Supporting data for "Establishment of a Macaca fascicularis gut microbiome gene catalog and comparison with the human, pig and mouse gut microbiomes"

Dataset type: Metagenomic
Data released on June 29, 2018

Li X; Liang S; Xia Z; Qu J; Liu H; Liu C; Yang H; Wang J; Madsen L; Hou Y; Li J; Jia H; Kristiansen K; Xiao L (2018): Supporting data for "Establishment of a Macaca fascicularis gut microbiome gene catalog and comparison with the human, pig and mouse gut microbiomes" GigaScience Database. http://dx.doi.org/10.5524/100470

DOI10.5524/100470

Macaca fascicularis, the cynomolgus macaque, is a widely used model in biomedical research and drug development as its genetics and physiology are close to humans. Detailed information on the cynomolgus macaque gut microbiota, the functional interplay between the gut microbiota and host physiology, and possible similarities to humans and other mammalians is very limited. The aim of this study was to construct the first cynomolgus macaque gut microbial gene catalog and compare this catalog to the human, pig, and mouse gut microbial gene catalogs. We performed metagenomic sequencing on fecal samples from twenty cynomolgus macaques and identified in total 1.9 million non-redundant bacterial genes of which 39.49% and 25.45% are present in the human and pig gut bacterial gene catalogs, respectively, whereas only 0.6% of the genes are present in the mouse gut bacterial gene catalog. By contrast, at the functional levels, more than 76% KOs are shared between the gut microbiota of all four mammalians. Thirty-two highly abundant bacterial genera could be defined as core genera of these mammalians. We demonstrated significant differences in the composition and functional potential of the gut microbiota as well as in the distribution of predicted bacterial phages sequences in cynomolgus macaques fed either a low-fat/high fiber diet or a high-fat/low fiber diet. Interestingly, the gut microbiota of cynomolgus macaques fed the high-fat/low fiber diet became more similar to the gut microbiota of humans.

Additional details

Accessions (data included in GigaDB):

BioProject: PRJEB22765





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
10A410656  organismal metagenomes Description:Stool sample from Macaca fascicularis ...
Alternative accession-SRA Sample:SAMEA104315429
Environment (material):fecal material [ENV_000002...
...
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11A410656  organismal metagenomes Description:Stool sample from Macaca fascicularis ...
Alternative accession-SRA Sample:SAMEA104315430
Environment (material):fecal material [ENV_000002...
...
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12A410656  organismal metagenomes Description:Stool sample from Macaca fascicularis ...
Alternative accession-SRA Sample:SAMEA104315431
Environment (material):fecal material [ENV_000002...
...
+
13A410656  organismal metagenomes Description:Stool sample from Macaca fascicularis ...
Alternative accession-SRA Sample:SAMEA104315432
Environment (material):fecal material [ENV_000002...
...
+
14A410656  organismal metagenomes Description:Stool sample from Macaca fascicularis ...
Alternative accession-SRA Sample:SAMEA104315433
Environment (material):fecal material [ENV_000002...
...
+
15A410656  organismal metagenomes Description:Stool sample from Macaca fascicularis ...
Alternative accession-SRA Sample:SAMEA104315434
Environment (material):fecal material [ENV_000002...
...
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16A410656  organismal metagenomes Description:Stool sample from Macaca fascicularis ...
Alternative accession-SRA Sample:SAMEA104315435
Environment (material):fecal material [ENV_000002...
...
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17A410656  organismal metagenomes Description:Stool sample from Macaca fascicularis ...
Alternative accession-SRA Sample:SAMEA104315436
Environment (material):fecal material [ENV_000002...
...
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18A410656  organismal metagenomes Description:Stool sample from Macaca fascicularis ...
Alternative accession-SRA Sample:SAMEA104315437
Environment (material):fecal material [ENV_000002...
...
+
19A410656  organismal metagenomes Description:Stool sample from Macaca fascicularis ...
Alternative accession-SRA Sample:SAMEA104315438
Environment (material):fecal material [ENV_000002...
...
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Displaying 1-10 of 20 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
annotationKEGG13.67 MB2018-06-22
annotationTAR74.32 MB2018-06-22
annotationUNKNOWN198.77 MB2018-06-22
Coding SequenceFASTA1.53 GB2018-06-22
Coding SequenceTAR969.42 MB2018-06-22
Mixed archiveTAR3.5 MB2018-07-04
protein sequenceFASTA623.5 MB2018-06-22
ReadmeTEXT2.33 KB2018-06-22
sequence assemblyTAR3.5 MB2018-06-22
Sequence assemblyTAR1.71 GB2018-06-22
Displaying 1-10 of 11 File(s).
Funding body Awardee Award ID Comments
National Natural Science Foundation of China L Xiao 81670606
Shenzhen Municipal Government of China J Li JSGG20160229172752028
Shenzhen Municipal Government of China H Jia JCYJ20160229172757249
National Natural Science Foundation of China X Li 81673850
Date Action
June 29, 2018 Dataset publish
June 29, 2018 File readme.txt updated
July 4, 2018 File scaftig.tar.gz updated
July 4, 2018 File readme.txt updated
July 4, 2018 Additional file pipeline_scripts.tar.gz added
July 19, 2018 File pipeline_scripts.tar.gz updated
July 19, 2018 pipeline_scripts.tar.gz: additional file attribute added
July 19, 2018 File pipeline_scripts.tar.gz updated
July 20, 2018 File contig.tar.gz updated
July 20, 2018 File scafSeq.tar.gz updated
July 20, 2018 File scaftig.tar.gz updated
July 20, 2018 File predicted_genes.tar.gz updated
July 20, 2018 File monkey.gene.set.fa updated
July 20, 2018 File monkey.gene.set.pep updated
July 20, 2018 File Carma.blastout.tax.anno updated
July 20, 2018 File kegg.KEGG.catalog updated
July 20, 2018 File pipeline_scripts.tar.gz updated
July 20, 2018 File taxonomic_abundance.tar.gz updated
July 20, 2018 File scaftig.tar.gz updated
July 20, 2018 File scaftig.tar.gz updated
July 20, 2018 readme.txt: additional file attribute added
July 20, 2018 File readme.txt updated