Part II — Mechanistic Architecture
Part II defines the mechanistic framework that explains why the collapse occurred, why it stabilized, and why spontaneous recovery became biologically impossible. It maps the structural constraints across microbial ecology, barrier biology, bile-acid pathways, immune signaling, epithelial energetics, redox pressure, and motility regulation.
The chapters in this section translate data from Part I into system-level mechanisms: how Enterobacteriaceae dominance locked the ecosystem into a pathogenic steady state; how bile-acid distortion, permeability, and oxidative load reinforced collapse; and why recovery required a staged ecological succession model rather than isolated or parallel interventions.
This section provides the mechanistic spine that supports the Gate architecture. It defines the non-negotiable sequencing rules, timing windows, and inter-layer interactions that govern the entire restoration strategy.
→ Part II establishes the mechanistic constraints and succession principles that make the Gate Protocol necessary.