GitHub Repository for: Opportunistic pathogens are prevalent across the culturable exogenous and endogenous microbiota of stable flies captured at a dairy facility

<p dir="ltr">GitHub link for manuscript: "Opportunistic pathogens are prevalent across the culturable exogenous and endogenous microbiota of stable flies captured at a dairy facility."</p><p dir="ltr">In this study, bacteria were cultured from internal homogenates and external surfaces of Stomoxys flies captured from a dairy farm in Wisconsin. Sample pool information is as follows:</p><p dir="ltr">D01A to D08A: Internal homogenate of flies caught near free-stall barn in July<br>D09A to D16A: Internal homogenate of flies caught near free-stall barn in August/September<br>T01A to T08A: External homogenate of flies caught near free-stall barn in July<br>T09A to T16A: External homogenate of flies caught near free-stall barn in August/September<br>D01C to D04C: Internal homogenate of flies caught near calf-hutches in July<br>D05C to D07C: Internal homogenate of flies caught near calf-hutches in August/September<br>T01C to T04C: External homogenate of flies caught near calf-hutches in July<br>T05C to T07C: External homogenate of flies caught near calf-hutches in August/September<br></p><p><br></p><p dir="ltr">Files in this repository:</p><p dir="ltr"><i>ArlingtonPathogenIncidence_DataSummary.xlsx</i> -> Excel file containing a summary of all bacterial isolates cultured from stable flies. The "Strains" tab provides information on the sample type, isolation media, partial 16S rRNA sequence, and taxonomic information. Remaining sheets provide a summary of incidence rates in different sample types for key bacterial taxa.<br><i>FisherTests -> R Script for fisher tests</i><br><i>Table_RImport.xlsx</i> -> Required input file showing the counts of key taxa in different sample types for R Script. The "total" column represents the number of fly pools for each sample type</p>