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Gigascience. 2018 May 1;7(5). doi: 10.1093/gigascience/giy055.

A gene catalogue of the Sprague-Dawley rat gut metagenome.

Pan H1, Guo R1,2,3, Zhu J2,3, Wang Q2,3,4, Ju Y2,3, Xie Y1, Zheng Y1,5, Wang Z2,3, Li T1, Liu Z6, Lu L6, Li F2,3,4, Tong B2,3, Xiao L2,3,7, Xu X2,3, Li R1, Yuan Z1, Yang H2,3, Wang J2,3, Kristiansen K2,3,8, Jia H1,2,3,9, Liu L1.

Author information

1
State Key Laboratory of Quality Research in Chinese Medicine/Macau Institute for Applied Research in Medicine and Health, Macao University of Science and Technology, Macao, China.
2
BGI-Shenzhen, Shenzhen 518083, China.
3
China National Genebank, BGI-Shenzhen, Shenzhen 518120, China.
4
BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
5
Fujian University of Traditional Chinese Medicine, No.1, Qiuyang Road, Minhoushangjie, Fuzhou, Fujian 350122, China.
6
International Institute for Translational Research of Traditional Chinese Medicine of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China.
7
Shenzhen Engineering Laboratory of Detection and Intervention of human intestinal microbiome, BGI-Shenzhen, Shenzhen 518083, China.
8
Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark.
9
Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China.

Abstract

Background:

Laboratory rats such as the Sprague-Dawley (SD) rats are an important model for biomedical studies in relation to human physiological or pathogenic processes. Here we report the first catalog of microbial genes in fecal samples from Sprague-Dawley rats.

Findings:

The catalog was established using 98 fecal samples from 49 SD rats, divided in 7 experimental groups, and collected at different time points 30 days apart. The established gene catalog comprises 5,130,167 non-redundant genes with an average length of 750 bp, among which 64.6% and 26.7% were annotated to phylum and genus levels, respectively. Functionally, 53.1%, 21.8%,and 31% of the genes could be annotated to KEGG orthologous groups, modules, and pathways, respectively.

Conclusions:

A comparison of rat gut metagenome catalogue with human or mouse revealed a higher pairwise overlap between rats and humans (2.47%) than between mice and humans (1.19%) at the gene level. Ninety-seven percent of the functional pathways in the human catalog were present in the rat catalogue, underscoring the potential use of rats for biomedical research.

PMID:
29762673
PMCID:
PMC5967468
DOI:
10.1093/gigascience/giy055
[Indexed for MEDLINE]
Free PMC Article

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