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SPIRE: a Searchable, Planetary-scale mIcrobiome REsource
Schmidt, T.; Fullam, F.; Ferretti, P.; Orakov, A.; Maistrenko, O.M.; Ruscheweyh, H.-J.; Letunic, I.; Duan, Y.; Van Rossum, T.; Sunagawa, S.; Mende, D.R.; Finn, R.D.; Kuhn, M.; Pedro Coelho, L.; Bork, P. (2023). SPIRE: a Searchable, Planetary-scale mIcrobiome REsource. Nucleic Acids Res. 52(D1): D777-D783. https://dx.doi.org/10.1093/nar/gkad943
In: Nucleic Acids Research. Information Retrieval: London. ISSN 0305-1048; e-ISSN 1362-4962
Peer reviewed article  
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  • Schmidt, T.
  • Fullam, F.
  • Ferretti, P.
  • Orakov, A.
  • Maistrenko, O.M.
  • Ruscheweyh, H.-J.
  • Letunic, I.
  • Duan, Y.
  • Van Rossum, T.
  • Sunagawa, S.
  • Mende, D.R.
  • Finn, R.D.
  • Kuhn, M.
  • Pedro Coelho, L.
  • Bork, P.
Abstract
    Meta’omic data on microbial diversity and function accrue exponentially in public repositories, but derived information is often siloed according to data type, study or sampled microbial environment. Here we present SPIRE, a Searchable Planetary-scale mIcrobiome REsource that integrates various consistently processed metagenome-derived microbial data modalities across habitats, geography and phylogeny. SPIRE encompasses 99 146 metagenomic samples from 739 studies covering a wide array of microbial environments and augmented with manually-curated contextual data. Across a total metagenomic assembly of 16 Tbp, SPIRE comprises 35 billion predicted protein sequences and 1.16 million newly constructed metagenome-assembled genomes (MAGs) of medium or high quality. Beyond mapping to the high-quality genome reference provided by proGenomes3 (http://progenomes.embl.de), these novel MAGs form 92 134 novel species-level clusters, the majority of which are unclassified at species level using current tools. SPIRE enables taxonomic profiling of these species clusters via an updated, custom mOTUs database (https://motu-tool.org/) and includes several layers of functional annotation, as well as crosslinks to several (micro-)biological databases. The resource is accessible, searchable and browsable via http://spire.embl.de.
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