OR = 0.101, 95%CI 0.015-0.666, p = 0.017), Turicibacter (OR = 0.043, 95%CI 0.007-0.273, p = 0.001), and Erysipelatoclostridium (OR = 0.194, 95%CI 0.040-0.926, p = 0.040) were protective factors against BD, while Intestinibacter (OR = 7.589, 95%CI 1.340-42.978, p = 0.022) might be a risk factor for BD. Conclusion Our study revealed the causal relationship between gut microbiota and BD. The microbiota that related to BD may become new biomarkers; provide new potential indicators and targets for the prevention and treatment of BD.
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Affiliation(s)
- Yu-Nan Li
- Department of Nephrology, Tianjin Medical University General Hospital, Tianjin, China
| | - Tong Chen
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Yang Xue
- Department of Nephrology, Tianjin Medical University General Hospital, Tianjin, China
| | - Jun-Ya Jia
- Department of Nephrology, Tianjin Medical University General Hospital, Tianjin, China
| | - Tie-Kun Yan
- Department of Nephrology, Tianjin Medical University General Hospital, Tianjin, China
| | - Peng-Cheng Xu
- Department of Nephrology, Tianjin Medical University General Hospital, Tianjin, China
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8
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Remesh AT, Viswanathan R. CrAss-Like Phages: From Discovery in Human Fecal Metagenome to Application as a Microbial Source Tracking Marker. FOOD AND ENVIRONMENTAL VIROLOGY 2024; 16:121-135. [PMID: 38413544 DOI: 10.1007/s12560-024-09584-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 01/24/2024] [Indexed: 02/29/2024]
Abstract
CrAss-like phages are a diverse group of bacteriophages genetically similar to the prototypical crAssphage (p-crAssphage), which was discovered in the human gut microbiome through a metagenomics approach. It was identified as a ubiquitous and highly abundant bacteriophage group in the gut microbiome. Initial co-occurrence analysis postulated Bacteroides spp. as the prospective bacterial host. Subsequent studies have confirmed multiple host species under Phylum Bacteroidetes and some Firmicutes. Detection of crAss-like phages in sewage-contaminated environmental water and robust correlation with enteric viruses and bacteria has culminated in their adoption as a microbial source tracking (MST) marker. Polymerase chain reaction (PCR) and real-time PCR assays have been developed utilizing the conserved genes in the p-crAssphage genome to detect human fecal contamination of different water sources, with high specificity. Numerous investigations have examined the implications of crAss-like phages in diverse disease conditions, including ulcerative colitis, obesity and metabolic syndrome, autism spectrum disorders, rheumatoid arthritis, atopic eczema, and other autoimmune disorders. These studies have unveiled associations between certain diseases and diminished abundance and diversity of crAss-like phages. This review offers insights into the diverse aspects of research on crAss-like phages, including their discovery, genomic characteristics, structure, taxonomy, isolation, molecular detection, application as an MST marker, and role as a gut microbiome modulator with consequential health implications.
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9
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Poulsen CS, Hesse D, Fernandes GR, Hansen TH, Kern T, Linneberg A, Van Espen L, Jørgensen T, Nielsen T, Alibegovic AC, Matthijnssens J, Pedersen O, Vestergaard H, Hansen T, Andersen MK. Characterization of the gut bacterial and viral microbiota in latent autoimmune diabetes in adults. Sci Rep 2024; 14:8315. [PMID: 38594375 PMCID: PMC11003976 DOI: 10.1038/s41598-024-58985-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: 10/13/2023] [Accepted: 04/05/2024] [Indexed: 04/11/2024] Open
Abstract
Latent autoimmune diabetes in adults (LADA) is a heterogeneous disease characterized by autoantibodies against insulin producing pancreatic beta cells and initial lack of need for insulin treatment. The aim of the present study was to investigate if individuals with LADA have an altered gut microbiota relative to non-diabetic control subjects, individuals with type 1 diabetes (T1D), and individuals with type 2 diabetes (T2D). Bacterial community profiling was performed with primers targeting the variable region 4 of the 16S rRNA gene and sequenced. Amplicon sequence variants (ASVs) were generated with DADA2 and annotated to the SILVA database. The gut virome was sequenced, using a viral particle enrichment and metagenomics approach, assembled, and quantified to describe the composition of the viral community. Comparison of the bacterial alpha- and beta-diversity measures revealed that the gut bacteriome of individuals with LADA resembled that of individuals with T2D. Yet, specific genera were found to differ in abundance in individuals with LADA compared with T1D and T2D, indicating that LADA has unique taxonomical features. The virome composition reflected the stability of the most dominant order Caudovirales and the families Siphoviridae, Podoviridae, and Inoviridae, and the dominant family Microviridae. Further studies are needed to confirm these findings.
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Affiliation(s)
- Casper S Poulsen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dan Hesse
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- Novo Nordisk A/S, Soeborg, Denmark
| | - Gabriel R Fernandes
- Biosystems Informatics, Institute René Rachou-Fiocruz Minas, Belo Horizonte, Brazil
| | - Tue H Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Timo Kern
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Clinical Microbiomics A/S, Copenhagen, Denmark
| | - Allan Linneberg
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lore Van Espen
- Department of Microbiology, Immunology & Transplantation, Rega Institute, Laboratory of Clinical & Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Torben Jørgensen
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
- Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Trine Nielsen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Amra C Alibegovic
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- Novo Nordisk A/S, Soeborg, Denmark
| | - Jelle Matthijnssens
- Department of Microbiology, Immunology & Transplantation, Rega Institute, Laboratory of Clinical & Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Center for Clinical Metabolic Research, Department of Medicine, Gentofte University Hospital, Copenhagen, Denmark
| | - Henrik Vestergaard
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- Department of Medicine, Bornholms Hospital, Rønne, Denmark
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Mette K Andersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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10
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Mo C, Bi J, Li S, Lin Y, Yuan P, Liu Z, Jia B, Xu S. The influence and therapeutic effect of microbiota in systemic lupus erythematosus. Microbiol Res 2024; 281:127613. [PMID: 38232494 DOI: 10.1016/j.micres.2024.127613] [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: 09/14/2023] [Revised: 12/18/2023] [Accepted: 01/09/2024] [Indexed: 01/19/2024]
Abstract
Systemic erythematosus lupus (SLE) is an autoimmune disease involving multiple organs that poses a serious risk to the health and life of patients. A growing number of studies have shown that commensals from different parts of the body and exogenous pathogens are involved in SLE progression, causing barrier disruption and immune dysregulation through multiple mechanisms. However, they sometimes alleviate the symptoms of SLE. Many factors, such as genetic susceptibility, metabolism, impaired barriers, food, and sex hormones, are involved in SLE, and the microbiota drives the development of SLE either by depending on or interacting with these factors. Among these, the crosstalk between genetic susceptibility, metabolism, and microbiota is a hot topic of research and is expected to lay the groundwork for the amelioration of the mechanism, diagnosis, and treatment of SLE. Furthermore, the microbiota has great potential for the treatment of SLE. Ideally, personalised therapeutic approaches should be developed in combination with more specific diagnostic methods. Herein, we provide a comprehensive overview of the role and mechanism of microbiota in lupus of the intestine, oral cavity, skin, and kidney, as well as the therapeutic potential of the microbiota.
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Affiliation(s)
- Chuzi Mo
- Department of Endodontics, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, Guangdong, China
| | - Jiaming Bi
- Department of Endodontics, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, Guangdong, China
| | - Siwei Li
- Department of Endodontics, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, Guangdong, China
| | - Yunhe Lin
- Department of Endodontics, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, Guangdong, China
| | - Peiyan Yuan
- Department of Endodontics, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhongjun Liu
- Department of Endodontics, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, Guangdong, China.
| | - Bo Jia
- Department of Oral and Maxillofacial Surgery, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, Guangdong, China.
| | - Shuaimei Xu
- Department of Endodontics, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, Guangdong, China.
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11
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Wang Y, Wang Z, Lu Q. Microbiome dynamics in rheumatic diseases. Curr Opin Rheumatol 2024; 36:134-141. [PMID: 37976078 DOI: 10.1097/bor.0000000000000993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
PURPOSE OF REVIEW Rheumatic disease are characterized by their autoimmune nature, frequently affecting joints, bones, muscles, blood vessels, and connective tissues. The onset of these conditions typically unfolds gradually and subtly. It is noteworthy that individuals with rheumatic diseases often experience shifts in their microbiome, specifically on mucosal surfaces. The purpose of this review is to delve into the intricate interplay between the microbiome, encompassing bacteria, viruses and fungi, and its role in the development and aggravation of various rheumatic diseases. Additionally, it aims to offer insights into microbiome-centered therapeutic approaches for patients in the field of rheumatology. RECENT FINDINGS The advent of next-generation sequencing has significantly improved our understanding of microbiome changes. Numerous studies have consistently revealed a strong link between rheumatism and the microbiome, especially in the oral and gut microbiota. SUMMARY A deeper comprehension of the microbiome's connection to rheumatism holds potential for enhancing disease diagnosis and treatment. Targeted therapeutic approaches, including probiotics, fecal microbiota transplantation, and combination therapies with medications, offer promising avenues for disease management.
