A gene catalogue of the Sprague-Dawley rat gut metagenome

Dataset type: Metagenomic
Data released on May 02, 2018

Pan H; Guo R; Zhu J; Wang Q; Ju Y; Xie Y; Zheng Y; Wang Z; Li T; Liu Z; Lu L; Li F; Tong B; Xiao L; Xu X; Li R; Yuan Z; Yang H; Wang J; Kristiansen K; Jia H; Liu L (2018): A gene catalogue of the Sprague-Dawley rat gut metagenome GigaScience Database. http://dx.doi.org/10.5524/100440

DOI10.5524/100440

Laboratory rats such as the Sprague-Dawley (SD) rats are important model for biomedical studies in relation to human physiological or pathogenic processes. Here we report on 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 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 base pairs (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 (KOs), 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. 97% of the functional pathways in the human catalog were present in the rat catalogue underscoring the potential use of rats for biomedical research.

Additional details

Read the peer-reviewed publication(s):

Pan, H., Guo, R., Zhu, J., Wang, Q., Ju, Y., Xie, Y., … Liu, L. (2018). A gene catalogue of the Sprague-Dawley rat gut metagenome. GigaScience, 7(5). doi:10.1093/gigascience/giy055

Accessions (data included in GigaDB):

BioProject: PRJEB22973





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
19-11436733  rat gut metagenome Description:HFD group, time point 1
Alternative accession-SRA Sample:ERS1971142
Alternative names:19A_RSZYD16111234
...
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19-51436733  rat gut metagenome Description:HFD group, time point 5
Alternative accession-SRA Sample:ERS1971338
Alternative names:215A_RSZYD16111283
...
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20-11436733  rat gut metagenome Description:HFD group, time point 1
Alternative accession-SRA Sample:ERS1971143
Alternative names:20A_RSZYD16111235
...
+
20-51436733  rat gut metagenome Description:HFD group, time point 5
Alternative accession-SRA Sample:ERS1971339
Alternative names:216A_RSZYD16111284
...
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2-11436733  rat gut metagenome Description:Normal group, time point 1
Alternative accession-SRA Sample:ERS1971125
Alternative names:2A_RSZYD16111217
...
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21-11436733  rat gut metagenome Description:HFD group, time point 1
Alternative accession-SRA Sample:ERS1971144
Alternative names:21A_RSZYD16111236
...
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21-51436733  rat gut metagenome Description:HFD group, time point 5
Alternative accession-SRA Sample:ERS1971340
Alternative names:217A_RSZYD16111285
...
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22-11436733  rat gut metagenome Description:MTX group, time point 1
Alternative accession-SRA Sample:ERS1971145
Alternative names:22A_RSZYD16111237
...
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22-51436733  rat gut metagenome Description:MTX group, time point 5
Alternative accession-SRA Sample:ERS1971341
Alternative names:218A_RSZYD16111286
...
+
23-11436733  rat gut metagenome Description:MTX group, time point 1
Alternative accession-SRA Sample:ERS1971146
Alternative names:23A_RSZYD16111238
...
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Displaying 21-30 of 98 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
Sequence assemblyUNKNOWN79.58 MB2018-04-24
Sequence assemblyUNKNOWN100.27 MB2018-04-24
Sequence assemblyUNKNOWN79.05 MB2018-04-24
Sequence assemblyUNKNOWN100.25 MB2018-04-24
Sequence assemblyUNKNOWN90.1 MB2018-04-24
Sequence assemblyUNKNOWN67.61 MB2018-04-24
Sequence assemblyUNKNOWN69.8 MB2018-04-24
Sequence assemblyUNKNOWN76.04 MB2018-04-24
Sequence assemblyUNKNOWN65.98 MB2018-04-24
Sequence assemblyUNKNOWN66.58 MB2018-04-24
Displaying 1-10 of 111 File(s).
Funding body Awardee Award ID Comments
Macau Technology Development Fund L Liu 102/2016/A3
Shenzhen Municipal Government of China H Jia JSGG20160229172752028
Shenzhen Municipal Government of China H Jia JCYJ20160229172757249
National Natural Science Foundation of China L Xiao 81670606
Date Action
May 2, 2018 Dataset publish
June 8, 2018 228A_RSZYD16111295.assembly.scaftig.gz: file attribute updated
June 8, 2018 File 228A_RSZYD16111295.assembly.scaftig.gz updated
July 9, 2018 Manuscript Link added : 10.1093/gigascience/giy055