Altered gut microbiota and microbial biomarkers associated with chronic kidney disease Original paper

What was studied?

This study investigated altered gut microbiota and microbial biomarkers associated with chronic kidney disease (CKD), using 16S rRNA sequencing to compare microbial composition between CKD patients and healthy controls. The central focus was identifying microbiota signatures—particularly genus-level phylotypes—that can distinguish CKD populations, track disease progression, and potentially inform earlier detection. The research revealed substantial shifts in the Firmicutes–Bacteroidetes balance, expansion of Proteobacteria, and enrichment of several taxa linked with uremic toxin metabolism. Among all microbial signatures evaluated, Lachnospira and Ruminococcus gnavus emerged as the strongest discriminatory biomarkers.

Who was studied?

The study enrolled 49 adults diagnosed with CKD and 24 healthy controls. Participants ranged in age from approximately 54 to 56 years and were screened to exclude confounders such as recent antibiotic, probiotic, or prebiotic use, as well as inflammatory or infectious diseases. Within the CKD group, 13 individuals were receiving hemodialysis, enabling additional comparison of microbial shifts attributable to renal replacement therapy. All subjects provided stool samples for microbial sequencing, creating a controlled dataset for identifying CKD-associated microbial changes.

Most important findings

The study demonstrated profound microbial dysbiosis in CKD. At the phylum level, CKD patients showed decreased Firmicutes and increased Bacteroidetes and Proteobacteria, a pattern frequently associated with inflammation and epithelial barrier dysfunction. Genus-level analysis identified 12 phylotypes enriched in CKD—including Bacteroides, Escherichia–Shigella, Parabacteroides, Ruminococcus gnavus, and Eggerthella—many of which are known contributors to uremic toxin pathways (p-cresol, indoxyl sulfate). Healthy controls were enriched in 19 genera, especially butyrate-producers such as Lachnospira, Roseburia, and Subdoligranulum. A subset of microbial biomarkers displayed strong diagnostic characteristics. Lachnospira best discriminated healthy controls (AUC 0.813), while Ruminococcus gnavus best classified CKD (AUC 0.764). Importantly, five genera showed distinct patterns related to CKD progression and dialysis exposure: Holdemanella, Megamonas, and Prevotella 2 declined progressively from healthy to nondialysis CKD to hemodialysis groups, while Dielma and Scardovia appeared only in CKD samples. These changes may represent early-to-late stage microbial transitions relevant for longitudinal monitoring. Microbiology.

Key implications

The study underscores that CKD is tightly linked to gut dysbiosis, marked by loss of protective short-chain-fatty-acid (SCFA) producing taxa and expansion of pathobionts capable of generating uremic toxins. The identification of genus-level biomarkers—especially Lachnospira, Ruminococcus gnavus, and the five progression-associated taxa—supports the feasibility of microbiome-based diagnostics. These microbial signatures could contribute to noninvasive detection of CKD, stratification of risk, and personalized therapeutic strategies. The findings also reinforce the mechanistic feedback loop between impaired renal function, uremic toxin accumulation, epithelial barrier disruption, and further microbial imbalance, highlighting the microbiome as a modifiable target in CKD management. Microbiology.

Citation

Lun H, Yang W, Zhao S, et al. Altered gut microbiota and microbial biomarkers associated with chronic kidney disease.MicrobiologyOpen. 2019;8:e678. doi:10.1002/mbo3.678