The core microbiome and dysbiosis of individual Phlebotomus argentipes sand flies across Bihar, India

Sand flies transmit Leishmania parasites across the world, causing the fatal disease visceral leishmaniasis (VL), and the highly disfiguring cutaneous leishmaniasis. India is one of 10 countries where 95% of VL cases occur, with 80% of Indian cases occurring in the northern Indian state Bihar. As the native microbiota of insect vectors are known to play a part in vectorial capacity, and may be exploited in vector control strategies, we sought to improve our knowledge of the microbiome of the sand fly Phlebotomus argentipes, the only VL vector in Bihar. The current knowledge of Ph. argentipes microbiota is restricted to the characterisation of pooled samples by aerobic culture. In this study we developed a pipeline to characterise the bacterial microbiota of individual Ph. argentipes samples, using 16S sequencing, and mitigating the challenges of low biomass and “kit-ome” contamination. Individual Ph. argentipes harbour a limited core microbiome of seven genera including Staphylococcus, Acinetobacter and Corynebacterium, and a highly-variable peripheral microbiome. A common dysbiotic state was discovered in Ph. argentipes sand flies, where single bacterial species dominate individual microbiomes. Furthermore, several pathogens causing currently emerging diseases are described, and the potential for sand flies to be novel vectors of these pathogens is discussed. Targets for paratransgenesis-based vector control strategies are identified, corroborating previous research into microbiota-mediated sand fly control strategies, and the next steps for implementing microbiome knowledge for VL control are outlined.