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An Open-Source QIIME2 and R Pipeline for Multi-Amplicon 16S rRNA Profiling: Validation and Application in Pediatric Microbiome Studies

ABSTRACT: This study presents a validated, open-source QIIME2- and R-based pipeline for 16S rRNA gene profiling using multi-amplicon sequencing. It aims to overcome the limitations of commercial, closed-source tools by offering a standardized and reproducible workflow. The pipeline was benchmarked against proprietary software using five mock communities and 12 child–caregiver fecal sample pairs, showing nearly identical microbial profiles, greater sequencing depth, and improved taxonomic resolution. High reproducibility (R = 0.99, p < 0.0001) was achieved across all datasets. Application to pediatric cancer samples revealed distinct Bifidobacterium variants in children whose microbiota closely matched their caregivers’. This highlights the pipeline’s utility in studying microbial relationships. Overall, the pipeline supports transparent, adaptable, and accurate microbiome analysis, advancing research in both clinical and experimental settings while promoting open-source solutions for reproducible science.

ORGANISM(S): unidentified

PROVIDER: GSE300047 | GEO | 2025/07/14

REPOSITORIES: GEO

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