Comparative analysis of the faecal virome of dogs with various inflammatory intestinal diseases
AuthorMoreno, Paloma Susana
AffiliationVeterinary and Agricultural Sciences Collected Works
Document TypePhD thesis
Access StatusThis item is embargoed and will be available on 2021-11-08. This item is currently available to University of Melbourne staff and students only, login required.
© 2019 Paloma Susana Moreno
Little is known about the population of viruses present in the intestine of dogs, the virome, despite advances in molecular biology techniques. The viral flora in the intestine of dogs has been mostly studied in disease settings, targeted to known pathogenic viruses. There is currently a gap in our knowledge of the faecal canine virome present in healthy conditions. This study aimed to identify and characterise the virome present in faeces of healthy dogs compared to the virome present in dogs with acute diarrhoea and dogs with chronic enteropathy. Faecal samples were collected from 8 healthy dogs, 8 dogs with acute diarrhoea and 8 dogs with chronic enteropathy. A viral enrichment protocol, using a mixture of endonucleases and bacterial filtration was used to enrich viral DNA and RNA. The total DNA and RNA isolated from the stool samples were amplified using a sequence-independent single-primer amplification (SISPA) protocol and subsequently sequenced by next-generation sequencing using the Illumina MiSeq platform at the Australian Genome Research Facility. Two bioinformatic pipelines were used to analyse the viral population present in each sample. After selecting high-quality reads (HQRs) and removing dog and bacterial sequences, sequence information was compared against CAMERA viral reference database in one pipeline and against the NCBI non-redundant nucleotide database in the other. Faecal samples from all groups showed a large occurrence of bacteriophages, from different families mainly under the order Caudovirales. Eukaryotic viruses were also identified. Consistent results, obtained from both bioinformatic analysis pipelines, were found for only 8 viral eukaryotic families. Interestingly, sequences with high similarity to viruses within the Astroviridae and Caliciviridae families were identified only in samples from the dogs with acute diarrhoea. Sequences similar to those of Picornaviridae were identified in one dog with acute diarrhoea and in one dog with chronic enteropathy. Only one group of sequences similar to a known virus family with known pathogenic members, Reoviridae, was identified in all groups (healthy and diarrhoeic samples). In conclusion, the largest proportion of viruses identified belonged to bacteriophages. The eukaryotic virome detected in this study contained viral sequences from a range of different virus families, including some with known enteric pathogens. These results were complemented with the complete genome characterisation of a canine kobuvirus, a canine astrovirus and a canine rotavirus. Furthermore, a prevalence analysis of these viruses, in a wider population, was performed. This project gives the first description of the canine faecal virome of healthy dogs and dogs with chronic enteropathy, thus contributing new knowledge that complements what was already known about the faecal virome of dogs with acute diarrhoea. Results from this study indicate that metagenomic analyses are useful for the investigation of viral populations in the faeces of dogs with various inflammatory intestinal diseases. Studies to further elucidate the epidemiological and biological relevance of these findings are warranted.
Keywordsfaecal virome; canine virome; metagenomics; bioinformatics; astrovirus; kobuvirus; rotavirus
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