Recent advances in high throughput sequencing have provided important insights on the diversity and functional capabilities of gut microbiota in various animals. Despite tremendous sampling efforts in mammalian systems, the community dynamics and assembly patterns of gut microbiota are poorly understood, and experimental demonstration of their nutritional benefits remains largely absent. To address these issues, this study develops Drosophila as a model system to study: 1) the diversity of the gut microbiota, by characterizing the gut microbiota composition of laboratory Drosophila melanogaster and other Drosophila species across phylogeny using high-throughput sequencing of the 16S rRNA gene, 2) the nutritional benefits of gut microbiota under different dietary regimes, by comparing the performance and nutritional responses between conventional and axenic (i.e. microbefree) flies onto diets of systematically-varied nutrient (yeast-glucose) content. Results from this project demonstrate that Drosophila has a low-diversity gut bacterial community that is amenable for studying gut microbiota functions. The taxonomic composition appears to be inconstant, with no evidence for core taxa or co-evolution between the host and its microbiota. However, elimination of the gut microbiota results in prolonged host development and nutritional response to diet. The gut bacteria promote host health under conditions of nutritional stress resulting from unbalanced diet by increasing micronutrient (vitamins B) availability and/or reducing excessive dietary sugar. Future investigations will include examining the nutritional functions of individual gut bacteria via re-associations with axenic flies, and testing congruence between taxonomic and functional (microbiome) profiles of the gut microbiota in response to changing diet.