1
|
Zhang Y, Zhong W, Liu W, Wang X, Lin G, Lin J, Fang J, Mou X, Jiang S, Huang J, Zhao W, Zheng Z. Uncovering specific taxonomic and functional alteration of gut microbiota in chronic kidney disease through 16S rRNA data. Front Cell Infect Microbiol 2024; 14:1363276. [PMID: 38707511 PMCID: PMC11066246 DOI: 10.3389/fcimb.2024.1363276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/01/2024] [Indexed: 05/07/2024] Open
Abstract
Introduction Chronic 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. Methods To 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. Results The 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. Discussion Our 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.
Collapse
Affiliation(s)
- Yangyang Zhang
- Department of Nephrology, Center of Kidney and Urology, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, China
| | - Weicong Zhong
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, China
| | - Wenting Liu
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, China
| | - Xiaohua Wang
- Department of Nephrology, Center of Kidney and Urology, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, China
| | - Gan Lin
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, China
| | - Jiawen Lin
- Department of Nephrology, Center of Kidney and Urology, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, China
| | - Junxuan Fang
- Department of Nephrology, Center of Kidney and Urology, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, China
| | - Xiangyu Mou
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, China
| | - Shan Jiang
- Department of Nephrology, Center of Kidney and Urology, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, China
| | - Jiayuan Huang
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, China
| | - Wenjing Zhao
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, China
| | - Zhihua Zheng
- Department of Nephrology, Center of Kidney and Urology, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, China
| |
Collapse
|
2
|
Hu ZQ, Hung YM, Chen LH, Lai LC, Pan MH, Chuang EY, Tsai MH. NURECON: A Novel Online System for Determining Nutrition Requirements Based on Microbial Composition. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024; 21:254-264. [PMID: 38568776 DOI: 10.1109/tcbb.2024.3349572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Dietary habits have been proven to have an impact on the microbial composition and health of the human gut. Over the past decade, researchers have discovered that gut microbiota can use nutrients to produce metabolites that have major implications for human physiology. However, there is no comprehensive system that specifically focuses on identifying nutrient deficiencies based on gut microbiota, making it difficult to interpret and compare gut microbiome data in the literature. This study proposes an analytical platform, NURECON, that can predict nutrient deficiency information in individuals by comparing their metagenomic information to a reference baseline. NURECON integrates a next-generation bacterial 16S rRNA analytical pipeline (QIIME2), metabolic pathway prediction tools (PICRUSt2 and KEGG), and a food compound database (FooDB) to enable the identification of missing nutrients and provide personalized dietary suggestions. Metagenomic information from total number of 287 healthy subjects was used to establish baseline microbial composition and metabolic profiles. The uploaded data is analyzed and compared to the baseline for nutrient deficiency assessment. Visualization results include gut microbial composition, related enzymes, pathways, and nutrient abundance. NURECON is a user-friendly online platform that provides nutritional advice to support dietitians' research or menu design.
Collapse
|
3
|
Wu PH, Tseng YF, Liu W, Chuang YS, Tai CJ, Tung CW, Lai KY, Kuo MC, Chiu YW, Hwang SJ, Hung WC, Lin YT. Exploring the Relationship between Gut Microbiome Composition and Blood Indole-3-acetic Acid in Hemodialysis Patients. Biomedicines 2024; 12:148. [PMID: 38255253 PMCID: PMC10813781 DOI: 10.3390/biomedicines12010148] [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: 12/05/2023] [Revised: 12/29/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
Indole-3-acetic acid (IAA), a protein-bound uremic toxin resulting from gut microbiota-driven tryptophan metabolism, increases in hemodialysis (HD) patients. IAA may induce endothelial dysfunction, inflammation, and oxidative stress, elevating cardiovascular and cognitive risk in HD patients. However, research on the microbiome-IAA association is limited. This study aimed to explore the gut microbiome's relationship with plasma IAA levels in 72 chronic HD patients aged over 18 (August 2016-January 2017). IAA levels were measured using tandem mass spectrometry, and gut microbiome analysis utilized 16s rRNA next-generation sequencing. Linear discriminative analysis effect size and random forest analysis distinguished microbial species linked to IAA levels. Patients with higher IAA levels had reduced microbial diversity. Six microbial species significantly associated with IAA levels were identified; Bacteroides clarus, Bacteroides coprocola, Bacteroides massiliensi, and Alisteps shahii were enriched in low-IAA individuals, while Bacteroides thetaiotaomicron and Fusobacterium varium were enriched in high-IAA individuals. This study sheds light on specific gut microbiota species influencing IAA levels, enhancing our understanding of the intricate interactions between the gut microbiota and IAA metabolism.
Collapse
Grants
- MOST 111-2314-B-037-032-MY3 Ministry of Science and Technology, Taiwan
- MOST 111-2314-B-037 -083 -MY3 Ministry of Science and Technology, Taiwan
- MOST 109-2314-B-037-088 Ministry of Science and Technology, Taiwan
- KMUH111-1M60 Kaohsiung Medical University Hospital, Taiwan
- KMUH111-1R73 Kaohsiung Medical University Hospital, Taiwan
- KMUH111-1M09 Kaohsiung Medical University Hospital, Taiwan
- KMUH110-0M13 Kaohsiung Medical University Hospital, Taiwan
- KMUH110-0M73 Kaohsiung Medical University Hospital, Taiwan
- KMUH110-0M12 Kaohsiung Medical University Hospital, Taiwan
- KT112P012 Kaohsiung Medical University, Taiwan
- NHRIKMU-111-I003 Kaohsiung Medical University, Taiwan
- NHRIKMU-111-I003-2 Kaohsiung Medical University, Taiwan
- NHRIKMU-111-I003-4 Kaohsiung Medical University, Taiwan
- NHRIKMU-111-I001-3 Kaohsiung Medical University, Taiwan
- NPUST-KMU-111-P001 Kaohsiung Medical University, Taiwan
- KMU-DK(B)110003 Kaohsiung Medical University, Taiwan
- KMUH-DK(B)110003-1 Kaohsiung Medical University, Taiwan
- KMU-DK(B)110003-2 Kaohsiung Medical University, Taiwan
- KMU-DK(B)110003-3 Kaohsiung Medical University, Taiwan
- KMU-DK(B)110003-4 Kaohsiung Medical University, Taiwan
- KMU-DK(B)110003-5 Kaohsiung Medical University, Taiwan
Collapse
Affiliation(s)
- Ping-Hsun Wu
- Division of Nephrology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (P.-H.W.); (M.-C.K.); (Y.-W.C.); (S.-J.H.)
