| Summary: | Differences in the gut microbial content of <i>Lutzomyia (Lu.) ayacuchensis</i>, a primary vector of Andean-type cutaneous leishmaniasis in Ecuador and Peru, may influence the susceptibility of these sand flies to infection by <i>Leishmania</i>. As a first step toward addressing this hypothesis, a comparative analysis of bacterial and fungal compositions from <i>Lu. ayacuchensis</i> populations with differential susceptibilities to <i>Leishmania</i> was performed. Bacterial 16S rRNA gene amplification and Illumina MiSeq sequencing approaches were used to characterize the bacterial composition in wild-caught populations from the Andean areas of Ecuador and southern Peru at which the sand fly species transmit <i>Leishmania</i> (<i>Leishmania</i>) <i>mexicana</i> and <i>Leishmania</i> (<i>Viannia</i>) <i>peruviana</i>, respectively, and a population from the northern Peruvian Andes at which the transmission of <i>Leishmania</i> by <i>Lu. ayacuchensis</i> has not been reported. In the present study, 59 genera were identified, 21 of which were widely identified and comprised more than 95% of all bacteria. Of the 21 dominant bacterial genera identified in the sand flies collected, 10 genera had never been detected in field sand flies. The Ecuador and southern Peru populations each comprised individuals of particular genera, while overlap was clearly observed between microbes isolated from different sites, such as the number of soil organisms. Similarly, <i>Corynebacterium</i> and <i>Micrococcus</i> were slightly more dominant bacterial genera in the southern Peru population, while <i>Ochrobactrum</i> was the most frequently isolated from other populations. On the other hand, fungi were only found in the southern Peru population and dominated by the <i>Papiliotrema</i> genus. These results suggest that variation in the insect gut microbiota may be elucidated by the ecological diversity of sand flies in Peru and Ecuador, which may influence susceptibility to <i>Leishmania</i> infection. The present study provides key insights for understanding the role of the microbiota during the course of <i>L.</i> (<i>L.</i>) <i>mexicana</i> and <i>L. (V.) peruviana</i> infections in this important vector.
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