Examining interactions between the microbiome and viral infection across Drosophila species

Microbiomes can influence the outcomes of virus infection, while viral infections can disrupt microbiome composition. These reciprocal interactions may contribute to patterns of host susceptibility, but it remains unclear whether microbiome-virus interactions are consistent across host species, or whether host evolutionary relationships influence microbiome variation and its association with viral susceptibility. Here, we investigate interactions between bacterial microbiomes and Drosophila C virus (DCV) infection across 32 Drosophilidae host species, using experimental infections and 16S rRNA amplicon sequencing. Using phylogenetic mixed models, we tested for phylogenetic structure in microbiome diversity and composition, and whether specific bacterial taxa were associated with among-species variation in viral load. Drosophilidae microbiomes were consistently dominated by a small number of bacterial genera and showed limited phylogenetic structuring. DCV infection was associated with a small reduction in bacterial richness, but microbiome composition was only weakly affected by wounding or infection and largely dominated by within-species variation. However, specific taxa were associated with large differences in viral replication, including reduced DCV load in flies harbouring Streptococcus before infection or Bacillus during infection. These results suggest that, at least in the conditions used in this study, microbiome composition may not generate strong, generalisable host phylogenetic patterns in virus susceptibility.