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Center for Big Data Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Research Center for Precision Environmental Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Yu-Fang Tseng
- Department of Family Medicine, Kaohsiung Municipal Hsiao-Kang Hospital, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Wangta Liu
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Yun-Shiuan Chuang
- Center for Big Data Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Research Center for Precision Environmental Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Family Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan;
| | - Chi-Jung Tai
- Department of Family Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan;
| | - Chun-Wei Tung
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli 350, Taiwan;
- Graduate Institute of Data Science, College of Management, Taipei Medical University, Taipei 110, Taiwan
| | - Kean-Yee Lai
- Post Baccalaureate Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Mei-Chuan Kuo
- Division of Nephrology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (P.-H.W.); (M.-C.K.); (Y.-W.C.); (S.-J.H.)
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Yi-Wen Chiu
- Division of Nephrology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (P.-H.W.); (M.-C.K.); (Y.-W.C.); (S.-J.H.)
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Shang-Jyh Hwang
- Division of Nephrology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (P.-H.W.); (M.-C.K.); (Y.-W.C.); (S.-J.H.)
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Wei-Chun Hung
- Department of Microbiology and Immunology, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Yi-Ting Lin
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Center for Big Data Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Research Center for Precision Environmental Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Family Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan;
| |
Collapse
|
4
|
Ramanathan K, Padmanabhan G, Gulilat H, Malik T. Salivary microbiome in kidney diseases: A narrative review. Cell Biochem Funct 2023; 41:988-995. [PMID: 37795946 DOI: 10.1002/cbf.3864] [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: 05/04/2023] [Revised: 09/01/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023]
Abstract
Many research has been conducted since the microbiota's discovery that have focused on the role it plays in health and disease. Microbiota can be divided into categories like intestinal, oral, respiratory, and skin microbiota based on the specific localized areas. To maintain homeostasis and control immunological response, the microbial populations live in symbiosis with the host. On the other hand, dysbiosis of the microbiota can cause diseases including kidney diseases and the deregulation of body functioning. We discuss the current understanding of how various kidney diseases are caused by the salivary microbiome (SM) in this overview. First, we review the studies on the salivary microbiota in diverse clinical situations. The importance of the SM in diabetic kidney disease, chronic kidney disease, membranous nephropathy, and IgA nephropathy is next highlighted. We conclude that the characteristics of the SM of patients with various kidney diseases have revealed the potential of salivary microbial markers as noninvasive tool for the detection of various kidney diseases.
Collapse
Affiliation(s)
- Kumaresan Ramanathan
- Department of Biomedical Sciences, Institute of Health, Faculty of Medical Sciences, Jimma University, Jimma, Ethiopia
| | | | - Henok Gulilat
- Department of Biomedical Sciences, Institute of Health, Faculty of Medical Sciences, Jimma University, Jimma, Ethiopia
| | - Tabarak Malik
- Department of Biomedical Sciences, Institute of Health, Faculty of Medical Sciences, Jimma University, Jimma, Ethiopia
| |
Collapse
|
5
|
Wang Z, Cui S, Zhang T, Wang W, Li J, Chen YQ, Zhu SL. Akkermansia muciniphila supplementation improves glucose tolerance in intestinal Ffar4 knockout mice during the daily light to dark transition. mSystems 2023; 8:e0057323. [PMID: 37787527 PMCID: PMC10654094 DOI: 10.1128/msystems.00573-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/11/2023] [Indexed: 10/04/2023] Open
Abstract
IMPORTANCE Alterations in the intestinal environment are associated with various diseases, and FFAR4 is abundantly enriched in the intestine, where it has been shown to have the ability to regulate intestinal hormone secretion and intestinal microbiota; here, we confirmed previous reports. Meanwhile, we found that intestinal FFAR4 regulates glucagon-like peptide 1 secretion by decreasing Akkermansia muciniphila abundance and show that such change is associated with the level of glucose utilization at ZT12 in mice. Intestinal FFAR4 deficiency leads to severely impaired glucose tolerance at the ZT12 moment in mice, and Akkermansia muciniphila supplementation ameliorates the abnormal glucose utilization at the ZT12 moment caused by FFAR4 deficiency, which is very similar to the dawn phenomenon in diabetic patients. Collectively, our data suggest that intestinal Ffar4 deteriorates glucose tolerance at the daily light to dark transition by affecting Akkermansia muciniphila.
Collapse
Affiliation(s)
- Zhe Wang
- Jiangnan University Medical Center, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Siyuan Cui
- Jiangnan University Medical Center, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - TingTing Zhang
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wei Wang
- Jiangnan University Medical Center, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - JiaYu Li
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Y. Q. Chen
- Jiangnan University Medical Center, Wuxi School of Medicine, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Sheng long Zhu
- Jiangnan University Medical Center, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| |
Collapse
|
6
|
Anegkamol W, Kamkang P, Hunthai S, Kaewwongse M, Taweevisit M, Chuaypen N, Rattanachaisit P, Dissayabutra T. The Usefulness of Resistant Maltodextrin and Chitosan Oligosaccharide in Management of Gut Leakage and Microbiota in Chronic Kidney Disease. Nutrients 2023; 15:3363. [PMID: 37571302 PMCID: PMC10420640 DOI: 10.3390/nu15153363] [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: 07/03/2023] [Revised: 07/14/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Microbiota-dysbiosis-induced gut leakage is a pathophysiologic change in chronic kidney disease (CKD), leading to the production of several uremic toxins and their absorption into the bloodstream to worsen the renal complications. We evaluate the benefits of resistant maltodextrin (RMD) and chitosan oligosaccharide (COS) supplements in cell culture and CKD-induced rats. The RMD exerted a significant anti-inflammatory effect in vitro and intestinal occludin and zonula occluden-1 up-regulation in CKD rats compared with inulin and COS. While all prebiotics slightly improved gut dysbiosis, RMD remarkably promoted the relative abundance and the combined abundance of Lactobacillus, Bifidobacteria, Akkermansia, and Roseburia in CKD rats. Supplements of RMD should be advantageous in the treatment of gut leakage and microbiota dysbiosis in CKD.
Collapse
Affiliation(s)
- Weerapat Anegkamol
- Metabolic Disease in Gastrointestinal and Urinary System Research Unit, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (W.A.); (P.K.); (S.H.); (N.C.); (P.R.)
| | - Panumas Kamkang
- Metabolic Disease in Gastrointestinal and Urinary System Research Unit, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (W.A.); (P.K.); (S.H.); (N.C.); (P.R.)
| | - Sittiphong Hunthai
- Metabolic Disease in Gastrointestinal and Urinary System Research Unit, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (W.A.); (P.K.); (S.H.); (N.C.); (P.R.)
| | - Maroot Kaewwongse
- Division of Physiology, School of Medical Sciences, University of Phayao, Phayao 56000, Thailand;
| | - Mana Taweevisit
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Natthaya Chuaypen
- Metabolic Disease in Gastrointestinal and Urinary System Research Unit, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (W.A.); (P.K.); (S.H.); (N.C.); (P.R.)
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pakkapon Rattanachaisit
- Metabolic Disease in Gastrointestinal and Urinary System Research Unit, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (W.A.); (P.K.); (S.H.); (N.C.); (P.R.)