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Affiliation(s)
- Yiqing Wang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing
- Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University
| | - Zijun Wang
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Qianjin Lu
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing
- Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University
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12
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Li Y, Ma J, Meng J, Li S, Zhang Y, You W, Sai X, Yang J, Zhang S, Sun W. Structural changes in the gut virome of patients with atherosclerotic cardiovascular disease. Microbiol Spectr 2024; 12:e0105023. [PMID: 38051048 PMCID: PMC10782949 DOI: 10.1128/spectrum.01050-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 10/31/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Existing studies have found that there is a close relationship between human virome and numerous diseases, and diseases may affect the diversity and composition of the virome; at the same time, changes in the virome will in turn affect the onset and progression of the disease. However, the composition and functional capabilities of the gut virome associated with atherosclerotic cardiovascular disease (ACVD) have not been systematically investigated. To our knowledge, this is the first study investigating the gut virome in patients with ACVD. We characterized the structural changes in the gut virome of ACVD patients, which may facilitate additional mechanistic, diagnostic, and interventional studies of ACVD and related diseases.
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Affiliation(s)
- Youshan Li
- Department of Peripheral Vascular Diseases II, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, 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 Key Laboratory of Acupuncture Neuromodulation, Beijing, China
| | - Xulin Sai
- Department of Peripheral Vascular Diseases II, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Jianfeng Yang
- Department of Peripheral Vascular Diseases II, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Shuo Zhang
- Department of Peripheral Vascular Diseases II, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Wen Sun
- Department of Traditional Chinese Medicine, Beijing Friendship Hospital, Capital Medical University, 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
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13
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Kalayci FNC, Ozen S. Possible Role of Dysbiosis of the Gut Microbiome in SLE. Curr Rheumatol Rep 2023; 25:247-258. [PMID: 37737528 DOI: 10.1007/s11926-023-01115-8] [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] [Accepted: 09/01/2023] [Indexed: 09/23/2023]
Abstract
PURPOSE OF REVIEW The resident gut microbiota serves as a double-edged sword that aids the host in multiple ways to preserve a healthy equilibrium and serve as early companions and boosters for the gradual evolution of our immune defensive layers; nevertheless, the perturbation of the symbiotic resident intestinal communities has a profound impact on autoimmunity induction, particularly in systemic lupus erythematosus (SLE). Herein, we seek to critically evaluate the microbiome research in SLE with a focus on intestinal dysbiosis. RECENT FINDINGS SLE is a complex and heterogeneous disorder with self-attack due to loss of tolerance, and there is aberrant excessive immune system activation. There is mounting evidence suggesting that intestinal flora disturbances may accelerate the formation and progression of SLE, presumably through a variety of mechanisms, including intestinal barrier dysfunction and leaky gut, molecular mimicry, bystander activation, epitope spreading, gender bias, and biofilms. Gut microbiome plays a critical role in SLE pathogenesis, and additional studies are warranted to properly define the impact of gut microbiome in SLE, which can eventually lead to new and potentially safer management approaches for this debilitating disease.
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Affiliation(s)
| | - Seza Ozen
- Department of Paediatric Rheumatology, Faculty of Medicine, Hacettepe University, Ankara, Turkey.
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14
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Tomofuji Y, Kishikawa T, Sonehara K, Maeda Y, Ogawa K, Kawabata S, Oguro-Igashira E, Okuno T, Nii T, Kinoshita M, Takagaki M, Yamamoto K, Arase N, Yagita-Sakamaki M, Hosokawa A, Motooka D, Matsumoto Y, Matsuoka H, Yoshimura M, Ohshima S, Nakamura S, Fujimoto M, Inohara H, Kishima H, Mochizuki H, Takeda K, Kumanogoh A, Okada Y. Analysis of gut microbiome, host genetics, and plasma metabolites reveals gut microbiome-host interactions in the Japanese population. Cell Rep 2023; 42:113324. [PMID: 37935197 DOI: 10.1016/j.celrep.2023.113324] [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: 06/05/2023] [Revised: 09/11/2023] [Accepted: 10/06/2023] [Indexed: 11/09/2023] Open
Abstract
Interaction between the gut microbiome and host plays a key role in human health. Here, we perform a metagenome shotgun-sequencing-based analysis of Japanese participants to reveal associations between the gut microbiome, host genetics, and plasma metabolome. A genome-wide association study (GWAS) for microbial species (n = 524) identifies associations between the PDE1C gene locus and Bacteroides intestinalis and between TGIF2 and TGIF2-RAB5IF gene loci and Bacteroides acidifiaciens. In a microbial gene ortholog GWAS, agaE and agaS, which are related to the metabolism of carbohydrates forming the blood group A antigen, are associated with blood group A in a manner depending on the secretor status determined by the East Asian-specific FUT2 variant. A microbiome-metabolome association analysis (n = 261) identifies associations between bile acids and microbial features such as bile acid metabolism gene orthologs including bai and 7β-hydroxysteroid dehydrogenase. Our publicly available data will be a useful resource for understanding gut microbiome-host interactions in an underrepresented population.
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Affiliation(s)
- Yoshihiko Tomofuji
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Tsurumi 230-0045, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan; Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo 113-8654, Japan.
| | - Toshihiro Kishikawa
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Department of Otorhinolaryngology-Head and Neck Surgery, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Department of Head and Neck Surgery, Aichi Cancer Center Hospital, Nagoya 464-8681, Japan
| | - Kyuto Sonehara
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Tsurumi 230-0045, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan; Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo 113-8654, Japan
| | - Yuichi Maeda
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan; Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Kotaro Ogawa
- Department of Neurology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Shuhei Kawabata
- Department of Neurosurgery, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Eri Oguro-Igashira
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Tatsusada Okuno
- Department of Neurology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Takuro Nii
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Makoto Kinoshita
- Department of Neurology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Masatoshi Takagaki
- Department of Neurosurgery, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Department of Pediatrics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita 565-0871, Japan
| | - Noriko Arase
- Department of Dermatology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Mayu Yagita-Sakamaki
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Akiko Hosokawa
- Department of Neurology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Department of Neurology, Suita Municipal Hospital, Suita 564-8567, Japan
| | - Daisuke Motooka
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan; Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan
| | - Yuki Matsumoto
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan
| | - Hidetoshi Matsuoka
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano 586-8521, Japan
| | - Maiko Yoshimura
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano 586-8521, Japan
| | - Shiro Ohshima
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano 586-8521, Japan
| | - Shota Nakamura
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan; Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan; Center for Infectious Disease Education and Research, Osaka University, Suita 565-0871, Japan
| | - Manabu Fujimoto
- Department of Dermatology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Hidenori Inohara
- Department of Otorhinolaryngology-Head and Neck Surgery, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Haruhiko Kishima
- Department of Neurosurgery, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Hideki Mochizuki
- Department of Neurology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Kiyoshi Takeda
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Center for Infectious Disease Education and Research, Osaka University, Suita 565-0871, Japan; WPI Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan
| | - Atsushi Kumanogoh
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan; Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Department of Immunopathology, Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Tsurumi 230-0045, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan; Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo 113-8654, Japan; Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita 565-0871, Japan; Center for Infectious Disease Education and Research, Osaka University, Suita 565-0871, Japan; Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Suita 565-0871, Japan.
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15
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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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16
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Wang H, Xu S, Li S, Su B, Sherrill-Mix S, Liang G. Virome in immunodeficiency: what we know currently. Chin Med J (Engl) 2023; 136:2647-2657. [PMID: 37914672 PMCID: PMC10684123 DOI: 10.1097/cm9.0000000000002899] [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: 07/30/2023] [Indexed: 11/03/2023] Open
Abstract
ABSTRACT Over the past few years, the human virome and its complex interactions with microbial communities and the immune system have gained recognition as a crucial factor in human health. Individuals with compromised immune function encounter distinctive challenges due to their heightened vulnerability to a diverse range of infectious diseases. This review aims to comprehensively explore and analyze the growing evidence regarding the role of the virome in immunocompromised disease status. By surveying the latest literature, we present a detailed overview of virome alterations observed in various immunodeficiency conditions. We then delve into the influence and mechanisms of these virome changes on the pathogenesis of specific diseases in immunocompromised individuals. Furthermore, this review explores the clinical relevance of virome studies in the context of immunodeficiency, highlighting the potential diagnostic and therapeutic gains from a better understanding of virome contributions to disease manifestations.
