Continent-wide structure of bacterial microbiomes of European Drosophila melanogaster suggests host-control

Abstract

The relative importance of host-control, environmental effects, and stochasticity in the assemblage of host-associated microbiomes has been much debated. With recent sampling efforts, the underpinnings of D. melanogaster's microbiome structure have become tractable on larger spatial scales. We analyzed the microbiome among fly populations that were sampled across Europe by the European Drosophila Population Consortium (DrosEU). We combined environmental data on climate and foodsubstrate, dense genomic data on host population structure, and microbiome profiling.Food-substrate, temperature, and host population-structure correlated with microbiomestructure. The microbes, whose abundance was co-structured with host populations, also differed in abundance between flies and their substrate in an independent survey, suggesting host-control. Patterns of enrichment and depletion of microbes between host and substrate were consistent with a model of host-control, where the host manipulates its microbiome for its benefit. Putative host-control was bacterial strain specific, supporting recent evidence for high specificity of D. melanogaster-microbe interaction.

Meta-analysis suggests the microbiome responds to Evolve and Resequence experiments inDrosophila melanogaster

“…There are both practical and biological reasons to exclude Wolbachia from most microbiome studies as it is intracellular, low abundance in the gut, has complex effects on host traits, overrepresentation in 16S rRNA profiling--all characteristics distinct from the more common bacteria in the fly microbiome, like Acetobacter and Lactobacillus [23,55,56]. Indeed, many studies in D. melanogaster either only use uninfected flies [23,39,45,46] or computationally remove Wolbachia reads during 16S rRNA microbiome analysis [24,[57][58][59][60]. We emphasize the importance of considering and testing the potential influence of Wolbachia on fly adaptation and trait variation.…”

“…Furthermore, recent studies suggest that Wolbachia may interact with other bacteria in the microbiome [55,56]. Finally, many studies in D. melanogaster exclude Wolbachia reads when analyzing microbial communities [24,[57][58][59][60], leaving an open question as to if Wolbachia is considered part of the Drosophila microbiome. To test the effect of Wolbachia on our inference, we removed the Anaplasmataceae family (all of which are Wolbachia in flies) reads from the communities, and then recalculated Shannon diversity through the same procedure as above.…”

The Predicted Metabolic Function of the Gut Microbiota ofDrosophila melanogaster

“…This choice of taxa enabled us to examine interactions among species of different taxonomic relatedness and metabolic function: within the Acetobacteraceae, the closely-related A. fabarum and A. pomorum are assigned to a different subgroup of Acetobacter from A. tropicalis (32); and the homofermentative L. plantarum and heterofermentative L. brevis are members of different 73 phylogenetic groups of Lactobacillus (33). Members of the genus Acetobacter and Lactobacillus are well represented across both field and lab Drosophila populations (34)(35)(36)(37) and have been widely used to investigate the impact of gut microbes on host physiology (14, [38][39][40]. The metabolic network for each species was reconstructed from annotated metabolism genes in the sequenced genome, and the networks for the different species in each community integrated into community models.…”