The holobiont's extracellular microbiome modulates the adaptation of an intracellular endosymbiont

Holobionts contain extra- and intracellular microbes that are typically studied in symbiotic and anatomical siloes. Here we demonstrate a previously unknown impact of the extracellular gut microbiome on the adaptation of a reproductive endosymbiont. Specifically, a paternal-effect embryonic lethality caused by Wolbachia-induced cytoplasmic incompatibility (CI) is attenuated by the gut microbiome. Gut microbiome-mediated variation in the CI phenotype causes key gene expression changes in the symbiosis and defining cell biological defects in the evolutionary conserved histone-to-protamine transition that drives CI. Reintroducing the gut microbiome into germ-free flies recapitulates the CI attenuation. Notably, the integrated holobiont exhibits significantly elevated gut microbiome and endosymbiont densities relative to isolated constituent rearing, highlighting a synergistic relationship. Finally, impacts of the symbionts on survival are independent and inversely related throughout development, and fitness changes are recapitulated when the gut microbiome is restored. Altogether, this study uncovers a gut-germline axis in which bacteria shape an entangled network of symbiotic functions within a holobiont. Interorgan, symbiotic relationships have far-reaching implications for the study of trait variation.