Bovine milk microbiota: comparison among three different DNA extraction protocols to identify a better approach for bacterial analysis. milk metagenome

Generating high-quality bacterial DNA for metagenomics characterization via shotgun or barcoded amplicons could be critical when starting from a matrix like milk, a complex biological fluid with high fat, protein, and calcium content. Here, bacterial DNA from one ultra-high temperature (UHT) commercial milk sample artificially spiked by a mock community (ZymoBIOMICS Microbial Community Standard) with a predetermined composition and from three bulk tank milk (raw milk) samples was isolated by three different protocols to evaluate the effect of the extraction procedures on milk microbiota composition and to identify the best approach for its characterization.For each extraction procedure, we performed at least 5 replicate experiments, in order to compensate for eventual one-time extraction differences. The performance and reproducibility of these protocols were assessed based on the quality and quantity of the DNA extracted, and bacterial community composition.

以脂肪、蛋白质与钙含量较高的复杂生物流体牛奶作为起始基质时，通过鸟枪法（shotgun）或带条形码扩增子（barcoded amplicons）开展宏基因组学（metagenomics）表征分析以获取高质量细菌DNA，往往至关重要。本研究中，研究人员采用三种不同的提取方案，对一份经预设组成的模拟群落（mock community，ZymoBIOMICS微生物群落标准品）人工掺入的超高温（UHT）市售牛奶样本，以及三份散装罐牛奶（生鲜乳）样本中的细菌DNA进行分离，以评估提取流程对牛奶微生物群组成的影响，并筛选出最优的牛奶微生物群表征方法。针对每种提取方案，我们均开展了至少5次重复实验，以抵消单次提取可能存在的偶然差异。研究基于提取所得DNA的质量与含量，以及细菌群落组成，对这些提取方案的性能与可重复性进行了评估。