Systematic Microbiome Dysbiosis Is Associated with IgA Nephropathy
ABSTRACT IgA nephropathy (IgAN) is reportedly associated with microbial dysbiosis. However, the microbiome dysregulation of IgAN patients across multiple niches remains unclear. To gain a systematic understanding of microbial dysbiosis, we conducted large-scale 16S rRNA gene sequencing in IgAN patie...
| 出版年: | Microbiology Spectrum |
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| 主要な著者: | , , , , , , , , , , , , , |
| フォーマット: | 論文 |
| 言語: | 英語 |
| 出版事項: |
American Society for Microbiology
2023-06-01
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| 主題: | |
| オンライン･アクセス: | https://journals.asm.org/doi/10.1128/spectrum.05202-22 |
| _version_ | 1851907200224591872 |
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| author | Fengtao Cai Chenfen Zhou Na Jiao Xinling Liang Zhiming Ye Wei Chen Qiongqiong Yang Hui Peng Ying Tang Chaoqun Niu Guoping Zhao Zefeng Wang Guoqing Zhang Xueqing Yu |
| author_facet | Fengtao Cai Chenfen Zhou Na Jiao Xinling Liang Zhiming Ye Wei Chen Qiongqiong Yang Hui Peng Ying Tang Chaoqun Niu Guoping Zhao Zefeng Wang Guoqing Zhang Xueqing Yu |
| author_sort | Fengtao Cai |
| collection | DOAJ |
| container_title | Microbiology Spectrum |
| description | ABSTRACT IgA nephropathy (IgAN) is reportedly associated with microbial dysbiosis. However, the microbiome dysregulation of IgAN patients across multiple niches remains unclear. To gain a systematic understanding of microbial dysbiosis, we conducted large-scale 16S rRNA gene sequencing in IgAN patients and healthy volunteers across 1,732 oral, pharynx, gut, and urine samples. We observed a niche-specific increase of several opportunistic pathogens, including Bergeyella and Capnocytophaga in the oral and pharynx, whereas some beneficial commensals decreased in IgAN patients. Similar alterations were also observed in the early versus advanced stage of chronic kidney disease (CKD) progression. Moreover, Bergeyella, Capnocytophaga, and Comamonas in the oral and pharynx were positively associated with creatinine and urea, indicating renal lesions. Random forest classifiers were developed by using the microbial abundance to predict IgAN, achieving an optimal accuracy of 0.879 in the discovery phase and 0.780 in the validation phase. IMPORTANCE This study provides microbial profiles of IgAN across multiple niches and underlines the potential of these biomarkers as promising, noninvasive tools with which to differentiate IgAN patients for clinical applications. |
| format | Article |
| id | doaj-art-b5d6d2b85539418e9c6f563c7fe3c4e2 |
| institution | Directory of Open Access Journals |
| issn | 2165-0497 |
| language | English |
| publishDate | 2023-06-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| spelling | doaj-art-b5d6d2b85539418e9c6f563c7fe3c4e22025-08-19T22:03:21ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972023-06-0111310.1128/spectrum.05202-22Systematic Microbiome Dysbiosis Is Associated with IgA NephropathyFengtao Cai0Chenfen Zhou1Na Jiao2Xinling Liang3Zhiming Ye4Wei Chen5Qiongqiong Yang6Hui Peng7Ying Tang8Chaoqun Niu9Guoping Zhao10Zefeng Wang11Guoqing Zhang12Xueqing Yu13School of Medicine, South China University of Technology, Guangzhou, ChinaNational Genomics Data Center & Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, ChinaNational Clinical Research Center for Child Health, the Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, ChinaDepartment of Nephrology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, ChinaDepartment of Nephrology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, ChinaDepartment of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, ChinaDepartment of Nephrology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, ChinaDepartment of Nephrology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, ChinaDepartment of Nephrology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, ChinaNational Genomics Data Center & Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, ChinaNational Genomics Data Center & Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, ChinaNational Genomics Data Center & Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, ChinaNational Genomics Data Center & Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, ChinaSchool of Medicine, South China University of Technology, Guangzhou, ChinaABSTRACT IgA nephropathy (IgAN) is reportedly associated with microbial dysbiosis. However, the microbiome dysregulation of IgAN patients across multiple niches remains unclear. To gain a systematic understanding of microbial dysbiosis, we conducted large-scale 16S rRNA gene sequencing in IgAN patients and healthy volunteers across 1,732 oral, pharynx, gut, and urine samples. We observed a niche-specific increase of several opportunistic pathogens, including Bergeyella and Capnocytophaga in the oral and pharynx, whereas some beneficial commensals decreased in IgAN patients. Similar alterations were also observed in the early versus advanced stage of chronic kidney disease (CKD) progression. Moreover, Bergeyella, Capnocytophaga, and Comamonas in the oral and pharynx were positively associated with creatinine and urea, indicating renal lesions. Random forest classifiers were developed by using the microbial abundance to predict IgAN, achieving an optimal accuracy of 0.879 in the discovery phase and 0.780 in the validation phase. IMPORTANCE This study provides microbial profiles of IgAN across multiple niches and underlines the potential of these biomarkers as promising, noninvasive tools with which to differentiate IgAN patients for clinical applications.https://journals.asm.org/doi/10.1128/spectrum.05202-22IgA nephropathyoralpharynxguturinemicrobiome |
| spellingShingle | Fengtao Cai Chenfen Zhou Na Jiao Xinling Liang Zhiming Ye Wei Chen Qiongqiong Yang Hui Peng Ying Tang Chaoqun Niu Guoping Zhao Zefeng Wang Guoqing Zhang Xueqing Yu Systematic Microbiome Dysbiosis Is Associated with IgA Nephropathy IgA nephropathy oral pharynx gut urine microbiome |
| title | Systematic Microbiome Dysbiosis Is Associated with IgA Nephropathy |
| title_full | Systematic Microbiome Dysbiosis Is Associated with IgA Nephropathy |
| title_fullStr | Systematic Microbiome Dysbiosis Is Associated with IgA Nephropathy |
| title_full_unstemmed | Systematic Microbiome Dysbiosis Is Associated with IgA Nephropathy |
| title_short | Systematic Microbiome Dysbiosis Is Associated with IgA Nephropathy |
| title_sort | systematic microbiome dysbiosis is associated with iga nephropathy |
| topic | IgA nephropathy oral pharynx gut urine microbiome |
| url | https://journals.asm.org/doi/10.1128/spectrum.05202-22 |
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