Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark.
Section for Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark.
Viruses. 2023 Oct 5;15(10):2051. doi: 10.3390/v15102051.
Studies into the viral fraction of complex microbial communities, like in the mammalian gut, have recently garnered much interest. Yet there is still no standardized protocol for extracting viruses from such samples, and the protocols that exist employ procedures that skew the viral community of the sample one way or another. The first step of the extraction pipeline often consists of the basic filtering of macromolecules and bacteria, yet even this affects the viruses in a strain-specific manner. In this study, we investigate a protocol for viral extraction based on ultrafiltration and how the choice of ultrafilter might influence the extracted viral community. Clinical samples (feces, vaginal swabs, and tracheal suction samples) were spiked with a mock community of known phages (T4, c2, Φ6, Φ29, Φx174, and Φ2972), filtered, and quantified using spot and plaque assays to estimate the loss in recovery. The enveloped Φ6 phage is especially severely affected by the choice of filter, but also tailed phages such as T4 and c2 have a reduced infectivity after ultrafiltration. We conclude that the pore size of ultrafilters may affect the recovery of phages in a strain- and sample-dependent manner, suggesting the need for greater thought when selecting filters for virus extraction.
对复杂微生物群落（如哺乳动物肠道）中的病毒部分进行的研究最近引起了广泛关注。然而，仍然没有从这类样本中提取病毒的标准化方案，而且现有的方案采用的方法会以某种方式使样本中的病毒群落发生偏斜。提取管道的第一步通常包括对大分子和细菌的基本过滤，但即使如此，这也会以菌株特异性的方式影响病毒。在这项研究中，我们研究了一种基于超滤的病毒提取方案，以及超滤器的选择如何影响提取的病毒群落。临床样本（粪便、阴道拭子和气管抽吸样本）中加入了已知噬菌体（T4、c2、Φ6、Φ29、Φx174 和 Φ2972）的模拟群落，然后进行过滤，并通过斑点和噬菌斑测定进行定量，以估计回收率的损失。包膜的 Φ6 噬菌体尤其受到滤器选择的严重影响，但 T4 和 c2 等长尾噬菌体在超滤后感染力也会降低。我们得出结论，超滤器的孔径可能会以菌株和样本依赖的方式影响噬菌体的回收率，这表明在选择用于病毒提取的滤器时需要更多的考虑。