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Affiliation(s)
- Hu Wang
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Siqi Xu
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Shuang Li
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Bin Su
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Scott Sherrill-Mix
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Guanxiang Liang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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17
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Abstract
The gut microbiome is a dense and metabolically active consortium of microorganisms and viruses located in the lower gastrointestinal tract of the human body. Bacteria and their viruses (phages) are the most abundant members of the gut microbiome. Investigating their biology and the interplay between the two is important if we are to understand their roles in human health and disease. In this review, we summarize recent advances in resolving the taxonomic structure and ecological functions of the complex community of phages in the human gut-the gut phageome. We discuss how age, diet, and geography can all have a significant impact on phageome composition. We note that alterations to the gut phageome have been observed in several diseases such as inflammatory bowel disease, irritable bowel syndrome, and colorectal cancer, and we evaluate whether these phageome changes can directly or indirectly contribute to disease etiology and pathogenesis. We also highlight how lack of standardization in studying the gut phageome has contributed to variation in reported results.
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Affiliation(s)
- Ciara A Tobin
- APC Microbiome Ireland, Cork, Ireland; , ,
- School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, Cork, Ireland; , ,
- School of Microbiology, University College Cork, Cork, Ireland
| | - Andrey N Shkoporov
- APC Microbiome Ireland, Cork, Ireland; , ,
- School of Microbiology, University College Cork, Cork, Ireland
- Department of Medicine, University College Cork, Cork, Ireland
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18
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Hu J, Ding J, Li X, Li J, Zheng T, Xie L, Li C, Tang Y, Guo K, Huang J, Liu S, Yan J, Peng W, Hou C, Wen L, Xu A, Zhou Z, Xiao Y. Distinct signatures of gut microbiota and metabolites in different types of diabetes: a population-based cross-sectional study. EClinicalMedicine 2023; 62:102132. [PMID: 37593224 PMCID: PMC10430172 DOI: 10.1016/j.eclinm.2023.102132] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/08/2023] [Accepted: 07/17/2023] [Indexed: 08/19/2023] Open
Abstract
Background Patients with type 1 diabetes (T1D) and type 2 diabetes (T2D) present intestinal disturbances. Recent epidemiological data have showed that, worldwide, over half of newly diagnosed T1D patients were adults. However, the gut microbial alterations in adult-onset T1D are unclear. We aimed to identify the signatures of gut microbiota and metabolites in patients with adult-onset T1D systematically, comparing with T2D patients and healthy controls (HCs). Methods This study enrolled 218 subjects from February 2019 to April 2022 (discovery cohort: 36 HCs, 51 patients with adult-onset T1D and 56 patients with T2D; validation cohort: 28 HCs, 27 patients with adult-onset T1D and 20 patients with T2D). Gut microbial profiles of the study subjects were investigated by metagenomic sequencing, and their faecal and serum metabolites were measured with targeted metabolomics. The study was registered on ClinicalTrials.gov (NCT05252728). Findings Patients with adult-onset T1D had significant differences in the composition of bacteria and their metabolites, characterized by notable depletion of short-chain fatty acid-producing bacteria, especially Eubacterium rectale. This was associated with a severe loss of phenolic acids and their derivatives, including gallic acid (associated with glucose metabolism) and 3,4-dihydroxyhydrocinnamic acid (linked with glucose metabolism and pancreatic beta cell autoimmunity). A predictive model based on six bacteria and six metabolites simultaneously discriminated adult-onset T1D from T2D and HCs with high accuracy. Interestingly, bacterial-viral or bacterial-fungal trans-kingdom relationships, especially positive correlations between bacteriophages and beneficial bacteria, were significantly reduced in adult-onset T1D compared to HCs. Interpretation Adult-onset T1D patients exhibit unique changes in host-microbiota-metabolite interactions. Gut microbiota and metabolite-based algorithms could be used as additional tools for differential diagnosis of different types of diabetes and beyond. Funding National Key Research and Development Program of China, the National Natural Science Foundation of China.
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Affiliation(s)
- Jingyi Hu
- National Clinical Research Centre for Metabolic Diseases, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Jin Ding
- National Clinical Research Centre for Metabolic Diseases, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xia Li
- National Clinical Research Centre for Metabolic Diseases, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
- School of Data Science, City University of Hong Kong, Hong Kong, China
| | - Tingting Zheng
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Lingxiang Xie
- National Clinical Research Centre for Metabolic Diseases, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Chenyu Li
- National Clinical Research Centre for Metabolic Diseases, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Yingxin Tang
- National Clinical Research Centre for Metabolic Diseases, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Keyu Guo
- National Clinical Research Centre for Metabolic Diseases, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Juan Huang
- National Clinical Research Centre for Metabolic Diseases, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Shanshan Liu
- National Clinical Research Centre for Metabolic Diseases, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Jianru Yan
- Department of Endocrinology, The First People's Hospital of Pingjiang, Pingjiang, Hunan, China
| | - Weijun Peng
- Department of Integrated Traditional Chinese and Western Medicine, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Can Hou
- National Clinical Research Centre for Metabolic Diseases, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Li Wen
- Section of Endocrinology, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Aimin Xu
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong, China
- Department of Medicine, The University of Hong Kong, Hong Kong, China
- Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong, China
| | - Zhiguang Zhou
- National Clinical Research Centre for Metabolic Diseases, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Yang Xiao
- National Clinical Research Centre for Metabolic Diseases, Key Laboratory of Diabetes Immunology, Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
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19
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Ding Y, Wan M, Li Z, Ma X, Zhang W, Xu M. Comparison of the gut virus communities between patients with Crohn's disease and healthy individuals. Front Microbiol 2023; 14:1190172. [PMID: 37396350 PMCID: PMC10311494 DOI: 10.3389/fmicb.2023.1190172] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/18/2023] [Indexed: 07/04/2023] Open
Abstract
Introduction The escalating incidence of Crohn's disease (CD), a debilitating ailment that ravages individuals and their families, has become a formidable issue over recent decades. Method In this study, fecal samples from patients with CD and healthy individuals were investigated by means of viral metagenomics. Results The fecal virome was analyzed and some suspected disease-causing viruses were described. A polyomavirus named HuPyV with 5,120 base pairs (bp) was found in the disease group. In a preliminary analysis employing large T region-specific primers, it was found that HuPyV was present in 3.2% (1/31) of healthy samples and 43.2% (16/37) of disease samples. Additionally, two other viruses from the anellovirus and CRESS-DNA virus families were found in fecal samples from CD patients. The complete genome sequences of these two viruses were described respectively, and the phylogenetic trees have been built using the anticipated amino acid sequences of the viral proteins. Discussion Further research is required to elucidate the relationship between these viruses and the onset and development of Crohn's disease.
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Affiliation(s)
- Yuzhu Ding
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Mengtian Wan
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Zheng Li
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xiao Ma
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Min Xu
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, Jiangsu, China
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20
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Lei Y, Liu Q, Li Q, Zhao C, Zhao M, Lu Q. Exploring the Complex Relationship Between Microbiota and Systemic Lupus Erythematosus. Curr Rheumatol Rep 2023; 25:107-116. [PMID: 37083877 DOI: 10.1007/s11926-023-01102-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2023] [Indexed: 04/22/2023]
Abstract
PURPOSE OF REVIEW Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by various autoantibodies and multi-organ. Microbiota dysbiosis in the gut, skin, oral, and other surfaces has a significant impact on SLE development. This article summarizes relevant research and provides new microbiome-related strategies for exploring the mechanisms and treating patients with SLE. RECENT FINDINGS SLE patients have disruptions in multiple microbiomes, with the gut microbiota (bacteria, viruses, and fungi) and their metabolites being the most thoroughly researched. This dysbiosis can promote SLE progression through mechanisms such as the leaky gut, molecular mimicry, and epigenetic regulation. Notwithstanding study constraints on the relationship between microbiota and SLE, specific interventions targeting the gut microbiota, such as probiotics, dietary management, and fecal microbiota transplantation, have emerged as promising SLE therapeutics.
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Affiliation(s)
- Yu Lei
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
- Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Qianmei Liu
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Qilin Li
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
- Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Cheng Zhao
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
- Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Ming Zhao
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China.
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China.
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China.
- Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, China.
| | - Qianjin Lu
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China.
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China.
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China.
- Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, China.
