A 16S rRNA-based meta-analysis of gut microbiota in diabetic nephropathy using QIIME2 and publicly available NGS...

Gut microbial profiles can differ significantly between diabetic nephropathy (DN), diabetic patients, and healthy controls (HCs). The exact microbial taxa involved in DN progression is yet to be fully characterized. Therefore, this study aims to compare the gut microbiota od DN patients with diabetic and healthy individuals. Accordingly, this study executes a pioneering metanalytical view using the publicly available datasets (National centre for biotechnology information) to evaluate DN associated variation in gut-microbiota diversity. We hypothesize that the DN patients should have a smaller number of beneficial microbes along with a greater fraction of pathogenic microbial composition relative to the other two groups. Specifically, this report utilizes quantitative insights into microbial ecology 2 (QIIME2) platform to identify an association between gut microbiota composition and DN advancement. This novelty provides distinctive nature to our work in comparison to the broader diabetes microbiome studies. Our study enables comprehensive taxonomic profiling, differential abundance testing, and alpha and beta diversity analyses across multiple studies. A total of six studies were included, comprising 684 samples from both DN patients and HCs. Post quality control check, these samples were processed using QIIME2 platform for taxonomic profiling and diversity analysis to characterize microbial dysbiosis in DN patients in relation to other two groups. Alpha diversity indicates insignificant trend towards reduction of microbial diversity as observed using the Kruskal-Wallis test, Shannon index, Observed features (richness), and Faith's PD analysis (p > 0.05). Additionally, beta diversity analyses revealed a trend toward microbial richness in DN compared to diabetic individuals and HCs, though differences were statically insignificant (P > 0.05). Taxonomic profiling showed a depletion of beneficial genera (e.g., Faecalibacterium, Roseburia, and Bifidobacterium) with false discovery rate (FDR)-adjusted p < 0.05. Contrarily, pathogenic and pro-inflammatory taxa including Escherichia-Shigella, Enterococcus, and Klebsiella showed higher abundance in the DN group (FDR-adjusted p < 0.05). These compositional shifts highlight pronounced gut dysbiosis during the transition from diabetes to DN, suggesting a potential association between gut-kidney axis.