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id="toc-EzBioCloud-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Ribosomal_Database_Project" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Ribosomal_Database_Project"> <div class="vector-toc-text"> <span class="vector-toc-numb">5.3</span> <span>Ribosomal Database Project</span> </div> </a> <ul id="toc-Ribosomal_Database_Project-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-SILVA" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#SILVA"> <div class="vector-toc-text"> <span class="vector-toc-numb">5.4</span> <span>SILVA</span> </div> </a> <ul id="toc-SILVA-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-GreenGenes" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#GreenGenes"> <div class="vector-toc-text"> <span class="vector-toc-numb">5.5</span> <span>GreenGenes</span> </div> </a> <ul id="toc-GreenGenes-sublist" class="vector-toc-list"> </ul> </li> </ul> </li> <li id="toc-References" class="vector-toc-list-item vector-toc-level-1 vector-toc-list-item-expanded"> <a class="vector-toc-link" href="#References"> <div class="vector-toc-text"> <span class="vector-toc-numb">6</span> <span>References</span> </div> </a> <ul id="toc-References-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-External_links" class="vector-toc-list-item vector-toc-level-1 vector-toc-list-item-expanded"> <a class="vector-toc-link" href="#External_links"> <div class="vector-toc-text"> <span class="vector-toc-numb">7</span> <span>External links</span> </div> </a> <ul id="toc-External_links-sublist" class="vector-toc-list"> </ul> </li> </ul> </div> </div> </nav> </div> </div> <div class="mw-content-container"> <main id="content" class="mw-body"> <header class="mw-body-header vector-page-titlebar"> <nav aria-label="Contents" class="vector-toc-landmark"> <div id="vector-page-titlebar-toc" class="vector-dropdown vector-page-titlebar-toc vector-button-flush-left" > <input type="checkbox" id="vector-page-titlebar-toc-checkbox" role="button" aria-haspopup="true" data-event-name="ui.dropdown-vector-page-titlebar-toc" class="vector-dropdown-checkbox " aria-label="Toggle the table of contents" > <label id="vector-page-titlebar-toc-label" for="vector-page-titlebar-toc-checkbox" class="vector-dropdown-label cdx-button cdx-button--fake-button cdx-button--fake-button--enabled cdx-button--weight-quiet cdx-button--icon-only " aria-hidden="true" ><span class="vector-icon mw-ui-icon-listBullet mw-ui-icon-wikimedia-listBullet"></span> <span class="vector-dropdown-label-text">Toggle the table of contents</span> </label> <div class="vector-dropdown-content"> <div id="vector-page-titlebar-toc-unpinned-container" class="vector-unpinned-container"> </div> </div> </div> </nav> <h1 id="firstHeading" class="firstHeading mw-first-heading"><span class="mw-page-title-main">16S ribosomal RNA</span></h1> <div id="p-lang-btn" class="vector-dropdown mw-portlet mw-portlet-lang" > <input type="checkbox" id="p-lang-btn-checkbox" role="button" aria-haspopup="true" data-event-name="ui.dropdown-p-lang-btn" class="vector-dropdown-checkbox mw-interlanguage-selector" aria-label="Go to an article in another language. Available in 19 languages" > <label id="p-lang-btn-label" for="p-lang-btn-checkbox" class="vector-dropdown-label cdx-button cdx-button--fake-button cdx-button--fake-button--enabled cdx-button--weight-quiet cdx-button--action-progressive mw-portlet-lang-heading-19" aria-hidden="true" ><span class="vector-icon mw-ui-icon-language-progressive mw-ui-icon-wikimedia-language-progressive"></span> <span class="vector-dropdown-label-text">19 languages</span> </label> <div class="vector-dropdown-content"> <div class="vector-menu-content"> <ul class="vector-menu-content-list"> <li class="interlanguage-link interwiki-ca mw-list-item"><a href="https://ca.wikipedia.org/wiki/ARN_ribos%C3%B2mic_16S" title="ARN ribosòmic 16S – Catalan" lang="ca" hreflang="ca" data-title="ARN ribosòmic 16S" data-language-autonym="Català" data-language-local-name="Catalan" class="interlanguage-link-target"><span>Català</span></a></li><li class="interlanguage-link interwiki-cs mw-list-item"><a href="https://cs.wikipedia.org/wiki/16S_rRNA" title="16S rRNA – Czech" lang="cs" hreflang="cs" data-title="16S rRNA" data-language-autonym="Čeština" data-language-local-name="Czech" class="interlanguage-link-target"><span>Čeština</span></a></li><li class="interlanguage-link interwiki-es mw-list-item"><a href="https://es.wikipedia.org/wiki/ARN_ribosomal_16S" title="ARN ribosomal 16S – Spanish" lang="es" hreflang="es" data-title="ARN ribosomal 16S" data-language-autonym="Español" data-language-local-name="Spanish" class="interlanguage-link-target"><span>Español</span></a></li><li class="interlanguage-link interwiki-fa mw-list-item"><a href="https://fa.wikipedia.org/wiki/%D8%A2%D8%B1%D8%A7%D9%86%E2%80%8C%D8%A7%DB%8C_%D8%B1%DB%8C%D8%A8%D9%88%D8%B2%D9%88%D9%85%DB%8C_%DB%B1%DB%B6%D8%A7%D8%B3" title="آران‌ای ریبوزومی ۱۶اس – Persian" lang="fa" hreflang="fa" data-title="آران‌ای ریبوزومی ۱۶اس" data-language-autonym="فارسی" data-language-local-name="Persian" class="interlanguage-link-target"><span>فارسی</span></a></li><li class="interlanguage-link interwiki-fr mw-list-item"><a href="https://fr.wikipedia.org/wiki/ARN_ribosomique_16S" title="ARN ribosomique 16S – French" lang="fr" hreflang="fr" data-title="ARN ribosomique 16S" data-language-autonym="Français" data-language-local-name="French" class="interlanguage-link-target"><span>Français</span></a></li><li class="interlanguage-link interwiki-gl mw-list-item"><a href="https://gl.wikipedia.org/wiki/ARNr_16S" title="ARNr 16S – Galician" lang="gl" hreflang="gl" data-title="ARNr 16S" data-language-autonym="Galego" data-language-local-name="Galician" class="interlanguage-link-target"><span>Galego</span></a></li><li class="interlanguage-link interwiki-ko mw-list-item"><a href="https://ko.wikipedia.org/wiki/16S_%EB%A6%AC%EB%B3%B4%EC%86%9C_RNA" title="16S 리보솜 RNA – Korean" lang="ko" hreflang="ko" data-title="16S 리보솜 RNA" data-language-autonym="한국어" data-language-local-name="Korean" class="interlanguage-link-target"><span>한국어</span></a></li><li class="interlanguage-link interwiki-id mw-list-item"><a href="https://id.wikipedia.org/wiki/RNA_ribosomal_16S" title="RNA ribosomal 16S – Indonesian" lang="id" hreflang="id" data-title="RNA ribosomal 16S" data-language-autonym="Bahasa Indonesia" data-language-local-name="Indonesian" class="interlanguage-link-target"><span>Bahasa Indonesia</span></a></li><li class="interlanguage-link interwiki-it mw-list-item"><a href="https://it.wikipedia.org/wiki/RNA_ribosomale_16S" title="RNA ribosomale 16S – Italian" lang="it" hreflang="it" data-title="RNA ribosomale 16S" data-language-autonym="Italiano" data-language-local-name="Italian" class="interlanguage-link-target"><span>Italiano</span></a></li><li