House flies are nuisance pests of cattle and serves as reservoirs, disseminators, and mechanical vectors of wide range of microbes, especially bacteria that could have acquired from animals and their waste. Examining the bacterial communities of individual house flies and assessing the effects of farm and location on community composition are essential to understand the role of house flies as a vector of bacteria in cattle operations. This study characterized bacterial communities of individual female house flies collected from dairy and beef cattle farms located in three geographic locations (Nebraska, Kansas, and Oklahoma) in USA. Bacterial community composition differed between farm types and also across their location. Highly prevalent bacterial communities included potential pathogenic taxa of human and animals such as Corynebacterium, Staphylococcus, Streptococcus, Enterobacteriaceae, Providencia, Acinetobacter, and Clostridium. Prevalence of cattle ocular disease pathogens: Moraxella bovis and M. bovoculi were greater in beef than dairy cattle farms. These results demonstrate the importance of house flies as a reservoir of potential pathogens in cattle operations and pose potential threats to disseminating around.