Metagenomics as a useful tool for the detection of faecal virome in swine

All living beings are naturally populated with many different symbiotic, commensal and pathogenic microorganisms that form complex communities. In addition to bacteria, archaea and microbial eukaryotes, viruses are a small part of this community. The totality of viruses in swine faeces, which are composed of eukaryotic viruses (porcine viruses), prokaryotic viruses (bacteriophages), transient viruses such as plant viruses and other viruses, is referred to as virome.

Here, the systemic effect of a monocausal respiratory infection with Influenza A virus H1N1pdm09 on the composition of the faecal virome was analyzed. Samples for virome analyses were taken before and 4, 21, and 31 days post infection (dpi). Shotgun DNA libraries of these faeces samples prepared from RNA were deep sequenced using Ion Torrent-sequencing and the resulting raw data were taxonomically classified using the software pipeline RIEMS (Reliable Information Extraction of Metagenomic Sequence datasets).

During the course of the experiment, infected swine were clinically inapparent and the highest virus shedding was observed 4 dpi. The most abundant viruses, which were constantly present in all days in all swine, comprised eukaryotic (Astroviridae, Picornaviridae) and prokaryotic (Podoviridae) viruses. In addition, transient viruses such as plant viruses (Endornaviridae) and other viruses (Nudiviridae) were detected sporadically.

Publication History

Article published online:
26 April 2021