- Department of Physiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Thasinas Dissayabutra
- Metabolic Disease in Gastrointestinal and Urinary System Research Unit, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (W.A.); (P.K.); (S.H.); (N.C.); (P.R.)
| |
Collapse
|
7
|
Gawey BJ, Khanna S. Clostridioides difficile Infection: Landscape and Microbiome Therapeutics. Gastroenterol Hepatol (N Y) 2023; 19:319-328. [PMID: 37706187 PMCID: PMC10496268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
Clostridioides difficile infection (CDI) is the leading cause of hospital-acquired diarrhea and is common in the community. Both younger individuals who may be healthy otherwise and older individuals with comorbid conditions are at risk for developing CDI, with the predominant risk factor being antibiotic use. Unlike other gastrointestinal infections, CDI is not self-limited, requires antimicrobial therapy, and tends to recur at high rates even without additional risk factor exposure. The goals of CDI management include controlling active symptoms and using a recurrence prevention strategy such as a narrow-spectrum antibiotic, tapered and pulsed regimens, antibody- based therapies (directed against toxin B), or microbiome restoration. In recent years, fecal microbiota transplantation (FMT) has been the most used modality to prevent recurrent CDI with high cure rates. Heterogeneity, lack of scalability, and serious adverse events from FMT have led to development of standardized microbiota restoration therapies (MRTs). The US Food and Drug Administration has approved 2 stool-derived MRTs for prevention of recurrent CDI: fecal microbiota, live-jslm, an enema-based therapy; and fecal microbiota spores, live-brpk, an oral therapy. A phase 3 trial for a synthetic oral MRT is underway. This article outlines the pathophysiology and treatment of CDI, focusing primarily on the gut microbiome and standardized MRTs.
Collapse
Affiliation(s)
- Brent J. Gawey
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Sahil Khanna
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| |
Collapse
|
8
|
Wang F, Li N, Ni S, Min Y, Wei K, Sun H, Fu Y, Liu Y, Lv D. The Effects of Specific Gut Microbiota and Metabolites on IgA Nephropathy-Based on Mendelian Randomization and Clinical Validation. Nutrients 2023; 15:nu15102407. [PMID: 37242290 DOI: 10.3390/nu15102407] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/02/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Although recent research suggests that alterations in gut microbiota and metabolites play a critical role in the pathophysiology of immunoglobulin A nephropathy (IgAN), the causal relationship between specific intestinal flora and metabolites and the risk of IgAN remains unclear. METHOD This study employed Mendelian randomization (MR) to investigate the causal association between gut microbiota and IgAN. To explore potential associations between gut microbiota and various outcomes, four MR methods were applied: inverse variance weighted (IVW), MR-Egger, weighted median, and weighted mode. If the results of the four methods are inconclusive, we prefer the IVW as the primary outcome. Additionally, MR-Egger, MR-PRESSO-Global, and Cochrane's Q tests were used to detect heterogeneity and pleiotropy. The stability of MR findings was assessed using the leave-one-out approach, and the strength of the causal relationship between exposure and outcome was tested using Bonferroni correction. Additional clinical samples were utilized to validate the results of Mendelian randomization, and the outcomes were visualized through an ROC curve, confusion matrix, and correlation analysis. RESULT This study examined a total of 15 metabolites and 211 microorganisms. Among them, eight bacteria and one metabolite were found to be associated with the risk of IgAN (p < 0.05). The Bonferroni-corrected test reveals that only Class. Actinobacteria (OR: 1.20, 95% CI: 1.07-1.36, p = 0.0029) have a significant causal relationship with IgAN. According to Cochrane's Q test, there is no substantial heterogeneity across different single-nucleotide polymorphisms (p > 0.05). Furthermore, MR-Egger and MR-PRESSO-Global tests (p > 0.05) showed no evidence of pleiotropy. No reverse causal association was found between the risk of IgAN and microbiota or metabolites (p > 0.05). Clinical specimens demonstrated the effectiveness and accuracy of Actinobacteria in distinguishing IgAN patients from those with other glomerular diseases (AUC = 0.9, 95% CI: 0.78-1.00). Additionally, our correlation analysis revealed a potential association between Actinobacteria abundance and increased albuminuria (r = 0.85) and poorer prognosis in IgAN patients (p = 0.01). CONCLUSION Through MR analysis, we established a causal link between Actinobacteria and the incidence of IgAN. Moreover, clinical validation using fecal samples indicated that Actinobacteria might be associated with the onset and poorer prognosis of IgAN. This finding could provide valuable biomarkers for early, noninvasive detection of the disease and potential therapeutic targets in IgAN.
Collapse
Affiliation(s)
- Fang Wang
- Institute of Nephrology, Liyang Hospital of Chinese Medicine, Liyang 213300, China
- Jiangsu Province Hospital of Traditional Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210000, China
| | - Ning Li
- Institute of Nephrology, Southeast University School of Medicine, Nanjing 210009, China
| | - Siming Ni
- Jiangsu Province Hospital of Traditional Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210000, China
| | - Yu Min
- Department of Biotherapy and National Clinical Research Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Kang Wei
- Yangzhou People's Hospital, Yangzhou University, Yangzhou 225000, China
| | - Hongbin Sun
- Jiangsu Province Hospital of Traditional Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210000, China
| | - Yuqi Fu
- Institute of Nephrology, Southeast University School of Medicine, Nanjing 210009, China
| | - Yalan Liu
- Jiangsu Province Hospital of Traditional Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210000, China
| | - Dan Lv
- Institute of Nephrology, Liyang Hospital of Chinese Medicine, Liyang 213300, China
- Jiangsu Province Hospital of Traditional Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210000, China
| |
Collapse
|
9
|
Voroneanu L, Burlacu A, Brinza C, Covic A, Balan GG, Nistor I, Popa C, Hogas S, Covic A. Gut Microbiota in Chronic Kidney Disease: From Composition to Modulation towards Better Outcomes-A Systematic Review. J Clin Med 2023; 12:jcm12051948. [PMID: 36902734 PMCID: PMC10003930 DOI: 10.3390/jcm12051948] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/22/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
BACKGROUND A bidirectional kidney-gut axis was described in patients with chronic kidney disease (CKD). On the one hand, gut dysbiosis could promote CKD progression, but on the other hand, studies reported specific gut microbiota alterations linked to CKD. Therefore, we aimed to systematically review the literature on gut microbiota composition in CKD patients, including those with advanced CKD stages and end-stage kidney disease (ESKD), possibilities to shift gut microbiota, and its impact on clinical outcomes. MATERIALS AND METHODS We performed a literature search in MEDLINE, Embase, Scopus, and Cochrane databases to find eligible studies using pre-specified keywords. Additionally, key inclusion and exclusion criteria were pre-defined to guide the eligibility assessment. RESULTS We retrieved 69 eligible studies which met all inclusion criteria and were analyzed in the present systematic review. Microbiota diversity was decreased in CKD patients as compared to healthy individuals. Ruminococcus and Roseburia had good power to discriminate between CKD patients and healthy controls (AUC = 0.771 and AUC = 0.803, respectively). Roseburia abundance was consistently decreased in CKD patients, especially in those with ESKD (p < 0.001). A model based on 25 microbiota dissimilarities had an excellent predictive power for diabetic nephropathy (AUC = 0.972). Several microbiota patterns were observed in deceased ESKD patients as compared to the survivor group (increased Lactobacillus, Yersinia, and decreased Bacteroides and Phascolarctobacterium levels). Additionally, gut dysbiosis was associated with peritonitis and enhanced inflammatory activity. In addition, some studies documented a beneficial effect on gut flora composition attributed to synbiotic and probiotic therapies. Large randomized clinical trials are required to investigate the impact of different microbiota modulation strategies on gut microflora composition and subsequent clinical outcomes. CONCLUSIONS Patients with CKD had an altered gut microbiome profile, even at early disease stages. Different abundance at genera and species levels could be used in clinical models to discriminate between healthy individuals and patients with CKD. ESKD patients with an increased mortality risk could be identified through gut microbiota analysis. Modulation therapy studies are warranted.
