Research Article: Characteristics of the tree shrew gut virome

Date Published: February 26, 2019

Publisher: Public Library of Science

Author(s): Linxia Chen, Wenpeng Gu, Chenxiu Liu, Wenguang Wang, Na Li, Yang Chen, Caixia Lu, Xiaomei Sun, Yuanyuan Han, Dexuan Kuang, Pinfen Tong, Jiejie Dai, Efrem Lim.

http://doi.org/10.1371/journal.pone.0212774

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.

Partial Text

The tree shrew (Tupaia belangeri) belongs to the family Tupaiidae, order Scandentia, which has a wide distribution in South Asia, Southeast Asia and Southwest China [1]. The tree shrew is a small mammal similar in appearance to squirrels and feeds on fruits, insects and small vertebrates [2]. Tupaia belangeri is the only representative in China and consists of six subspecies: T. belangeri gaoligongensis, T. belangeri modesta, T. belangeri yaoshanensis, T. belangeri tonquinia, T. belangeri yunalis and T. belangeri chinensis [3]. Previous studies [4–5] showed that the tree shrew has a closer relationship with humans than did rodents in terms of physiological function, biochemical metabolism and genomic signatures. Due to its unique characteristics, such as small body size, low cost of maintenance, life span and short reproductive cycle, the tree shrew has been increasingly used in laboratory analyses in recent years. Several studies have used this animal for the construction of human disease models, such as models for hepatitis virus, influenza virus, cytomegalovirus, herpes simplex virus, and dengue virus [6–8].

The viral metagenomics method has been employed to identify both commensal viruses and viral pathogens successfully in recent years and has the potential to detect most viruses through sequence similarity searches [11, 25]. Due to considerable genetic homology with both humans and primates, the tree shrew was considered to be a model for studies on viral infection and preclinical drug development [2]. This study indicated that the value of tree shrew as a model animal was increased because of the presence of a fecal virome.

 

Source:

http://doi.org/10.1371/journal.pone.0212774

 

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