Characterization of prokaryotic and microeukaryotic microbiomes of larval pools of mosquitoes sampled in three different countries (Kenya, Guinea Conakry and Burkina Faso) and in laboratory maintained Anopheles lineages.. Comprehensive ecological and geographic characterization of eukaryotic and prokaryotic microbiomes in African Anopheles

Exposure of mosquitoes and their arthropod ancestors to numerous eukaryotic and prokaryotic microbes in their associated microbiomes has probably helped shape the innate immune system. To our knowledge, a comprehensive metagenomic catalogue of the eukaryotic microbiome has not been reported from any insect. Here we employ a novel approach to preferentially deplete host 18S ribosomal gene amplicons in order to reveal the composition of the eukaryotic microbial communities of Anopheles larvae sampled in Kenya, Burkina Faso and Republic of Guinea (Conakry). To determine composition of the eukaryotic microbiome, taxonomic profiling was combined with sequence similarity matching and phylogenetic placement. Notably, the natural eukaryotic microbiome includes aquatic members of the phylum Apicomplexa, relatives of Plasmodium. The eukaryotic microbiome of Anopheles larvae sampled in Kenya is particularly dominated by a novel apicomplexan in the Neogregarinorida lineage. Species richness of the eukaryotic microbiome was not significantly different across sites from East to West Africa, while species richness of the prokaryotic microbiome was significantly lower in larvae sampled in West as compared to East Africa. The microbiome composition in laboratory-maintained Anopheles displayed lower species richness and less diverse community composition of both eukaryotes and prokaryotes, as compared to mosquitoes from the wild population. Laboratory colonies share microbiome members with wild samples, but despite being maintained in the same insectary with the same water and food sources, prokaryotic microbiome variation amongst colonies is maintained, suggesting a genetic influence on microbiome composition. These results provide a foundation to identify and measure the taxa of the Anopheles eukaryotic microbiome. This is a necessary step to understanding their role in vector biology, immunity and pathogen transmission. Natural microbial taxa in the phylum Apicomplexa could induce interference or competition against the apicomplexan Plasmodium within the vector, and other members of the eukaryotic microbiome may offer candidates for new vector control tools.