Collapse
Affiliation(s)
- Luminita Voroneanu
- Nephrology Department, Dialysis and Renal Transplant Center, “Dr. C.I. Parhon” University Hospital, 700503 Iasi, Romania
- Faculty of Medicine, ‘Grigore T. Popa’ University of Medicine, 700115 Iasi, Romania
| | - Alexandru Burlacu
- Faculty of Medicine, ‘Grigore T. Popa’ University of Medicine, 700115 Iasi, Romania
- Department of Interventional Cardiology, Cardiovascular Diseases Institute “Prof. Dr. George I.M. Georgescu”, 700503 Iasi, Romania
| | - Crischentian Brinza
- Faculty of Medicine, ‘Grigore T. Popa’ University of Medicine, 700115 Iasi, Romania
- Department of Interventional Cardiology, Cardiovascular Diseases Institute “Prof. Dr. George I.M. Georgescu”, 700503 Iasi, Romania
| | - Andreea Covic
- Nephrology Department, Dialysis and Renal Transplant Center, “Dr. C.I. Parhon” University Hospital, 700503 Iasi, Romania
- Faculty of Medicine, ‘Grigore T. Popa’ University of Medicine, 700115 Iasi, Romania
- Correspondence:
| | - Gheorghe G. Balan
- Faculty of Medicine, ‘Grigore T. Popa’ University of Medicine, 700115 Iasi, Romania
- Institute of Gastroenterology and Hepatology, St. 1 Spiridon Emergency County Hospital, 700111 Iasi, Romania
| | - Ionut Nistor
- Nephrology Department, Dialysis and Renal Transplant Center, “Dr. C.I. Parhon” University Hospital, 700503 Iasi, Romania
- Faculty of Medicine, ‘Grigore T. Popa’ University of Medicine, 700115 Iasi, Romania
| | - Cristina Popa
- Faculty of Medicine, ‘Grigore T. Popa’ University of Medicine, 700115 Iasi, Romania
| | - Simona Hogas
- Nephrology Department, Dialysis and Renal Transplant Center, “Dr. C.I. Parhon” University Hospital, 700503 Iasi, Romania
- Faculty of Medicine, ‘Grigore T. Popa’ University of Medicine, 700115 Iasi, Romania
| | - Adrian Covic
- Nephrology Department, Dialysis and Renal Transplant Center, “Dr. C.I. Parhon” University Hospital, 700503 Iasi, Romania
- Faculty of Medicine, ‘Grigore T. Popa’ University of Medicine, 700115 Iasi, Romania
| |
Collapse
|
10
|
Gut microbiome studies in CKD: opportunities, pitfalls and therapeutic potential. Nat Rev Nephrol 2023; 19:87-101. [PMID: 36357577 DOI: 10.1038/s41581-022-00647-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2022] [Indexed: 11/12/2022]
Abstract
Interest in gut microbiome dysbiosis and its potential association with the development and progression of chronic kidney disease (CKD) has increased substantially in the past 6 years. In parallel, the microbiome field has matured considerably as the importance of host-related and environmental factors is increasingly recognized. Past research output in the context of CKD insufficiently considered the myriad confounding factors that are characteristic of the disease. Gut microbiota-derived metabolites remain an interesting therapeutic target to decrease uraemic (cardio)toxicity. However, future studies on the effect of dietary and biotic interventions will require harmonization of relevant readouts to enable an in-depth understanding of the underlying beneficial mechanisms. High-quality standards throughout the entire microbiome analysis workflow are also of utmost importance to obtain reliable and reproducible results. Importantly, investigating the relative composition and abundance of gut bacteria, and their potential association with plasma uraemic toxins levels is not sufficient. As in other fields, the time has come to move towards in-depth quantitative and functional exploration of the patient's gut microbiome by relying on confounder-controlled quantitative microbial profiling, shotgun metagenomics and in vitro simulations of microorganism-microorganism and host-microorganism interactions. This step is crucial to enable the rational selection and monitoring of dietary and biotic intervention strategies that can be deployed as a personalized intervention in CKD.
Collapse
|
11
|
Li N, Wang Y, Wei P, Min Y, Yu M, Zhou G, Yuan G, Sun J, Dai H, Zhou E, He W, Sheng M, Gao K, Zheng M, Sun W, Zhou D, Zhang L. Causal Effects of Specific Gut Microbiota on Chronic Kidney Diseases and Renal Function-A Two-Sample Mendelian Randomization Study. Nutrients 2023; 15:nu15020360. [PMID: 36678231 PMCID: PMC9863044 DOI: 10.3390/nu15020360] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/02/2023] [Accepted: 01/05/2023] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Targeting the gut microbiota may become a new therapeutic to prevent and delay the progression of chronic kidney disease (CKD). Nonetheless, the causal relationship between specific intestinal flora and CKD is still unclear. MATERIALS AND METHOD To identify genetically predicted microbiota, we used summary data from genome-wide association studies on gut microbiota in 18340 participants from 24 cohorts. Furthermore, we genetically predicted the causal relationship between 211 gut microbiotas and six phenotypes (outcomes) (CKD, estimated glomerular filtration rate (eGFR), urine albumin to creatinine ratio (UACR), dialysis, rapid progress to CKD, and rapid decline of eGFR). Four Mendelian randomization (MR) methods, including inverse variance weighted (IVW), MR-Egger, weighted median, and weighted mode were used to investigate the casual relationship between gut microbiotas and various outcomes. The result of IVW was deemed as the primary result. Then, Cochrane's Q test, MR-Egger, and MR-PRESSO Global test were used to detect heterogeneity and pleiotropy. The leave-one method was used for testing the stability of MR results and Bonferroni-corrected was used to test the strength of the causal relationship between exposure and outcome. RESULTS Through the MR analysis of 211 microbiotas and six clinical phenotypes, a total of 36 intestinal microflora were found to be associated with various outcomes. Among them, Class Bacteroidia (=-0.005, 95% CI: -0.001 to -0.008, p = 0.002) has a strong causality with lower eGFR after the Bonferroni-corrected test, whereas phylum Actinobacteria (OR = 1.0009, 95%CI: 1.0003-1.0015, p = 0.0024) has a strong causal relationship with dialysis. The Cochrane's Q test reveals that there is no significant heterogeneity between various single nucleotide polymorphisms. In addition, no significant level of pleiotropy was found according to MR-Egger and MR-PRESSO Global tests. CONCLUSIONS Through the two-sample MR analysis, we identified the specific intestinal flora that has a causal relationship with the incidence and progression of CKD at the level of gene prediction, which may provide helpful biomarkers for early disease diagnosis and potential therapeutic targets for CKD.
