Engineered Microbiome

Engineered strain seed 40%

Nutrient / prebiotic level 50%

Population

Engineered %

Therapeutic output

0 u/s

Diversity index

0.00

How it works

Engineered cells (teal capsules) and native community members (grey capsules) compete for space and nutrients inside the host niche. Engineered cells continuously secrete a therapeutic molecule (small glowing particles) while alive. The kill-switch simulates a genetic biocontainment circuit that triggers programmed death of the engineered population on demand.

dN_i/dt = r_i · N_i · (1 − N_total/K) − d_i · N_i
diversity (Shannon) H = −Σ p_i · ln(p_i)

Engineered strain seed — starting fraction of engineered vs native cells at colonisation.
Nutrient / prebiotic level — raises growth rate r for all strains and total carrying capacity K.
Kill-switch — instantly raises the engineered strain's death rate, simulating an inducible biocontainment circuit.
Environment — gut vs soil changes the visual niche; the same logistic competition applies to both.

This captures the central engineering trade-off in microbiome design: enough engineered abundance to deliver a therapeutic dose, balanced against containment so the strain does not persist or spread uncontrolled.

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