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Data released on May 14, 2015

Supporting data for the dynamics and stabilization of the Human gut microbiome during the first year of life.

Al-Aama, J, Y; Backhed, F; Bergman, S; Colding, C; Dahlgren, J; Feng, Q; Jia, H; Khan, M, T; Kotowska, D; Kovatcheva-Datchary, P; Kristiansen, K; Lee, Y, S; Li, J; Li, Y; Madsen, L; Peng, Y; Roswall, J; Tremaroli, V; Wang, J; Xia, Y; Xiao, L; Xie, H; Yin, Y; Zhang, D; Zhang, J; Zhong, H (2015): Supporting data for the dynamics and stabilization of the Human gut microbiome during the first year of life. GigaScience Database. http://dx.doi.org/10.5524/100145 RIS BibTeX Text

Here we performed metagenomic shotgun sequencing on fecal samples from 98 full-term Swedish infants (new born, 4-months and 12-months old) and their mothers; assembled gut microbial genomes and constructed reference gene catalogs from the cohort. We generated 1.52 Tb paired-end reads of high-quality sequences (average 3.99 Gb per sample). A gene catalog was constructed for each time point based on de novo assembly and metagenomic gene prediction; and functionally annotated using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. We also assembled a total of 4,356 microbial genomes (>0.9 MB) de novo; by binning assembled contigs according to abundance variations across samples. These de novo assembled genomes were complemented by 1,147 genomes from the National Center for Biotechnology Information (NCBI) Bacteria/Archaea genome database. All genomes were subsequently clustered into 690 unique metagenomic operational taxonomic units (MetaOTUs) that were equivalent to species-level classifications. Of these, 373 were annotated to species, the remaining 317 represent novel species related to known species. We constructed the metaOTUs profile by mapping reads to our metaOTUs sequences.

Contact Submitter

Related manuscripts:

doi:10.1016/j.chom.2015.04.004

Accessions (data included in GigaDB):

ENA : ERP005989

Metagenomic

http://gigadb.org/images/uploads/image_upload/Images_199.png

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
10_12M408170Human gut metagenome human gut metagenome Life stage:infant
Diet:no breastfeeding
Family relationship:mother is 10_M
...
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103_12M408170Human gut metagenome human gut metagenome Parturition mechanism:Caesarian section(HP:0011410...
Life stage:infant
Diet:no breastfeeding
...
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103_4M408170Human gut metagenome human gut metagenome Parturition mechanism:Caesarian section(HP:0011410...
Life stage:infant
Diet:Bottle feeding
...
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103_B408170Human gut metagenome human gut metagenome Parturition mechanism:Caesarian section(HP:0011410...
Life stage:infant
Diet:Breast feeding
...
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103_M408170Human gut metagenome human gut metagenome Days after parturition:4
Description:Baby's mother
Life stage:adult
...
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10_4M408170Human gut metagenome human gut metagenome Life stage:infant
Diet:Breast feeding
Family relationship:mother is 10_M
...
+
105_12M408170Human gut metagenome human gut metagenome Life stage:infant
Diet:no breastfeeding
Family relationship:mother is 105_M
...
+
105_4M408170Human gut metagenome human gut metagenome Life stage:infant
Diet:Breast feeding
Family relationship:mother is 105_M
...
+
105_B408170Human gut metagenome human gut metagenome Life stage:infant
Diet:Breast feeding
Family relationship:mother is 105_M
...
+
105_M408170Human gut metagenome human gut metagenome Days after parturition:5
Description:Baby's mother
Life stage:adult
...
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Displaying 1-10 of 392 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 
Coding sequenceFASTA456.62 MB2015-05-14
Protein sequenceFASTA318.7 MB2015-05-14
Coding sequenceFASTA280.45 MB2015-05-14
Protein sequenceFASTA195.09 MB2015-05-14
OtherUNKNOWN236.67 MB2015-05-14
OtherUNKNOWN3.68 MB2015-05-14
OtherUNKNOWN106.84 MB2015-05-14
OtherUNKNOWN3.6 MB2015-05-14
OtherUNKNOWN61.62 MB2015-05-14
OtherUNKNOWN3.22 MB2015-05-14
Displaying 1-10 of 22 File(s).

History:

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