An observational study of the presence and variability of the microbiota composition of goat herd milk related to mainstream and artisanal farm management

Goat milk is produced on mainstream and artisanal farms. It was expected that the farm management may influence the microbial population of the milk. Therefore, we investigated the bacterial content and microbiota composition of raw milk in relation to Dutch goat farm management. After amplicon sequencing we analyzed the taxa at phylum and genus levels, and used the relative values enabling to provide information about the variation among the different samples. On ten farms our results indicated that the number of bacterial colony forming units and microbiota composition of the milk, directly after milking was variable among farms and not related to the farm management system. At the phylum level the phyla Firmicutes, Actinobacteria, Proteobacteria, and to a minor extend Bacteriodota were the dominant phyla in the raw goat milk, together usually comprising 90% of the total bacterial phyla. The most dominant genera were Staphylococcus, Pseudomonas, Lactococcus, Microbacteria, Acinetobacteria, and Corinebacteria. The number of bacterial phyla and genera does not differ between the mainstream and artisanal farms, although the Shannon index may be numerically higher in the mainstream farms as compared to artisanal farms. In addition, the variability is higher among artisanal farms, which may be due to less standardization of the management. The milk microbiota composition differed among farms. Repeated sampling of a farm showed that this changed over time. The lactic acid producing bacteria showed a similar pattern. Variable microbiota richness amount and diversity of microorganisms were present in different farming systems. We concluded that farm-specific management and sampling moment were the major determining factors for the milk microbiota composition.