Dietary composition modulate gut microbiota and related biomarkers in patients with chronic kidney disease Original paper

What was studied?

This original research article examined how dietary composition modulates the gut microbiota and related biomarkers in chronic kidney disease (CKD), focusing on how a low-protein, high-fiber diet compared with a high-protein, low-fiber diet shapes microbial signatures relevant to CKD progression. Gut microbiota in CKD was the central focus, with the study assessing how specific microbiome patterns, microbial metabolites such as TMAO, and inflammatory cytokines differ according to diet. Using 16S rRNA sequencing, plasma biomarker assays, and fecal BCoAT quantification, the research mapped the relationship between dietary macronutrient patterns and microbial shifts that contribute to uremic toxin accumulation and systemic inflammation.

Who was studied?

The study evaluated 135 adults with non-dialysis CKD stages G3–G4 and compared them against 19 healthy controls. All CKD participants were recruited from an outpatient nephrology clinic and stratified into dietary subgroups based on three-day diet records: high-protein/high-fiber, high-protein/low-fiber, low-protein/high-fiber, and low-protein/low-fiber. Participants with immunomodulatory therapy, pre/pro/synbiotic use, or abnormal bowel habits were excluded to avoid confounding effects on gut microbiota. Biological samples—including blood, urine, and stool—were collected within five days of dietary assessment.

Most important findings

The study revealed substantial gut dysbiosis in CKD patients, with significant reductions in SCFA-producing bacteria such as Bifidobacterium, Ruminococcus, Subdoligranulum, Coprococcus, Eubacterium ruminantium group, and Faecalibacterium compared with healthy controls. The harmful genus Lachnoclostridium was enriched in CKD and is known to promote TMAO generation. CKD participants also showed markedly elevated TMAO and I-FABP levels, indicating increased microbial toxin load and impaired intestinal barrier integrity. Dietary subgroup analysis highlighted clear differences: the low-protein, high-fiber (LP-HF) group displayed greater abundance of beneficial SCFA producers, including Lachnospiraceae NK4A136 and the Eubacterium ruminantium group, while the high-protein, low-fiber (HP-LF) group exhibited increased proteolytic and potentially pathogenic genera such as Romboutsia, Clostridium sensu stricto 1, and Klebsiella. These bacterial patterns were consistent with functional pathway predictions showing increased alcohol fermentation pathways in the HP-LF subgroup. TMAO and pro-inflammatory cytokines IL-18 and MCP-1 were significantly higher in HP-LF participants, connecting microbial signatures to systemic inflammation.

Key implications

The findings underscore diet as a modifiable driver of gut microbiota composition and inflammatory burden in CKD. A fiber-rich, low-protein dietary pattern enhances SCFA-producing bacteria, reduces pathogenic proteolytic taxa, lowers TMAO levels, and diminishes inflammatory cytokines linked to renal decline. These data support integrating microbiome-targeted dietary counseling into CKD management, potentially slowing progression through modulation of the gut–kidney axis. The results also reinforce the clinical value of microbial signatures—such as SCFA-producer depletion and proteolytic bacteria enrichment—as biomarkers for dietary responsiveness and CKD risk stratification.

Citation

Udomkarnjananun S, Chuaypen N, Metta K, et al. Dietary composition modulate gut microbiota and related biomarkers in patients with chronic kidney disease.Scientific Reports. 2025;15:36274. doi:10.1038/s41598-025-20266-5