Drosophila melanogaster is one of the most widely used model systems in biology. However, little is known about its associated bacterial community. As a first step towards understanding these communities, we compared bacterial 16S rRNA gene sequence libraries recovered from 11 natural populations of adult D. melanogaster. Bacteria from these sequence libraries were grouped into 74 distinct taxa, spanning the phyla Proteobacteria, Bacteroidetes, and Firmicutes, which were unevenly spread across host populations. Summed across populations, the distribution of abundance of genera was closely fit by a power law. We observed differences among host population locations both in bacterial community richness and in composition. Despite this significant spatial variation, no relationship was observed between species richness and a variety of abiotic factors, such as temperature and latitude. Overall, bacterial communities associated with adult D. melanogaster hosts are diverse and differ across host populations.Insects harbor diverse microbial communities (11,29,34,65), and interactions between hosts and their microbes can range from mutualistic, such as the interaction between termites and their gut microbes (8,65), to parasitic, such as the interaction of the bacterium Paenibacillus larvae (American foulbrood) in honeybees (62). Some of these interactions are relatively well characterized, owing to their economic importance or because of their remarkable biology. However, the exact nature of many other potentially interesting and experimentally tractable insect-microbe interactions, specifically those between microbes and the major insect model systems, remains poorly understood.In addition to the immediate association between insect hosts and the bacterial communities they harbor, the bacteria that insects carry can also associate with and affect the fitness of other hosts through vector transmission. The most common vector-borne zoonotic inflammatory disease in the United States, Lyme disease (caused by Borrelia burgdorferi), is transmitted by the deer tick, Ixodes scapularis, and infected more than 23,000 people in 2002 (26). In addition, Erwinia carotova, responsible for soft rot in many species of plants and for significant economic losses, can be vector transmitted by a variety of insects, including Drosophila melanogaster (38). Clearly, vector-borne bacterial infections can have large economic and health impacts and are important determinants of fitness for a variety of potential hosts.It is estimated that approximately 99% of the bacteria in nature are unculturable (3). With the advent of molecular techniques, such as PCR and genome sequencing, and metagenomic approaches, researchers have uncovered an astonishing level of microbial diversity in natural habitats, ranging from soil (7, 54, 69) and marine environments (23,64,69,70) to the human gut (25). The same techniques are currently being applied to understanding the microbiota of a range of insects (11,29,34,47,53,55,56,65). For example, using such sequence-b...