Multilayer defense collapse model and rare taxa-based early warning for solid-state vinegar fermentation stagnation:...

Fermentation stagnation is a persistent challenge in industrial vinegar production, yet its microecological mechanisms remain poorly understood. Here, we conducted time series metagenomic analysis comparing normal and stagnant solid state acetic acid fermentation, and propose the Multilayer Defense Collapse (MDC) model as a unifying framework for stagnation mechanisms. We found fermentation stagnation represents a cascade collapse of four progressive defense layers rather than a single-point failure. Initial perturbation first impairs community network resilience, manifesting as community simplification with 72% reduction in species richness and synchronous viral diversity loss. Metabolic monopoly by core functional bacteria then weakens through triple reconfiguration involving genus-level replacement of lactic acid bacteria, reduced acetic acid bacterial contribution, and limited pathogen penetration. The acidic chemical barrier subsequently fails through both barrier weakening and quorum sensing-mediated active breakthrough. Antimicrobial peptide defense ultimately collapses with 74% AMP decline, driving the system into a dysregulated steady state characterized by broad-spectrum resistome expansion. Random forest analysis further showed that rare taxa, rather than core bacteria, serve as the most sensitive early warning indicators, with 20-50 sentinel species sufficient for high-accuracy classification. This study provides a mechanistic framework for fermentation stagnation and offers potential early-warning indicator and graded intervention.