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Data released on September 01, 2016

A catalogue of the pig gut microbiome

Chatelier, E, L; Doré, J; Estellé, J; Feng, Q; Jia, H; Kiilerich, P; Kjeldsen, N, J; Li, J; Liang, S; Liu, C; Maguin, E; Pedersen, A, O; Pons, N; Prifti, E; Ramayo-Caldas, Y; Xia, Z; Xiao, L; Ehrlich, S, D; Xu, X; Madsen, L; Kristiansen, K; Rogel-Gaillard, C; Wang, J (2016): A catalogue of the pig gut microbiome GigaScience Database. http://dx.doi.org/10.5524/100187 RIS BibTeX Text

The pig is a major species for livestock and biomedicine. We established a comprehensive catalogue of gut microbial genes based on faecal samples of 287 pigs from France, Denmark and China. 7.7 million non-redundant genes representing 719 metagenomic species were identified by deep metagenome sequencing. The pig and human catalogues share 12.6 % and 9.3 % of their genes, respectively, a higher proportion than that shared between the mouse and human catalogues. Importantly, 78 % and 96% of the functional pathways are shared, underscoring the potential use of pigs for biomedical research. The pig gut microbiota is influenced by gender, age and breed. Analysis of the prevalence of antibiotic resistance genes confirmed the efficiency of eliminating antibiotics from animal diet to reduce the risk of dissemination associated with farming systems. The pig microbiome gene catalogue provides a useful resource for metagenomics-based research in biomedicine and for sustainable knowledge-based pig farming.

Contact Submitter

Related manuscripts:

doi:10.1038/nmicrobiol.2016.161

Accessions (data included in GigaDB):

BioProject: PRJEB11755

Metagenomic

http://gigadb.org/images/data/cropped/100187.jpg

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
BHZ-10B1510822pig gut metagenome Age:NA
Submitted to insdc:ERS970354
Body product:feces
...
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BHZ-11B1510822pig gut metagenome Age:NA
Submitted to insdc:ERS970355
Body product:feces
...
+
BHZ-12B1510822pig gut metagenome Age:NA
Submitted to insdc:ERS970356
Body product:feces
...
+
BHZ-1B1510822pig gut metagenome Age:NA
Submitted to insdc:ERS970357
Body product:feces
...
+
BHZ-2B1510822pig gut metagenome Age:NA
Submitted to insdc:ERS970358
Body product:feces
...
+
BHZ-3B1510822pig gut metagenome Age:NA
Submitted to insdc:ERS970359
Body product:feces
...
+
BHZ-4B1510822pig gut metagenome Age:NA
Submitted to insdc:ERS970360
Body product:feces
...
+
BHZ-5B1510822pig gut metagenome Age:NA
Submitted to insdc:ERS970361
Body product:feces
...
+
BHZ-6B1510822pig gut metagenome Age:NA
Submitted to insdc:ERS970362
Body product:feces
...
+
BHZ-7B1510822pig gut metagenome Age:NA
Submitted to insdc:ERS970363
Body product:feces
...
+
Displaying 1-10 of 295 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
OtherUNKNOWN-0 KB2016-02-02
OtherUNKNOWN-0 KB2016-02-02
OtherUNKNOWN412.33 KB2016-02-02
OtherUNKNOWN775.46 KB2016-02-02
OtherUNKNOWN1.05 MB2016-02-02
OtherUNKNOWN578.15 KB2016-02-02
OtherUNKNOWN282.82 KB2016-02-02
OtherUNKNOWN1.37 MB2016-02-02
OtherUNKNOWN23.12 MB2016-02-02
Coding sequenceFASTA1.58 GB2016-02-02
Displaying 1-10 of 21 File(s).

History:

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