Next generation sequencing, insect microbiomes, and the confounding effect of Wolbachia: a case study using Drosophila suzukii Matsumura (Diptera: Drosophilidae)

Abstract

Next generation sequencing (NGS) increasingly is being used to characterize the gut microbiome of insects to provide insights into the ecology and biology of the host, but results may be confounded by co-occurring infections of Wolbachia bacteria in the cells of the host. We illustrate this issue using spotted winged drosophila (SWD), Drosophila suzukii Matsumura, 1931 (Diptera: Drosophilidae) as an example. With a polymerase chain reaction based assay, we detected Wolbachia in 20 percent of flies collected from sites in British Columbia, Alberta, and Newfoundland and Labrador, Canada. With NGS, we determined that the total microbiome of infected flies was dominated by Wolbachia (ave. of 98.8%) with average values of bacterial richness and diversity 1.4- and 22-fold lower than that of co-occurring, uninfected flies (ave. of 0.6% Wolbachia). We review options available to address the confounding factor of Wolbachia, which vary with the presence of infections in the population, the prevalence of infected individuals in the population, and the titre of Wolbachia in infected individuals. Understanding this issue and how it can be resolved is of broad importance, given that an estimated 40 percent of terrestrial arthropod species harbour Wolbachia infections.