Characteristics of the farms.

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.

山羊奶产自规模化商业农场与手工特色养殖农场。此前研究推测，农场管理模式可能会影响羊奶中的微生物种群。为此，本研究针对荷兰山羊养殖场的管理模式，对原奶的细菌含量与微生物群组成展开了调研。
通过扩增子测序（amplicon sequencing），我们分别在门（phylum）与属（genus）水平对分类单元进行分析，并利用相对丰度值以呈现不同样本间的差异情况。针对10家养殖场的研究结果显示，挤奶后即刻采集的羊奶样本中，细菌菌落形成单位（colony forming units，CFU）数量与微生物群组成在不同农场间存在差异，且与农场管理体系并无关联。
在门水平上，厚壁菌门（Firmicutes）、放线菌门（Actinobacteria）、变形菌门（Proteobacteria）以及少量拟杆菌门（Bacteroidota，原文拼写为Bacteriodota）为山羊原奶中的优势菌门，这四类菌门的总相对丰度通常可达细菌总群落的90%。优势菌属则包括葡萄球菌属（Staphylococcus）、假单胞菌属（Pseudomonas）、乳球菌属（Lactococcus）、微杆菌属（Microbacterium，原文拼写为Microbacteria）、不动杆菌属（Acinetobacter，原文拼写为Acinetobacteria）以及棒状杆菌属（Corynebacterium，原文拼写为Corinebacteria）。
规模化商业农场与手工特色养殖农场间的细菌门、属数量并无显著差异，不过规模化农场的香农指数（Shannon index）数值上可能略高于手工特色养殖农场。
此外，手工特色养殖农场间的微生物群差异度更高，这可能源于其管理标准化程度较低。
不同农场的羊奶微生物群组成存在显著差异。对同一农场的重复采样结果显示，微生物群组成会随时间发生变化。
乳酸菌（lactic acid producing bacteria）的分布模式也呈现出类似的变化规律。
不同养殖系统下的羊奶微生物群丰富度与多样性存在显著差异。
本研究最终得出结论：农场专属的管理模式与采样时机是影响羊奶微生物群组成的两大核心决定因素。