Advances in genome sequencing technology have revolutionized the study of microorganisms. Recent genome-wide association studies (GWAS) on gut microbiota revealed fascinating discoveries about the effect of microbiota on our health. In this thesis, Drosophila Melanogaster samples were used to investigate the associations between the host's genotype and microbiota. The meta-analysis of microbiota data was performed using PhyloMAF, a novel, and comprehensive microbiome meta-analysis framework. The resulting microbial abundance tables were analyzed using alpha and phylogenetic beta bio-diversity metrics, which were used in the microbiome GWAS study. Significant variant associations were further analyzed in the post-GWAS analysis. The results of our study show that several genomic variants are significantly associated with bio-diversity estimates. Among identified variants, few were found to be associated with more specific phenotypes. Particularly, the gene involved in folate transport and linked to folate malabsorption was found to be associated with Proteobacteria. The latter for its part was found to be one of the primary phyla containing the highest number of genes responsible for de-novo folate synthesis. Similarly, the fly gene related to immune function with the human homologous gene linked to the inflammatory gut disease was found to be associated with the Acetobacter genus. This genus based on the literature survey was found to be associated with an immune deficiency in a fruit fly. In summary, this research revealed captivating findings of genetic factors associated with fruit fly microbiota. The limitations and future directions were stated in order to provide the basis for future prospective studies.