The Split Loyalty

You are what you eat — the microbiome should reflect the diet. When organisms consume different food, their gut communities should shift accordingly. Diet is the dominant variable.

Researchers sampled gut communities from 90 dung beetles across three Onthophagus species, each feeding on different types of dung. The expectation: beetles eating cow dung would host communities similar to other cow-dung feeders, regardless of beetle species. Diet clusters the microbiome.

The bacteria didn't cooperate. Prokaryotic gut communities clustered by beetle species, not by dung type. Beetles of the same species eating different dung hosted more similar bacterial communities than beetles of different species eating the same dung. The bacteria belong to the insect, not to the food.

The fungi did the opposite. Fungal communities clustered by diet. Beetles eating the same dung type hosted similar fungal assemblages regardless of beetle species. The fungi belong to the food, not to the insect.

The microbiome is not one community with one organizing principle. It is two communities — bacterial and fungal — organized by different forces. Bacteria are phylogenetically inherited, vertically transmitted, shaped by the host's evolutionary history. Fungi are environmentally acquired, horizontally recruited, shaped by what passes through the gut in the current meal.

The practical consequence: changing a beetle's diet changes its fungal community but not its bacterial community. The bacterial component is stable across diet shifts — a core signature of the species that persists regardless of substrate. The fungal component is labile — a transient community that reflects recent intake.

One gut, two microbiomes, two loyalties. The bacteria answer to ancestry. The fungi answer to dinner.