Universitet A gene catalogue of the Sprague-Dawley rat gut

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. Received: 19 October 2017; Revised: 22 March 2018; Accepted: 4 May 2018 C © The Author(s) 2018. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

[1]  Huijue Jia,et al.  A gene catalogue of the Sprague-Dawley rat gut metagenome , 2018, GigaScience.

[2]  N. Segata,et al.  Shotgun metagenomics, from sampling to analysis , 2017, Nature Biotechnology.

[3]  M. Redinbo,et al.  The role of the microbiome in cancer development and therapy , 2017, CA: a cancer journal for clinicians.

[4]  Huijue Jia,et al.  Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention , 2017, Nature Medicine.

[5]  J. Raes,et al.  The resilience of the intestinal microbiota influences health and disease , 2017, Nature Reviews Microbiology.

[6]  William Tottey,et al.  Fecal microbiota variation across the lifespan of the healthy laboratory rat , 2017, Gut microbes.

[7]  Hui Jiang,et al.  A reference human genome dataset of the BGISEQ-500 sequencer , 2017, GigaScience.

[8]  Jun Wang,et al.  Whether Probiotic Supplementation Benefits Rheumatoid Arthritis Patients: A Systematic Review and Meta-Analysis , 2017 .

[9]  T. Spector,et al.  Shotgun Metagenomics of 250 Adult Twins Reveals Genetic and Environmental Impacts on the Gut Microbiome. , 2016, Cell systems.

[10]  S. Lynch,et al.  The Human Intestinal Microbiome in Health and Disease. , 2016, The New England journal of medicine.

[11]  Liang Liu,et al.  Simultaneous Determination of Multiple Components in Guanjiekang in Rat Plasma via the UPLC–MS/MS Method and Its Application in Pharmacokinetic Study , 2016, Molecules.

[12]  Xun Xu,et al.  A reference gene catalogue of the pig gut microbiome , 2016, Nature Microbiology.

[13]  C. Huttenhower,et al.  The healthy human microbiome , 2016, Genome Medicine.

[14]  T. R. Licht,et al.  A catalog of the mouse gut metagenome , 2015, Nature Biotechnology.

[15]  Qiang Feng,et al.  The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment , 2015, Nature Medicine.

[16]  Jeroen Raes,et al.  Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates , 2015, Gut.

[17]  Jens Roat Kultima,et al.  An integrated catalog of reference genes in the human gut microbiome , 2014, Nature Biotechnology.

[18]  Peer Bork,et al.  MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit , 2012, PloS one.

[19]  Qiang Feng,et al.  A metagenome-wide association study of gut microbiota in type 2 diabetes , 2012, Nature.

[20]  Siu-Ming Yiu,et al.  IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth , 2012, Bioinform..

[21]  James Versalovic,et al.  The Human Microbiome and Its Potential Importance to Pediatrics , 2012, Pediatrics.

[22]  Alison S. Waller,et al.  Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data , 2012, PloS one.

[23]  L. Lao,et al.  A new rat model of bone cancer pain. , 2012, Methods in molecular biology.

[24]  Georg Schett,et al.  The pathogenesis of rheumatoid arthritis. , 2011, The New England journal of medicine.

[25]  Miriam L. Land,et al.  Trace: Tennessee Research and Creative Exchange Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification Recommended Citation Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification , 2022 .

[26]  Siu-Ming Yiu,et al.  SOAP2: an improved ultrafast tool for short read alignment , 2009, Bioinform..

[27]  M. Hegen,et al.  Utility of animal models for identification of potential therapeutics for rheumatoid arthritis , 2007, Annals of the rheumatic diseases.

[28]  Ying Xie,et al.  Manipulation of the induction of adjuvant arthritis in Sprague-Dawley rats , 2006, Inflammation Research.

[29]  Adam Godzik,et al.  Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..

[30]  P. Ramarao,et al.  Combination of high-fat diet-fed and low-dose streptozotocin-treated rat: a model for type 2 diabetes and pharmacological screening. , 2005, Pharmacological research.

[31]  B. Cronstein,et al.  Low-Dose Methotrexate: A Mainstay in the Treatment of Rheumatoid Arthritis , 2005, Pharmacological Reviews.

[32]  J. Cristol,et al.  Involvement of oxidative stress and NADPH oxidase activation in the development of cardiovascular complications in a model of insulin resistance, the fructose-fed rat. , 2005, Atherosclerosis.

[33]  B. Balkan,et al.  Selective breeding for diet-induced obesity and resistance in Sprague-Dawley rats. , 1997, The American journal of physiology.

[34]  C. Pearson,et al.  Studies of arthritis and other lesions induced in rats by the injection of mycobacterial adjuvant. VII. Pathologic details of the arthritis and spondylitis. , 1963, The American journal of pathology.

[35]  C. Pearson,et al.  Studies of arthritis and other lesions induced in rats by injection of mycobacterial adjuvant. II. Evidence that the disease is a disseminated immunologic response to exogenous antigen. , 1960, Journal of immunology.