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21
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Tomofuji Y, Sonehara K, Kishikawa T, Maeda Y, Ogawa K, Kawabata S, Nii T, Okuno T, Oguro-Igashira E, Kinoshita M, Takagaki M, Yamamoto K, Kurakawa T, Yagita-Sakamaki M, Hosokawa A, Motooka D, Matsumoto Y, Matsuoka H, Yoshimura M, Ohshima S, Nakamura S, Inohara H, Kishima H, Mochizuki H, Takeda K, Kumanogoh A, Okada Y. Reconstruction of the personal information from human genome reads in gut metagenome sequencing data. Nat Microbiol 2023:10.1038/s41564-023-01381-3. [PMID: 37188815 DOI: 10.1038/s41564-023-01381-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 04/12/2023] [Indexed: 05/17/2023]
Abstract
Human DNA present in faecal samples can result in a small number of human reads in gut shotgun metagenomic sequencing data. However, it is presently unclear how much personal information can be reconstructed from such reads, and this has not been quantitatively evaluated. Such a quantitative evaluation is necessary to clarify the ethical concerns related to data sharing and to enable efficient use of human genetic information in stool samples, such as for research and forensics. Here we used genomic approaches to reconstruct personal information from the faecal metagenomes of 343 Japanese individuals with associated human genotype data. Genetic sex could be accurately predicted based on the sequencing depth of sex chromosomes for 97.3% of the samples. Individuals could be re-identified from the matched genotype data based on human reads recovered from the faecal metagenomic data with 93.3% sensitivity using a likelihood score-based method. This method also enabled us to predict the ancestries of 98.3% of the samples. Finally, we performed ultra-deep shotgun metagenomic sequencing of five faecal samples as well as whole-genome sequencing of blood samples. Using genotype-calling approaches, we demonstrated that the genotypes of both common and rare variants could be reconstructed from faecal samples. This included clinically relevant variants. Our approach can be used to quantify personal information contained within gut metagenome data.
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Affiliation(s)
- Yoshihiko Tomofuji
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Suita, Japan.
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan.
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
| | - Kyuto Sonehara
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Toshihiro Kishikawa
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Suita, Japan
- Department of Otorhinolaryngology-Head and Neck Surgery, Graduate School of Medicine, Osaka University, Suita, Japan
- Department of Head and Neck Surgery, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Yuichi Maeda
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Kotaro Ogawa
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Shuhei Kawabata
- Department of Neurosurgery, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Takuro Nii
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Tatsusada Okuno
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Eri Oguro-Igashira
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Makoto Kinoshita
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Masatoshi Takagaki
- Department of Neurosurgery, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Suita, Japan
- Department of Pediatrics, Graduate School of Medicine, Osaka University, Suita, Japan
- Laboratory of Statistical Immunology, WPI Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Takashi Kurakawa
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Mayu Yagita-Sakamaki
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Akiko Hosokawa
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Japan
- Department of Neurology, Suita Municipal Hospital, Suita, Japan
| | - Daisuke Motooka
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Yuki Matsumoto
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Hidetoshi Matsuoka
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano, Japan
| | - Maiko Yoshimura
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano, Japan
| | - Shiro Ohshima
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano, Japan
| | - Shota Nakamura
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Japan
| | - Hidenori Inohara
- Department of Otorhinolaryngology-Head and Neck Surgery, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Haruhiko Kishima
- Department of Neurosurgery, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Hideki Mochizuki
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Kiyoshi Takeda
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Japan
- WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Atsushi Kumanogoh
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
- Department of Immunopathology, Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Suita, Japan.
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan.
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
- Laboratory of Statistical Immunology, WPI Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan.
- Center for Infectious Disease Education and Research, Osaka University, Suita, Japan.
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22
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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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23
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Smith L, Goldobina E, Govi B, Shkoporov AN. Bacteriophages of the Order Crassvirales: What Do We Currently Know about This Keystone Component of the Human Gut Virome? Biomolecules 2023; 13:584. [PMID: 37189332 PMCID: PMC10136315 DOI: 10.3390/biom13040584] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 05/17/2023] Open
Abstract
The order Crassvirales comprises dsDNA bacteriophages infecting bacteria in the phylum Bacteroidetes that are found in a variety of environments but are especially prevalent in the mammalian gut. This review summarises available information on the genomics, diversity, taxonomy, and ecology of this largely uncultured viral taxon. With experimental data available from a handful of cultured representatives, the review highlights key properties of virion morphology, infection, gene expression and replication processes, and phage-host dynamics.
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24
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Chu Y, Meng Q, Yu J, Zhang J, Chen J, Kang Y. Strain-Level Dynamics Reveal Regulatory Roles in Atopic Eczema by Gut Bacterial Phages. Microbiol Spectr 2023; 11:e0455122. [PMID: 36951555 PMCID: PMC10101075 DOI: 10.1128/spectrum.04551-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/06/2023] [Indexed: 03/24/2023] Open
Abstract
The vast population of bacterial phages or viruses (virome) plays pivotal roles in the ecology of human microbial flora and health conditions. Obstacles, including poor viral sequence inference, strain-sensitive virus-host relationship, and the high diversity among individuals, hinder the in-depth understanding of the human virome. We conducted longitudinal studies of the virome based on constructing a high-quality personal reference metagenome (PRM). By applying long-read sequencing for representative samples, we could build a PRM of high continuity that allows accurate annotation and abundance estimation of viruses and bacterial species in all samples of the same individual by aligning short sequencing reads to the PRM. We applied this approach to a series of fecal samples collected for 6 months from a 2-year-old boy who had experienced a 2-month flare-up of atopic eczema (dermatitis) in this period. We identified 31 viral strains in the patient's gut microbiota and deciphered their strain-level relationship to their bacterial hosts. Among them, a lytic crAssphage developed into a dozen substrains and coordinated downregulation in the catabolism of aromatic amino acids (AAAs) in their host bacteria which govern the production of immune-active AAA derivates. The metabolic alterations confirmed based on metabolomic assays cooccurred with symptom remission. Our PRM-based analysis provides an easy approach for deciphering the dynamics of the strain-level human gut virome in the context of entire microbiota. Close temporal correlations among virome alteration, microbial metabolism, and disease remission suggest a potential mechanism for how bacterial phages in microbiota are intimately related to human health. IMPORTANCE The vast populations of viruses or bacteriophages in human gut flora remain mysterious. However, poor annotation and abundance estimation remain obstacles to strain-level analysis and clarification of their roles in microbiome ecology and metabolism associated with human health and diseases. We demonstrate that a personal reference metagenome (PRM)-based approach provides strain-level resolution for analyzing the gut microbiota-associated virome. When applying such an approach to longitudinal samples collected from a 2-year-old boy who has experienced a 2-month flare-up of atopic eczema, we observed thriving substrains of a lytic crAssphage, showing temporal correlation with downregulated catabolism of aromatic amino acids, lower production of immune-active metabolites, and remission of the disease. The PRM-based approach is practical and powerful for strain-centric analysis of the human gut virome, and the underlying mechanism of how strain-level virome dynamics affect disease deserves further investigation.
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Affiliation(s)
- Yanan Chu
- Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
| | - Qingren Meng
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Jun Yu
- University of Chinese Academy of Sciences, Beijing, China
| | - Juan Zhang
- Department of Pediatric, Peking University Third Hospital, Beijing, China
| | - Jing Chen
- Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
| | - Yu Kang
- Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
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25
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Park EH, Kang EH, Lee YJ, Ha YJ. Impact of early age at menopause on disease outcomes in postmenopausal women with rheumatoid arthritis: a large observational cohort study of Korean patients with rheumatoid arthritis. RMD Open 2023; 9:rmdopen-2022-002722. [PMID: 36792311 PMCID: PMC9933755 DOI: 10.1136/rmdopen-2022-002722] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 01/31/2023] [Indexed: 02/17/2023] Open
Abstract
OBJECTIVES To assess the differences in clinical outcomes between patients with rheumatoid arthritis (RA) with early menopause (EM) (<45 years) and usual menopause (UM) (≥45 years) and to identify the impact of EM on longitudinal changes in RA activity and patient-reported outcomes (PROs). METHODS We recruited 2878 postmenopausal women with RA from the Korean Observational Study Network for Arthritis. Patients were examined at baseline and for 5 consecutive years using the Simplified Disease Activity Index (SDAI), Health Assessment Questionnaire-Disability Index (HAQ-DI) and other PROs. Generalised estimating equation (GEE) analyses were performed among patients with a baseline SDAI of >11 to evaluate the impact of EM on longitudinal changes in RA activity and PROs. RESULTS The EM group (n=437) was younger than the UM group (n=2441), but the RA duration was similar between the two groups. The EM group was more educated and more likely to be seronegative at enrolment. Moreover, the EM group demonstrated higher disease activity and worse PROs for global assessment, fatigue, sleep disturbance and health-related quality of life (HRQoL) (all p<0.05) at baseline. The GEE model revealed that EM significantly influenced the rate of SDAI change (β=1.265, p=0.004) after adjusting for age, RA duration, biologics use and SDAI at baseline. The EM group was also significantly associated with increased HAQ-DI scores and decreased EQ-5D-utility values during the 5-year follow-up period. CONCLUSION Patients with RA and EM demonstrate higher disease activity and poorer HRQoL. Furthermore, EM significantly affects the longitudinal changes in disease activity and PROs in patients with RA.
