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SPIRE: a Searchable, Planetary-scale mIcrobiome REsource

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Item Type:Article
Title:SPIRE: a Searchable, Planetary-scale mIcrobiome REsource
Creators Name:Schmidt, T.S.B. and Fullam, A. and Ferretti, P. and Orakov, A. and Maistrenko, O.M. and Ruscheweyh, H.J. and Letunic, I. and Duan, Y. and Van Rossum, T. and Sunagawa, S. and Mende, D.R. and Finn, R.D. and Kuhn, M. and Pedro Coelho, L. and 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.
Keywords:Factual Databases, Metagenome, Metagenomics, Microbiota
Source:Nucleic Acids Research
Publisher:Oxford University Press
Page Range:D777-D783
Date:5 January 2024
Official Publication:https://doi.org/10.1093/nar/gkad943
PubMed:View item in PubMed

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