House flies (Musca domestica L.) are vectors of human and animal pathogens at livestock operations. Microbial communities in flies are acquired from, and correlate with, their local environment. However, variation among microbial communities carried by flies from farms in different geographical areas is not well understood. We characterized bacterial communities of female house flies collected from beef and dairy farms in Oklahoma, Kansas, and Nebraska and further evaluated the prevalence of antibiotic resistance genes in bacteria within flies. We evaluated the influence of farm type and farm location on bacterial communities, diversity, pathogenic bacteria strains and prevalence of antibiotic resistance genes. These data can be used for better understanding of abundance and prevalence of bacterial communities in house flies associated with livestock operations. These data were collected in September 2019. Abbreviations used include Operational Taxonomic Units(OTUs), Canonical Correspondence analysis (CCA), Infectious Bovine Keratoconjunctivitis (IBK), Anti Microbial Resistance (AMR), and Antibiotic Resistance Genes (ARGs).
The raw Illumina MiSeq sequence data for this project can be found here: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA863664 Resources in this dataset:

Resource title: Metadata for Microbiome of House Fly Associated with Cattle Farms File name: Metadata for Microbiome of House Fly Associated with Cattle Farms.xlsx Resource description: This spreadsheet links the raw sequence reads on NCBI with data on farm type, farm location and sample type.