Characteristics of the tree shrew gut virome

Abstract

The tree shrew ( Tupaia belangeri ) has been proposed as an alternative laboratory animal to primates in biomedical research in recent years. However, characteristics of the tree shrew gut virome remain unclear. In this study, the metagenomic analysis method was used to identify the features of gut virome from fecal samples of this animal. Results showed that 5.80% of sequence reads in the libraries exhibited significant similarity to sequences deposited in the viral reference database (NCBI non-redundant nucleotide databases, viral protein databases and ACLAME database), and these reads were further classified into three major orders: Caudovirales (58.0%), Picornavirales (16.0%), and Herpesvirales (6.0%). Siphoviridae (46.0%), Myoviridae (45.0%), and Podoviridae (8.0%) comprised most Caudovirales . Picornaviridae (99.9%) and Herpesviridae (99.0%) were the primary families of Picornavirales and Herpesvirales , respectively. According to the host types and nucleic acid classifications, all of the related viruses in this study were divided into bacterial phage (61.83%), animal-specific virus (34.50%), plant-specific virus (0.09%), insect-specific virus (0.08%) and other viruses (3.50%). The dsDNA virus accounted for 51.13% of the total, followed by ssRNA (33.51%) and ssDNA virus (15.36%). This study provides an initial understanding of the community structure of the gut virome of tree shrew and a baseline for future tree shrew virus investigation.

Fishing for the Virome of Tropical Tuna

“…Although the liver and gut are well-known bacterial niches in vertebrates [ 16 ], bacteriophages represented no more than 20% of the assigned contigs in our samples, suggesting that eukaryotic viruses may prevail in fish digestive organs [ 17 ]. This strongly differs from observations in other vertebrates such as birds and mammals, where phages were found to be predominant within the gut microflora [ 18 , 19 , 20 ]. However, Ramírez-Martínez et al (2018) [ 21 ] also demonstrated that eukaryotic viruses were dominant in the fecal virome of various wild migratory duck species.…”

The ecogenomics of dsDNA bacteriophages in feces of stabled and feral horses

“…Despite significant progress in the understanding of bacteriophage ecology in the human gut, data on other animal species are scarce. Although a significant number of metagenomic datasets from various species have been published [29] , [30] , [31] , [32] , the vast majority of these studies focus on the detection and interpretation of animal viruses, and bacteriophages have not been given significant attention. Only a few studies give emphasis to bacteriophage diversity in these samples, although this is limited to identifying differences between healthy and diseased states in rhesus monkeys [33] , [34] or specifically focusing on the diversity of ssDNA viruses [35] .…”

Cloacal virome of an ancient host lineage – the tuatara (Sphenodon punctatus) – reveals abundant and diverse diet-related viruses

“…A major limitation of metatranscriptomics is that the true host range of many viruses often cannot be determined. Cloacal swabs and faecal samples are particularly challenging to identify viral-host associations as a high proportion of the total viral sequences identified are often dietary-related (33,40–42). Indeed, 48 of the 49 novel viruses identified in this study were likely dietary-related and, consequently, the hosts of these viral sequences remain unclear.…”