House flies are common pests in agricultural facilities and serve as an important vectors of human and animal pathogens. Microbial communities associated with house flies are acquired from the environments within which they live and feed upon. The extent to which such microbial communities vary between flies originating from similar agricultural facilities yet separated across a large geographical distances have not been well described. In this study, we used high throughput sequencing of bacterial 16S rDNA to characterize bacterial communities of female house flies collected from dairy and feedlot cattle farms in Nebraska, Kansas and Oklahoma. Bacterial community composition in the house flies varied significantly between farm types and across geographic locations. Species richness and Shannon diversity indices were greater (14 and 18 %, respectively) in flies collected from feedlots compared to dairy cattle farms. Abundance of the most dominant bacterial taxa (Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria) differed significantly among geographic locations. Abundance of Proteobacteria and Bacteroidetes also differed between farm types. Furthermore, potential human and animal pathogenic taxa such as Acinetobacter, Providencia, unclassified Enterobacteriaceae, Enterococcus and Ignatzschineria were more abundant in house flies collected from dairy farms whereas Prevotella, Alloprevotella, Turicibacter, Clostridium_IX, unclassified Clostridiales and Moraxella were more abundant in feedlot flies. These results demonstrate that the diversity and structure of bacterial communities in female house flies are significantly influenced by farm type and geographic location, and that adult female house flies serve as a potential reservoir for human and animal pathogenic bacteria.
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