Spatiotemporal variation of bacterial communities in female house flies sssociated with beef cattle farms

Bacterial communities of house flies are shaped by food and developmental resources in their surrounding environment. Variations in microbial communities between flies originating from similar agricultural facilities yet separated across large geographical areas and time are largely unexplored. Here, we used high-throughput sequencing of 16S rRNA gene to characterize bacterial communities of female house flies collected once per month (July-October 2020) from beef cattle farms in Kansas, Oklahoma and Texas. Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria were the most dominant and prevalent bacterial phyla in flies. Highly prevalent taxa (core microbiome) included potential pathogens of humans and livestock such as Staphylococcus, Escherichia, Providencia, Enterococcus, Turicibacter and Moraxella. While prevalence was 100% across sites, abundance of Staphylococcus was significantly higher in flies from southern geographic locations. The opposite trend was observed in abundances of Prevotella and Turicibacter whose abundance also varied across sites and between sampling times. Bacterial species richness increased from northern to southern geographic regions. The lowest species richness was observed in September and the highest in October. Bacterial community compositions of individual flies from the same sampling date and geographic location were more similar indicating the pronounced effect of both variables on fly carriage of bacteria. These results demonstrated that composition and diversity of bacterial communities in house flies are significantly influenced by geographic location and sampling time, and female house flies pose a risk as reservoirs and disseminators of human and animal pathogens.