Effect of the microbiome on pathogen susceptibility across four Drosophilidae species

The host microbiota has been shown to play an important role in host susceptibility to infections in some systems. However, less is known about whether microbiota-mediated effects are consistent across host species as our understanding of these interactions might be affected by publication bias. Following on from a large study of 36 species of Drosophilidae challenged with four bacterial pathogens, we identified two candidate host species that might have protective microbiome based on low susceptibility and high abundance of the culturable microbiota; we selected two other species for comparison. We tested whether germ-reduced flies, and flies with a natural or re-constituted microbiome, varied in their susceptibility to systemic infection of two bacterial pathogens (Providencia rettgeri and Staphylococcus aureus) and one viral pathogen (Drosophila C Virus).The composition and abundance of the bacterial microbiota varied between species and microbiome treatments. Significant interactions were found between host species and pathogen, and between host species and microbiome treatment, but not between pathogen and microbiome treatment. The natural microbiota exerted limited effects on pathogens in a small number of interactions. For example, the microbiome composition affected bacterial and DCV infections in D. putrida; bacterial infection in Z. davidi, and DCV infection in D. melanogaster. Re-constituting the microbiome with a single bacterial species largely did not improve the host survival relative to germ-reduced or normal flies. While there are always challenges to manipulating microbiomes, especially across multiple host species, our results showed host microbiota play limited roles on survival in systemic infection in these four species. This work demonstrates caution is required when generalizing about potential beneficial impact of microbiomes.