Alterations of gut microbes and their correlation with clinical features in middle and end-stages chronic kidney disease Original paper

What was studied?

Alterations of gut microbes and their correlation with clinical features in middle and end-stage chronic kidney disease was examined by profiling fecal microbiome composition in patients with CKD and ESRD using 16S rRNA sequencing, with the aim of identifying microbiome signatures linked to disease progression and clinical biomarkers.

Who was studied?

The study analyzed 13 adults aged 22–76 years hospitalized with confirmed CKD or ESRD at the Third Xiangya Hospital, China. Seven individuals had CKD and six had ESRD. Clinical data included renal indices (eGFR, creatinine, BUN), inflammatory markers, electrolytes, and dialysis status; individuals using confounding medications such as probiotics or antimicrobials were excluded.

Most important findings

The gut microbiome showed progressive simplification from CKD to ESRD, marked by reduced alpha diversity and a notable contraction of high-abundance taxa. Firmicutes remained dominant across groups, but ESRD samples displayed lower richness and larger sample-to-sample variation. At the genus level, CKD samples exhibited higher relative abundance of Escherichia-Shigella, Blautia, Fusicatenibacter, and Faecalibacterium, whereas ESRD samples were enriched in Enterococcus, Subdoligranulum, Lactobacillus, and Staphylococcus. Differential abundance analysis showed ESRD-associated increases in Faecalitalea, Enterococcus, Staphylococcus, Geobacter, Dubosiella, Raoultibacter, Helicobacter, and Corynebacterium—many of which have pathogenic or proinflammatory potential. Conversely, short-chain fatty acid (SCFA)–producing genera such as Faecalibacterium, Phascolarctobacterium, Lachnospira, Megamonas, and Hungatella were significantly depleted, indicating a loss of microbial metabolites with anti-inflammatory and nephroprotective properties. Correlations between gut microbes and clinical biomarkers were pronounced in CKD but diminished in ESRD. Canonical Correspondence Analysis revealed β₂-microglobulin (b2-MG) as the strongest clinical determinant of microbial structure. Mantel testing indicated that intermediate- and rare-abundance genera showed significant positive associations with creatinine, phosphorus, parathyroid hormone, and BNP in CKD, while ESRD showed positive associations with b2-MG and sodium. Notably, Phascolarctobacterium displayed a strong negative correlation with b2-MG in ESRD, suggesting disease-linked suppression of beneficial SCFA-producing taxa.

Key implications

This study reinforces that microbiome degradation accelerates with kidney function decline, culminating in ESRD-associated dominance of dysbiotic, potentially pathogenic taxa and loss of beneficial butyrate-producing microbes. The findings underscore the clinical relevance of microbial signatures—especially decreases in Faecalibacterium and Phascolarctobacterium and increases in Enterococcus and Staphylococcus—as potential noninvasive indicators of CKD severity. The identification of b2-MG as a major driver of microbiome shifts highlights the interplay between systemic toxin burden and gut dysbiosis. These results suggest opportunities for leveraging microbiome-based diagnostics and interventions to monitor CKD progression, mitigate inflammation, and preserve gut-kidney axis function.

Citation

Chen H, Wang J, Ouyang Q, Peng X, Yu Z, Wang J, Huang J. Alterations of gut microbes and their correlation with clinical features in middle and end-stages chronic kidney disease. Front Cell Infect Microbiol. 2023;13:1105366. doi:10.3389/fcimb.2023.1105366