Longitudinal sampling of 6 farms in the Auvergne region (France) provided bi-weekly samples of milk (cow level), feces (cow level), litter (farm level) and milk filter (farm level), which were investigated for - mastitis pathogens, quantified by qPCR using Pathoproof commercial kit and laboratory-made range (included in qPCR pathogen file and qPCR pathogen range file) - bacterial abundance, quantified by 16S gene qPCR (included in metadata) - immune cells abunance, quantified weekly by AgroLabs laboratory (included in metadata) -information on farm practices and antibiotic treatments (included in metadata)

This data was then analyzed to identify pathogen profiles associated with mastitis, using the R workflow (included in R files pathogen preprocessing and pathogen analysis)