TY - JOUR
T1 - SPIRE
T2 - a Searchable, Planetary-scale mIcrobiome REsource
AU - Schmidt, Thomas S. B.
AU - Fullam, Anthony
AU - Ferretti, Pamela
AU - Orakov, Askarbek
AU - Maistrenko, Oleksandr M.
AU - Ruscheweyh, Hans-Joachim
AU - Letunic, Ivica
AU - Duan, Yiqian
AU - van Rossum, Thea
AU - Sunagawa, Shinichi
AU - Mende, Daniel R.
AU - Finn, Robert D.
AU - Kuhn, Michael
AU - Pedro Coelho, Luis
AU - Bork, Peer
N1 - Publisher Copyright: © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.
PY - 2024/1/5
Y1 - 2024/1/5
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85181852683&partnerID=8YFLogxK
U2 - https://doi.org/10.1093/nar/gkad943
DO - https://doi.org/10.1093/nar/gkad943
M3 - Article
C2 - 37897342
SN - 0305-1048
VL - 52
SP - D777-D783
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - D1
ER -