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Abstract:
The diversity and structure of the intestinal microbial community has a strong influence on life history. To understand how
hosts and microbes interact, model organisms with comparatively simple microbial communities, such as the fruit fly (Drosophila
melanogaster), offer key advantages. However, studies of the Drosophila microbiome are limited to a single point in time,
because flies are typically sacrificed for DNA extraction. In order to test whether noninvasive approaches, such as sampling of fly
feces, could be a means to assess fly-associated communities over time on the same cohort of flies, we compared the microbial
communities of fly feces, dissected fly intestines, and whole flies across three different Drosophila strains. Bacterial species identified
in either whole flies or isolated intestines were reproducibly found in feces samples. Although the bacterial communities of
feces and intestinal samples were not identical, they shared similarities and obviously the same origin. In contrast to material
from whole flies and intestines, feces samples were not compromised by Wolbachia spp. infections, which are widespread in laboratory
and wild strains. In a proof-of-principle experiment, we showed that simple nutritional interventions, such as a high-fat
diet or short-term starvation, had drastic and long-lasting effects on the micobiome. Thus, the analysis of feces can supplement
the toolbox for microbiome studies in Drosophila, unleashing the full potential of such studies in time course experiments where
multiple samples from single populations are obtained during aging, development, or experimental manipulations.