class="interlanguage-link interwiki-ka mw-list-item"><a href="https://ka.wikipedia.org/wiki/16S_%E1%83%A0-%E1%83%A0%E1%83%9C%E1%83%9B" title="16S რ-რნმ – Georgian" lang="ka" hreflang="ka" data-title="16S რ-რნმ" data-language-autonym="ქართული" data-language-local-name="Georgian" class="interlanguage-link-target"><span>ქართული</span></a></li><li class="interlanguage-link interwiki-hu mw-list-item"><a href="https://hu.wikipedia.org/wiki/16S_riboszom%C3%A1lis_RNS" title="16S riboszomális RNS – Hungarian" lang="hu" hreflang="hu" data-title="16S riboszomális RNS" data-language-autonym="Magyar" data-language-local-name="Hungarian" class="interlanguage-link-target"><span>Magyar</span></a></li><li class="interlanguage-link interwiki-mk mw-list-item"><a href="https://mk.wikipedia.org/wiki/16S_%D1%80%D0%B8%D0%B1%D0%BE%D0%B7%D0%BE%D0%BC%D0%BD%D0%B0_%D0%A0%D0%9D%D0%9A" title="16S рибозомна РНК – Macedonian" lang="mk" hreflang="mk" data-title="16S рибозомна РНК" data-language-autonym="Македонски" data-language-local-name="Macedonian" class="interlanguage-link-target"><span>Македонски</span></a></li><li class="interlanguage-link interwiki-ja mw-list-item"><a href="https://ja.wikipedia.org/wiki/16S%E3%83%AA%E3%83%9C%E3%82%BD%E3%83%BC%E3%83%A0RNA" title="16SリボソームRNA – Japanese" lang="ja" hreflang="ja" data-title="16SリボソームRNA" data-language-autonym="日本語" data-language-local-name="Japanese" class="interlanguage-link-target"><span>日本語</span></a></li><li class="interlanguage-link interwiki-uz mw-list-item"><a href="https://uz.wikipedia.org/wiki/16S_rRNK" title="16S rRNK – Uzbek" lang="uz" hreflang="uz" data-title="16S rRNK" data-language-autonym="Oʻzbekcha / ўзбекча" data-language-local-name="Uzbek" class="interlanguage-link-target"><span>Oʻzbekcha / ўзбекча</span></a></li><li class="interlanguage-link interwiki-pt mw-list-item"><a href="https://pt.wikipedia.org/wiki/ARN_ribossomal_16S" title="ARN ribossomal 16S – Portuguese" lang="pt" hreflang="pt" data-title="ARN ribossomal 16S" data-language-autonym="Português" data-language-local-name="Portuguese" class="interlanguage-link-target"><span>Português</span></a></li><li class="interlanguage-link interwiki-ro mw-list-item"><a href="https://ro.wikipedia.org/wiki/ARN_ribozomal_16s" title="ARN ribozomal 16s – Romanian" lang="ro" hreflang="ro" data-title="ARN ribozomal 16s" data-language-autonym="Română" data-language-local-name="Romanian" class="interlanguage-link-target"><span>Română</span></a></li><li class="interlanguage-link interwiki-ru badge-Q17559452 badge-recommendedarticle mw-list-item" title="recommended article"><a href="https://ru.wikipedia.org/wiki/16S_%D1%80%D0%A0%D0%9D%D0%9A" title="16S рРНК – Russian" lang="ru" hreflang="ru" data-title="16S рРНК" data-language-autonym="Русский" data-language-local-name="Russian" class="interlanguage-link-target"><span>Русский</span></a></li><li class="interlanguage-link interwiki-uk mw-list-item"><a href="https://uk.wikipedia.org/wiki/16S_%D1%80%D0%A0%D0%9D%D0%9A" title="16S рРНК – Ukrainian" lang="uk" hreflang="uk" data-title="16S рРНК" data-language-autonym="Українська" data-language-local-name="Ukrainian" class="interlanguage-link-target"><span>Українська</span></a></li><li class="interlanguage-link interwiki-zh mw-list-item"><a href="https://zh.wikipedia.org/wiki/16S_%E6%A0%B8%E7%B3%96%E4%BD%93RNA" title="16S 核糖体RNA – Chinese" lang="zh" hreflang="zh" data-title="16S 核糖体RNA" data-language-autonym="中文" data-language-local-name="Chinese" class="interlanguage-link-target"><span>中文</span></a></li> </ul> <div class="after-portlet after-portlet-lang"><span class="wb-langlinks-edit wb-langlinks-link"><a href="https://www.wikidata.org/wiki/Special:EntityPage/Q1209205#sitelinks-wikipedia" title="Edit interlanguage links" class="wbc-editpage">Edit links</a></span></div> </div> </div> </div> </header> <div class="vector-page-toolbar"> <div class="vector-page-toolbar-container"> <div id="left-navigation"> <nav aria-label="Namespaces"> <div id="p-associated-pages" class="vector-menu vector-menu-tabs mw-portlet mw-portlet-associated-pages" > <div class="vector-menu-content"> <ul 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class="vector-body" aria-labelledby="firstHeading" data-mw-ve-target-container> <div class="vector-body-before-content"> <div class="mw-indicators"> </div> <div id="siteSub" class="noprint">From Wikipedia, the free encyclopedia</div> </div> <div id="contentSub"><div id="mw-content-subtitle"></div></div> <div id="mw-content-text" class="mw-body-content"><div class="mw-content-ltr mw-parser-output" lang="en" dir="ltr"><style data-mw-deduplicate="TemplateStyles:r1236090951">.mw-parser-output .hatnote{font-style:italic}.mw-parser-output div.hatnote{padding-left:1.6em;margin-bottom:0.5em}.mw-parser-output .hatnote i{font-style:normal}.mw-parser-output .hatnote+link+.hatnote{margin-top:-0.5em}@media print{body.ns-0 .mw-parser-output .hatnote{display:none!important}}</style><div role="note" class="hatnote navigation-not-searchable">For the mitochondrially encoded 16S RNA, see <a href="/wiki/MT-RNR2" title="MT-RNR2">MT-RNR2</a>.</div> <div class="shortdescription nomobile noexcerpt noprint searchaux" style="display:none">RNA component</div> <style data-mw-deduplicate="TemplateStyles:r1251242444">.mw-parser-output .ambox{border:1px solid #a2a9b1;border-left:10px solid #36c;background-color:#fbfbfb;box-sizing:border-box}.mw-parser-output .ambox+link+.ambox,.mw-parser-output .ambox+link+style+.ambox,.mw-parser-output .ambox+link+link+.ambox,.mw-parser-output .ambox+.mw-empty-elt+link+.ambox,.mw-parser-output .ambox+.mw-empty-elt+link+style+.ambox,.mw-parser-output .ambox+.mw-empty-elt+link+link+.ambox{margin-top:-1px}html body.mediawiki .mw-parser-output .ambox.mbox-small-left{margin:4px 1em 4px 0;overflow:hidden;width:238px;border-collapse:collapse;font-size:88%;line-height:1.25em}.mw-parser-output .ambox-speedy{border-left:10px solid #b32424;background-color:#fee7e6}.mw-parser-output .ambox-delete{border-left:10px solid #b32424}.mw-parser-output .ambox-content{border-left:10px solid #f28500}.mw-parser-output .ambox-style{border-left:10px solid #fc3}.mw-parser-output .ambox-move{border-left:10px solid #9932cc}.mw-parser-output .ambox-protection{border-left:10px solid #a2a9b1}.mw-parser-output .ambox .mbox-text{border:none;padding:0.25em 0.5em;width:100%}.mw-parser-output .ambox .mbox-image{border:none;padding:2px 0 2px 0.5em;text-align:center}.mw-parser-output .ambox .mbox-imageright{border:none;padding:2px 0.5em 2px 0;text-align:center}.mw-parser-output .ambox .mbox-empty-cell{border:none;padding:0;width:1px}.mw-parser-output .ambox .mbox-image-div{width:52px}@media(min-width:720px){.mw-parser-output .ambox{margin:0 10%}}@media print{body.ns-0 .mw-parser-output .ambox{display:none!important}}</style><table class="box-Missing_information plainlinks metadata ambox ambox-content" role="presentation"><tbody><tr><td class="mbox-image"><div class="mbox-image-div"><span typeof="mw:File"><a href="/wiki/File:Wiki_letter_w.svg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/en/thumb/6/6c/Wiki_letter_w.svg/44px-Wiki_letter_w.svg.png" decoding="async" width="44" height="44" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/en/thumb/6/6c/Wiki_letter_w.svg/66px-Wiki_letter_w.svg.png 1.5x, //upload.wikimedia.org/wikipedia/en/thumb/6/6c/Wiki_letter_w.svg/88px-Wiki_letter_w.svg.png 2x" data-file-width="44" data-file-height="44" /></a></span></div></td><td class="mbox-text"><div class="mbox-text-span">This article <b>is missing information</b> about Rfam SSU_rRNA_bacteria, SSU_rRNA_archaea.