Symbiosis is an intimate association between unrelated organisms, which has been essential in the evolutionary diversifi cation of eukaryotes (Moran and Yun 2015). Insects frequently share long-term and stable relationships with heritable bacteria which has enabled them to become the most diverse and successful animals on earth (Dale and Moran 2006, Brownlie and Johnson 2009, Gibson and Hunter 2009). Most bacterial symbionts in insects cannot be cultivated independently and they may be present in the low titer in the host (Oliver et al. 2010). The symbionts may be diffi cult to cultivate because of their slow growth, microaerophilic lifestyle, requirement for specifi c host metabolites and/or the loss and inactivation of genes, which reduces their independence (Pontes and Dale 2006). Microbial diversity and ecology can be studied without cultivation using the 16S ribosomal DNA (rDNA) sequencing approach (Klindworth et al. 2013, Vetrovsky and Baldrian 2013). The 16S rDNA is particularly suitable because it is ubiquitous in eukaryotes and only weakly affected by horizontal gene transfer, so conserved regions can be used to design taxon-specifi c primers and hybridization probes (Daubin et al. 2003). In addition, variable regions within the 16S rDNA can be used to classify microbial diversity (Vetrovsky and Baldrian 2013). The rapid development of nextgeneration sequencing technologies has therefore provided a new approach for the analysis of biodiversity, revealing the “rare biosphere” within different host organisms (Klindworth et al. 2013).