Creation of an new mouse gut gene catalog with special features:
- more diverse samples from different studies (12 Vendors incl. wild mice and various gut locations)
- clustering-free approach: all-in-one assembly, keeping track of each ORF to contigs to bins
- higher taxonomic resolution and more accuracy by using contigs for annotation
- 16S rRNA gene integration via linkage to bins
- expansion by 20,927 MAGs from sample-wise assembly of 871 mouse gut metagenomic samples, representing 1,296 species
- Pipelines and Tutorials to process you own data
See our paper for details.
An integrated metagenome catalog enables new insights into the murine gut microbiome
Till R. Lesker, Abilash C. Durairaj, Eric. J.C. Gálvez, Ilias Lagkouvardos, John F. Baines, Thomas Clavel, Alexander Sczyrba, Alice C. McHardy, Till Strowig. Cell reports 30, no. 9 (2020): 2909-2922.
https://doi.org/10.1016/j.celrep.2020.02.036
Please download the files by using the links in the table, use script provided here: download all iMGMC data or use alternative download at Zenodo.
| Description | Size | Link |
|---|---|---|
| Catalog ORF sequences | 1 GB | iMGMC-GeneID.fasta.gz |
| Full assembly contigs | 1.3 GB | iMGMC-ConitgID.fasta.gz |
| Mapping File (GeneID->ContigID->BinID) | 30 MB | iMGMC-map-Gene-Contig-Bin.tab.gz |
| Taxonomic annotations | 42 MB | iMGMC_map_taxonomy.tar.gz |
| Functional annotations | 38 MB | iMGMC_map_functionality.tar.gz |
| 16S rRNA sequences | 2 MB | iMGMC-16SrRNAgenes.fasta |
| Description | Size | Link |
|---|---|---|
| integrated MAGs | 0.5 GB | iMGMC_MAGs.tar.gz |
| representative mMAGs (n=1296) | 1 GB | iMGMC-mMAGs-dereplicated_genomes.tar.gz |
| representative hqMAGs (n=830) | 0.7 GB | iMGMC-hqMAGs-dereplicated_genomes.tar.gz |
| all mMAGs (n=20,927) | 15 GB | iMGMC-mMAGs.tar.gz |
| Annotations by CheckM, dRep-Clustering, GTDB-Tk | 2 MB | MAG-annotation_CheckM_dRep_GTDB-Tk.tar.gz |
| Functional annotations (hqMAGs by eggNOG mapper v2) | 187 MB | hqMAGs.emapper.annotations.gz |
For species abundance determination you can use CoverM or our bbmap-pipeline.
Accession codes of the used gut metagenome sequences: European Nucleotide Archive: ERP008710, ERA473426, PRJEB32890 and to the Metagenomics Rapid Genomes/Metagenomes (MG-RAST) with ID 4661127.3/ mgp5130
The following files are additional or updated data. The mainly effects annotations files like KEGG-database links and taxonomic descriptions from GTDB.
| Description | Size | Link |
|---|---|---|
| translated ORF sequences | 0.7 GB | iMGMC-GeneID.proteins.gz |
| KEGG KofamScan 03/20 | 14 MB | iMGMC-GeneID-KofamScan.fasta.gz |
| mMAGs Taxonomy GTDB-Tk-v1.3 rs95 | 1 MB | iMGMC-mMAGs-GTDB-Tk_v1.3.0-r95.tsv |
We recommend the use of Bioconda
Instruction to process your own WGS samples with iMGMC
Using MAGs with iMGMC/sMAGS with your own WGS samples
Instruction to process your own samples 16S rRNA amplicon samples with PICRUSt and iMGMC
Instruction to work with iMGMC-IMNGS data
Code for assembly, binning and 16S rRNA gene reconstruction
Code for linking 16S rRNA genes to bins
Code for the generation and clustering of single-wise assembly MAGs
Code for the evaluation of single-wise assembly MAGs versus all-in-one assembly MAGs
Explore MAG abundances with CoverM and Krona Plot
Compare MAGs abundances with CoverM and R heatmap
Ordination of samples by gene and KO profiles
Please open an issue if the problem cannot be solved. We will need to know how to reproduce your problem.
Xiao, Liang, et al. "A catalog of the mouse gut metagenome." Nature biotechnology 33.10 (2015): 1103-1108. http://doi.org/10.1038/nbt.3353
Wang, Jun, et al. "Dietary history contributes to enterotype-like clustering and functional metagenomic content in the intestinal microbiome of wild mice." Proceedings of the National Academy of Sciences 111.26 (2014): E2703-E2710. http://doi.org/10.1073/pnas.1402342111
Lagkouvardos, Ilias, et al. "The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota." Nature microbiology 1 (2016): 16131. http://doi.org/10.1038/nmicrobiol.2016.131
Acknowledgements: TS was funded by the Helmholtz Association (VH-NG-933), by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation, STR-1343/1 and STR-1343/2) and the European Union (StG337251). JFB was funded by the DFG under Germany`s Excellence Strategy – EXC 22167-390884018 and by the DFG Collaborative Research Center (CRC) 1182 “Origin and Function of Metaorganisms”. TC received funding from the DFG (project CL481/2-1 and grants within Collaborative Research Center 1382).