Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark.
Department of Environmental Science, Aarhus University, 4000 Roskilde, Denmark.
Viruses. 2021 May 21;13(6):959. doi: 10.3390/v13060959.
Isolating single phages using plaque assays is a laborious and time-consuming process. Whether single isolated phages are the most lyse-effective, the most abundant in viromes, or those with the highest ability to make plaques in solid media is not well known. With the increasing accessibility of high-throughput sequencing, metaviromics is often used to describe viruses in environmental samples. By extracting and sequencing metaviromes from organic waste with and without exposure to a host-of-interest, we show a host-related phage community's shift, as well as identify the most enriched phages. Moreover, we isolated plaque-forming single phages using the same virome-host matrix to observe how enrichments in liquid media correspond to the metaviromic data. In this study, we observed a significant shift ( = 0.015) of the 47 identified putative phages with a minimum twofold change above zero in read abundance when adding a DC3000 host. Surprisingly, it appears that only two out of five plaque-forming phages from the same organic waste sample, targeting the strain, were highly abundant in the metavirome, while the other three were almost absent despite host exposure. Lastly, our sequencing results highlight how long reads from Oxford Nanopore elevates the assembly quality of metaviromes, compared to short reads alone.
使用噬菌斑分析法分离单一噬菌体是一项费力且耗时的过程。单一分离噬菌体是否最具裂解效率、最丰富存在于病毒组中，或者在固体培养基中形成噬菌斑的能力最高，目前还不太清楚。随着高通量测序的普及，宏病毒组学常用于描述环境样本中的病毒。通过提取并对含有和不含有目标宿主的有机废物进行宏病毒组测序，我们展示了与宿主相关的噬菌体群落的变化，并鉴定了最丰富的噬菌体。此外，我们使用相同的病毒组-宿主基质分离形成噬菌斑的单一噬菌体，以观察液体培养基中的富集情况如何与宏病毒组数据相对应。在这项研究中，当添加一个 DC3000 宿主时，我们观察到 47 种已识别的假定噬菌体中有 47 种（= 0.015）发生了显著变化，其读长丰度至少增加了两倍。令人惊讶的是，尽管暴露于宿主，但来自同一有机废物样本、针对 菌株的五个形成噬菌斑的噬菌体中，似乎只有两个在宏病毒组中高度丰富，而另外三个则几乎不存在。最后，我们的测序结果强调了与单独使用短读长相比，Oxford Nanopore 的长读长如何提高宏病毒组的组装质量。