<span class="hide-when-compact"> Please expand the article to include this information. Further details may exist on the <a href="/wiki/Talk:16S_ribosomal_RNA" title="Talk:16S ribosomal RNA">talk page</a>.</span> <span class="date-container"><i>(<span class="date">December 2020</span>)</i></span></div></td></tr></tbody></table> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:010_small_subunit-1FKA.gif" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/9/90/010_small_subunit-1FKA.gif/220px-010_small_subunit-1FKA.gif" decoding="async" width="220" height="220" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/9/90/010_small_subunit-1FKA.gif 1.5x" data-file-width="320" data-file-height="320" /></a><figcaption>Molecular structure of the 30S Subunit from <i><a href="/wiki/Thermus_thermophilus" title="Thermus thermophilus">Thermus thermophilus</a></i>. Proteins are shown in blue and the single RNA strand in a pale orange-brown colour.<sup id="cite_ref-Schluenzen_1-0" class="reference"><a href="#cite_note-Schluenzen-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup></figcaption></figure> <p><b>16<a href="/wiki/Svedberg" title="Svedberg">S</a> ribosomal RNA</b> (or 16<a href="/wiki/Svedberg" title="Svedberg">S</a> <a href="/wiki/RRNA" class="mw-redirect" title="RRNA">rRNA</a>) is the RNA component of the <a href="/wiki/30S" class="mw-redirect" title="30S">30S</a> subunit of a <a href="/wiki/Prokaryotic" class="mw-redirect" title="Prokaryotic">prokaryotic</a> <a href="/wiki/Ribosome" title="Ribosome">ribosome</a> (<a href="/wiki/SSU_rRNA" title="SSU rRNA">SSU rRNA</a>). It binds to the <a href="/wiki/Shine-Dalgarno_sequence" class="mw-redirect" title="Shine-Dalgarno sequence">Shine-Dalgarno sequence</a> and provides most of the SSU structure. </p><p>The genes coding for it are referred to as <b>16S rRNA genes</b> and are used in reconstructing <a href="/wiki/Phylogenetics" title="Phylogenetics">phylogenies</a>, due to the slow rates of <a href="/wiki/Evolution" title="Evolution">evolution</a> of this region of the gene.<sup id="cite_ref-woese1977_2-0" class="reference"><a href="#cite_note-woese1977-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> <a href="/wiki/Carl_Woese" title="Carl Woese">Carl Woese</a> and <a href="/wiki/George_E._Fox" title="George E. Fox">George E. Fox</a> were two of the people who pioneered the use of 16S rRNA in phylogenetics in 1977.<sup id="cite_ref-Woese_1990_3-0" class="reference"><a href="#cite_note-Woese_1990-3"><span class="cite-bracket">[</span>3<span class="cite-bracket">]</span></a></sup> Multiple sequences of the 16S rRNA gene can exist within a single <a href="/wiki/Bacterium" class="mw-redirect" title="Bacterium">bacterium</a>.<sup id="cite_ref-pmid17071787_4-0" class="reference"><a href="#cite_note-pmid17071787-4"><span class="cite-bracket">[</span>4<span class="cite-bracket">]</span></a></sup> </p> <meta property="mw:PageProp/toc" /> <div class="mw-heading mw-heading2"><h2 id="Functions">Functions</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=16S_ribosomal_RNA&action=edit&section=1" title="Edit section: Functions"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <ul><li>Like the <a href="/wiki/23S_ribosomal_RNA" title="23S ribosomal RNA">large (23S) ribosomal RNA</a>, it has a structural role, acting as a scaffold defining the positions of the <a href="/wiki/Ribosomal_protein" title="Ribosomal protein">ribosomal proteins</a>.</li> <li>The <a href="/wiki/Directionality_(molecular_biology)" title="Directionality (molecular biology)">3<span class="nowrap" style="padding-left:0.15em;">′</span>-end</a> contains the anti-<a href="/wiki/Shine-Dalgarno_sequence" class="mw-redirect" title="Shine-Dalgarno sequence">Shine-Dalgarno sequence</a>, which binds upstream to the AUG <a href="/wiki/Start_codon" title="Start codon">start codon</a> on the <a href="/wiki/MRNA" class="mw-redirect" title="MRNA">mRNA</a>. The 3<span class="nowrap" style="padding-left:0.15em;">′</span>-end of 16S RNA binds to the proteins S1 and S21 which are known to be involved in initiation of <a href="/wiki/Protein_synthesis" class="mw-redirect" title="Protein synthesis">protein synthesis</a><sup id="cite_ref-5" class="reference"><a href="#cite_note-5"><span class="cite-bracket">[</span>5<span class="cite-bracket">]</span></a></sup></li> <li>Interacts with 23S, aiding in the binding of the two ribosomal subunits (<a href="/wiki/50S" class="mw-redirect" title="50S">50S</a> and <a href="/wiki/30S" class="mw-redirect" title="30S">30S</a>)</li> <li>Stabilizes correct codon-anticodon pairing in the <a href="/wiki/A-site" title="A-site">A-site</a> by forming a <a href="/wiki/Hydrogen_bond" title="Hydrogen bond">hydrogen bond</a> between the N1 atom of <a href="/wiki/Adenine" title="Adenine">adenine</a> residues 1492 and 1493 and the 2<span class="nowrap" style="padding-left:0.15em;">′</span>OH group of the mRNA backbone.</li></ul> <div class="mw-heading mw-heading2"><h2 id="Structure">Structure</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=16S_ribosomal_RNA&action=edit&section=2" title="Edit section: Structure"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <figure class="mw-halign-center" typeof="mw:File/Thumb"><a href="/wiki/File:16S.svg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/a/a6/16S.svg/600px-16S.svg.png" decoding="async" width="600" height="626" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/a/a6/16S.svg/900px-16S.svg.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/a/a6/16S.svg/1200px-16S.svg.png 2x" data-file-width="819" data-file-height="855" /></a><figcaption>SSU Ribosomal RNA, bacteria and archaea. From Woese 1987.<sup id="cite_ref-6" class="reference"><a href="#cite_note-6"><span class="cite-bracket">[</span>6<span class="cite-bracket">]</span></a></sup></figcaption></figure> <div class="mw-heading mw-heading2"><h2 id="Universal_primers">Universal primers</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=16S_ribosomal_RNA&action=edit&section=3" title="Edit section: Universal primers"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The 16S rRNA gene is used for <a href="/wiki/Phylogenetics" title="Phylogenetics">phylogenetic</a> studies<sup id="cite_ref-Weisburg_7-0" class="reference"><a href="#cite_note-Weisburg-7"><span class="cite-bracket">[</span>7<span class="cite-bracket">]</span></a></sup> as it is highly conserved between different species of bacteria and archaea.