Dataset Open Access

iMGMC - integrated Mouse Gut Metagenomic Catalog

Lesker, Till Robin; Strowig, Till


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  <identifier identifierType="DOI">10.5281/zenodo.3631711</identifier>
  <creators>
    <creator>
      <creatorName>Lesker, Till Robin</creatorName>
      <givenName>Till Robin</givenName>
      <familyName>Lesker</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-3085-6438</nameIdentifier>
      <affiliation>Helmholtz Centre for Infection Research</affiliation>
    </creator>
    <creator>
      <creatorName>Strowig, Till</creatorName>
      <givenName>Till</givenName>
      <familyName>Strowig</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-0185-1459</nameIdentifier>
      <affiliation>Helmholtz Centre for Infection Research</affiliation>
    </creator>
  </creators>
  <titles>
    <title>iMGMC - integrated Mouse Gut Metagenomic Catalog</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2020</publicationYear>
  <subjects>
    <subject>mouse gut</subject>
    <subject>metagenome</subject>
    <subject>gene catalog</subject>
    <subject>Metagenome-assembled genomes (MAGs)</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2020-01-31</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/3631711</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsPartOf" resourceTypeGeneral="Preprint">10.1101/528737</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsPartOf" resourceTypeGeneral="JournalArticle">10.1016/j.celrep.2020.02.036</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.3631710</relatedIdentifier>
  </relatedIdentifiers>
  <version>1</version>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;&lt;em&gt;Creation of an new mouse gut gene catalog with special features:&lt;/em&gt;&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;more diverse samples from different studies (12 Vendors incl. wild mice and various gut locations)&lt;/li&gt;
	&lt;li&gt;clustering-free approach: all-in-one assembly, keeping track of each ORF to contigs to bins&lt;/li&gt;
	&lt;li&gt;higher taxonomic resolution and more accuracy by using contigs for annotation&lt;/li&gt;
	&lt;li&gt;16S rRNA gene integration via linkage to bins&lt;/li&gt;
	&lt;li&gt;expansion by 20,927 MAGs from sample-wise assembly of 871 mouse gut metagenomic samples, representing 1,296 species&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;Code used:&amp;nbsp;&lt;a href="https://github.com/tillrobin/iMGMC"&gt;https://github.com/tillrobin/iMGMC&lt;/a&gt;&lt;/p&gt;

&lt;p&gt;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 (&amp;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.&lt;/p&gt;

&lt;p&gt;Genecatalog:&lt;/p&gt;

&lt;p&gt;Description&amp;nbsp;&amp;nbsp; &amp;nbsp;Size&amp;nbsp;&amp;nbsp; Filename&lt;br&gt;
Catalog ORF sequences&amp;nbsp;&amp;nbsp; &amp;nbsp;1 GB&amp;nbsp;&amp;nbsp; &amp;nbsp;iMGMC-GeneID.fasta.gz&lt;br&gt;
Full assembly contigs&amp;nbsp;&amp;nbsp; &amp;nbsp;1.3 GB&amp;nbsp;&amp;nbsp; &amp;nbsp;iMGMC-ConitgID.fasta.gz&lt;br&gt;
Mapping File (GeneID-&amp;gt;ContigID-&amp;gt;BinID)&amp;nbsp;&amp;nbsp; &amp;nbsp;30 MB&amp;nbsp;&amp;nbsp; &amp;nbsp;iMGMC-map-Gene-Contig-Bin.tab.gz&lt;br&gt;
Taxonomic annotations&amp;nbsp;&amp;nbsp; &amp;nbsp;40 MB&amp;nbsp;&amp;nbsp; &amp;nbsp;iMGMC_map_taxonomy.tar.gz&lt;br&gt;
Functional annotations&amp;nbsp;&amp;nbsp; &amp;nbsp;36 MB&amp;nbsp;&amp;nbsp; &amp;nbsp;iMGMC_map_functionality.tar.gz&lt;br&gt;
16S rRNA sequences&amp;nbsp;&amp;nbsp; &amp;nbsp;2 MB&amp;nbsp;&amp;nbsp; &amp;nbsp;iMGMC-16SrRNAgenes.fasta&lt;/p&gt;

&lt;p&gt;Metagenome-assembled genomes (MAGs) :&lt;/p&gt;

&lt;p&gt;Description&amp;nbsp;&amp;nbsp; &amp;nbsp;Size&amp;nbsp;&amp;nbsp; &amp;nbsp;Filename&lt;br&gt;
integrated MAGs&amp;nbsp;&amp;nbsp; &amp;nbsp;0.5 GB&amp;nbsp;&amp;nbsp; &amp;nbsp;iMGMC_MAGs.tar.gz&lt;br&gt;
representave mMAGs (n=1296)&amp;nbsp;&amp;nbsp; &amp;nbsp;1 GB&amp;nbsp;&amp;nbsp; &amp;nbsp;iMGMC-mMAGs-dereplicated_genomes.tar.gz&lt;br&gt;
representave hqMAGs (n=830)&amp;nbsp;&amp;nbsp; &amp;nbsp;0.7 GB&amp;nbsp;&amp;nbsp; &amp;nbsp;iMGMC-hqMAGs-dereplicated_genomes.tar.gz&lt;br&gt;
all mMAGs (n=20,927)&amp;nbsp;&amp;nbsp; &amp;nbsp;15 GB&amp;nbsp;&amp;nbsp; &amp;nbsp;iMGMC-mMAGs.tar.gz&lt;br&gt;
Annotations by CheckM, dRep-Clustering, GTDB-Tk&amp;nbsp;&amp;nbsp; &amp;nbsp;2 MB&amp;nbsp;&amp;nbsp; &amp;nbsp;MAG-annotation_CheckM_dRep_GTDB-Tk.tar.gz&lt;br&gt;
Functional annotations (hqMAGs by eggNOG mapper v2)&amp;nbsp;&amp;nbsp; &amp;nbsp;187 MB&amp;nbsp;&amp;nbsp; &amp;nbsp;hqMAGs.emapper.annotations.gz&lt;/p&gt;

&lt;p&gt;&amp;nbsp;&lt;/p&gt;</description>
    <description descriptionType="Other">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).</description>
  </descriptions>
</resource>
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