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Abstract:
The fruit fly Drosophila is a classic model organism to study adaptation as well as the relationship between genetic variation
and phenotypes. Although associated bacterial communities might be important for many aspects of Drosophila biology,
knowledge about their diversity, composition, and factors shaping them is limited. We used 454-based sequencing of a
variable region of the bacterial 16S ribosomal RNA gene to characterize the bacterial communities associated with wild and
laboratory Drosophila isolates. In order to specifically investigate effects of food source and host species on bacterial
communities, we analyzed samples from wild Drosophila melanogaster and D. simulans collected from a variety of natural
substrates, as well as from adults and larvae of nine laboratory-reared Drosophila species. We find no evidence for host
species effects in lab-reared flies; instead, lab of origin and stochastic effects, which could influence studies of Drosophila
phenotypes, are pronounced. In contrast, the natural Drosophila–associated microbiota appears to be predominantly
shaped by food substrate with an additional but smaller effect of host species identity. We identify a core member of this
natural microbiota that belongs to the genus Gluconobacter and is common to all wild-caught flies in this study, but absent
from the laboratory. This makes it a strong candidate for being part of what could be a natural D. melanogaster and D.
simulans core microbiome. Furthermore, we were able to identify candidate pathogens in natural fly isolates.