<sup id="cite_ref-pmid14612235_8-0" class="reference"><a href="#cite_note-pmid14612235-8"><span class="cite-bracket">[</span>8<span class="cite-bracket">]</span></a></sup> <a href="/wiki/Carl_Woese" title="Carl Woese">Carl Woese</a> pioneered this use of 16S rRNA in 1977.<sup id="cite_ref-woese1977_2-1" class="reference"><a href="#cite_note-woese1977-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> It is suggested that 16S rRNA gene can be used as a reliable <a href="/wiki/Molecular_clock" title="Molecular clock">molecular clock</a> because 16S rRNA sequences from distantly related bacterial lineages are shown to have similar functionalities.<sup id="cite_ref-9" class="reference"><a href="#cite_note-9"><span class="cite-bracket">[</span>9<span class="cite-bracket">]</span></a></sup> Some <a href="/wiki/Thermophile" title="Thermophile">thermophilic</a> <a href="/wiki/Archaea" title="Archaea">archaea</a> (e.g. order <a href="/wiki/Thermoproteales" title="Thermoproteales">Thermoproteales</a>) contain 16S rRNA gene <a href="/wiki/Intron" title="Intron">introns</a> that are located in highly conserved regions and can impact the <a href="/wiki/Annealing_(biology)" class="mw-redirect" title="Annealing (biology)">annealing</a> of "universal" <a href="/wiki/Primer_(molecular_biology)" title="Primer (molecular biology)">primers</a>.<sup id="cite_ref-Jay_10-0" class="reference"><a href="#cite_note-Jay-10"><span class="cite-bracket">[</span>10<span class="cite-bracket">]</span></a></sup> Mitochondrial and <a href="/wiki/Chloroplast" title="Chloroplast">chloroplastic</a> rRNA are also amplified.<sup id="cite_ref-11" class="reference"><a href="#cite_note-11"><span class="cite-bracket">[</span>11<span class="cite-bracket">]</span></a></sup> </p><p>The most common primer pair was devised by Weisburg <i>et al.</i> (1991)<sup id="cite_ref-Weisburg_7-1" class="reference"><a href="#cite_note-Weisburg-7"><span class="cite-bracket">[</span>7<span class="cite-bracket">]</span></a></sup> and is currently referred to as 27F and 1492R; however, for some applications shorter <a href="/wiki/Amplicon" title="Amplicon">amplicons</a> may be necessary, for example for 454 sequencing with titanium chemistry the primer pair 27F-534R covering V1 to V3.<sup id="cite_ref-12" class="reference"><a href="#cite_note-12"><span class="cite-bracket">[</span>12<span class="cite-bracket">]</span></a></sup> Often 8F is used rather than 27F. The two primers are almost identical, but 27F has an M instead of a C. AGAGTTTGATC<b>M</b>TGGCTCAG compared with 8F.<sup id="cite_ref-:5_13-0" class="reference"><a href="#cite_note-:5-13"><span class="cite-bracket">[</span>13<span class="cite-bracket">]</span></a></sup> </p> <table class="wikitable"> <tbody><tr> <th>Primer name</th> <th>Sequence (5<span class="nowrap" style="padding-left:0.15em;">′</span>–3<span class="nowrap" style="padding-left:0.15em;">′</span>)</th> <th><abbr title="Reference">Ref.</abbr> </th></tr> <tr> <td>8F</td> <td>AGA GTT TGA TCC TGG CTC AG</td> <td><sup id="cite_ref-Eden_14-0" class="reference"><a href="#cite_note-Eden-14"><span class="cite-bracket">[</span>14<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-James_G_15-0" class="reference"><a href="#cite_note-James_G-15"><span class="cite-bracket">[</span>15<span class="cite-bracket">]</span></a></sup> </td></tr> <tr> <td>27F </td> <td>AGA GTT TGA TC<b>M</b> TGG CTC AG </td> <td><sup id="cite_ref-:5_13-1" class="reference"><a href="#cite_note-:5-13"><span class="cite-bracket">[</span>13<span class="cite-bracket">]</span></a></sup> </td></tr> <tr> <td>336R</td> <td>ACT GCT GCS YCC CGT AGG AGT CT</td> <td><sup id="cite_ref-Weirdner_16-0" class="reference"><a href="#cite_note-Weirdner-16"><span class="cite-bracket">[</span>16<span class="cite-bracket">]</span></a></sup> </td></tr> <tr> <td>337F</td> <td>GAC TCC TAC GGG AGG CWG CAG</td> <td><sup id="cite_ref-17" class="reference"><a href="#cite_note-17"><span class="cite-bracket">[</span>17<span class="cite-bracket">]</span></a></sup> </td></tr> <tr> <td>518R</td> <td>GTA TTA CCG CGG CTG CTG G</td> <td> </td></tr> <tr> <td>533F</td> <td>GTG CCA GCM GCC GCG GTA A</td> <td> </td></tr> <tr> <td>785F</td> <td>GGA TTA GAT ACC CTG GTA</td> <td> </td></tr> <tr> <td>806R</td> <td>GGA CTA CVS GGG TAT CTA AT</td> <td><sup id="cite_ref-18" class="reference"><a href="#cite_note-18"><span class="cite-bracket">[</span>18<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-19" class="reference"><a href="#cite_note-19"><span class="cite-bracket">[</span>19<span class="cite-bracket">]</span></a></sup> </td></tr> <tr> <td>907R</td> <td>CCG TCA ATT CCT TTR AGT TT</td> <td> </td></tr> <tr> <td>928F</td> <td>TAA AAC TYA AAK GAA TTG ACG GG</td> <td><sup id="cite_ref-Weirdner_16-1" class="reference"><a href="#cite_note-Weirdner-16"><span class="cite-bracket">[</span>16<span class="cite-bracket">]</span></a></sup> </td></tr> <tr> <td>1100F</td> <td>YAA CGA GCG CAA CCC</td> <td> </td></tr> <tr> <td>1100R</td> <td>GGG TTG CGC TCG TTG</td> <td> </td></tr> <tr> <td>U1492R</td> <td>GGT TAC CTT GTT ACG ACT T</td> <td><sup id="cite_ref-Eden_14-1" class="reference"><a href="#cite_note-Eden-14"><span class="cite-bracket">[</span>14<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-James_G_15-1" class="reference"><a href="#cite_note-James_G-15"><span class="cite-bracket">[</span>15<span class="cite-bracket">]</span></a></sup> </td></tr> <tr> <td>1492R</td> <td>CGG TTA CCT TGT TAC GAC TT</td> <td><sup id="cite_ref-HC_Jiang_20-0" class="reference"><a href="#cite_note-HC_Jiang-20"><span class="cite-bracket">[</span>20<span class="cite-bracket">]</span></a></sup> </td></tr></tbody></table> <div class="mw-heading mw-heading3"><h3 id="PCR_and_NGS_applications">PCR and NGS applications</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=16S_ribosomal_RNA&action=edit&section=4" title="Edit section: PCR and NGS applications"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>In addition to highly conserved primer binding sites, 16S rRNA gene sequences contain <a href="/wiki/Hypervariable_region" title="Hypervariable region">hypervariable regions</a> that can provide species-specific signature sequences useful for identification of bacteria.