A gene catalogue of the Sprague-Dawley rat gut metagenome

GigaScience
Hudan PanLiang Liu

Abstract

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. 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. 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.

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Citations

Aug 20, 2019·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Mengfan YueYue Dai
Aug 4, 2020·Environmental Microbiology·Carlos M DuarteXabier Irigoien
May 16, 2018·GigaScience·Hudan PanLiang Liu
Aug 28, 2020·Gut Microbes·Mirna ČokloSandra Kraljević Pavelić
Apr 2, 2021·Bioinformatics·Seth CommichauxMihai Pop
May 6, 2021·Therapeutic Advances in Gastroenterology·Fenghua XuYanling Wei
May 19, 2021·FEMS Microbiology Letters·Yuping YangXiaoyan Wang
Jun 13, 2021·Genomics, Proteomics & Bioinformatics·Zhuye JieHuijue Jia
Aug 16, 2021·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Chen ChenHuijue Jia
Oct 19, 2021·Frontiers in Cellular and Infection Microbiology·Lydia ZeibichRosa Krajmalnik-Brown
May 1, 2021·FEMS Microbiology Reviews·Ilana Zilber-Rosenberg, Eugene Rosenberg

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Datasets Mentioned

BETA
PRJEB22973

Methods Mentioned

BETA
Assay

Software Mentioned

SOAPaligner2
BLASTP
Prodigal
IDBA
HIT
- UD
house Perl script
SOAP aligner
Kmer
CD

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