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. 2019 Feb 26;14(2):e0212774.
doi: 10.1371/journal.pone.0212774. eCollection 2019.

Characteristics of the tree shrew gut virome

Linxia Chen  1   2 , Wenpeng Gu  1   3 , Chenxiu Liu  1 , Wenguang Wang  1 , Na Li  1 , Yang Chen  4 , Caixia Lu  1 , Xiaomei Sun  1 , Yuanyuan Han  1 , Dexuan Kuang  1 , Pinfen Tong  1 , Jiejie Dai  1
Affiliations

Characteristics of the tree shrew gut virome

Linxia Chen et al. PLoS One. .

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.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Taxonomic distributions of the virus-related sequences of the tree shrew gut virome.
A. The left pie-chart showed the reads alignment results; the right one indicated the taxonomic distributions of orders; B. The proportions of taxonomic distributions of families for each order.
Fig 2
Fig 2. The relative abundance of the top 10 virus-related reads at different distribution levels and total taxonomic distributions.
A. The bar graph of relative abundance for top 10 families in this study; B. The bar graph of relative abundance for top 10 genera in this study; C. The bar graph of relative abundance for top 10 species in this study; D. Total composition ratio of taxonomic distributions shown by Krona.
Fig 3
Fig 3. Phylogenetic analysis of the 3’UTR region of adenovirus.
The red area indicated the best match result between sequence in this study with reference adenovirus (AF258784.1).
Fig 4
Fig 4. Phylogenetic analysis of the top virus species in the tree shrew gut virome.
A.Phylogenetic tree of Cercopithecine herpesvirus 5 with tree shrew contig; Three cluster groups were generated by using MEGA 6.0, and shown by different colors. B. Phylogenetic tree of Theilovirus with tree shrew contig; Three cluster groups were generated by using MEGA 6.0, and shown by different colors. C.The diagram of base substitutions between African bat icavirus A and tree shrew contig; Yellow areas indicated the positions of base changes. D. The diagram of base substitutions between Cosavirus JMY-2014 and tree shrew contig.Yellow areas indicated the positions of base changes.
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