<sup id="cite_ref-21" class="reference"><a href="#cite_note-21"><span class="cite-bracket">[</span>21<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-22" class="reference"><a href="#cite_note-22"><span class="cite-bracket">[</span>22<span class="cite-bracket">]</span></a></sup> As a result, 16S rRNA gene sequencing has become prevalent in <a href="/wiki/Medical_microbiology" title="Medical microbiology">medical microbiology</a> as a rapid and cheap alternative to <a href="/wiki/Phenotype" title="Phenotype">phenotypic</a> methods of bacterial identification.<sup id="cite_ref-23" class="reference"><a href="#cite_note-23"><span class="cite-bracket">[</span>23<span class="cite-bracket">]</span></a></sup> Although it was originally used to identify bacteria, 16S sequencing was subsequently found to be capable of reclassifying bacteria into completely new <a href="/wiki/Species" title="Species">species</a>,<sup id="cite_ref-24" class="reference"><a href="#cite_note-24"><span class="cite-bracket">[</span>24<span class="cite-bracket">]</span></a></sup> or even <a href="/wiki/Genus" title="Genus">genera</a>.<sup id="cite_ref-Weisburg_7-2" class="reference"><a href="#cite_note-Weisburg-7"><span class="cite-bracket">[</span>7<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-25" class="reference"><a href="#cite_note-25"><span class="cite-bracket">[</span>25<span class="cite-bracket">]</span></a></sup> It has also been used to describe new species that have never been successfully cultured.<sup id="cite_ref-26" class="reference"><a href="#cite_note-26"><span class="cite-bracket">[</span>26<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-27" class="reference"><a href="#cite_note-27"><span class="cite-bracket">[</span>27<span class="cite-bracket">]</span></a></sup> With <a href="/wiki/Third-generation_sequencing" title="Third-generation sequencing">third-generation sequencing</a> coming to many labs, simultaneous identification of thousands of 16S rRNA sequences is possible within hours, allowing <a href="/wiki/Third-generation_sequencing#Metagenomics" title="Third-generation sequencing">metagenomic</a> studies, for example of <a href="/wiki/Gut_flora" class="mw-redirect" title="Gut flora">gut flora</a>.<sup id="cite_ref-pmid25226019_28-0" class="reference"><a href="#cite_note-pmid25226019-28"><span class="cite-bracket">[</span>28<span class="cite-bracket">]</span></a></sup> In samples collected from patients with confirmed infections, 16S rRNA next-generation sequencing (NGS) demonstrated enhanced detection in 40% of cases compared to traditional culture methods; moreover, pre-sampling antibiotic consumption did not significantly affect the sensitivity of 16S NGS.<sup id="cite_ref-29" class="reference"><a href="#cite_note-29"><span class="cite-bracket">[</span>29<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Hypervariable_regions">Hypervariable regions</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=16S_ribosomal_RNA&action=edit&section=5" title="Edit section: Hypervariable regions"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The bacterial 16S gene contains nine hypervariable regions (V1–V9), ranging from about 30 to 100 <a href="/wiki/Base_pair" title="Base pair">base pairs</a> long, that are involved in the secondary structure of the <a href="/wiki/30S" class="mw-redirect" title="30S">small ribosomal subunit</a>.<sup id="cite_ref-pmid6462918_30-0" class="reference"><a href="#cite_note-pmid6462918-30"><span class="cite-bracket">[</span>30<span class="cite-bracket">]</span></a></sup> The degree of conservation varies widely between hypervariable regions, with more conserved regions correlating to higher-level taxonomy and less conserved regions to lower levels, such as genus and species.<sup id="cite_ref-:0_31-0" class="reference"><a href="#cite_note-:0-31"><span class="cite-bracket">[</span>31<span class="cite-bracket">]</span></a></sup> While the entire 16S sequence allows for comparison of all hypervariable regions, at approximately 1,500 base pairs long it can be prohibitively expensive for studies seeking to identify or characterize diverse bacterial communities.<sup id="cite_ref-:0_31-1" class="reference"><a href="#cite_note-:0-31"><span class="cite-bracket">[</span>31<span class="cite-bracket">]</span></a></sup> These studies commonly utilize the <a href="/wiki/Illumina_dye_sequencing" title="Illumina dye sequencing">Illumina platform</a>, which produces reads at rates 50-fold and 12,000-fold less expensive than 454 <a href="/wiki/Pyrosequencing" title="Pyrosequencing">pyrosequencing</a> and <a href="/wiki/Sanger_sequencing" title="Sanger sequencing">Sanger sequencing</a>, respectively.<sup id="cite_ref-32" class="reference"><a href="#cite_note-32"><span class="cite-bracket">[</span>32<span class="cite-bracket">]</span></a></sup> While cheaper and allowing for deeper community coverage, Illumina sequencing only produces reads 75–250 base pairs long (up to 300 base pairs with Illumina MiSeq), and has no established protocol for reliably assembling the full gene in community samples.<sup id="cite_ref-:1_33-0" class="reference"><a href="#cite_note-:1-33"><span class="cite-bracket">[</span>33<span class="cite-bracket">]</span></a></sup> Full hypervariable regions can be assembled from a single Illumina run, however, making them ideal targets for the platform.<sup id="cite_ref-:1_33-1" class="reference"><a href="#cite_note-:1-33"><span class="cite-bracket">[</span>33<span class="cite-bracket">]</span></a></sup> </p><p>While 16S hypervariable regions can vary dramatically between bacteria, the 16S gene as a whole maintains greater length homogeneity than its eukaryotic counterpart (<a href="/wiki/18S_ribosomal_RNA" title="18S ribosomal RNA">18S ribosomal RNA</a>), which can make <a href="/wiki/Sequence_alignment" title="Sequence alignment">alignments</a> easier.<sup id="cite_ref-pmid8811093_34-0" class="reference"><a href="#cite_note-pmid8811093-34"><span class="cite-bracket">[</span>34<span class="cite-bracket">]</span></a></sup> Additionally, the 16S gene contains highly conserved sequences between hypervariable regions, enabling the design of universal primers that can reliably produce the same sections of the 16S sequence across different <a href="/wiki/Taxon" title="Taxon">taxa</a>.<sup id="cite_ref-:2_35-0" class="reference"><a href="#cite_note-:2-35"><span class="cite-bracket">[</span>35<span class="cite-bracket">]</span></a></sup> Although no hypervariable region can accurately classify all bacteria from <a href="/wiki/Domain_(biology)" title="Domain (biology)">domain</a> to species, some can reliably predict specific taxonomic levels.<sup id="cite_ref-:0_31-2" class="reference"><a href="#cite_note-:0-31"><span class="cite-bracket">[</span>31<span class="cite-bracket">]</span></a></sup> Many community studies select semi-conserved hypervariable regions like the V4 for this reason, as it can provide resolution at the phylum level as accurately as the full 16S gene.