Bacterial diversity associated with Drosophila in the laboratory and in the natural environment
Fabian Staubach, John F. Baines, Sven Kuenzel, Elisabeth M. Bik, Dmitri A. Petrov
(Submitted on 14 Nov 2012)
All higher organisms are associated with bacterial communities. Bacteria have a range of effects on their metazoan hosts from being indispensable for survival to being lethal pathogens. Because bacteria have phenotypic effects on their hosts, they can also be involved in host adaptation to the environment. The fruit fly Drosophila is a classic model organism to study adaptation as well as the relationship between genetic variation and phenotypes. Recently, Drosophila has received attention in immunology and studies of host-microbe interaction. Although bacterial communities associated with Drosophila might be important for many aspects of Drosophila biology, little is known about their diversity and composition or the factors shaping these communities. We used 454-based sequencing of a variable region of the bacterial 16S ribosomal 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 flies collected from a variety of natural substrates, as well as from adults and larvae of nine laboratory-reared Drosophila species. We find substantial variation of bacterial communities within and between laboratories that could interfere with phenotype studies. We show that bacterial communities associated with wild-caught Drosophila contain more bacterial species than laboratory-raised flies, but that they are on average less diverse than vertebrate communities. The natural Drosophila-associated microbiota appears to be predominantly shaped by food substrate with an additional but smaller effect of host species identity.