Structure, function, and quantitative biology of the Drosophila gut microbiome

Drosophila melanogaster is one of the most powerful animal models for developmental genetics, and it has a relatively simple microbiome. Flies can easily be reared germ-free, then reassociated with defined microbial strains to study colonization and bacterial effects on the fly, making a highly tractable model for microbiome studies. This review provides a biological background on the Drosophila microbiome for quantitative researchers interested in using the system. We discuss the current understanding of which microbes compose the fly gut microbiome, how they colonize, how they affect the fly, and how the overall microbiome structure influences its function. We also discuss existing large data sets and quantitative theory of the Drosophila microbiome.