<sup id="cite_ref-:0_31-3" class="reference"><a href="#cite_note-:0-31"><span class="cite-bracket">[</span>31<span class="cite-bracket">]</span></a></sup> While lesser-conserved regions struggle to classify new species when higher order taxonomy is unknown, they are often used to detect the presence of specific pathogens. In one study by Chakravorty et al. in 2007, the authors characterized the V1–V8 regions of a variety of pathogens in order to determine which hypervariable regions would be most useful to include for disease-specific and broad <a href="/wiki/Assay" title="Assay">assays</a>.<sup id="cite_ref-:3_36-0" class="reference"><a href="#cite_note-:3-36"><span class="cite-bracket">[</span>36<span class="cite-bracket">]</span></a></sup> Amongst other findings, they noted that the V3 region was best at identifying the genus for all pathogens tested, and that V6 was the most accurate at differentiating species between all <a href="/wiki/Notifiable_diseases_in_USA" class="mw-redirect" title="Notifiable diseases in USA">CDC-watched pathogens</a> tested, including <a href="/wiki/Anthrax" title="Anthrax">anthrax</a>.<sup id="cite_ref-:3_36-1" class="reference"><a href="#cite_note-:3-36"><span class="cite-bracket">[</span>36<span class="cite-bracket">]</span></a></sup> </p><p>While 16S hypervariable region analysis is a powerful tool for bacterial taxonomic studies, it struggles to differentiate between closely related species.<sup id="cite_ref-:2_35-1" class="reference"><a href="#cite_note-:2-35"><span class="cite-bracket">[</span>35<span class="cite-bracket">]</span></a></sup> In the families <i><a href="/wiki/Enterobacteriaceae" title="Enterobacteriaceae">Enterobacteriaceae</a></i>, <i><a href="/wiki/Clostridiaceae" title="Clostridiaceae">Clostridiaceae</a></i>, and <i><a href="/wiki/Peptostreptococcaceae" title="Peptostreptococcaceae">Peptostreptococcaceae</a></i>, species can share up to 99% sequence similarity across the full 16S gene.<sup id="cite_ref-:4_37-0" class="reference"><a href="#cite_note-:4-37"><span class="cite-bracket">[</span>37<span class="cite-bracket">]</span></a></sup> As a result, the V4 sequences can differ by only a few <a href="/wiki/Nucleotide" title="Nucleotide">nucleotides</a>, leaving reference databases unable to reliably classify these bacteria at lower taxonomic levels.<sup id="cite_ref-:4_37-1" class="reference"><a href="#cite_note-:4-37"><span class="cite-bracket">[</span>37<span class="cite-bracket">]</span></a></sup> By limiting 16S analysis to select hypervariable regions, these studies can fail to observe differences in closely related taxa and group them into single taxonomic units, therefore underestimating the total diversity of the sample.<sup id="cite_ref-:2_35-2" class="reference"><a href="#cite_note-:2-35"><span class="cite-bracket">[</span>35<span class="cite-bracket">]</span></a></sup> Furthermore, bacterial genomes can house multiple 16S genes, with the V1, V2, and V6 regions containing the greatest intraspecies diversity.<sup id="cite_ref-pmid14612235_8-1" class="reference"><a href="#cite_note-pmid14612235-8"><span class="cite-bracket">[</span>8<span class="cite-bracket">]</span></a></sup> While not the most precise method of classifying bacterial species, analysis of the hypervariable regions remains one of the most useful tools available to bacterial community studies.<sup id="cite_ref-:4_37-2" class="reference"><a href="#cite_note-:4-37"><span class="cite-bracket">[</span>37<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading2"><h2 id="Promiscuity_of_16S_rRNA_genes">Promiscuity of 16S rRNA genes</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=16S_ribosomal_RNA&action=edit&section=6" title="Edit section: Promiscuity of 16S rRNA genes"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>Under the assumption that evolution is driven by <a href="/wiki/Vertical_transmission" title="Vertical transmission">vertical transmission</a>, 16S rRNA genes have long been believed to be species-specific, and infallible as genetic markers inferring phylogenetic relationships among <a href="/wiki/Prokaryotes" class="mw-redirect" title="Prokaryotes">prokaryotes</a>. However, a growing number of observations suggest the occurrence of <a href="/wiki/Horizontal_transfer" class="mw-redirect" title="Horizontal transfer">horizontal transfer</a> of these genes. In addition to observations of natural occurrence, transferability of these genes is supported experimentally using a specialized <i><a href="/wiki/Escherichia_coli" title="Escherichia coli">Escherichia coli</a></i> genetic system. Using a <a href="/wiki/Null_mutant" class="mw-redirect" title="Null mutant">null mutant</a> of <i>E. coli</i> as host, growth of the mutant strain was shown to be complemented by foreign 16S rRNA genes that were phylogenetically distinct from <i>E. coli</i> at the phylum level.<sup id="cite_ref-38" class="reference"><a href="#cite_note-38"><span class="cite-bracket">[</span>38<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-39" class="reference"><a href="#cite_note-39"><span class="cite-bracket">[</span>39<span class="cite-bracket">]</span></a></sup> Such functional compatibility was also seen in <i><a href="/wiki/Thermus_thermophilus" title="Thermus thermophilus">Thermus thermophilus</a></i>.<sup id="cite_ref-40" class="reference"><a href="#cite_note-40"><span class="cite-bracket">[</span>40<span class="cite-bracket">]</span></a></sup> Furthermore, in <i>T. thermophilus</i>, both complete and partial gene transfer was observed. Partial transfer resulted in spontaneous generation of apparently random <a href="/wiki/Chimera_(genetics)" title="Chimera (genetics)">chimera</a> between host and foreign bacterial genes. Thus, 16S rRNA genes may have evolved through multiple mechanisms, including vertical inheritance and <a href="/wiki/Horizontal_gene_transfer" title="Horizontal gene transfer">horizontal gene transfer</a>; the frequency of the latter may be much higher than previously thought.<sup id="cite_ref-41" class="reference"><a href="#cite_note-41"><span class="cite-bracket">[</span>41<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading2"><h2 id="16S_ribosomal_databases">16S ribosomal databases</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=16S_ribosomal_RNA&action=edit&section=7" title="Edit section: 16S ribosomal databases"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The 16S rRNA gene is used as the standard for classification and identification of microbes, because it is present in most microbes and shows proper changes.