Supporting data for "A catalog of microbial genes from the bovine rumen reveals the determinants of herbivory"

Dataset type: Metagenomic
Data released on April 27, 2018

Li J; Zhong H; Ramayo-Caldas Y; Terrapon N; Lombard V; Potocki-Veronese G; Estellé J; Popova M; Yang Z; Zhang H; Li F; Tang S; Chen W; Chen B; Li J; Guo J; Martin C; Maguin E; Xu X; Yang H; Wang J; Kristiansen K; Henrissat B; D Ehrlich SS; Morgavi DP (2018): Supporting data for "A catalog of microbial genes from the bovine rumen reveals the determinants of herbivory" GigaScience Database. http://dx.doi.org/10.5524/100391

DOI10.5524/100391

The rumen microbiome is responsible for the unique nature of ruminants. A thorough knowledge of the genetic potential of rumen symbiotic microbes is therefore crucial for the sustainability of ruminant production systems. Using deep metagenome sequencing we identified 13,825,880 non-redundant prokaryote genes from the bovine rumen and constructed 324 high quality metagenomic species. These metagenomic species were prevalent in the rumen of 77 cattle fed various diets whereas known rumen microbial genomes were less abundant. Compared to human, pig and mouse gut metagenome catalogs, the rumen is richer in functions and microbial species associated to the degradation of lignocellulosic material and production of methane. Genes coding for enzymes that deconstruct lignocellulosic substrates showed a particularly high richness that is otherwise impossible to infer from available genomes or shallow metagenomics sequencing. These data bring new insights on functions, enzymes and microbes of the rumen, critical to understand phenotypes and biological processes.

Additional details

Read the peer-reviewed publication(s):

Li, J., Zhong, H., Ramayo-Caldas, Y., Terrapon, N., Lombard, V., Potocki-Veronese, G., … Morgavi, D. P. (2018). A catalog of microbial genes from the bovine rumen reveals the determinants of herbivory. doi:10.1101/272690





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
0081-a1218275  bovine metagenome Description:eukaryote-depleted rumen microbiota of...
Geographic location (latitude and longitude):45.71...
Geographic location (country and/or sea,region):Fr...
...
+
100058-a1218275  bovine metagenome Description:eukaryote-depleted rumen microbiota of...
Geographic location (latitude and longitude):45.71...
Geographic location (country and/or sea,region):Fr...
...
+
2009040-a1218275  bovine metagenome Description:eukaryote-depleted rumen microbiota of...
Geographic location (latitude and longitude):45.71...
Geographic location (country and/or sea,region):Fr...
...
+
3042-a1218275  bovine metagenome Description:eukaryote-depleted rumen microbiota of...
Geographic location (latitude and longitude):45.71...
Geographic location (country and/or sea,region):Fr...
...
+
553-B1218275  bovine metagenome Description:eukaryote-depleted rumen microbiota of...
Geographic location (latitude and longitude):45.71...
Geographic location (country and/or sea,region):Fr...
...
+
7049-a1218275  bovine metagenome Description:eukaryote-depleted rumen microbiota of...
Geographic location (latitude and longitude):45.71...
Geographic location (country and/or sea,region):Fr...
...
+
An.5521218275  bovine metagenome Description:eukaryote-depleted rumen microbiota of...
Geographic location (latitude and longitude):45.71...
Geographic location (country and/or sea,region):Fr...
...
+
An.5541218275  bovine metagenome Description:eukaryote-depleted rumen microbiota of...
Geographic location (latitude and longitude):45.71...
Geographic location (country and/or sea,region):Fr...
...
+
An.5551218275  bovine metagenome Description:eukaryote-depleted rumen microbiota of...
Geographic location (latitude and longitude):45.71...
Geographic location (country and/or sea,region):Fr...
...
+
An.5831218275  bovine metagenome Description:eukaryote-depleted rumen microbiota of...
Geographic location (latitude and longitude):45.71...
Geographic location (country and/or sea,region):Fr...
...
+
Displaying 1-10 of 87 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
fastaFASTA574.68 MB2018-04-19
fastaFASTA853.16 MB2018-04-19
fastaFASTA2.97 GB2018-04-19
fastaFASTA813.91 MB2018-04-19
fastaFASTA624.67 MB2018-04-19
fastaFASTA156.54 MB2018-04-19
fastaFASTA160.94 MB2018-04-19
fastaFASTA234.76 MB2018-04-19
fastaFASTA629.23 MB2018-04-19
fastaFASTA419.18 MB2018-04-19
Displaying 1-10 of 18 File(s).
Funding body Awardee Award ID Comments
National Science Foundation of China J Li 31601073
Shenzhen Municipal Government of China J Li JSGG20160229172752028
Shenzhen Municipal Government of China J Li CXB201108250098A Shenzhen Key Laboratory of Human commensal Microorganisms and Health Research
European Commission B Henrissat FP/2007/2013 Seventh Framework Program
European Research Council B Henrissat 322820
Agence Nationale de la Recherche ES Dusko ANR-11-DPBS-0001
European Commission G Aumont 267196 Marie-Curie FP7 COFUND People Programme
Date Action
April 26, 2018 Dataset publish