X-Gutor: a high-fidelity in vitro platform for long-term gut microbiome recovery

Abstract

In vitro gut microbiome-culturing models are essential for studying host-microbe interactions, yet achieving high microbial recovery and long-term stability remains a long-standing challenge. Here we devise X-Gutor, an ecologically designed in vitro platform that recapitulates the monogastric digestive system with precise control of pH, redox potential, and a mucin-based biofilm matrix. Using an integrated assessment framework, microbial source tracking, a curated gut metabolism database (GutDB), and short-chain fatty acid profiling, we benchmarked gut community recovery. Building on this platform, HanGutor and PigGutor were developed to recover 96.27{+/-}4.92% and 90.48{+/-}5.95% of human and swine gut microbiota, respectively. Ecological fine-tuning revealed that redox potential drives the Prevotella-Bacteroides trade-off and that spatial biofilm structure suppresses cheater (Succinivibrio) growth. The X-Gutor provides a scalable, modular platform for gut microbiome engineering, dietary intervention, and microbiota-targeted therapy development.