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Background The causative agent of Chagas disease,  Trypanosoma cruzi , and its nonpathogenic relative,  Trypanosoma rangeli , are transmitted by haematophagous triatomines and undergo a crucial ontogenetic phase in the insect’s intestine. In the process, the parasites interfere with the host immune system as well as the microbiome present in the digestive tract potentially establishing an environment advantageous for development. However, the coherent interactions between host, pathogen and microbiota have not yet been elucidated in detail. We applied a metagenome shotgun sequencing approach to study the alterations in the microbiota of  Rhodnius prolixus , a major vector of Chagas disease, after exposure to  T. cruzi  and  T. rangeli  focusing also on the functional capacities present in the intestinal microbiome of the insect. Results The intestinal microbiota of  R. prolixus  was dominated by the bacterial orders  Enterobacterales ,  Corynebacteriales ,  Lactobacillales ,  Clostridiales  and  Chlamydiales , whereas the latter conceivably originated from the blood used for pathogen exposure. The anterior and posterior midgut samples of the exposed insects showed a reduced overall number of organisms compared to the control group. However, we also found enriched bacterial groups after exposure to  T. cruzi  as well as  T rangeli . While the relative abundance of  Enterobacterales  and  Corynebacteriales  decreased considerably, the  Lactobacillales , mainly composed of the genus  Enterococcus , developed as the most abundant taxonomic group. This applies in particular to vectors challenged with  T. rangeli  and at early timepoints after exposure to vectors challenged with  T. cruzi . Furthermore, we were able to reconstruct four metagenome-assembled genomes from the intestinal samples and elucidate their unique metabolic functionalities within the triatomine microbiome, including the genome of a recently described insect symbiont,  Candidatus Symbiopectobacterium , and the secondary metabolites producing bacteria  Kocuria  spp. Conclusions Our results facilitate a deeper understanding of the processes that take place in the intestinal tract of triatomine vectors during colonisation by trypanosomal parasites and highlight the influential aspects of pathogen-microbiota interactions. In particular, the mostly unexplored metabolic capacities of the insect vector’s microbiome are clearer, underlining its role in the transmission of Chagas disease.

Exposure to Trypanosoma parasites induces changes in the microbiome of the Chagas disease vector Rhodnius prolixus