16S rRNA Gene Amplicon Sequencing Dataset of Gut Microbiota from Chronic Kidney Disease Patients and Healthy Controls in Baghdad, Iraq
Description
A comprehensive dataset profiling the gut microbiome of patients diagnosed with chronic kidney disease (CKD) who are not receiving dialysis. This cross-sectional observational study includes clinical, socio-demographic, and high-throughput metagenomic sequencing data from 154 patients aged 18 to 70 years, recruited from Al-Karama Teaching Hospital, Al-Noor Center, and Al-Hayat Center. The dataset integrates structured questionnaire outputs, clinical profiles (including age, gender, body weight, smoking status, medical history, disease stage, serum creatinine levels, and GFR), and 16S rRNA gene sequencing data. This dataset was generated to support the comparative metagenomic analysis of gut microbiota across different CKD stages. It enables comprehensive microbial profiling, including Alpha and Beta diversity indices, taxonomy distribution, and composition comparisons between CKD patients and healthy controls. The Mendeley Data repository contains both raw and processed datasets generated from the 16S rRNA sequencing analysis. The repository includes the feature abundance tables (ASV representative sequences in FASTA format, taxonomy assignment tables, sample metadata, diversity analysis results, distance matrices, and PCoA coordinates. The raw sequencing outputs are stored in the "Raw" folder, while the processed and filtered datasets used for downstream analyses are available in the "Processed" folder. All scripts and workflow files used for bioinformatics processing, statistical analysis, and figure generation are provided in the "Code" folder.
Files
Steps to reproduce
1. Sampling & DNA Isolation: Socio-demographic/clinical data and stool samples were collected from 154 CKD patients and healthy controls. Genomic DNA was isolated using MagicPure®️ Stool and Soil Genomic DNA Kit (TransGen Biotech, China) with mechanical/thermal lysis. Quality/purity were assessed via NanoDrop, and 20 samples proceeded to sequencing. 2. Library Prep & Sequencing: Amplicon libraries were prepared and checked via Agilent TapeStation (D1000). 16 libraries passed QC (peaks 571–623 bp) and 4 failed. High-throughput sequencing was executed on the Illumina platform, and BCL files were converted to FASTQ via bcl-convert. 3. Bioinformatics Processing: Raw reads were processed using Cutadapt (v3.2) for trimming (forward: 250 bp, reverse: 200 bp). Denoising, merging, and chimera removal were performed using DADA2 (v1.18.0) in R. ASVs <350 bp were filtered out, and normalization was done using QIIME (v1.9.0). 4. Taxonomy & Diversity Analysis: Taxonomic assignment was performed against the NCBI_16S database using a Naive Bayesian Classifier. Alpha diversity (Chao1, Shannon, Simpson) was evaluated via Mann-Whitney U test. Phylogeny was done via MAFFT and FastTreeMP. Beta diversity (Bray-Curtis, UniFrac) and PCoA/UPGMA were computed via QIIME (v1.9.0), with group variances checked by PERMANOVA.
Institutions
- University of BaghdadBaghdad, Baghdad