The General Composition of the Faecal Virome of Pigs Depends on Age, but Not on Feeding with a Probiotic Bacterium

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.

ELM: Enhanced lowest common ancestor based method for detecting a pathogenic virus from a large sequence dataset

“…These results were consistent with abundant virus genera described in the literature (Sachsenroder et al 2014). However, we failed to identify pig stool-associated small circular DNA virus in dataset 5 (Table 4).…”

“…(2) Taxonomic classification based on the LCA is performed using MEGAN under the top 10% score filter (Huson et al 2007). (Sachsenroder et al 2014), this virus is the novel pig stool-associated single-stranded DNA virus, which is not assigned to a specific genus.…”

“…were obtained by 454 GS FLX Titanium sequencing (Sachsenroder et al 2014). In these benchmark tests, the BLAST searches were performed on a workstation with an Intel Sandy Bridge CPU 2.6 GHz processor.…”

Metagenomic analysis of viromes of dromedary camel fecal samples reveals large number and high diversity of circoviruses and picobirnaviruses

“…Although subclinical infections are common, circovirus infections have been suggested to be associated with psittacine beak and feather disease, infectious chicken anemia, circovirus disease of pigeons, and the postweaning multisystemic wasting syndrome of pigs (Biagini et al, 2011). Among the metagenomic studies on fecal samples of other mammals, only one study on fecal samples of pigs showed a comparable high number of sequences from the Circoviridae family (Table 1) (Sachsenroder et al, 2014). At least five metagenomic studies did not show any circovirus sequence (Lager et al, 2012;Li et al, 2011a;Li et al, 2011b;Smits et al, 2013;van den Brand et al, 2012).…”

Pathogens, faecal indicators and human-specific microbial source-tracking markers in sewage

“…Regarding the virome, the results show the same trends as in humans; there is predominance of bacteriophages and animal viruses more or less specific to the animal species, great diversity and concentrations one to two log units higher than for bacteria (Sachsenröder et al . ; Zhang et al . ).…”