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Affiliation(s)
- Eun Hye Park
- Division of Rheumatology, Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul, Korea,Division of Rheumatology, Department of Internal Medicine, Chung-Ang University Gwangmyeong Hospital, Gwangmyeong, Korea
| | - Eun Ha Kang
- Division of Rheumatology, Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea,Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Yun Jong Lee
- Division of Rheumatology, Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea,Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - You-Jung Ha
- Division of Rheumatology, Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea .,Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
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26
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Chen B, Cao J, Liu W, Zhang Y, Liu Y, Wang M, Xiao F, Ma J, Wang J, Zhang X. Disturbed gut virome with potent interferonogenic property in systemic lupus erythematosus. Sci Bull (Beijing) 2023; 68:295-304. [PMID: 36697300 DOI: 10.1016/j.scib.2023.01.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/22/2022] [Accepted: 01/16/2023] [Indexed: 01/19/2023]
Abstract
Accumulating evidence suggests an essential role of disturbed gut microbiota in the etiopathogenesis of systemic lupus erythematosus (SLE), but it remains unclear as to gut virome. In this study, fecal virus-like particles (VLPs) isolated from 76 non-treated SLE patients and 75 healthy controls were subjected to gut virome profiling. The proportion of bacteriophages was significantly elevated in the SLE gut, and the altered viral taxa were correlated with clinical parameters. Gut virome and bacteriome were closely associated with each other in SLE patients. The combination of gut viral and bacterial markers displayed better performance in distinguishing SLE patients from healthy controls. Further, VLPs from non-treated SLE patients promoted interferon-α production in an epithelial cell line and human immune cells. Intriguingly, the interferon-stimulatory capacity diminished in VLPs from post-treated SLE patients. Our findings may shed novel insights into SLE pathogenesis. Further in-depth understanding of gut virome might help develop future biomarkers and therapeutics for SLE patients.
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Affiliation(s)
- Beidi Chen
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, China; Division of Rheumatology and Immunology, Peking University Third Hospital, Beijing 100191, China
| | - Jiabao Cao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Wei Liu
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Yuqing Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Yudong Liu
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Min Wang
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Fei Xiao
- The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Beijing Institute of Geriatrics, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Jie Ma
- The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Beijing Institute of Geriatrics, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Jun Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China.
| | - Xuan Zhang
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, China.
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27
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Tanaka Y. What are the hot topics in Japanese rheumatology? Go above and beyond. RMD Open 2023; 9:rmdopen-2022-002819. [PMID: 36717187 PMCID: PMC9887709 DOI: 10.1136/rmdopen-2022-002819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 01/02/2023] [Indexed: 01/31/2023] Open
Abstract
Japanese rheumatology and immunology have contributed to progress in the field and advancement of rheumatology, including postmarketing surveillance, development of IL-6-targeting therapy and concept of drug tapering, have accelerated in the 21st century. The 67th Annual Scientific Meeting of the Japan College of Rheumatology, held on Fukuoka on 24 April 2023-26 April 2023, will go ahead and beyond such an advancement. Profound discussion on future perspectives such as precision medicine, the elucidation of pathology and genome-based drug discovery by multilayered integration with various types of omics information, information on metabolome and proteome of blood metabolites, and database of target proteins and compounds for drug discovery will be discussed.
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Affiliation(s)
- Yoshiya Tanaka
- The First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health Japan, Kitakyushu, Fukuoka, Japan
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28
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Chen C, Yan Q, Yao X, Li S, Lv Q, Wang G, Zhong Q, Tang F, Liu Z, Huang Y, An Y, Zhou J, Zhang Q, Zhang A, Ullah H, Zhang Y, Liu C, Zhu D, Li H, Sun W, Ma W. Alterations of the gut virome in patients with systemic lupus erythematosus. Front Immunol 2023; 13:1050895. [PMID: 36713446 PMCID: PMC9874095 DOI: 10.3389/fimmu.2022.1050895] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/23/2022] [Indexed: 01/13/2023] Open
Abstract
Background Systemic lupus erythematosus (SLE) is a systemic autoimmune disease that has been linked to the dysbiosis of the gut microbiome and virome. However, the potential characterization of the gut virome in SLE patients needs to be explored more extensively. Methods Herein, we analyzed the gut viral community of 16 SLE patients and 31 healthy controls using both bulk and virus-like particle (VLP)-based metagenomic sequencing of their fecal samples. A total of 15,999 non-redundant viral operational taxonomic units (vOTUs) were identified from the metagenomic assembled contigs and used for gut virome profiling. Results SLE patients exhibited a significant decrease in gut viral diversity in the bulk metagenome dataset, but this change was not significant in the VLP metagenome dataset. Also, considerable alterations of the overall gut virome composition and remarkable changes in the viral family compositions were observed in SLE patients compared with healthy controls, as observed in both two technologies. We identified 408 vOTUs (177 SLE-enriched and 231 control-enriched) with significantly different relative abundances between patients and controls in the bulk virome, and 18 vOTUs (17 SLE-enriched in 1 control-enriched) in the VLP virome. The SLE-enriched vOTUs included numerous Siphoviridae, Microviridae, and crAss-like viruses and were frequently predicted to infect Bacteroides, Parabacteroides, and Ruminococcus_E, while the control-enriched contained numerous members of Siphoviridae and Myoviridae and were predicted to infect Prevotella and Lachnospirales_CAG-274. We explored the correlations between gut viruses and bacteria and found that some Lachnospirales_CAG-274 and Hungatella_A phages may play key roles in the virus-bacterium network. Furthermore, we explored the gut viral signatures for disease discrimination and achieved an area under the receiver operator characteristic curve (AUC) of above 0.95, suggesting the potential of the gut virome in the prediction of SLE. Conclusion Our findings demonstrated the alterations in viral diversity and taxonomic composition of the gut virome of SLE patients. Further research into the etiology of SLE and the gut viral community will open up new avenues for treating and preventing SLE and other autoimmune diseases.
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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
| | - Qiulong Yan
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Xueming Yao
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | | | - Qingbo Lv
- Puensum Genetech Institute, Wuhan, China,College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Guangyang Wang
- 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
| | - Fang Tang
- 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
| | - Ying Huang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Yang An
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Jing Zhou
- 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
| | | | - Hayan Ullah
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan, China
| | - Can Liu
- 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
| | - Hufan Li
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Wen Sun
- Key Laboratory of Health Cultivation of the Ministry of Education, Beijing University of Chinese Medicine, Beijing, China,*Correspondence: Wen Sun, ; Wukai Ma,
| | - Wukai Ma
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China,*Correspondence: Wen Sun, ; Wukai Ma,
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29
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Nii T, Maeda Y, Motooka D, Naito M, Matsumoto Y, Ogawa T, Oguro-Igashira E, Kishikawa T, Yamashita M, Koizumi S, Kurakawa T, Okumura R, Kayama H, Murakami M, Sakaguchi T, Das B, Nakamura S, Okada Y, Kumanogoh A, Takeda K. Genomic repertoires linked with pathogenic potency of arthritogenic Prevotella copri isolated from the gut of patients with rheumatoid arthritis. Ann Rheum Dis 2023; 82:621-629. [PMID: 36627170 PMCID: PMC10176341 DOI: 10.1136/ard-2022-222881] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 12/30/2022] [Indexed: 01/12/2023]
Abstract
OBJECTIVES Prevotella copri is considered to be a contributing factor in rheumatoid arthritis (RA). However, in some non-Westernised countries, healthy individuals also harbour an abundance of P. copri in the intestine. This study investigated the pathogenicity of RA patient-derived P. copri (P. copri RA) compared with healthy control-derived P. copri (P. copri HC). METHODS We obtained 13 P. copri strains from the faeces of patients with RA and healthy controls. Following whole genome sequencing, the sequences of P. copri RA and P. copri HC were compared. To analyse the arthritis-inducing ability of P. copri, we examined two arthritis models (1) a collagen-induced arthritis model harbouring P. copri under specific-pathogen-free conditions and (2) an SKG mouse arthritis model under P. copri-monocolonised conditions. Finally, to evaluate the ability of P. copri to activate innate immune cells, we performed in vitro stimulation of bone marrow-derived dendritic cells (BMDCs) by P. copri RA and P. copri HC. RESULTS Comparative genomic analysis revealed no apparent differences in the core gene contents between P. copri RA and P. copri HC, but pangenome analysis revealed the high genome plasticity of P. copri. We identified a P. copri RA-specific genomic region as a conjugative transposon. In both arthritis models, P. copri RA-induced more severe arthritis than P. copri HC. In vitro BMDC stimulation experiments revealed the upregulation of IL-17 and Th17-related cytokines (IL-6, IL-23) by P. copri RA. CONCLUSION Our findings reveal the genetic diversity of P. copri, and the genomic signatures associated with strong arthritis-inducing ability of P. copri RA. Our study contributes towards elucidation of the complex pathogenesis of RA.
