Evaluation of 16S rRNA Bioinformatics Analysis Pipelines Using Ion Torrent Sequencing for Gastrointestinal Microbiome and Cancer Research
With the advent of high-throughput genome sequencing, the human gut microbiome has been extensively characterized and linked to numerous diseases, including cancer. However, metagenomic results are known to vary depending on sequencing platform, library preparation protocol, hypervariable region (HVR) targeted, and bioinformatics workflow. In particular, there is currently no consensus on the optimal strategy for analyzing 16S rRNA data generated with the Ion Torrent (Thermo Fisher Scientific) platform when focusing on a single HVR.In this study, we evaluate eight different 16S bioinformatics pipelines, including Ion Reporter and several open-source alternatives. Performance was assessed within a compositional data analysis framework, using a well-characterized mock community previously defined by DNA shotgun sequencing (ZymoBIOMICS) as ground truth.Our objective is to provide an evidence-based benchmark to guide researchers in selecting the bioinformatics pipeline best aligned with their analytical goals.