It takes three to tango : tripartite interaction between cabbage root flies their gut microbiome and host plant defense compounds Plants are constantly attacked by herbivores. To defend themselves they produce chemical compounds. The plant family Brassicaceae synthesizes glucosinolates (GSL) that are hydrolyzed to toxic isothiocyanates (ITCs) and other compounds during herbivory. Several insect herbivores adapted to their host plant defense system. Microbial communities can play a crucial role in allowing insects to thrive in recalcitrant habitats and feed on toxic food sources. However adaptation mechanisms in belowground herbivores and the role of gut bacterial communities (GBCs) in this adaptation process remained uninvestigated so far. This thesis aims to understand the molecular mechanisms underpinning the adaptation of the cabbage root fly D. radicum and the turnip root fly D. floralis larvae to the GSL ITC defense system in their host plants. Biochemical response of roots to D. radicum and D. floralis infestation indicated that the larvae of both Delia species are exposed to the GSL ITC system while feeding. To elucidate molecular mechanisms that underlie the adaptation processes of Delia species to their host plants defense system the genome of D. radicum was assembled and annotated. A combination of metabolomic and transcriptomic analyses revealed that the larvae possess the enzymatic machinery to detoxify ITCs by activating the mercapturic acid conjugation pathway and a hydrolytic pathway. Both mechanisms are likely the results of co evolutionary processes with their host plants. In addition 16S amplicon sequencing revealed that the larval GBCs responded to ITCs and likely express their own detoxification mechanism (hydrolytic pathway). How essential the GBCs are for the larvae to detoxify ITCs remains an unanswered question. The results of this thesis provide a knowledge base for understanding mechanisms that underpin co evolutionary processes between host plants and belowground herbivores.