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Affiliation(s)
- Takuro Nii
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
- Department of Respiratory Medicine, Clinical Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
- National Hospital Organization Osaka Toneyama Medical Center, Osaka, Japan
| | - Yuichi Maeda
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
- Department of Respiratory Medicine, Clinical Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
| | - Daisuke Motooka
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Mariko Naito
- Department of Microbiology and Oral Infection, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Yuki Matsumoto
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Takao Ogawa
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
- Department of Respiratory Medicine, Clinical Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Eri Oguro-Igashira
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
- Department of Respiratory Medicine, Clinical Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Toshihiro Kishikawa
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan
- Department of Otorhinolaryngology-Head and Neck Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
- Department of Head and Neck Surgery, Aichi Cancer Center Hospital, Aichi, Japan
| | - Makoto Yamashita
- Research & Innovation Center, Kyowa Hakko Bio Co., Ltd, Ibaraki, Japan
| | - Satoshi Koizumi
- Research & Innovation Center, Kyowa Hakko Bio Co., Ltd, Ibaraki, Japan
| | - Takashi Kurakawa
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Ryu Okumura
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Hisako Kayama
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
- WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Institute for Advanced Co-Creation Studies, Osaka University, Osaka, Japan
| | - Mari Murakami
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
- WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Taiki Sakaguchi
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
- WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Bhabatosh Das
- Molecular Genetics Laboratory, Infection and Immunology Division, Translational Health Science and Technology Institute, Faridabad, India
| | - Shota Nakamura
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan
| | - Yukinori Okada
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan
- Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine, Clinical Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan
| | - Kiyoshi Takeda
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan
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Dagar S, Singh J, Saini A, Kumar Y, Chhabra S, Minz RW, Rani L. Gut bacteriome, mycobiome and virome alterations in rheumatoid arthritis. Front Endocrinol (Lausanne) 2023; 13:1044673. [PMID: 36699026 PMCID: PMC9868751 DOI: 10.3389/fendo.2022.1044673] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/20/2022] [Indexed: 01/11/2023] Open
Abstract
Rheumatoid arthritis (RA) is a chronic destructive autoimmune disease of the joints which causes significant pain, functional disability, and mortality. Although aberrant immune cell activation induced by the imbalance between T helper Th1/Th17 and Treg cells is implicated in the RA development, its etiopathogenesis remains unclear. The presence of mucosal inflammation and systemic IgA-isotype-autoantibodies (anti-citrullinated peptide antibodies and rheumatoid factor) in pre-clinical RA supports the mucosal origin hypothesis involving altered microbiota in disease development. The gut microbiota comprises diverse bacteria, fungal and viral components, which are critical in developing host immunity. Alterations in microbial abundance are known to exacerbate or attenuate immune responses in the gut microenvironment subsequently affecting the joints. Further, these changes can provide biomarkers for disease activity and outcome in RA. Most of the research till date has been focused on describing gut bacterial components in RA. Studies on gut mycobiome and virome components in RA are relatively new and burgeoning field. Given the paucity of mycobiome or virome specific studies in RA, this review, discusses the recent findings on alterations in gut bacterial, fungal, and viral components as well as their role in regulating the spectrum of immune-pathogenic events occurring in RA which might be explored in future as a potential therapeutic target. Further, we provide an overview on inter-kingdom interactions between bacteria, fungi, and viruses in RA. The current understanding on gut microbiota modulation for managing RA is also summarised.
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Affiliation(s)
| | | | | | | | | | | | - Lekha Rani
- Department of Immunopathology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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31
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Tardov MV, Talapbek S, Sturov NV, Popova EV, Boldin AV, Rusanova EI, Suvorova NN. [Gut microbiota in patients with relapsing-remitting multiple sclerosis]. Zh Nevrol Psikhiatr Im S S Korsakova 2023; 123:8-15. [PMID: 36719114 DOI: 10.17116/jnevro20231230118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Microorganisms in human life play a huge role: in particular, those that coexist with the host organism, inhabiting the skin, upper respiratory tract, external genitalia and especially the digestive tract. The intestinal microbiota, including bacteriome, mycobiome and virome, not only takes part in the digestion process, but also provides the synthesis of a number of vitamins. The intestinal microbiome also serves as the basis for a system of extensive bidirectional neuroendocrine pathways that connect microbiota with various regions of the central nervous system, the hypothalamic-pituitary-adrenal system, and the peripheral parts of the autonomic nervous system. This system of connections has got the name of gut-brain axis and has attracted close attention of scientists over the past two decades, since a targeted impact on the intestinal flora is potentially capable of changing the nature of nervous system regulatory influences on the whole body. It is especially important to study patterns of functioning of the gut-brain axis in patients with the nervous system pathology, namely neurodegenerative and demyelinating diseases. Methods for their treatment continue to improve, and perhaps the correction of the gut microbiotic composition will serve as an additional therapeutic approach. The review article describes current views on the role of the intestinal microbiota, provides the latest data on the composition of bacteriome, mycobiome, and virome in patients with relapsing-remitting multiple sclerosis.
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Affiliation(s)
- M V Tardov
- Peoples' Friendship University of Russia, Moscow, Russia
| | - Sh Talapbek
- Peoples' Friendship University of Russia, Moscow, Russia
| | - N V Sturov
- Peoples' Friendship University of Russia, Moscow, Russia
| | - E V Popova
- Moscow City Clinical Hospital 24, Moscow, Russia
| | - A V Boldin
- Sechenov First Moscow State Medical University, Moscow, Russia
| | - E I Rusanova
- Peoples' Friendship University of Russia, Moscow, Russia
| | - N N Suvorova
- Consultative and Diagnostic Center No. 6 of the Moscow Health Department, Moscow, Russia
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32
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Tomofuji Y, Kishikawa T, Maeda Y, Ogawa K, Otake-Kasamoto Y, Kawabata S, Nii T, Okuno T, Oguro-Igashira E, Kinoshita M, Takagaki M, Oyama N, Todo K, Yamamoto K, Sonehara K, Yagita M, Hosokawa A, Motooka D, Matsumoto Y, Matsuoka H, Yoshimura M, Ohshima S, Shinzaki S, Nakamura S, Iijima H, Inohara H, Kishima H, Takehara T, Mochizuki H, Takeda K, Kumanogoh A, Okada Y. Prokaryotic and viral genomes recovered from 787 Japanese gut metagenomes revealed microbial features linked to diets, populations, and diseases. CELL GENOMICS 2022; 2:100219. [PMID: 36778050 PMCID: PMC9903723 DOI: 10.1016/j.xgen.2022.100219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/27/2022] [Accepted: 10/31/2022] [Indexed: 12/03/2022]
Abstract
We reconstructed 19,084 prokaryotic and 31,395 viral genomes from 787 Japanese gut metagenomes as Japanese metagenome-assembled genomes (JMAG) and Japanese Virus Database (JVD), which are large microbial genome datasets for a single population. Population-specific enrichment of the Bacillus subtilis and β-porphyranase among the JMAG could derive from the Japanese traditional food natto (fermented soybeans) and nori (laver), respectively. Dairy-related Enterococcus_B lactis and Streptococcus thermophilus were nominally associated with the East Asian-specific missense variant rs671:G>A in ALDH2, which was associated with dairy consumption. Of the species-level viral genome clusters in the JVD, 62.9% were novel. The β crAss-like phage composition was low among the Japanese but relatively high among African and Oceanian peoples. Evaluations of the association between crAss-like phages and diseases showed significant disease-specific associations. Our large catalog of virus-host pairs identified the positive correlation between the abundance of the viruses and their hosts.
