Effect of the microbiome on pathogen susceptibility across four Drosophilidae species

Microbiome have been shown to play an important role in host susceptibility to infections in some hosts. However, less is known about whether microbiota-mediated effects are consistent across host species, as our understanding of such interactions may 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 microbiomes based on low susceptibility and high abundance of culturable microbiota; we selected two other host species for comparison. We tested whether germ-reduced flies, and flies with natural or re-constituted microbiomes varied in their susceptibility to systemic infection with 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 host species and microbiome treatments. We found an overall interaction between host species and pathogen type, confirming previous work that host species vary in their susceptibility in a pathogen specific manner. Similarly, we found that microbiome treatments had differing effects on host survival among host species, although some effect sizes tended to be small. In D. putrida individuals with manipulated microbiomes showed increased susceptibility to all pathogens tested; in other hosts altered susceptibility was pathogen dependent. While there are always challenges to manipulating microbiomes, especially across multiple host species, our results indicate that host microbiota play limited roles on survival in systemic infection in these four species. This work demonstrates that caution is required when generalizing about potential beneficial impact of microbiomes.