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Data released on June 30, 2014

Metagenomic

Supporting data for the paper: "An integrated catalog of reference genes in the human gut microbiome".

Li, J; Jia, H; Cai, X; Zhong, H; Feng, Q; Sunagawa, S; Arumugam, M; Kultima, JR; Prifti, E; Nielsen, T; Juncker, A; Manichanh, C; Chen, B; Zhang, W; Levenez, F; Wang, J; Xu, X; Xiao, L; Liang, S; Zhang, D; Zhang, Z; Chen, W; Zhao, H; Al-Aama, JY; Edris, S; Yang, H; Wang, J; Hansen, T; Nielsen, HB; Brunak, S; Kristiansen, K; Guarner, F; Pedersen, O; Doré, J; Ehrlich, SD; MetaHIT consortium; Bork, P; Wang, J (2014): Supporting data for the paper: "An integrated catalog of reference genes in the human gut microbiome". GigaScience Database. http://dx.doi.org/10.5524/100064 RIS BibTeX Text

Here we sequenced 249 fecal samples from European adults, leading to a total of 760 samples in the Metagenome of the Human Intestinal Tract (MetaHIT) project. All 6.4TB whole-genome shotgun sequencing data from 1267 fecal samples in MetaHIT, the Human Microbiome Project (HMP) and our diabetes study on Chinese adults were processed with the MOCAT pipeline. The resulting gene catalogs were merged using CD-HIT and complemented with genes from 511 sequenced human gut-related prokaryotic genomes that were present in our gut metagenomes. The final high-quality integrated reference catalog of the human gut microbiome contains 9,879,896 non-redundant genes. The genes were phylogenetically annotated according to 3449 bacterial and archaeal genomes and draft genomes from NCBI, and functionally annotated using orthologous groups from the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) databases. In addition, 11 samples from the Chinese cohort were re-extracted using the MetaHIT DNA extraction protocol and shotgun-sequenced to compare with the original data generated by a slightly different DNA extraction protocol.

Related manuscripts:

doi:10.1038/nbt.2942

Accessions (data not in GigaDB):

ENA: ERP000108
ENA: ERP002061
ENA: ERP003612
ENA: ERP004605
ENA: SRP002163
ENA: SRP011011
ENA: SRP008047

Projects:


Samples:

Sample ID Taxonomic ID Common name Genbank name Scientific name Sample attributes
158256496-stool1 408170 Human gut metagenome human gut metagenome
158337416-stool1 408170 Human gut metagenome human gut metagenome
158337416-stool2 408170 Human gut metagenome human gut metagenome
158458797-stool1 408170 Human gut metagenome human gut metagenome
158479027-stool1 408170 Human gut metagenome human gut metagenome
158499257-stool1 408170 Human gut metagenome human gut metagenome
158499257-stool2 408170 Human gut metagenome human gut metagenome
158742018-stool1 408170 Human gut metagenome human gut metagenome
158802708-stool1 408170 Human gut metagenome human gut metagenome
158802708-stool2 408170 Human gut metagenome human gut metagenome

Files (FTP site) (Aspera):Aspera user name: gigadb , password: gigadb Table Settings
Items per page:

File Name Sample ID File Type File Format Size Release Date

readme.txt

Readme TEXT 1 4 29502.88 KB 2013-09-15

3CGC.clstr.gz

Other UNKNOWN 2 9 170013559162.14 MB 2013-09-15

3CGC.fa.gz

Coding sequence FASTA 3 10 19055112381.77 GB 2013-09-15

AGC.clstr.gz

Other UNKNOWN 2 9 323864711308.86 MB 2013-09-15

AGC.fa.gz

Coding sequence FASTA 2 9 692436363660.36 MB 2013-09-15

CGC.clstr.gz

Other UNKNOWN 2 9 437188592416.94 MB 2013-09-15

CGC.fa.gz

Coding sequence FASTA 2 9 891937240850.62 MB 2013-09-15

EGC.clstr.gz

Other UNKNOWN 3 10 15437468601.44 GB 2013-09-15

EGC.fa.gz

Coding sequence FASTA 3 10 19664183041.83 GB 2013-09-15

IGC.clstr.gz

Other UNKNOWN 2 8 9622268391.77 MB 2013-09-15