Collapse
Affiliation(s)
- Ning Li
- Division of Nephrology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
| | - Yi Wang
- Division of Nephrology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
| | - Ping Wei
- Division of Nephrology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
| | - Yu Min
- Department of Biotherapy and National Clinical Research Center, Sichuan University, Chengdu 610041, China
| | - Manshu Yu
- Division of Nephrology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
| | - Guowei Zhou
- Division of Nephrology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
| | - Gui Yuan
- Division of Nephrology, Department of Medicine, University of Connecticut, School of Medicine, Farmington, CT 06030, USA
| | - Jinyi Sun
- Division of Nephrology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
| | - Huibo Dai
- Division of Nephrology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
| | - Enchao Zhou
- Division of Nephrology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
| | - Weiming He
- Division of Nephrology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
| | - Meixiao Sheng
- Division of Nephrology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
| | - Kun Gao
- Division of Nephrology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
| | - Min Zheng
- Division of Nephrology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
| | - Wei Sun
- Division of Nephrology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
| | - Dong Zhou
- Division of Nephrology, Department of Medicine, University of Connecticut, School of Medicine, Farmington, CT 06030, USA
- Correspondence: (D.Z.); (L.Z.)
| | - Lu Zhang
- Division of Nephrology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
- Correspondence: (D.Z.); (L.Z.)
| |
Collapse
|
12
|
Liu W, Huang J, Liu T, Hu Y, Shi K, Zhou Y, Zhang N. Changes in gut microbial community upon chronic kidney disease. PLoS One 2023; 18:e0283389. [PMID: 36952529 PMCID: PMC10035866 DOI: 10.1371/journal.pone.0283389] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 03/08/2023] [Indexed: 03/25/2023] Open
Abstract
With the increasing incidence and mortality of chronic kidney disease (CKD), targeted therapies for CKD have been explored constantly. The important role of gut microbiota on CKD has been emphasized increasingly, it is necessary to analyze the metabolic mechanism of CKD patients from the perspective of gut microbiota. In this study, bioinformatics was used to analyze the changes of gut microbiota between CKD and healthy control (HC) groups using 315 samples from NCBI database. Diversity analysis showed significant changes in evenness compared to the HC group. PCoA analysis revealed significant differences between the two groups at phylum level. In addition, the F/B ratio was higher in CKD group than in HC group, suggesting the disorder of gut microbiota, imbalance of energy absorption and the occurrence of metabolic syndrome in CKD group. The study found that compared with HC group, the abundance of bacteria associated with impaired kidney was increased in CKD group, such as Ralstonia and Porphyromonas, which were negatively associated with eGFR. PICRUSt2 was used to predict related functions and found that different pathways between the two groups were mainly related to metabolism, involving the metabolism of exogenous and endogenous substances, as well as Glycerophospholipid metabolism, which provided evidence for exploring the relationship between gut microbiota and lipid metabolism. Therefore, in subsequent studies, special attention should be paid to these bacteria and metabolic pathway, and animal experiments and metabolomics studies should be conducted explore the association between bacterial community and CKD, as well as the therapeutic effects of these microbial populations on CKD.
Collapse
Affiliation(s)
- Wu Liu
- Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jiaqi Huang
- Department of Radiation Oncology, Peking University Third Hospital, Beijing, China
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
| | - Tong Liu
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, China
| | - Yutian Hu
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, China
| | - Kaifeng Shi
- Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yi Zhou
- Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Department of Graduate Student, Beijing University of Chinese Medicine, Beijing, China
| | - Ning Zhang
- Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| |
Collapse
|
13
|
Wu YY, Cheng CX, Yang L, Ye QQ, Li WH, Jiang JY. Characterization of Gut Microbiome in the Mud Snail Cipangopaludina cathayensis in Response to High-Temperature Stress. Animals (Basel) 2022; 12:ani12182361. [PMID: 36139220 PMCID: PMC9494996 DOI: 10.3390/ani12182361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/30/2022] [Accepted: 09/07/2022] [Indexed: 11/29/2022] Open
Abstract
Simple Summary This study investigated the effects of high-temperature stress on the intestinal microbiome of Cipangopaludina cathayensis. High-temperature exposure significantly changed the intestinal microbiota structure of C. cathayensis. The relative abundance of putatively beneficial bacteria decreased, whereas the relative abundance of putatively pathogenic bacteria increased after thermal stress. Consistent with the trends of change in the intestinal microbiota, the high-temperature treatment inhibited some carbohydrate metabolism pathways and induced certain disease-related pathways. Thermal stress disrupts the homeostasis of gut microbiota, which may lead to disease outbreak in C. cathayensis. Abstract The mud snail Cipangopaludina cathayensis is a widely distributed species in China. Particularly in Guangxi province, mud snail farming contributes significantly to the economic development. However, global warming in recent decades poses a serious threat to global aquaculture production. The rising water temperature is harmful to aquatic animals. The present study explored the effects of high temperature on the intestinal microbiota of C. cathayensis. Snail intestinal samples were collected from the control and high-temperature groups on days 3 and 7 to determine the gut microbiota composition and diversity. Gut bacterial community composition was investigated using high-throughput sequencing of the V3–V4 region of bacterial 16S rRNA genes. Our results suggested that thermal stress altered the gut microbiome structure of C. cathayensis. At the phylum level, Proteobacteria, Bacteroidetes, and Firmicutes were dominant in C. cathayensis gut microbiota. The T2 treatment (32 ± 1 °C, day 7) significantly decreased the relative abundance of Firmicutes, Actinobacteria, and Deinococcus-Thermus. In T2, the abundance of several genera of putatively beneficial bacteria (Pseudomonas, Aeromonas, Rhodobacter, and Bacteroides) decreased, whereas the abundance of Halomonas—a pathogenic bacterial genus—increased. The functional prediction results indicated that T2 treatment inhibited some carbohydrate metabolism pathways and induced certain disease-related pathways (e.g., those related to systemic lupus erythematosus, Vibrio cholerae infection, hypertrophic cardiomyopathy, and shigellosis). Thus, high temperature profoundly affected the community structure and function of C. cathayensis gut microbiota. The results provide insights into the mechanisms associated with response of C. cathayensis intestinal microbiota to global warming.
