Dataset Open Access

iMGMC - integrated Mouse Gut Metagenomic Catalog

Lesker, Till Robin; Strowig, Till


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  "description": "<p><em>Creation of an new mouse gut gene catalog with special features:</em></p>\n\n<ul>\n\t<li>more diverse samples from different studies (12 Vendors incl. wild mice and various gut locations)</li>\n\t<li>clustering-free approach: all-in-one assembly, keeping track of each ORF to contigs to bins</li>\n\t<li>higher taxonomic resolution and more accuracy by using contigs for annotation</li>\n\t<li>16S rRNA gene integration via linkage to bins</li>\n\t<li>expansion by 20,927 MAGs from sample-wise assembly of 871 mouse gut metagenomic samples, representing 1,296 species</li>\n</ul>\n\n<p>Code used:&nbsp;<a href=\"https://github.com/tillrobin/iMGMC\">https://github.com/tillrobin/iMGMC</a></p>\n\n<p>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 (&lt;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.</p>\n\n<p>Genecatalog:</p>\n\n<p>Description&nbsp;&nbsp; &nbsp;Size&nbsp;&nbsp; Filename<br>\nCatalog ORF sequences&nbsp;&nbsp; &nbsp;1 GB&nbsp;&nbsp; &nbsp;iMGMC-GeneID.fasta.gz<br>\nFull assembly contigs&nbsp;&nbsp; &nbsp;1.3 GB&nbsp;&nbsp; &nbsp;iMGMC-ConitgID.fasta.gz<br>\nMapping File (GeneID-&gt;ContigID-&gt;BinID)&nbsp;&nbsp; &nbsp;30 MB&nbsp;&nbsp; &nbsp;iMGMC-map-Gene-Contig-Bin.tab.gz<br>\nTaxonomic annotations&nbsp;&nbsp; &nbsp;40 MB&nbsp;&nbsp; &nbsp;iMGMC_map_taxonomy.tar.gz<br>\nFunctional annotations&nbsp;&nbsp; &nbsp;36 MB&nbsp;&nbsp; &nbsp;iMGMC_map_functionality.tar.gz<br>\n16S rRNA sequences&nbsp;&nbsp; &nbsp;2 MB&nbsp;&nbsp; &nbsp;iMGMC-16SrRNAgenes.fasta</p>\n\n<p>Metagenome-assembled genomes (MAGs) :</p>\n\n<p>Description&nbsp;&nbsp; &nbsp;Size&nbsp;&nbsp; &nbsp;Filename<br>\nintegrated MAGs&nbsp;&nbsp; &nbsp;0.5 GB&nbsp;&nbsp; &nbsp;iMGMC_MAGs.tar.gz<br>\nrepresentave mMAGs (n=1296)&nbsp;&nbsp; &nbsp;1 GB&nbsp;&nbsp; &nbsp;iMGMC-mMAGs-dereplicated_genomes.tar.gz<br>\nrepresentave hqMAGs (n=830)&nbsp;&nbsp; &nbsp;0.7 GB&nbsp;&nbsp; &nbsp;iMGMC-hqMAGs-dereplicated_genomes.tar.gz<br>\nall mMAGs (n=20,927)&nbsp;&nbsp; &nbsp;15 GB&nbsp;&nbsp; &nbsp;iMGMC-mMAGs.tar.gz<br>\nAnnotations by CheckM, dRep-Clustering, GTDB-Tk&nbsp;&nbsp; &nbsp;2 MB&nbsp;&nbsp; &nbsp;MAG-annotation_CheckM_dRep_GTDB-Tk.tar.gz<br>\nFunctional annotations (hqMAGs by eggNOG mapper v2)&nbsp;&nbsp; &nbsp;187 MB&nbsp;&nbsp; &nbsp;hqMAGs.emapper.annotations.gz</p>\n\n<p>&nbsp;</p>", 
  "license": "https://creativecommons.org/licenses/by/4.0/legalcode", 
  "creator": [
    {
      "affiliation": "Helmholtz Centre for Infection Research", 
      "@id": "https://orcid.org/0000-0002-3085-6438", 
      "@type": "Person", 
      "name": "Lesker, Till Robin"
    }, 
    {
      "affiliation": "Helmholtz Centre for Infection Research", 
      "@id": "https://orcid.org/0000-0003-0185-1459", 
      "@type": "Person", 
      "name": "Strowig, Till"
    }
  ], 
  "url": "https://zenodo.org/record/3631711", 
  "datePublished": "2020-01-31", 
  "isPartOf": [
    {
      "@id": "https://doi.org/10.1101/528737", 
      "@type": "ScholarlyArticle"
    }, 
    {
      "@id": "https://doi.org/10.1016/j.celrep.2020.02.036", 
      "@type": "ScholarlyArticle"
    }
  ], 
  "version": "1", 
  "keywords": [
    "mouse gut", 
    "metagenome", 
    "gene catalog", 
    "Metagenome-assembled genomes (MAGs)"
  ], 
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  "identifier": "https://doi.org/10.5281/zenodo.3631711", 
  "@id": "https://doi.org/10.5281/zenodo.3631711", 
  "@type": "Dataset", 
  "name": "iMGMC - integrated Mouse Gut Metagenomic Catalog"
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