The porcine enteric microbiota is currently extensively studied, taking advantage of developments in high-throughput sequencing technologies. However, the viral part of the microbiota, the virome, is being lightly explored, and the impact of the pretreatments used before sequencing the viruses is barely considered. In this study, the impacts of filtration, RNase and DNase treatments on virus reads recovery and diversity after sequencing on a MiSeq platform were assessed on fecal samples individually taken at <3, 5, 12 and 20 weeks from two piglets. None of the four pretreatment series affected the virus read averages or influenced diversity, but the samples with the higher proportion of reads corresponding to an entry in the “nt” database were those receiving the least number of pretreatments. The enzymatic pretreatments affected the detection of the single-stranded RNA viruses of Aichivirus C, porcine astrovirus, Sapovirus and posavirus, which is worrisome, as these viruses can be involved in swine diarrhea. If enzymatic pretreatments are used when sequencing using a high-throughput method, it may impact single-stranded RNA virus recovery, but not the overall virome diversity. Therefore, filtrated samples may be the better option, reducing the amount of bacterial genetic material while preserving the virus reads.

利用高通量测序技术的发展，目前对猪肠道微生物群进行了广泛的研究。然而，微生物群的病毒部分，即病毒组，正在被轻松探索，并且几乎没有考虑在对病毒进行测序之前使用的预处理的影响。在这项研究中，在 MiSeq 平台上测序后，过滤、RNase 和 DNase 处理对病毒读数恢复和多样性的影响是对在小于 3、5、12 和 20 周时从两只仔猪中单独采集的粪便样本进行评估的。四个预处理系列都没有影响病毒读取平均值或影响多样性，但与“nt”数据库中的条目对应的读取比例较高的样本是那些接受最少预处理的样本。爱知病毒C、猪星状病毒、沙波病毒和波沙病毒，令人担忧，因为这些病毒可能与猪腹泻有关。如果在使用高通量方法测序时使用酶预处理，它可能会影响单链 RNA 病毒的恢复，但不会影响整体病毒组多样性。因此，过滤样本可能是更好的选择，在保留病毒读数的同时减少细菌遗传物质的数量。