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Most associations between animals and their gut microbiota are dynamic, involving sustained transfer of food-associated microbial cells into the gut and shedding of microorganisms into the external environment with feces, but the interacting effects of host and microbial factors on the composition of the internal and external microbial communities are poorly understood. This study on laboratory cultures of the fruit flyDrosophila melanogaster reared in continuous contact with their food revealed time-dependent changes of the microbial communities in the food that were strongly influenced by the presence and abundance ofDrosophila . When germfreeDrosophila eggs were aseptically added to nonsterile food, the microbiota in the food and flies converged to a composition dramatically different from that in fly-free food, showing thatDrosophila has microbiota-independent effects on the food microbiota. The microbiota in both the flies that developed from unmanipulated eggs (bearing microorganisms) and the associated food was dominated by the bacteria most abundant on the eggs, demonstrating effective vertical transmission via surface contamination of eggs. Food coinoculated with a four-species defined bacterial community ofAcetobacter andLactobacillus species revealed the progressive elimination ofLactobacillus from the food bearing few or noDrosophila , indicating the presence of antagonistic interactions betweenAcetobacter andLactobacillus. Drosophila at high densities ameliorated theAcetobacter/Lactobacillus antagonism, enablingLactobacillus to persist. This study withDrosophila demonstrates how animals can have major, coordinated effects on the composition of microbial communities in the gut and immediate environment.

The Host as the Driver of the Microbiota in the Gut and External Environment of Drosophila melanogaster