GitHub Repository for: Stable-Fly-Microbiome

Raw data and scripts for: Stable flies are bona fide carriers of mastitis-associated bacteria.

Hematophagous Stomoxys (stable) fly populations in dairy barns are sustained by a constant availability of cattle hosts and manure, which serve as major reservoirs of both zoonotic and opportunistic bacterial pathogens. However, the composition of the Stomoxys fly microbiota, the mechanisms by which flies acquire their microbiome, and the ability of potentially pathogenic bacteria to colonize and persist in fly hosts remain to be investigated. Here, we longitudinally collected fly and manure samples from two connected dairy facilities. High throughput 16S rRNA gene amplicon sequencing was then used to characterize and compare bacterial communities present on or within flies and in manure collected from the same facility, while culture-dependent methods were used to verify the viability of clinically relevant bacteria.

Scripts for each analysis are written in R. Each directory contains necessary files and code to recreate each figure and all data analyses reported in the manuscript. To repeat the analysis, clone the repository, and then run each script. Do not cd into the cloned repository.