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Affiliation(s)
- Yoshihiko Tomofuji
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita 565-0871, Japan,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan,Corresponding author
| | - Toshihiro Kishikawa
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita 565-0871, Japan,Department of Otorhinolaryngology-Head and Neck Surgery, Osaka University Graduate School of Medicine, Suita 565-0871, Japan,Department of Head and Neck Surgery, Aichi Cancer Center Hospital, Nagoya 464-8681, Japan
| | - Yuichi Maeda
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan,Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan,Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Kotaro Ogawa
- Department of Neurology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Yuriko Otake-Kasamoto
- Department of Gastroenterology and Hepatology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Shuhei Kawabata
- Department of Neurosurgery, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Takuro Nii
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan,Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Tatsusada Okuno
- Department of Neurology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Eri Oguro-Igashira
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan,Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Makoto Kinoshita
- Department of Neurology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Masatoshi Takagaki
- Department of Neurosurgery, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Naoki Oyama
- Department of Stroke Medicine, Kawasaki Medical School, Kurashiki 701-0192, Japan
| | - Kenichi Todo
- Department of Neurology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita 565-0871, Japan,Department of Pediatrics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan,Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita 565-0871, Japan
| | - Kyuto Sonehara
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita 565-0871, Japan,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan
| | - Mayu Yagita
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan,Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Akiko Hosokawa
- Department of Neurology, Suita Municipal Hospital, Suita 564-8567, Japan
| | - Daisuke Motooka
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan,Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan
| | - Yuki Matsumoto
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan
| | - Hidetoshi Matsuoka
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano 586-8521, Japan
| | - Maiko Yoshimura
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano 586-8521, Japan
| | - Shiro Ohshima
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano 586-8521, Japan
| | - Shinichiro Shinzaki
- Department of Gastroenterology and Hepatology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Shota Nakamura
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan,Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan
| | - Hideki Iijima
- Department of Gastroenterology and Hepatology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Hidenori Inohara
- Department of Otorhinolaryngology-Head and Neck Surgery, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Haruhiko Kishima
- Department of Neurosurgery, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Tetsuo Takehara
- Department of Gastroenterology and Hepatology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Hideki Mochizuki
- Department of Neurology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Kiyoshi Takeda
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan,WPI Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan
| | - Atsushi Kumanogoh
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan,Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan,Department of Immunopathology, Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita 565-0871, Japan,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan,Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita 565-0871, Japan,Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Tsurumi 230-0045, Japan,Center for Infectious Disease Education and Research, Osaka University, Suita 565-0871, Japan,Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan,Corresponding author
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Fujimoto K, Miyaoka D, Uematsu S. Characterization of the human gut virome in metabolic and autoimmune diseases. Inflamm Regen 2022; 42:32. [PMID: 36316749 PMCID: PMC9623931 DOI: 10.1186/s41232-022-00218-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 06/27/2022] [Indexed: 11/05/2022] Open
Abstract
The intestinal microbiome is dominated by bacteria and plays a pivotal role in the occurrence and development of disease, including several metabolic and autoimmune disorders. While intestinal viral communities, primarily made up of bacteriophages, are also thought to play a role in disease pathogenesis in the gastrointestinal tract, they have received much less attention than intestinal bacteria. Thus, there is limited information about the relationship between bacteriophages and disease. This review explores a potential role for the intestinal viral microbiome in various metabolic and autoimmune diseases.
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Affiliation(s)
- Kosuke Fujimoto
- Department of Immunology and Genomics, Graduate School of Medicine, Osaka Metropolitan University, 1-4-3 Asahi-machi, Abeno-ku, Osaka, 545-8585 Japan ,grid.26999.3d0000 0001 2151 536XDivision of Metagenome Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639 Japan ,grid.26999.3d0000 0001 2151 536XDivision of Innate Immune Regulation, International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639 Japan
| | - Daichi Miyaoka
- Department of Immunology and Genomics, Graduate School of Medicine, Osaka Metropolitan University, 1-4-3 Asahi-machi, Abeno-ku, Osaka, 545-8585 Japan
| | - Satoshi Uematsu
- Department of Immunology and Genomics, Graduate School of Medicine, Osaka Metropolitan University, 1-4-3 Asahi-machi, Abeno-ku, Osaka, 545-8585 Japan ,grid.26999.3d0000 0001 2151 536XDivision of Metagenome Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639 Japan ,grid.26999.3d0000 0001 2151 536XDivision of Innate Immune Regulation, International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639 Japan ,grid.26999.3d0000 0001 2151 536XCollaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
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Guo R, Li S, Zhang Y, Zhang Y, Wang G, Ullah H, Ma Y, Yan Q. Dysbiotic Oral and Gut Viromes in Untreated and Treated Rheumatoid Arthritis Patients. Microbiol Spectr 2022; 10:e0034822. [PMID: 36040159 PMCID: PMC9603985 DOI: 10.1128/spectrum.00348-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 08/03/2022] [Indexed: 11/20/2022] Open
Abstract
Rheumatoid arthritis (RA) is influenced by oral and gut bacteria; however, much less is known about the relationship between oral or gut viromes and RA. Here, we performed whole-oral- and whole-gut-virome analyses based on shotgun sequencing of 497 samples. A comparative analysis of the oral and gut viromes in healthy controls and untreated and treated RA patients was performed, and system interaction networks among viruses, bacteria, and RA-associated clinical indices were constructed to address the potential relationship between the virome and RA by principal-coordinate analysis, distance-based redundancy analysis, permutational multivariate analysis, Spearman correlation coefficient analysis, and random-forest model analysis. The results showed that the viromes could be profiled in dental plaque, saliva, and fecal samples, among which saliva had the highest within-sample diversity. Importantly, significantly different diversities and compositions of the oral (i.e., dental plaque and saliva) viromes were observed not only between RA patients and healthy controls but also between untreated and treated RA patients, yet there were relatively minor differences in the gut viromes. Furthermore, to understand how these viruses affected the bacteriome, a virus-bacterium interaction network was constructed from dental plaque, saliva, and fecal samples of RA patients. Additionally, some RA-associated oral taxa, including Lactococcus phage (vOTU70), Bacteroides vulgatus, Lactococcus lactis, Escherichia coli, and Neisseria elongata, were correlated with the RA-related clinical indices. Whole-virome analysis illustrated the potential role of the oral and gut viromes in affecting our body either directly or via bacteria, which characterized neglected and new candidates contributing to the development of RA. IMPORTANCE Our results demonstrated community variation among dental plaque, saliva, and fecal viromes. In oral and gut samples from untreated and treated RA patients, the perturbance of viral composition and the correlation network of microbes and RA-associated clinical indices might be involved in the pathogenicity of RA. The findings in this study expand the knowledge of the potential role of oral and gut viral communities in the development of RA and may contribute to research on correlations between viruses and other diseases.
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Affiliation(s)
- Ruochun Guo
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
- Puensum Genetech Institute, Wuhan, China
| | - Shenghui Li
- Puensum Genetech Institute, Wuhan, China
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Yu Zhang
- Puensum Genetech Institute, Wuhan, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan, 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
| | - Yufang Ma
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Qiulong Yan
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
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35
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Yaigoub H, Fath N, Tirichen H, Wu C, Li R, Li Y. Bidirectional crosstalk between dysbiotic gut microbiota and systemic lupus erythematosus: What is new in therapeutic approaches? Clin Immunol 2022; 244:109109. [PMID: 36087683 DOI: 10.1016/j.clim.2022.109109] [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: 07/25/2022] [Revised: 08/25/2022] [Accepted: 08/30/2022] [Indexed: 11/18/2022]
Abstract
Systemic lupus erythematosus is an autoimmune disease characterized by chronic inflammation and multiple organs damage. Its pathogenesis is complex and involves multiple factors including gut microbiota. Accumulating evidence indicates the interaction of microbial communities with the host immune system to maintain a state of homeostasis. Imbalances within the gut microbial composition and function may contribute to the development of many autoimmune diseases including SLE. In this review, we aim to highlight the dysregulation of commensal bacteria and their metabolites in the gastrointestinal tract and the resulting autoimmune responses in lupus and to decrypt the cross-link between the altered gut microbiota and the immune system in the SLE condition. We also provide new insights into targeting gut microbiota as a promising therapeutic approach to treat and manage SLE.
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Affiliation(s)
- Hasnaa Yaigoub
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Nada Fath
- Comparative Anatomy Unit, Department of Biological and Pharmacological Veterinary Sciences, Hassan II Agronomy and Veterinary Medicine Institute, Rabat-Instituts, Rabat, Morocco
| | - Hasna Tirichen
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Changxin Wu
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Rongshan Li
- Department of Nephrology, The Fifth Hospital (Shanxi Provincial People's Hospital) of Shanxi Medical University, Taiyuan, China; Shanxi Provincial Key Laboratory of Kidney Disease, Taiyuan, China
| | - Yafeng Li
- Department of Nephrology, The Fifth Hospital (Shanxi Provincial People's Hospital) of Shanxi Medical University, Taiyuan, China; Shanxi Provincial Key Laboratory of Kidney Disease, Taiyuan, China; Academy of Microbial Ecology, Shanxi Medical University, Taiyuan, China.