Collapse
Affiliation(s)
- Yang-Yang Wu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin 541004, China
| | - Chun-Xing Cheng
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin 541004, China
| | - Liu Yang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin 541004, China
| | - Quan-Qing Ye
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin 541004, China
| | - Wen-Hong Li
- College of Animal Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, China
- Correspondence: (W.-H.L.); (J.-Y.J.); Tel.: +86-159-9447-9761 (W.-H.L.); +86-183-7830-1237 (J.-Y.J.)
| | - Jiao-Yun Jiang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin 541004, China
- Correspondence: (W.-H.L.); (J.-Y.J.); Tel.: +86-159-9447-9761 (W.-H.L.); +86-183-7830-1237 (J.-Y.J.)
| |
Collapse
|
14
|
Liu F, Sheng J, Hu L, Zhang B, Guo W, Wang Y, Gu Y, Jiang P, Lin H, Lydia B, Sun Y, Tang Y, Gu C, Wei S, Zhai Q, Chen W, Feng N. Salivary microbiome in chronic kidney disease: what is its connection to diabetes, hypertension, and immunity? J Transl Med 2022; 20:387. [PMID: 36059002 PMCID: PMC9441058 DOI: 10.1186/s12967-022-03602-5] [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: 05/11/2022] [Accepted: 08/19/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The association between oral dysbiosis and chronic kidney disease (CKD) has gained increasing attention in recent years. Diabetes and hypertension are the most common conditions in CKD. However, a case-control study with matched confounding variables on the salivary microbiome in CKD and the influence of diabetes and hypertension on the microbiome has never been reported. METHODS In our study, we compared the salivary microbiome profile between patients with CKD and healthy controls (HC) using 16S ribosomal DNA sequencing and examine its association with diabetes, hypertension, and immunity. RESULTS We observed that the bacterial community was skewed in the saliva of CKD, with increased Lautropia and Pseudomonas, and decreased Actinomyces, Prevotella, Prevotella 7, and Trichococcus. No difference in the bacterial community between the CKD patients complicated with and without diabetes, and between those with and without hypertension. Prevotella 7 declined in CKD patients with/without hypertension with respect to HC, while Pseudomonas increased in CKD patients with/without hypertension. Pseudomonas was negatively associated with immunoglobin G in CKD patients. Both CKD patients with positive and negative antistreptolysin O had declined Prevotella 7 and Trichococcus compared to HC, whereas increased Pseudomonas. CONCLUSIONS Our study identifies a distinct bacterial saliva microbiome in CKD patients characterized by alteration in composition. We unravel here that the co-occurrence diseases of diabetes and hypertension are not associated with specific bacterial alterations, suggesting that bacterial dysbiosis in saliva plays a role in renal damage regardless of the occurrence of diabetes and hypertension.
Collapse
Affiliation(s)
- Fengping Liu
- Wuxi School of Medicine, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Jiayi Sheng
- Department of Urology, Wuxi No.2 People's Hospital, Affiliated Wuxi Second Hospital of Nanjing Medical University, Wuxi, 214000, Jiangsu, China
| | - Lei Hu
- Department of Urology, Wuxi No.2 People's Hospital, Affiliated Wuxi Second Hospital of Nanjing Medical University, Wuxi, 214000, Jiangsu, China
| | - Bin Zhang
- Department of Urology, the First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, China
| | - Wei Guo
- Department of Urology, Wuxi No.2 People's Hospital, Affiliated Wuxi Second Hospital of Nanjing Medical University, Wuxi, 214000, Jiangsu, China
| | - Yang Wang
- Department of Urology, Wuxi No.2 People's Hospital, Affiliated Wuxi Second Hospital of Nanjing Medical University, Wuxi, 214000, Jiangsu, China
| | - Yifeng Gu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, 310003, Zhejiang, China
| | - Peng Jiang
- Department of Urology, Wuxi No.2 People's Hospital, Affiliated Wuxi Second Hospital of Nanjing Medical University, Wuxi, 214000, Jiangsu, China
| | - Hao Lin
- Department of Urology, Wuxi No.2 People's Hospital, Affiliated Wuxi Second Hospital of Nanjing Medical University, Wuxi, 214000, Jiangsu, China
| | - Brako Lydia
- Wuxi School of Medicine, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Yifan Sun
- Department of Urology, Wuxi No.2 People's Hospital, Affiliated Wuxi Second Hospital of Nanjing Medical University, Wuxi, 214000, Jiangsu, China
| | - Yifan Tang
- Department of Urology, Wuxi No.2 People's Hospital, Affiliated Wuxi Second Hospital of Nanjing Medical University, Wuxi, 214000, Jiangsu, China
| | - Chaoqun Gu
- School of Medicine, Nantong University, Nantong, 226019, Jiangsu, China
| | - Shichao Wei
- School of Medicine, Nantong University, Nantong, 226019, Jiangsu, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology and School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.
| | - Weiguo Chen
- Department of Urology, the First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, China.
| | - Ninghan Feng
- Department of Urology, Wuxi No.2 People's Hospital, Affiliated Wuxi Second Hospital of Nanjing Medical University, Wuxi, 214000, Jiangsu, China.
| |
Collapse
|
15
|
Jiang JY, Li WH, Wu YY, Cheng CX, Ye QQ, Feng JX, Xie ZX. Effects of cadmium exposure on intestinal microflora of Cipangopaludina cathayensis. Front Microbiol 2022; 13:984757. [PMID: 36003941 PMCID: PMC9393624 DOI: 10.3389/fmicb.2022.984757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 07/21/2022] [Indexed: 01/04/2023] Open
Abstract
As one of the most environmentally toxic heavy metals, cadmium (Cd) has attracted the attention of researchers globally. In particular, Guangxi, a province in southwestern China, has been subjected to severe Cd pollution due to geogenic processes and anthropogenic activities. Cd can be accumulated in aquatic animals and transferred to the human body through the food chain, with potential health risks. The aim of the present study was to explore the effects of waterborne Cd exposure (0.5 mg/L and 1.5 mg/L) on the intestinal microbiota of mudsnail, Cipangopaludina cathayensis, which is favored by farmers and consumers in Guangxi. Gut bacterial community composition was investigated using high-throughput sequencing of the V3–V4 segment of the bacterial 16S rRNA gene. Our results indicated that C. cathayensis could tolerate low Cd (0.5 mg/L) stress, while Cd exposure at high doses (1.5 mg/L) exerted considerable effects on microbiota composition. At the phylum level, Proteobacteria, Bacteroidetes, and Firmicutes were the dominant phyla in the mudsnail gut microbiota. The relative abundances of Bacteroidetes increased significantly under high Cd exposure (H14) (p < 0.01), with no significant change in the low Cd exposure (L14) treatment. The dominant genera with significant differences in relative abundance were Pseudomonas, Cloacibacterium, Acinetobacter, Dechloromonas, and Rhodobacter. In addition, Cd exposure could significantly alter the pathways associated with metabolism, cellular processes, environmental information processing, genetic information processing, human diseases, and organismal systems. Notably, compared to the L14 treatment, some disease-related pathways were enriched, while some xenobiotic and organic compound biodegradation and metabolism pathways were significantly inhibited in the H14 group. Overall, Cd exposure profoundly influenced community structure and function of gut microbiota, which may in turn influence C. cathayensis gut homeostasis and health.
