Seasonal and geographical influences on the bulk tank milk microbiota

Season and location have been shown previously to influence the microbiota of raw milk, especially in pasture-based systems. However, correlations between the raw milk microbiota and specific climatic variables or the chemical composition of milk have not been investigated. This study examined differences in the raw milk microbiota from a number of different locations across Ireland over a 12-month period, and studied the associations with climatic variables and the chemical composition. More specifically, shotgun metagenomic sequencing was used to investigate the microbiota of bulk tank raw milk collected from 9 locations (n=241) over this time. Although the raw milk microbiota was highly diverse, a core microbiota was found, with Pseudomonas_E, Lactococcus, Acinetobacter and Leuconostoc present in all samples. Diversity significantly differed by season and location, with seasonality and geography contributing 11.8% and 10.5% to the variation in the microbiota. Functional and antibiotic resistance profiles also differed by season and location. Many climatic variables were found to significantly impact the raw milk microbiota. Mean daily temperature was associated with several mastitis-related taxa and also correlated with the fat content of milk. Ultimately, this study expands our understanding of the interconnected nature of the microbiota, environment/climate variables and chemical composition of raw milk and provides evidence of a season- and location-specific microbiota.