Exploring Enterotype Characteristics of Chronic Kidney Disease Stages 3-5 Based on the Partitioning Around Medoids Clustering Algorithm

Background: Recent studies have been shown growing interest in gut microbiota and chronic kidney disease (CKD). Our preliminary studies found that Yishen Qingli Huoxue formula is effective in treating CKD stage 3-5. However, there is still individual variability in comprehensive treatment and disease regression. Previous studies have indicated that individual variability may be closely related to microbial enrichment or depletion. Methods: This study aimed to characterize enterotypes in patients with CKD stages 3-5 to construct partial microecological pathways for CKD prevention and treatment. The study included 60 patients with CKD stages 3-5 from the Department of Nephrology of Jiangsu Provincial Hospital of Chinese Medicine and 30 controls who were recruited during the same period. Classification of enterotypes in CKD stages 3-5 was performed by the partitioning around medoids (PAM) clustering algorithm based on the genus level with the control as the baseline. Information mining was utilized to analyze the dependence of enterotype on environmental factors, and marker genera corresponding to different enterotypes were identified based on Tukey Honestly Significant Difference (HSD) and Receiver Operating Characteristic (ROC) curve analysis. Results: Patients with CKD stages 3-5 could be categorized into three enterotypes, the formation of which was weakly dependent on environmental factors. The three enterotypes were dominated by commensal ( Bacteroides, Klebsiella ), conditionally pathogenic ( Escherichia-Shigella, Ruminococcus gnavus ), and short-chain fatty acid-producing bacteria ( Bifidobacterium, Faecalibacterium ), respectively. They were characterized by Bacteroides, Erysipelatoclostridium , and Alistipes , respectively, as marker genera. Conclusion: The standardization of enterotypes provides a basis for precise intervention and management of traditional chinese medicine for CKD patients.