A Reproducible Meta-Analytic Pipeline for Quantifying Ecological Bottlenecks, Alpha Diversity Decay, and Core Biomarker Fluctuations in Ex Vivo Human Gut Microbiota Fermentations

Ex vivo continuous-flow bioreactor systems are foundational in mechanistic microbiome research, allowing researchers to evaluate compound fermentations under tight experimental parameters. However, migrating a complex multi-phyla ecosystem from an in vivo environment to an artificial vessel triggers an immediate selective pressure event. This report details an independent, reproducible statistical validation workflow in R designed to isolate and measure this baseline "bioreactor drift". Using a public Metagenomic Species Pan-genome (MSP) relative abundance matrix, I track taxonomic distribution changes and targeted species survival profiles. Non-parametric analysis confirms an acute 87.9% collapse in Observed Taxonomic Richness along with a fundamental restructuring of community entropy. This open-science pipeline provides a robust framework for downstream intervention benchmarking.