Choice of Ultrafilter affects Recovery Rate of Bacteriophages

Studies into the viral fraction of the microbiota have recently garnered much interest. Yet there is still no standardized protocol for extracting viruses from samples, and the protocols that exist are fraught with procedures that skew the viral community of the sample one way or another. The first step of the extraction pipeline often consists of 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 viral community. Especially the enveloped F6 phage is severely affected by choice of filter, but also tailed phages such as T4 and c2 have a reduced infectivity after ultrafiltration. We postulate that the cause of this bias might be the retention of bacterial debris capable of inactivating specific phages in filters with smaller pore sizes, suggesting the need for greater thought when selecting filters for virus extraction.