<sup id="cite_ref-pmid25118885_42-0" class="reference"><a href="#cite_note-pmid25118885-42"><span class="cite-bracket">[</span>42<span class="cite-bracket">]</span></a></sup> Type strains of 16S rRNA gene sequences for most bacteria and archaea are available on public databases, such as <a href="/wiki/National_Center_for_Biotechnology_Information" title="National Center for Biotechnology Information">NCBI</a>. However, the quality of the sequences found on these databases is often not validated. Therefore, secondary databases that collect only 16S rRNA sequences are widely used. </p> <div class="mw-heading mw-heading3"><h3 id="MIMt">MIMt</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=16S_ribosomal_RNA&action=edit&section=8" title="Edit section: MIMt"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>MIMt is a compact non-redundant 16S database for a rapid metagenomic samples identification. It is composed of 39.940 full 16S sequences belonging to 17,625 well classified bacteria and archaea species. All sequences were obtained from complete genomes deposited in NCBI and for each of the sequences full taxonomic hierarchy is provided. It contains no redundancy, so only one representative for each species was considered avoiding same sequences from differente strains, isolates or patovars resulting in a very fast tool for microorganisms identification, compatible with any classification software (QIIME, Mothur, DADA, etc).<sup id="cite_ref-43" class="reference"><a href="#cite_note-43"><span class="cite-bracket">[</span>43<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="EzBioCloud">EzBioCloud</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=16S_ribosomal_RNA&action=edit&section=9" title="Edit section: EzBioCloud"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>EzBioCloud database, formerly known as <a href="/wiki/EzTaxon_Database" title="EzTaxon Database">EzTaxon</a>, consists of a complete hierarchical taxonomic system containing 62,988 bacteria and archaea species/phylotypes which includes 15,290 valid published names as of September 2018. Based on the phylogenetic relationship such as maximum-likelihood and OrthoANI, all species/subspecies are represented by at least one 16S rRNA gene sequence. The EzBioCloud database is systematically curated and updated regularly which also includes novel candidate species. Moreover, the website provides bioinformatics tools such as ANI calculator, ContEst16S and 16S rRNA DB for QIIME and Mothur pipeline.<sup id="cite_ref-44" class="reference"><a href="#cite_note-44"><span class="cite-bracket">[</span>44<span class="cite-bracket">]</span></a></sup>^^ </p> <div class="mw-heading mw-heading3"><h3 id="Ribosomal_Database_Project">Ribosomal Database Project</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=16S_ribosomal_RNA&action=edit&section=10" title="Edit section: Ribosomal Database Project"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The Ribosomal Database Project (RDP) is a curated database that offers ribosome data along with related programs and services. The offerings include phylogenetically ordered alignments of ribosomal RNA (rRNA) sequences, derived phylogenetic trees, rRNA secondary structure diagrams and various software packages for handling, analyzing and displaying alignments and trees. The data are available via ftp and electronic mail. Certain analytic services are also provided by the electronic mail server.<sup id="cite_ref-45" class="reference"><a href="#cite_note-45"><span class="cite-bracket">[</span>45<span class="cite-bracket">]</span></a></sup> Due to its large size the RDP database is often used as the basis for bioinformatic tool development and creating manually curated databases.<sup id="cite_ref-46" class="reference"><a href="#cite_note-46"><span class="cite-bracket">[</span>46<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="SILVA">SILVA</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=16S_ribosomal_RNA&action=edit&section=11" title="Edit section: SILVA"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p><a href="/wiki/SILVA_ribosomal_RNA_database" title="SILVA ribosomal RNA database">SILVA</a> provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/<a href="/wiki/18S_ribosomal_RNA" title="18S ribosomal RNA">18S</a>, <a href="/wiki/Small_subunit" class="mw-redirect" title="Small subunit">SSU</a>) and large subunit (<a href="/wiki/23S_ribosomal_RNA" title="23S ribosomal RNA">23S</a>/<a href="/wiki/28S_ribosomal_RNA" title="28S ribosomal RNA">28S</a>, <a href="/wiki/Large_subunit" class="mw-redirect" title="Large subunit">LSU</a>) ribosomal RNA (rRNA) sequences for all three domains of life as well as a suite of search, primer-design and alignment tools (Bacteria, Archaea and Eukarya).<sup id="cite_ref-47" class="reference"><a href="#cite_note-47"><span class="cite-bracket">[</span>47<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="GreenGenes">GreenGenes</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=16S_ribosomal_RNA&action=edit&section=12" title="Edit section: GreenGenes"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>GreenGenes is a quality controlled, comprehensive 16S rRNA gene reference database and taxonomy based on a <i>de novo</i> phylogeny that provides standard operational taxonomic unit sets. Beware that it utilizes taxonomic terms proposed from phylogenetic methods applied years ago between 2012 and 2013. Since then, a variety of novel phylogenetic methods have been proposed for Archaea and Bacteria.<sup id="cite_ref-48" class="reference"><a href="#cite_note-48"><span class="cite-bracket">[</span>48<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-49" class="reference"><a href="#cite_note-49"><span class="cite-bracket">[</span>49<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading2"><h2 id="References">References</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=16S_ribosomal_RNA&action=edit&section=13" title="Edit section: References"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <div class="mw-references-wrap mw-references-columns"><ol class="references"> <li id="cite_note-Schluenzen-1"><span class="mw-cite-backlink"><b><a href="#cite_ref-Schluenzen_1-0">^</a></b></span> <span class="reference-text"><style data-mw-deduplicate="TemplateStyles:r1238218222">.mw-parser-output cite.citation{font-style:inherit;word-wrap:break-word}.mw-parser-output .citation q{quotes:"\"""\"""'""'"}.mw-parser-output .citation:target{background-color:rgba(0,127,255,0.133)}.mw-parser-output .id-lock-free.id-lock-free a{background:url("//upload.wikimedia.org/wikipedia/commons/6/65/Lock-green.svg")right 0.1em center/9px no-repeat}.mw-parser-output .id-lock-limited.id-lock-limited a,.mw-parser-output .id-lock-registration.id-lock-registration a{background:url("//upload.wikimedia.org/wikipedia/commons/d/d6/Lock-gray-alt-2.svg")right 0.1em center/9px no-repeat}.mw-parser-output .id-lock-subscription.id-lock-subscription a{background:url("//upload.wikimedia.org/wikipedia/commons/a/aa/Lock-red-alt-2.svg")right 0.1em center/9px no-repeat}.mw-parser-output .cs1-ws-icon