🦠 The Honey Bee Gut Microbiome

About this simulation

A worker bee's gut hosts a small, specialised community of bacteria — mainly Lactobacillus, Bifidobacterium, Gilliamella and Snodgrassella — concentrated in the ileum and rectum at the rear of the digestive tract. This cutaway shows that hindgut region as a ring of amber "core" bacteria lining the gut wall, while pathogens such as Nosema-type invaders (shown in red) try to establish in the midgut.

How it works

• Every frame the simulation runs a simple population model: core bacteria grow toward a diversity-dependent ceiling and actively suppress pathogens (colonisation resistance).
• Pesticide/antibiotic stress kills core bacteria directly and weakens that suppression, letting pathogens bloom.
• Higher pathogen pressure increases how aggressively invaders try to colonise the gut.
• A wildflower diet supplies more diverse pollen nutrients, boosting core bacteria growth; a monoculture diet slows it.

Controls

• Microbiome diversity — richness of the starting bacterial community; higher diversity raises the core bacteria's carrying capacity and resilience.
• Pesticide / antibiotic stress — simulates sub-lethal chemical exposure that disrupts gut flora.
• Pathogen pressure — how strongly opportunistic pathogens are trying to invade the gut.
• Forage diversity — switches between a wildflower mix and a single-crop monoculture diet.
• ↺ Reset gut — restarts the population model. Drag to rotate, scroll to zoom.

Did you know?

A healthy hindgut community can occupy so much of the epithelial surface and out-compete for nutrients so effectively that it measurably blocks pathogens like Nosema ceranae and certain trypanosomatids from establishing — one reason gut health is now tracked as a colony-health indicator alongside varroa loads and queen performance.