Abstract
BackgroundThe pig faecal virome, which comprises the community of viruses present in pig faeces, is complex and consists of pig viruses, bacteriophages, transiently passaged plant viruses and other minor virus species. Only little is known about factors influencing its general composition. Here, the effect of the probiotic bacterium Enterococcus faecium (E. faecium) NCIMB 10415 on the pig faecal virome composition was analysed in a pig feeding trial with sows and their piglets, which received either the probiotic bacterium or not.ResultsFrom 8 pooled faecal samples derived from the feeding trial, DNA and RNA virus particles were prepared and subjected to process-controlled Next Generation Sequencing resulting in 390,650 sequence reads. In average, 14% of the reads showed significant sequence identities to known viruses. The percentage of detected mammalian virus sequences was highest (55–77%) in the samples of the youngest piglets and lowest (8–10%) in the samples of the sows. In contrast, the percentage of bacteriophage sequences increased from 22–44% in the youngest piglets to approximately 90% in the sows. The dominating mammalian viruses differed remarkably among 12 day-old piglets (kobuvirus), 54 day-old piglets (boca-, dependo- and pig stool-associated small circular DNA virus [PigSCV]) and the sows (PigSCV, circovirus and “circovirus-like” viruses CB-A and RW-A). In addition, the Shannon index, which reflects the diversity of sequences present in a sample, was generally higher for the sows as compared to the piglets. No consistent differences in the virome composition could be identified between the viromes of the probiotic bacterium-treated group and the control group.ConclusionThe analysis indicates that the pig faecal virome shows a high variability and that its general composition is mainly dependent on the age of the pigs. Changes caused by feeding with the probiotic bacterium E. faecium could not be demonstrated using the applied metagenomics method.
Highlights
The viral community present in faeces is composed of a variety of viruses originating from the gut tissue, from intestinal microorganisms or from ingested food
Samples derived from different continents had been analysed in these studies, the general composition was found to be similar
Sows and their piglets received either no probiotic bacterium or approximately 56106 cfu/g E. faecium NCIMB 10415, which was fed with their diet starting at 28 days ante partum
Summary
The viral community present in faeces is composed of a variety of viruses originating from the gut tissue, from intestinal microorganisms or from ingested food. The composition of the faecal virome of pigs has been studied recently [2,10,11]. Samples derived from different continents had been analysed in these studies, the general composition was found to be similar. The majority of the detected virus sequences belonged to bacteriophages and pig viruses. Most of the bacteriophage sequences originated from viruses belonging to the families Siphoviridae, Microviridae and Myoviridae [10]. The pig faecal virome, which comprises the community of viruses present in pig faeces, is complex and consists of pig viruses, bacteriophages, transiently passaged plant viruses and other minor virus species. The effect of the probiotic bacterium Enterococcus faecium (E. faecium) NCIMB 10415 on the pig faecal virome composition was analysed in a pig feeding trial with sows and their piglets, which received either the probiotic bacterium or not
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