Data

  Gene Catalog Reference

  Gene profile, taxonomic profile, KO profile

  Data download link and phenotype

  Gene Annotation

File format specification :

Unique IDGene ID
Unique nameGene Name
Length of nucleotide sequenceGene Length
Ratio of speciesNumber of genes annotated to the corresponding species
Ratio of species (%)Number of genes annotated to the corresponding species (%)
Average % identityAverage identity of annotated species
NCBI tax_idTaxonomy id
NCBI taxonomyTaxonomy species
Annotated KO(s) for a gene(prokaryotes)Annotated prokaryotes KO(s) for a gene
prokaryotes % identityIdentity of annotated prokaryotes KO(s)
Annotated KO(s) for a gene(fungi)Annotated fungi KO(s) for a gene
fungi % identityIdentity of annotated fungi KO(s)
Best_Hit_AROARO term of top hit in CARD
Best_IdentitiesPercent identity of match to top hit in CARD
Drug ClassARO Categorization
Resistance MechanismARO Categorization
AMR Gene FamilyARO Categorization

Summary

Gene catalogSample sizeNumber of genesTotal length(bp)Average length(bp)N50(bp)N90(bp)Max length(bp)Min length(bp)
Macaque201,991,1691,507,900,19475799940240,851102

* N50: it is the length for which the collection of all contigs of that length or longer contains at least half of the total of the lengths of the contigs
* N90: it is the length for which the collection of all contigs of that length or longer contains at least 90% of the total of the lengths of the contigs

#ORFsSequence Length(bp)Average length (bp)N50 (bp)N90 (bp)Max lengthMin length% annotated on Phylum level% annotated on Genus level% annotated on KO
10,930,6387,236,097,080659.2387331847,49615053.45%36.05%58.69%

* ORFs: open reading frame
* N50: it is the length for which the collection of all contigs of that length or longer contains at least half of the total of the lengths of the contigs
* N90: it is the length for which the collection of all contigs of that length or longer contains at least 90% of the total of the lengths of the contigs
* KO: KEGG orthologue group
See our paper for details.

  Gene length

  Number of genes assembled from only one cohort or multiple cohorts

  Phylum composition

  Genus composition

Reference

1. Xie, H. et al. Shotgun Metagenomics of 250 Adult Twins Reveals Genetic and Environmental Impacts on the Gut Microbiome. Cell Syst. 0, 32–46 (2016).

s Xiaoping Li, Suisha Liang, Zhongkui Xia, Jing Qu, Huan Liu, Chuan Liu, Huanming Yang, Jian Wang, Lise Madsen, Yong Hou, Junhua Li, Huijue Jia, Karsten Kristiansen, Liang Xiao; Establishment of a Macaca fascicularis gut microbiome gene catalog and comparison with the human, pig, and mouse gut microbiomes, GigaScience, Volume 7, Issue 9, 1 September 2018, giy100, https://doi.org/10.1093/gigascience/giy100

Xiao, L., Feng, Q., Liang, S., Sonne, S. B., Xia, Z., Qiu, X., … Kristiansen, K. (2015). A catalog of the mouse gut metagenome. Nature Biotechnology, 33(10), 1103–1108. doi:10.1038/nbt.3353

1. Xiao, L. et al. A reference gene catalogue of the pig gut microbiome. Nat. Microbiol. 1, 1–6 (2016).

Pan H, Guo R, Zhu J, et al. A gene catalogue of the Sprague-Dawley rat gut metagenome[J]. GigaScience, 2018, 7(5): giy055.