Gut Microbiome Alternative Stable States

The gut microbiome doesn't drift smoothly between compositions — it tends to settle into one of a small number of self-reinforcing configurations and resist leaving. This simulator renders that behavior as a real bistable (cusp-catastrophe) potential landscape: a ball representing the community's overall composition rolls under diet-driven tilt and competitive-exclusion curvature, while an instanced colony of thousands of virtual microbial cells changes its fiber-fermenter/protein-fermenter mixture live to match. Push the diet slider far enough and one stable state disappears outright (a bifurcation); fire an antibiotic pulse and, if it's strong enough to cross the barrier between wells, the community can resettle permanently into the other state — a concrete illustration of why microbiome recovery after antibiotics is so often incomplete.