斯普拉格-道利大鼠肠道宏基因组的基因目录。
A gene catalogue of the Sprague-Dawley rat gut metagenome.
机构信息
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.
BGI-Shenzhen, Shenzhen 518083, China.
出版信息
Gigascience. 2018 May 1;7(5). doi: 10.1093/gigascience/giy055.
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.
背景
实验大鼠（如 Sprague-Dawley 大鼠）是研究人类生理或发病过程的重要生物医学模型。本研究首次报道了 Sprague-Dawley 大鼠粪便样本中的微生物基因目录。
发现
该目录基于 49 只 Sprague-Dawley 大鼠的 98 个粪便样本建立，这些大鼠分为 7 个实验组，在 30 天的不同时间点采集。建立的基因目录包含 5130167 个非冗余基因，平均长度为 750bp，其中 64.6%和 26.7%分别注释到门和属水平。从功能上看，分别有 53.1%、21.8%和 31%的基因可注释到 KEGG 直系同源群、模块和途径。
结论
大鼠肠道宏基因组目录与人类或小鼠的比较显示，在基因水平上，大鼠与人类的基因重叠度（2.47%）高于大鼠与小鼠（1.19%）。人类目录中 97%的功能途径也存在于大鼠目录中，这突出了大鼠在生物医学研究中的潜在用途。
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