Collapse
Affiliation(s)
- Jiao-yun Jiang
- College of Life Science and Technology, Guangxi University, Nanning, China
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Normal University, Guilin, China
| | - Wen-hong Li
- College of Life Science and Technology, Guangxi University, Nanning, China
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yang-yang Wu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Normal University, Guilin, China
| | - Chun-xing Cheng
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Normal University, Guilin, China
| | - Quan-qing Ye
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Normal University, Guilin, China
| | - Jia-xun Feng
- College of Life Science and Technology, Guangxi University, Nanning, China
| | - Zhi-xun Xie
- College of Life Science and Technology, Guangxi University, Nanning, China
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- *Correspondence: Zhi-xun Xie,
| |
Collapse
|
16
|
Tian Y, Gu C, Yan F, Gu Y, Feng Y, Chen J, Sheng J, Hu L, Jiang P, Guo W, Feng N. Alteration of Skin Microbiome in CKD Patients Is Associated With Pruritus and Renal Function. Front Cell Infect Microbiol 2022; 12:923581. [PMID: 35837475 PMCID: PMC9274276 DOI: 10.3389/fcimb.2022.923581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/24/2022] [Indexed: 12/02/2022] Open
Abstract
Dysbiotic gut microbiome in chronic kidney disease (CKD) patients has been extensively explored in recent years. Skin microbiome plays a crucial role in patients with skin diseases or even systemic disorders. Pruritus is caused by the retention of uremic solutes in the skin. Until now, no studies have investigated the role of skin microbiome in CKD and its association with pruritus. Here, we aim to examine the bacterial profile of skin microbiome in CKD and whether it is correlated to pruritus. A total of 105 CKD patients and 38 healthy controls (HC) were recruited. Skin swab was used to collect skin samples at the antecubital fossa of participants. Bacterial 16S rRNA genes V3–V4 region was sequenced on NovaSeq platform. On the day of skin sample collection, renal function was assessed, and numeric rating scale was used to measure pruritus severity. Principal coordinate analysis (PCoA) revealed a significant difference in bacterial composition between the groups of CKD and HC. A depletion of bacterial diversity was observed in CKD patients. Akkermansia, Albimonas, Escherichia–Shigella, etc. showed significant higher abundance in CKD patients, whereas Flavobacterium, Blastomonas, Lautropia, etc. significantly declined in patients. Escherichia–Shigella achieved an acceptable diagnostic biomarker with area under the curve (AUC) value of 0.784 in the receiver operating characteristics (ROC) curve. In addition, CKD patients with pruritus (P-CKD) had a different bacterial community comparing to those without pruritus (non-P-CKD) and HC group. Several bacterial genera showing significant difference between P-CKD and non-P-CKD/HC, such as Oribacterium, significantly declined in P-CKD patients than that in the HC group, and Methylophaga significantly increased in P-CKD patients compared to that in HC subjects. Escherichia–Shigella was positively associated with the levels of pruritus severity, blood urea nitrogen (BUN), uric acid, and urine protein; Oribacterium was negatively associated with pruritus severity, whereas it was positively associated with estimated glomerular filtration rate (eGFR) and 24-h urine volume. The dysbiotic of skin microbiome in CKD patients and its association with pruritus and renal function shed a light on skin probiotics.
Collapse
Affiliation(s)
- Yu Tian
- Department of Urology, Wuxi No. 2 People’s Hospital, Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Chaoqun Gu
- Department of Urology, Wuxi No. 2 People’s Hospital, Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Feng Yan
- Department of Nephrology, Wuxi No. 2 People’s Hospital, Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Yifeng Gu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yangkun Feng
- School of Medicine, Nantong University, Nantong, China
| | - Jie Chen
- Department of Urology, Wuxi No. 2 People’s Hospital, Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Jiayi Sheng
- Department of Urology, Wuxi No. 2 People’s Hospital, Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Lei Hu
- Department of Urology, Wuxi No. 2 People’s Hospital, Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Peng Jiang
- Department of Urology, Wuxi No. 2 People’s Hospital, Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
- *Correspondence: Peng Jiang, ; Wei Guo, ; Ninghan Feng,
| | - Wei Guo
- Department of Urology, Wuxi No. 2 People’s Hospital, Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
- *Correspondence: Peng Jiang, ; Wei Guo, ; Ninghan Feng,
| | - Ninghan Feng
- Department of Urology, Wuxi No. 2 People’s Hospital, Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
- *Correspondence: Peng Jiang, ; Wei Guo, ; Ninghan Feng,
| |
Collapse
|
17
|
Abstract
Chronic kidney disease (CKD) is a worldwide public health issue and has ultimately progressed to an end-stage renal disease that requires life-long dialysis or renal transplantation. However, the underlying molecular mechanism of these pathological development and progression remains to be fully understood. The human gut microbiota is made up of approximately 100 trillion microbial cells including anaerobic and aerobic species. In recent years, more and more evidence has indicated a clear association between dysbiosis of gut microbiota and CKD including immunoglobulin A (IgA) nephropathy, diabetic kidney disease, membranous nephropathy, chronic renal failure and end-stage renal disease. The current review describes gut microbial dysbiosis and metabolites in patients with CKD thus helping to understand human disease. Treatment with prebiotics, probiotics and natural products can attenuate CKD through improving dysbiosis of gut microbiota, indicating a novel intervention strategy in patients with CKD. This review also discusses therapeutic options, such as prebiotics, probiotics and natural products, for targeting dysbiosis of gut microbiota in patients to provide more specific concept-driven therapy strategy for CKD treatment.
