Uncovering specific taxonomic and functional alteration of gut microbiota in chronic kidney disease through 16S rRNA data
IntroductionChronic kidney disease (CKD) is worldwide healthcare burden with growing incidence and death rate. Emerging evidence demonstrated the compositional and functional differences of gut microbiota in patients with CKD. As such, gut microbial features can be developed as diagnostic biomarkers...
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Frontiers Media S.A.
2024-04-01
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| Series: | Frontiers in Cellular and Infection Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fcimb.2024.1363276/full |
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| author | Yangyang Zhang Weicong Zhong Wenting Liu Xiaohua Wang Gan Lin Jiawen Lin Junxuan Fang Xiangyu Mou Shan Jiang Jiayuan Huang Wenjing Zhao Zhihua Zheng |
| author_facet | Yangyang Zhang Weicong Zhong Wenting Liu Xiaohua Wang Gan Lin Jiawen Lin Junxuan Fang Xiangyu Mou Shan Jiang Jiayuan Huang Wenjing Zhao Zhihua Zheng |
| author_sort | Yangyang Zhang |
| collection | DOAJ |
| description | IntroductionChronic kidney disease (CKD) is worldwide healthcare burden with growing incidence and death rate. Emerging evidence demonstrated the compositional and functional differences of gut microbiota in patients with CKD. As such, gut microbial features can be developed as diagnostic biomarkers and potential therapeutic target for CKD.MethodsTo eliminate the outcome bias arising from factors such as geographical distribution, sequencing platform, and data analysis techniques, we conducted a comprehensive analysis of the microbial differences between patients with CKD and healthy individuals based on multiple samples worldwide. A total of 980 samples from six references across three nations were incorporated from the PubMed, Web of Science, and GMrepo databases. The obtained 16S rRNA microbiome data were subjected to DADA2 processing, QIIME2 and PICRUSt2 analyses.ResultsThe gut microbiota of patients with CKD differs significantly from that of healthy controls (HC), with a substantial decrease in the microbial diversity among the CKD group. Moreover, a significantly reduced abundance of bacteria Faecalibacterium prausnitzii (F. prausnitzii) was detected in the CKD group through linear discriminant analysis effect size (LEfSe) analysis, which may be associated with the alleviating effects against CKD. Notably, we identified CKD-depleted F. prausnitzii demonstrated a significant negative correlation with three pathways based on predictive functional analysis, suggesting its potential role in regulating systemic acidbase disturbance and pro-oxidant metabolism.DiscussionOur findings demonstrated notable alterations of gut microbiota in CKD patients. Specific gut-beneficial microbiota, especially F. prausnitzii, may be developed as a preventive and therapeutic tool for CKD clinical management. |
| first_indexed | 2024-04-24T07:44:18Z |
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| id | doaj.art-208a15f64a6e47ddb15ec1cb6d11630c |
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| language | English |
| last_indexed | 2024-04-24T07:44:18Z |
| publishDate | 2024-04-01 |
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| record_format | Article |
| series | Frontiers in Cellular and Infection Microbiology |
| spelling | doaj.art-208a15f64a6e47ddb15ec1cb6d11630c2024-04-19T04:36:05ZengFrontiers Media S.A.Frontiers in Cellular and Infection Microbiology2235-29882024-04-011410.3389/fcimb.2024.13632761363276Uncovering specific taxonomic and functional alteration of gut microbiota in chronic kidney disease through 16S rRNA dataYangyang Zhang0Weicong Zhong1Wenting Liu2Xiaohua Wang3Gan Lin4Jiawen Lin5Junxuan Fang6Xiangyu Mou7Shan Jiang8Jiayuan Huang9Wenjing Zhao10Zhihua Zheng11Department of Nephrology, Center of Kidney and Urology, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, ChinaShenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, ChinaShenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, ChinaDepartment of Nephrology, Center of Kidney and Urology, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, ChinaShenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, ChinaDepartment of Nephrology, Center of Kidney and Urology, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, ChinaDepartment of Nephrology, Center of Kidney and Urology, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, ChinaShenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, ChinaDepartment of Nephrology, Center of Kidney and Urology, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, ChinaShenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, ChinaShenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, ChinaDepartment of Nephrology, Center of Kidney and Urology, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, ChinaIntroductionChronic kidney disease (CKD) is worldwide healthcare burden with growing incidence and death rate. Emerging evidence demonstrated the compositional and functional differences of gut microbiota in patients with CKD. As such, gut microbial features can be developed as diagnostic biomarkers and potential therapeutic target for CKD.MethodsTo eliminate the outcome bias arising from factors such as geographical distribution, sequencing platform, and data analysis techniques, we conducted a comprehensive analysis of the microbial differences between patients with CKD and healthy individuals based on multiple samples worldwide. A total of 980 samples from six references across three nations were incorporated from the PubMed, Web of Science, and GMrepo databases. The obtained 16S rRNA microbiome data were subjected to DADA2 processing, QIIME2 and PICRUSt2 analyses.ResultsThe gut microbiota of patients with CKD differs significantly from that of healthy controls (HC), with a substantial decrease in the microbial diversity among the CKD group. Moreover, a significantly reduced abundance of bacteria Faecalibacterium prausnitzii (F. prausnitzii) was detected in the CKD group through linear discriminant analysis effect size (LEfSe) analysis, which may be associated with the alleviating effects against CKD. Notably, we identified CKD-depleted F. prausnitzii demonstrated a significant negative correlation with three pathways based on predictive functional analysis, suggesting its potential role in regulating systemic acidbase disturbance and pro-oxidant metabolism.DiscussionOur findings demonstrated notable alterations of gut microbiota in CKD patients. Specific gut-beneficial microbiota, especially F. prausnitzii, may be developed as a preventive and therapeutic tool for CKD clinical management.https://www.frontiersin.org/articles/10.3389/fcimb.2024.1363276/fullchronic kidney diseasegut microbiota16S rRNAbiomarkerprobiotics |
| spellingShingle | Yangyang Zhang Weicong Zhong Wenting Liu Xiaohua Wang Gan Lin Jiawen Lin Junxuan Fang Xiangyu Mou Shan Jiang Jiayuan Huang Wenjing Zhao Zhihua Zheng Uncovering specific taxonomic and functional alteration of gut microbiota in chronic kidney disease through 16S rRNA data Frontiers in Cellular and Infection Microbiology chronic kidney disease gut microbiota 16S rRNA biomarker probiotics |
| title | Uncovering specific taxonomic and functional alteration of gut microbiota in chronic kidney disease through 16S rRNA data |
| title_full | Uncovering specific taxonomic and functional alteration of gut microbiota in chronic kidney disease through 16S rRNA data |
| title_fullStr | Uncovering specific taxonomic and functional alteration of gut microbiota in chronic kidney disease through 16S rRNA data |
| title_full_unstemmed | Uncovering specific taxonomic and functional alteration of gut microbiota in chronic kidney disease through 16S rRNA data |
| title_short | Uncovering specific taxonomic and functional alteration of gut microbiota in chronic kidney disease through 16S rRNA data |
| title_sort | uncovering specific taxonomic and functional alteration of gut microbiota in chronic kidney disease through 16s rrna data |
| topic | chronic kidney disease gut microbiota 16S rRNA biomarker probiotics |
| url | https://www.frontiersin.org/articles/10.3389/fcimb.2024.1363276/full |
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