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Objectives  As in most organisms, the surface of the fruit fly  Drosophila melanogaster  is associated with bacteria. To examine whether this association depends on cuticle quality, we isolated and quantified surface bacteria in normal and melanized flies applying a new and simple protocol.    Results  On wild flies maintained in the laboratory, we identified two persistently culturable species as  Lactobacillus plantarum  and  Acetobacter pomorum  by 16S rDNA sequencing. For quantification, we showered single flies for DNA extraction avoiding the rectum to prevent contamination from the gut. In quantitative PCR analyses, we determined the relative abundance of these two species in surface wash samples. On average, we found 17-times more  A. pomorum  than  L. plantarum . To tentatively study the importance of the cuticle for the interaction of the surface with these bacteria, applying Crispr/Cas9 gene editing in the initial wild flies, we generated flies mutant for the  ebony  gene needed for cuticle melanisation and determined the  L. plantarum  to  A. pomorum  ratio on these flies. We found that the ratio between the two bacterial species reversed on  ebony  flies. We hypothesize that the cuticle chemistry is crucial for surface bacteria composition. This finding may inspire future studies on cuticle-microbiome interactions.    Supplementary Information  The online version contains supplementary material available at 10.1186/s13104-021-05766-7.

Ratio between Lactobacillus plantarum and Acetobacter pomorum on the surface of Drosophila melanogaster adult flies depends on cuticle melanisation