Abstract
Introduction of microbial contaminations in the dairy value chain starts at the farm level and the initial microbial composition may severely affect the production of high-quality dairy products. Therefore, understanding the farm-to-farm variation and longitudinal shifts in the composition of the bulk tank milk microbiota is fundamental to increase the quality and reduce the spoilage and waste of milk and dairy products. In this study, we performed a double experiment to study long- and short-term longitudinal shifts in microbial composition using 16S rRNA gene amplicon sequencing. We analyzed milk from 37 farms, that had also been investigated two years earlier, to understand the stability and overall microbial changes over a longer time span. In addition, we sampled bulk tank milk from five farms every 1–2 weeks for up to 7 months to observe short-term changes in microbial composition. We demonstrated that a persistent and farm-specific microbiota is found in bulk tank milk and that changes in composition within the same farm are mostly driven by bacterial genera associated with mastitis (e.g., Staphylococcus and Streptococcus). On a long-term, we detected that major shift in milk microbiota were not correlated with farm settings, such as milking system, number of cows and quality of the milk but other factors, such as weather and feeding, may have had a greater impact on the main shifts in composition of the bulk tank milk microbiota. Our results provide new information regarding the ecology of raw milk microbiota at the farm level.
Highlights
Production of high-quality dairy products requires a high-quality raw milk
Between 2017 and 2019, three farms switched from tie stall pipeline milking system (TSP) to automatic milking systems (AMS) in area A while no such changes were registered in area B
As the milk samples were collected in the same manner, from the same farms and in the same period of the year, our experimental design allowed us to look beyond variation connected to season, FIGURE 5 | Pairwise differential abundance of the most abundant genera which account for over 95% of the total milk microbiota
Summary
The initial microbial quality of raw milk is one of the most important parameters used by the dairy industry to assess the milk prior to production It is important for the dairy industry to avoid the introduction in the dairy chain of spoilage microbes that can cause quality-deterioration of milk products. Knowing and understanding the composition and Longitudinal Study of the Bulk Tank Milk Microbiota temporal changes, as well as the potential causes of these changes in the community structure of raw milk is important for the dairy industry. This can inform action to reduce spoilage and limit economical costs and food waste caused by quality problems
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