Livestock forensics: Utilizing stable fly microbiome profiles as investigative tools and to monitor agricultural health

Within the livestock industry, insects and the pathogens they harbor present legal concerns and agricultural health threats. Recently, residents in North Carolina successfully sued the world’s largest pork producer under nuisance laws; fly infestation was a chief complaint. Fly populations also have the potential to play a role in agroterrorism. There are over 30 animal diseases on the bioterrorism list including many bacteria, several of which have the potential to be mechanically transmitted by stable flies (Stomoxys calcitrans). These include species like Bacillus anthracis, Francisella tularensis, and several Brucella species. Stable fly infestation or an outbreak of associated disease would warrant origin determination and host identification. The microbiome of S. calcitrans larvae and their substrate has been assessed, but not from various locations. This has not to our knowledge been attempted with adults. Stable flies present a novel perspective for use in environmental monitoring, specifically around livestock facilities. Surveillance for this fly differs from traditional dipteran monitoring sources because they feed on blood from live animals, and not excrement or dead tissue. This presents an alternative to traditional filth fly sampling by offering a clearer snapshot of the microbiome of a live host within their environment while limiting the interference of the necrobiome. This research aims to identify a baseline laboratory stable fly microbiome and utilize it in comparison to the microbial communities associated with wild flies sourced from an exotic wildlife park, beef cattle and dairy facilities. Flies and environmental samples were collected for analysis from each location.