  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.