Collapse
Affiliation(s)
- Ying-Yong Zhao
- Faculty of Life Science & Medicine, Northwest University, Xi’an 710069, Shaanxi, China
| |
Collapse
|
18
|
Hu J, Wei S, Gu Y, Wang Y, Feng Y, Sheng J, Hu L, Gu C, Jiang P, Tian Y, Guo W, Lv L, Liu F, Zou Y, Yan F, Feng N. Gut Mycobiome in Patients With Chronic Kidney Disease Was Altered and Associated With Immunological Profiles. Front Immunol 2022; 13:843695. [PMID: 35784313 PMCID: PMC9245424 DOI: 10.3389/fimmu.2022.843695] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Objectives Mounting evidence suggests that bacterial dysbiosis and immunity disorder are associated with patients with chronic kidney disease (CKD), but the mycobiome is beginning to gain recognition as a fundamental part of our microbiome. We aim to characterize the profile of the mycobiome in the gut of CKD patients and its correlation to serum immunological profiles. Methods and materials Ninety-two CKD patients and sex-age-body mass index (BMI)-matched healthy controls (HCs) were recruited. Fresh samples were collected using sterile containers. ITS transcribed spacer ribosomal RNA gene sequencing was performed on the samples. An immunoturbidimetric test was used to assess the serum levels of immunological features. Results The CKD cohort displayed a different microbial community from that in the HC cohort according to principal coordinate analysis (PCoA). (P=0.001). The comparison of the two cohorts showed that the CKD cohort had significantly higher gut microbial richness and diversity (P<0.05). The CKD cohort had lower abundances of Candida, Bjerkandera, Rhodotorula, and Ganoderma compared to the HC cohort, while it had higher Saccharomyces (P<0.05). However, the microbial community alteration was inconsistent with the severity of kidney damage in patients, as only patients in CKD stage 1~3 had differed microbial community concerning for HCs based on PCoA (P<0.05). The serum concentration of the kappa light chain in CKD patients was positively associated with Saccharomyces, whereas the it was negatively associated with Ganoderma (P<0.05). Conclusions Not only was gut mycobiome dysbiosis observed in CKD patients, but the dysbiosis was also associated with the immunological disorder. These findings suggest that therapeutic strategies targeting gut mycobiome might be effective.
Collapse
Affiliation(s)
- Jialin Hu
- Department of Urology, Affiliated Wuxi No.2 Hospital, Nantong University, Wuxi, China
| | - Shichao Wei
- Department of Urology, Affiliated Wuxi No.2 Hospital, Nantong University, Wuxi, China
| | - Yifeng Gu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yang Wang
- Department of Urology, Affiliated Wuxi No.2 Hospital, Nantong University, Wuxi, China
| | - Yangkun Feng
- School of Medicine, Nantong University, Nantong, China
| | - Jiayi Sheng
- Department of Urology, Affiliated Wuxi No.2 Hospital, Nanjing Medical University, Wuxi, China
| | - Lei Hu
- Department of Urology, Affiliated Wuxi No.2 Hospital, Nanjing Medical University, Wuxi, China
| | - Chaoqun Gu
- Department of Urology, Affiliated Wuxi No.2 Hospital, Nantong University, Wuxi, China
| | - Peng Jiang
- Department of Urology, Affiliated Wuxi No.2 Hospital, Nantong University, Wuxi, China
| | - Yu Tian
- Department of Nephrology, Affiliated Wuxi No.2 Hospital, Nanjing Medical University, Wuxi, China
| | - Wei Guo
- Department of Urology, Affiliated Wuxi No.2 Hospital, Nantong University, Wuxi, China
| | - Longxian Lv
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Fengping Liu
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Yeqing Zou
- School of Basic Medicine, Jiangsu Vocational College of Medicine, Yancheng, China
| | - Feng Yan
- Department of Nephrology, Affiliated Wuxi No.2 Hospital, Nanjing Medical University, Wuxi, China
| | - Ninghan Feng
- Department of Urology, Affiliated Wuxi No.2 Hospital, Nantong University, Wuxi, China
| |
Collapse
|
19
|
Dai X, Chen L, Liu M, Liu Y, Jiang S, Xu T, Wang A, Yang S, Wei W. Effect of 6-Methoxybenzoxazolinone on the Cecal Microbiota of Adult Male Brandt's Vole. Front Microbiol 2022; 13:847073. [PMID: 35422782 PMCID: PMC9002351 DOI: 10.3389/fmicb.2022.847073] [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: 01/01/2022] [Accepted: 02/28/2022] [Indexed: 11/28/2022] Open
Abstract
The anti-microbial effects of plant secondary metabolite (PSM) 6-methoxybenzoxazolinone (6-MBOA) have been overlooked. This study investigated the effect of 6-MBOA on the cecal microbiota of adult male Brandt’s voles (Lasiopodomys brandtii), to evaluate its effect on the physiology of mammalian herbivores. The growth of voles was inhibited by 6-MBOA. A low dose of 6-MBOA enhanced the observed species, as well as the Chao1 and abundance-based coverage estimator (ACE) indices and introduced changes in the structure of cecal microbiota. The abundance of the phylum Tenericutes, classes Mollicutes and Negativicutes, order Selenomonadales, families Ruminococcaceae and Veillonellaceae, genera Quinella, Caproiciproducens, Anaerofilum, Harryflintia, and unidentified Spirochaetaceae in the cecal microbiota was enhanced upon administration of a low dose of 6-MBOA, which also inhibited glucose metabolism and protein digestion and absorption in the cecal microbiota. 6-MBOA treatment also stimulated butyrate production and dose-dependently enhanced the metabolism of xenobiotics in the cecal microbiome. Our findings indicate that 6-MBOA can affect Brandt’s voles by inducing changes in the abundance of cecal bacteria, thereby, altering the contents of short-chain fatty acids (SCFAs) and pathway intermediates, ultimately inhibiting the growth of voles. Our research suggests that 6-MBOA could potentially act as a digestion-inhibiting PSM in the interaction between mammalian herbivores and plants.
Collapse
Affiliation(s)
- Xin Dai
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Lin Chen
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Mengyue Liu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Ying Liu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Siqi Jiang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Tingting Xu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Aiqin Wang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Shengmei Yang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Wanhong Wei
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| |
Collapse
|
20
|
Abstract
PURPOSE OF REVIEW Growing evidence show the importance of gut/kidney axis in renal diseases. Advances in gut microbiome sequencing, associated metabolites, detection of gut permeability and inflammation provide new therapeutic strategies targeting gut for kidney diseases and particularly for Immunoglobulin A (IgA) nephropathy (IgAN). RECENT FINDINGS The diversity and composition of gut flora have been recently deeply explored in kidney diseases. Modulation and depletion of microbiota in animal models allowed the understanding of molecular mechanisms involved in the crosstalk between gut, immune system and kidney. New clinical trials in order to positively modulate microbiota result in improvement of gastrointestinal disorders and inflammation in patients suffering with kidney diseases. SUMMARY The investigation of gut alterations in kidney diseases open new therapeutic strategies. In IgAN, targeted treatments for intestinal inflammation and modifications of gut microbiota seem promising.
Collapse
Affiliation(s)
- Renato C Monteiro
- INSERM UMR1149, Center of Research on Inflammation CRI, CNRS ERL8252
- Inflamex Laboratory of Excellence, Paris University
- Immunology Department, Bichat Hospital, AP-HP, DHU Apollo, Paris
| | - Laureline Berthelot
- Center of Research in Transplantation and Immunology CRTI, UMR1064, INSERM, Nantes University, Nantes, France
| |
Collapse
|