Gut Microbiome Diversity Simulator

Gut ecosystem

Dietary fiber 50%

Antibiotic dose 0%

Processed sugar 20%

Shannon diversity H

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Dominant phylum

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Ecosystem status

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How it works

Five bacterial phyla share one gut niche and compete for the same fermentable resources. Each phylum's fitness rises or falls with what you feed the system — fiber favors the fermenters (Bacteroidetes, Actinobacteria, Akkermansia), antibiotics knock back everything except the resistant opportunist Proteobacteria, and processed sugar without fiber lets that same opportunist bloom. Populations follow replicator dynamics: a phylum's share of the community grows only if its fitness beats the community average.

dpᵢ/dt = pᵢ·(fᵢ − f̄),  f̄ = Σ pⱼfⱼ
H = −Σ pᵢ·ln(pᵢ)   (Shannon diversity index)

Dietary fiber — feeds short-chain-fatty-acid producers (Bacteroidetes, Actinobacteria, Akkermansia); low fiber starves them out.
Antibiotic dose — suppresses nearly every phylum's growth rate, but resistant Proteobacteria is barely touched and fills the vacated niche.
Processed sugar — bypasses fiber-fermenting specialists and directly favors fast-growing, pro-inflammatory Proteobacteria.
Shannon diversity H — a healthy gut sits high (many phyla near-balanced); a collapse toward one dominant phylum drives H down toward dysbiosis, the pattern seen in obesity, IBD and antibiotic-associated C. difficile infection.

Real-world relevance: this is the same competitive-exclusion dynamic behind why a course of antibiotics can leave the gut vulnerable to opportunistic infection, and why high-fiber diets are associated with a more resilient, diverse microbiome.

Firmicutes Bacteroidetes Actinobacteria Proteobacteria Akkermansia

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