Beyond the Single Vessel: A Reproducible Comparative Analysis of Alpha Diversity Across Ex Vivo Gut Microbiota Platforms

Ex vivo continuous-flow bioreactors serve as critical translational proxies for investigating human gut microbial ecology without host physiological confounding factors. However, transitioning native donor stool into synthetic vessels induces an acute selective pressure event—termed 'bioreactor drift'—that restructures community architecture. Here, I report a harmonized cross-dataset comparative reanalysis evaluating community Shannon Diversity Entropy ( H' ) shifts across two distinct continuous-culture architectures: single-stage Mini Chemostat Arrays and Multi-Stage Simulator of the Human Intestinal Microbial Ecosystem (SHIME) platforms. Evaluating n = 40 harmonized profile points across baseline donor stool (In_Vivo_Baseline) and stabilized vessel cultures (Ex_Vivo_Stabilized), Mini-Chemostat Arrays exhibited significant phylum-level community entropy decay (median baseline H' = 0.963, IQR = 0.045 vs. stabilized H' = 0.886, IQR = 0.061; Δ H' = -0.077; W = 12.0, p = 0.0046). Conversely, multi-stage SHIME profiles retained high entropy, displaying a modest increase post-stabilization (median baseline H' = 0.947, IQR = 0.031 vs. stabilized H' = 0.988, IQR = 0.032; Δ H' = +0.041; W = 80.0, p = 0.0258). A direct non-parametric comparison of stabilized vessel profiles confirmed higher steady-state phylum-level diversity in the SHIME dataset ( W = 8, p = 0.001706). While these observational differences are consistent with the hypothesis that spatial gradients and regional compartmentalization may contribute to community stability, platform architecture is confounded with source study conditions. These results establish platform-associated benchmark metrics and provide a reproducible pipeline for cross-study continuous-culture evaluation.