Data
Gene Catalog Reference
amino acid sequences (amino acid sequences, fasta)
Gene profile, taxonomic profile, KO profile
KO profile (KO abundance profile table for 20 Macaca fascicularis feces samples)
class profile (class abundance profile table for 20 Macaca fascicularis feces samples)
family profile (family abundance profile table for 20 Macaca fascicularis feces samples)
genus profile (genus abundance profile table for 20 Macaca fascicularis feces samples)
order profile (order abundance profile table for 20 Macaca fascicularis feces samples)
phylum profile (phylum abundance profile table for 20 Macaca fascicularis feces samples)
species profile (species abundance profile table for 20 Macaca fascicularis feces samples)
superkingdom profile (superkingdom abundance profile table of 20 Macaca fascicularis feces samples)
Data download link and phenotype
Gene Annotation
kegg (functional annotation based on the Kyoto Encyclopedia of Genes and Genomes(KEGG) database)
File format specification :
| Unique ID | Gene ID |
| Unique name | Gene Name |
| Length of nucleotide sequence | Gene Length |
| Ratio of species | Number of genes annotated to the corresponding species |
| Ratio of species (%) | Number of genes annotated to the corresponding species (%) |
| Average % identity | Average identity of annotated species |
| NCBI tax_id | Taxonomy id |
| NCBI taxonomy | Taxonomy species |
| Annotated KO(s) for a gene(prokaryotes) | Annotated prokaryotes KO(s) for a gene |
| prokaryotes % identity | Identity of annotated prokaryotes KO(s) |
| Annotated KO(s) for a gene(fungi) | Annotated fungi KO(s) for a gene |
| fungi % identity | Identity of annotated fungi KO(s) |
| Best_Hit_ARO | ARO term of top hit in CARD |
| Best_Identities | Percent identity of match to top hit in CARD |
| Drug Class | ARO Categorization |
| Resistance Mechanism | ARO Categorization |
| AMR Gene Family | ARO Categorization |
Summary
| Gene catalog | Sample size | Number of genes | Total length(bp) | Average length(bp) | N50(bp) | N90(bp) | Max length(bp) | Min length(bp) |
| Macaque | 20 | 1,991,169 | 1,507,900,194 | 757 | 999 | 402 | 40,851 | 102 |
* 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
| #ORFs | Sequence Length(bp) | Average length (bp) | N50 (bp) | N90 (bp) | Max length | Min length | % annotated on Phylum level | % annotated on Genus level | % annotated on KO |
| 10,930,638 | 7,236,097,080 | 659.23 | 873 | 318 | 47,496 | 150 | 53.45% | 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.
China National GeneBank(CNGB)
Jinsha Road, Dapeng District, Shenzhen
Contact datasubs@cngb.org for questions about data submission.