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36
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Xu W, Xu L, Xu C. Relationship between Helicobacter pylori infection and gastrointestinal microecology. Front Cell Infect Microbiol 2022; 12:938608. [PMID: 36061875 PMCID: PMC9433739 DOI: 10.3389/fcimb.2022.938608] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 08/04/2022] [Indexed: 11/13/2022] Open
Abstract
The prevalence of Helicobacter pylori (H. pylori) infection has exceeded 50% worldwide, and it is considered a high-risk factor for chronic gastritis, peptic ulcer, gastric adenocarcinoma, gastroesophageal reflux disease and functional dyspepsia. H. pylori drug resistance is a common problem worldwide. In recent years, the relationship between H. pylori infection and gastrointestinal microecology has received much attention. H. pylori infection changes the structure and composition of gastrointestinal microflora by regulating the gastrointestinal microecological environment, local pH value, cytokines and antimicrobial peptides, and immune response and then plays a crucial role in the occurrence and development of digestive system tumors, liver metabolism and extragastrointestinal diseases. The quadruple strategy of H. pylori eradication can also aggravate gastrointestinal microflora disorder. However, probiotics can reduce intestinal flora changes and imbalances through different mechanisms, thus enhancing the efficacy of H. pylori eradication therapy and reducing adverse reactions caused by eradication therapy. Therefore, this paper reviews the relationship between H. pylori infection and gastrointestinal microecology and its clinical application, providing a basis for clinical treatment.
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Affiliation(s)
- Wenting Xu
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Liming Xu
- Department of Pathology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chengfu Xu
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- *Correspondence: Chengfu Xu,
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37
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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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Abstract
CONTEXT Thyroid eye disease (TED), a vision-threatening and disfiguring autoimmune process, has thwarted our efforts to understand its pathogenesis and develop effective and safe treatments. Recent scientific advances have facilitated improved treatment options. OBJECTIVE Review historically remote and recent advances in understanding TED. DESIGN/SETTING/PARTICIPANTS PubMed was scanned using search terms including thyroid-associated ophthalmopathy, thyroid eye disease, Graves' orbitopathy, autoimmune thyroid disease, and orbital inflammation. MAIN OUTCOME MEASURES Strength of scientific evidence, size, scope, and controls of clinical trials/observations. RESULTS Glucocorticoid steroids are widely prescribed systemic medical therapy. They can lessen inflammation-related manifestations of TED but fail to reliably reduce proptosis and diplopia, 2 major causes of morbidity. Other current therapies include mycophenolate, rituximab (anti-CD20 B cell-depleting monoclonal antibody), tocilizumab (interleukin-6 receptor antagonist), and teprotumumab (IGF-I receptor inhibitor). Several new therapeutic approaches have been proposed including targeting prostaglandin receptors, vascular endothelial growth factor, mTOR, and cholesterol pathways. Of potentially greater long-term importance are attempts to restore immune tolerance. CONCLUSION Despite their current wide use, steroids may no longer enjoy first-tier status for TED as more effective and better tolerated medical options become available. Multiple current and emerging therapies, the rationales for which are rooted in theoretical and experimental science, promise better options. These include teprotumumab, rituximab, and tocilizumab. Restoration of immune tolerance could ultimately become the most effective and safe medical management for TED.
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Affiliation(s)
- Terry J Smith
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, Division of Metabolism, Endocrinology, and Diabetes, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48105, USA
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Chen Y, Lin J, Xiao L, Zhang X, Zhao L, Wang M, Li L. Gut microbiota in systemic lupus erythematosus: A fuse and a solution. J Autoimmun 2022; 132:102867. [PMID: 35932662 DOI: 10.1016/j.jaut.2022.102867] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 07/05/2022] [Indexed: 12/13/2022]
Abstract
Gut commensals help shape and mold host immune system and deeply influence human health. The disease spectrum of mankind that gut microbiome may associate with is ever-growing, but the mechanisms are still enigmas. Characterized by loss of self-tolerance and sustained self-attack, systemic lupus erythematosus (SLE) is labeled with chronic inflammation, production of autoantibodies and multisystem injury, which so far are mostly incurable. Gut microbiota and their metabolites, now known as important environmental triggers of local/systemic immune responses, have been proposed to be involved in SLE development and progression probably through the following mechanisms: translocation beyond their niches; molecular mimicry to cross-activate immune response targeting self-antigens; epitope spreading to expand autoantibodies spectrum; and bystander activation to promote systemic inflammation. Gut microbiota which varies between individuals may also influence the metabolism and bio-transformation of disease-modifying anti-rheumatic drugs, thus associated with the efficacy and toxicity of these drugs, adding another explanation for heterogenic therapeutic responses. Modulation of gut microbiota via diet, probiotics/prebiotics, antibiotics/phages, fecal microbiota transplantation, or helminth to restore immune tolerance and homeostasis is expected to be a promising neoadjuvant therapy for SLE. We reviewed the advances in this territory and discussed the application prospect of modulating gut microbiota in controlling SLE.
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Affiliation(s)
- Yanfei Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, China; Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Jin Lin
- Department of Rheumatology, The First Affiliated Hospital, College of Medicine, Zhejiang University, China
| | - Lanlan Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, China; Department of Rheumatology, The First Affiliated Hospital, College of Medicine, Zhejiang University, China
| | - Xuan Zhang
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Clinical Immunology Center, Chinese Academy of Medical Sciences & Peking Union Medical College, NO.1 Da Hua Road, Dong Dan, Beijing, 100730, China
| | - Lidan Zhao
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology, Beijing, 100730, China
| | - Min Wang
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Clinical Immunology Center, Chinese Academy of Medical Sciences & Peking Union Medical College, NO.1 Da Hua Road, Dong Dan, Beijing, 100730, China.
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, China; Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China.
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40
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Shkoporov AN, Turkington CJ, Hill C. Mutualistic interplay between bacteriophages and bacteria in the human gut. Nat Rev Microbiol 2022; 20:737-749. [PMID: 35773472 DOI: 10.1038/s41579-022-00755-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 12/12/2022]
Abstract
Bacteriophages (phages) are often described as obligate predators of their bacterial hosts, and phage predation is one of the leading forces controlling the density and distribution of bacterial populations. Every 48 h half of all bacteria on Earth are killed by phages. Efficient killing also forms the basis of phage therapy in humans and animals and the use of phages as food preservatives. In turn, bacteria have a plethora of resistance systems against phage attack, but very few bacterial species, if any, have entirely escaped phage predation. However, in complex communities and environments such as the human gut, this antagonistic model of attack and counter-defence does not fully describe the scope of phage-bacterium interactions. In this Review, we explore some of the more mutualistic aspects of phage-bacterium interactions in the human gut, and we suggest that the relationship between phages and their bacterial hosts in the gut is best characterized not as a fight to the death between enemies but rather as a mutualistic relationship between partners.
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Affiliation(s)
- Andrey N Shkoporov
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland. .,Department of Medicine, University College Cork, Cork, Ireland.
| | | | - Colin Hill
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland.
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41
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Zuo W, Michail S, Sun F. Metagenomic Analyses of Multiple Gut Datasets Revealed the Association of Phage Signatures in Colorectal Cancer. Front Cell Infect Microbiol 2022; 12:918010. [PMID: 35782128 PMCID: PMC9240273 DOI: 10.3389/fcimb.2022.918010] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/12/2022] [Indexed: 12/24/2022] Open
Abstract
The association of colorectal cancer (CRC) and the human gut microbiome dysbiosis has been the focus of several studies in the past. Many bacterial taxa have been shown to have differential abundance among CRC patients compared to healthy controls. However, the relationship between CRC and non-bacterial gut microbiome such as the gut virome is under-studied and not well understood. In this study we conducted a comprehensive analysis of the association of viral abundances with CRC using metagenomic shotgun sequencing data of 462 CRC subjects and 449 healthy controls from 7 studies performed in 8 different countries. Despite the high heterogeneity, our results showed that the virome alpha diversity was consistently higher in CRC patients than in healthy controls (p-value <0.001). This finding is in sharp contrast to previous reports of low alpha diversity of prokaryotes in CRC compared to healthy controls. In addition to the previously known association of Podoviridae, Siphoviridae and Myoviridae with CRC, we further demonstrate that Herelleviridae, a newly constructed viral family, is significantly depleted in CRC subjects. Our interkingdom association analysis reveals a less intertwined correlation between the gut virome and bacteriome in CRC compared to healthy controls. Furthermore, we show that the viral abundance profiles can be used to accurately predict CRC disease status (AUROC >0.8) in both within-study and cross-study settings. The combination of training sets resulted in rather generalized and accurate prediction models. Our study clearly shows that subjects with colorectal cancer harbor a distinct human gut virome profile which may have an important role in this disease.
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Affiliation(s)
- Wenxuan Zuo
- Quantitative and Computational Biology Department, University of Southern California, Los Angeles, CA, United States
| | - Sonia Michail
- Department of Pediatrics, Keck School of Medicine of the University of Southern California, Los Angeles, CA, United States
| | - Fengzhu Sun
- Quantitative and Computational Biology Department, University of Southern California, Los Angeles, CA, United States
- *Correspondence: Fengzhu Sun,
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