Dataset Open Access

iMGMC - integrated Mouse Gut Metagenomic Catalog

Lesker, Till Robin; Strowig, Till

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

Code used: https://github.com/tillrobin/iMGMC

The vast complexity of host-associated microbial ecosystems requires host-specific reference catalogs to survey the functions and diversity of these communities. We generated a comprehensive resource, the integrated mouse gut metagenome catalog (iMGMC), comprising 4.6 million unique genes and 660 metagenome-assembled genomes (MAGs) with many of them (485 MAGs, 73%) linked to reconstructed full-length 16S rRNA gene sequences. iMGMC enables unprecedented coverage and taxonomic resolution of the mouse gut microbiota, i.e. more than 92% of MAGs lack species-level representatives in public repositories (<95% ANI match). The integration of MAGs and 16S rRNA gene data allows a more accurate prediction of functional profiles of communities than based on 16S rRNA amplicons alone. Accompanying iMGMC we provide a set of MAGs representing 1,296 gut bacteria obtained through complementary assembly strategies. We envision that integrated resources such as iMGMC together with MAG collections will enhance the resolution of numerous existing and future sequencing-based studies.

Genecatalog:

Description    Size   Filename
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    40 MB    iMGMC_map_taxonomy.tar.gz
Functional annotations    36 MB    iMGMC_map_functionality.tar.gz
16S rRNA sequences    2 MB    iMGMC-16SrRNAgenes.fasta

Metagenome-assembled genomes (MAGs) :

Description    Size    Filename
integrated MAGs    0.5 GB    iMGMC_MAGs.tar.gz
representave mMAGs (n=1296)    1 GB    iMGMC-mMAGs-dereplicated_genomes.tar.gz
representave 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

 

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).
Files (20.6 GB)
Name Size
hqMAGs.emapper.annotations.gz
md5:d4afcb3987c47098850cf3a69447796e
196.5 MB Download
iMGMC-16SrRNAgenes.fasta
md5:56a4c3e4a3adfe027cb29f888ece3d1b
2.0 MB Download
iMGMC-ConigID.fasta.gz
md5:32a6219d4323cdcc10b275b60a314179
1.4 GB Download
iMGMC-GeneID.fasta.gz
md5:293bb3922237dea87df9cac8d9e7600f
1.1 GB Download
iMGMC-hqMAGs-dereplicated_genomes.tar.gz
md5:58d2aabd73ec9b580d2aeade4b949057
744.1 MB Download
iMGMC-MAGs.tar.gz
md5:71ab991698b358ac37729477b6d05615
579.7 MB Download
iMGMC-map-Gene-Contig-Bin.tab.gz
md5:c65b1e54f9d856ca745809b8f4d6092b
32.7 MB Download
iMGMC-mMAGs-dereplicated_genomes.tar.gz
md5:434b0a269af6bc11bb1dd22acc17eb33
1.0 GB Download
iMGMC-mMAGs.tar.gz
md5:9eedd41d115127701e0cb2b6ac3eed29
15.4 GB Download
iMGMC_map_functionality.tar.gz
md5:d1b64aecd3d397d009f036a0a313e736
38.2 MB Download
iMGMC_map_taxonomy.tar.gz
md5:2cc20450e5bf5f783ccc1894b19aaf8d
41.8 MB Download
MAG-annotation_CheckM_dRep_GTDB-Tk.tar.gz
md5:b011dd70e8c8005c252aedba537a9178
1.9 MB Download
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