{"id":1400,"date":"2024-05-07T10:26:47","date_gmt":"2024-05-07T10:26:47","guid":{"rendered":"https:\/\/www.embl.org\/about\/info\/planetary-biology\/?page_id=1400"},"modified":"2026-09-10T08:44:23","modified_gmt":"2026-09-10T08:44:23","slug":"spire","status":"publish","type":"page","link":"https:\/\/www.embl.org\/about\/info\/planetary-biology\/projects\/spire\/","title":{"rendered":"SPIRE"},"content":{"rendered":"\n<div class=\"vf-grid | vf-grid__col-3\"><div class=\"vf-grid__col--span-2\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<p class=\"vf-lede\">Searchable Planetary-scale mIcrobiome REsource.<\/p>\n<!--\/vf-lede-->\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">SPIRE integrates metagenome-derived microbial data modalities across habitats, geography and phylogeny.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n\n\n\n<figure class=\"vf-figure wp-block-image  | vf-figure--align vf-figure--align-centered  size-full is-resized\"><a href=\"https:\/\/spire.embl.de\/\" target=\"_blank\" rel=\"noreferrer noopener\"><img loading=\"lazy\" decoding=\"async\" width=\"520\" height=\"516\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/about\/info\/planetary-biology\/wp-content\/uploads\/2024\/05\/spire.jpeg\" alt=\"\" class=\"wp-image-1526\" style=\"width:500px\" srcset=\"https:\/\/www.embl.org\/about\/info\/planetary-biology\/wp-content\/uploads\/2024\/05\/spire.jpeg 520w, https:\/\/www.embl.org\/about\/info\/planetary-biology\/wp-content\/uploads\/2024\/05\/spire-300x298.jpeg 300w, https:\/\/www.embl.org\/about\/info\/planetary-biology\/wp-content\/uploads\/2024\/05\/spire-150x150.jpeg 150w\" sizes=\"auto, (max-width: 520px) 100vw, 520px\" \/><\/a><\/figure>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">SPIRE is a recently published platform with the aim to provide an integrated view of microbial diversity at various taxonomic granularities, at genome and at gene level, across known microbial habitats. It is a \u201cone-stop-shop\u201d for microbial data, integrated and consistently processed across habitats and phylogeny, at global scales. SPIRE is derived from ~100k metagenomic samples in 739 studies encompassing ~500Tbp of publicly available raw metagenomes, and holds five main types of data: <\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>manually curated contextual data, including annotations against a custom \u201cmicrontology\u201d<\/li>\n\n\n\n<li>16Tbp worth of metagenomic assemblies (contigs)<\/li>\n\n\n\n<li>35 billion metagenomic open reading frames (ORFs) called from these contigs, functionally annotated in various ways<\/li>\n\n\n\n<li>1.16 million metagenome-assembled genomes (MAGs) of medium or high quality, co-clustered with isolate genomes into ~120 thousand species-level clusters and <\/li>\n\n\n\n<li>custom mOTU database to allow taxonomic profiling against these species-level clusters<\/li>\n<\/ul>\n\n\n\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Publication<\/strong><br><em>Nucleic Acids Research<\/em>, Volume 52, Issue D1, 5 January 2024, Pages D777-D783&nbsp; <a href=\"https:\/\/doi.org\/10.1093\/nar\/gkad943\">https:\/\/doi.org\/10.1093\/nar\/gkad943<\/a><\/p>\n\n\n\n<div style=\"height:60px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h3 class=\"wp-block-heading\">Collaborators<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">Coelho, Queensland University of Technology<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Schmidt, University College Cork<\/p>\n\n\n\n<p class=\"vf-u-margin__bottom--800 wp-block-paragraph\"><\/p>\n\n<\/div>\n<\/div>\n\n\n<div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<h3 class=\"wp-block-heading\">Project lead<\/h3>\n\n\n<div class=\"vf-content-hub-html\" data-cache=\"64fed8e3\">\n      <!-- Generated by: http:\/\/content.embl.org\/api\/v1\/pattern.html?filter-content-type=person&amp;filter-field-contains%5Bfield_person_full_name%5D=Michael%20Kuhn&amp;filter-fields-empty=field_person_visible_internally&amp;filter-ref-entity%5Bfield_person_positions%5D%5Btitle%5D=&amp;filter-ref-entity%5Bfield_person_positions%5D%5Bfield_position_primary%5D=1&amp;hide%5B0%5D=1&amp;limit=1&amp;pattern=vf-profile-inline -->\n                \n                            <article class=\"vf-profile vf-profile--very-easy vf-profile--medium vf-profile--inline\" data-embl-js-conditional-edit=\"80856\">\n              <img decoding=\"async\" class=\"vf-profile__image\" src=\"https:\/\/content.embl.org\/\/sites\/default\/files\/styles\/medium\/public\/persons\/CP-60003014.jpg?itok=GrqpwbNi\" alt=\"image of Michael Kuhn\" \/>\n      \n              <h3 class=\"vf-profile__title\">\n                      <a href=\"https:\/\/www.embl.org\/people\/person\/mkuhn\" class=\"vf-profile__link\">Michael Kuhn<\/a>\n                  <\/h3>\n      \n              <p class=\"vf-profile__job-title\">\n          Research Staff Scientist \/ Coordinator\n        <\/p>\n      \n              <p class=\"vf-profile__text\">\n          Bork Group\n        <\/p>\n      \n      \n      \n      \n      \n              <p class=\"vf-profile__uuid\">\n          <span>ORCID:<\/span>\n          <a class=\"vf-profile__link vf-profile__link--secondary\" href=\"https:\/\/europepmc.org\/authors\/0000-0002-2841-872X\">\n            0000-0002-2841-872X\n          <\/a>\n        <\/p>\n            <a class=\"vf-text vf-text--body-r vf-link embl-conditional-edit\" rel=\"noopener noreferrer nofollow\" href=\"\/node\/80856\/80856\" target=\"_blank\">\n        Edit\n      <\/a>\n    <\/article>\n  <\/div>\n\n\n\n<\/div>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":2,"featured_media":0,"parent":714,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"template-title-left-aligned.php","meta":{"_acf_changed":false,"footnotes":""},"embl_taxonomy":[],"class_list":["post-1400","page","type-page","status-publish","hentry"],"acf":[],"embl_taxonomy_terms":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/about\/info\/planetary-biology\/wp-json\/wp\/v2\/pages\/1400","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.embl.org\/about\/info\/planetary-biology\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.embl.org\/about\/info\/planetary-biology\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.embl.org\/about\/info\/planetary-biology\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.embl.org\/about\/info\/planetary-biology\/wp-json\/wp\/v2\/comments?post=1400"}],"version-history":[{"count":11,"href":"https:\/\/www.embl.org\/about\/info\/planetary-biology\/wp-json\/wp\/v2\/pages\/1400\/revisions"}],"predecessor-version":[{"id":129405,"href":"https:\/\/www.embl.org\/about\/info\/planetary-biology\/wp-json\/wp\/v2\/pages\/1400\/revisions\/129405"}],"up":[{"embeddable":true,"href":"https:\/\/www.embl.org\/about\/info\/planetary-biology\/wp-json\/wp\/v2\/pages\/714"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/about\/info\/planetary-biology\/wp-json\/wp\/v2\/media?parent=1400"}],"wp:term":[{"taxonomy":"embl_taxonomy","embeddable":true,"href":"https:\/\/www.embl.org\/about\/info\/planetary-biology\/wp-json\/wp\/v2\/embl_taxonomy?post=1400"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}