a{background:url("//upload.wikimedia.org/wikipedia/commons/4/4c/Wikisource-logo.svg")right 0.1em center/12px no-repeat}body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-free a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-limited a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-registration a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-subscription a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .cs1-ws-icon a{background-size:contain;padding:0 1em 0 0}.mw-parser-output .cs1-code{color:inherit;background:inherit;border:none;padding:inherit}.mw-parser-output .cs1-hidden-error{display:none;color:var(--color-error,#d33)}.mw-parser-output .cs1-visible-error{color:var(--color-error,#d33)}.mw-parser-output .cs1-maint{display:none;color:#085;margin-left:0.3em}.mw-parser-output .cs1-kern-left{padding-left:0.2em}.mw-parser-output .cs1-kern-right{padding-right:0.2em}.mw-parser-output .citation .mw-selflink{font-weight:inherit}@media screen{.mw-parser-output .cs1-format{font-size:95%}html.skin-theme-clientpref-night .mw-parser-output .cs1-maint{color:#18911f}}@media screen and (prefers-color-scheme:dark){html.skin-theme-clientpref-os .mw-parser-output .cs1-maint{color:#18911f}}</style><cite id="CITEREFSchluenzenTociljZarivachHarms2000" class="citation journal cs1">Schluenzen F, Tocilj A, Zarivach R, Harms J, Gluehmann M, Janell D, et al. 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(July 2006). <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1489311">"Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB"</a>. <i>Applied and Environmental Microbiology</i>. <b>72</b> (7): 5069–5072. <a href="/wiki/Bibcode_(identifier)" class="mw-redirect" title="Bibcode (identifier)">Bibcode</a>:<a rel="nofollow" class="external text" href="https://ui.adsabs.harvard.edu/abs/2006ApEnM..72.5069D">2006ApEnM..72.5069D</a>. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1128%2Faem.03006-05">10.1128/aem.03006-05</a>. <a href="/wiki/PMC_(identifier)" class="mw-redirect" title="PMC (identifier)">PMC</a> <span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1489311">1489311</a></span>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/16820507">16820507</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=Applied+and+Environmental+Microbiology&rft.atitle=Greengenes%2C+a+chimera-checked+16S+rRNA+gene+database+and+workbench+compatible+with+ARB&rft.volume=72&rft.issue=7&rft.pages=5069-5072&rft.date=2006-07&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC1489311%23id-name%3DPMC&rft_id=info%3Apmid%2F16820507&rft_id=info%3Adoi%2F10.1128%2Faem.03006-05&rft_id=info%3Abibcode%2F2006ApEnM..72.5069D&rft.aulast=DeSantis&rft.aufirst=TZ&rft.au=Hugenholtz%2C+P&rft.au=Larsen%2C+N&rft.au=Rojas%2C+M&rft.au=Brodie%2C+EL&rft.au=Keller%2C+K&rft.au=Huber%2C+T&rft.au=Dalevi%2C+D&rft.au=Hu%2C+P&rft.au=Andersen%2C+GL&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC1489311&rfr_id=info%3Asid%2Fen.wikipedia.org%3A16S+ribosomal+RNA" class="Z3988"></span></span> </li> <li id="cite_note-49"><span class="mw-cite-backlink"><b><a href="#cite_ref-49">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFMcDonaldPriceGoodrichNawrocki2012" class="citation journal cs1">McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, et al. (March 2012). <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3280142">"An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea"</a>. <i>The ISME Journal</i>. <b>6</b> (3): 610–618. <a href="/wiki/Bibcode_(identifier)" class="mw-redirect" title="Bibcode (identifier)">Bibcode</a>:<a rel="nofollow" class="external text" href="https://ui.adsabs.harvard.edu/abs/2012ISMEJ...6..610M">2012ISMEJ...6..610M</a>. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1038%2Fismej.2011.139">10.1038/ismej.2011.139</a>. <a href="/wiki/PMC_(identifier)" class="mw-redirect" title="PMC (identifier)">PMC</a> <span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3280142">3280142</a></span>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/22134646">22134646</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=The+ISME+Journal&rft.atitle=An+improved+Greengenes+taxonomy+with+explicit+ranks+for+ecological+and+evolutionary+analyses+of+bacteria+and+archaea&rft.volume=6&rft.issue=3&rft.pages=610-618&rft.date=2012-03&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC3280142%23id-name%3DPMC&rft_id=info%3Apmid%2F22134646&rft_id=info%3Adoi%2F10.1038%2Fismej.2011.139&rft_id=info%3Abibcode%2F2012ISMEJ...6..610M&rft.aulast=McDonald&rft.aufirst=D&rft.au=Price%2C+MN&rft.au=Goodrich%2C+J&rft.au=Nawrocki%2C+EP&rft.au=DeSantis%2C+TZ&rft.au=Probst%2C+A&rft.au=Andersen%2C+GL&rft.au=Knight%2C+R&rft.au=Hugenholtz%2C+P&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC3280142&rfr_id=info%3Asid%2Fen.wikipedia.org%3A16S+ribosomal+RNA" class="Z3988"></span></span> </li> </ol></div> <div class="mw-heading mw-heading2"><h2 id="External_links">External links</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=16S_ribosomal_RNA&action=edit&section=14" title="Edit section: External links"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <ul><li><a rel="nofollow" class="external text" href="http://depts.washington.edu/molmicdx/mdx/tests/bctseq.shtml">University of Washington Laboratory Medicine: Molecular Diagnosis | Bacterial Sequencing</a></li> <li><a rel="nofollow" class="external text" href="http://mimt.bu.biopolis.pt/">MIMt 16S database</a></li> <li><a rel="nofollow" class="external text" href="http://rdp.cme.msu.edu/">The Ribosomal Database Project</a> <a rel="nofollow" class="external text" href="https://web.archive.org/web/20200819061707/http://rdp.cme.msu.edu/">Archived</a> 2020-08-19 at the <a href="/wiki/Wayback_Machine" title="Wayback Machine">Wayback Machine</a></li> <li><a rel="nofollow" class="external text" href="http://serc.carleton.edu/microbelife/research_methods/genomics/ribosome.html">Ribosomes and Ribosomal RNA: <i>(rRNA)</i></a></li> <li><a rel="nofollow" class="external text" href="http://www.arb-silva.de/">SILVA rRNA database</a></li> <li><a rel="nofollow" class="external text" href="https://web.archive.org/web/20111021102728/http://greengenes.lbl.gov/cgi-bin/nph-index.cgi/">Greengenes: 16S rDNA data and tools</a></li> <li><a rel="nofollow" class="external text" href="https://web.archive.org/web/20130928154318/http://eztaxon-e.ezbiocloud.net/">EzBioCloud</a></li></ul> <div class="navbox-styles"><style data-mw-deduplicate="TemplateStyles:r1129693374">.mw-parser-output .hlist dl,.mw-parser-output .hlist ol,.mw-parser-output .hlist ul{margin:0;padding:0}.mw-parser-output .hlist dd,.mw-parser-output .hlist dt,.mw-parser-output .hlist li{margin:0;display:inline}.mw-parser-output .hlist.inline,.mw-parser-output .hlist.inline dl,.mw-parser-output .hlist.inline ol,.mw-parser-output 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title="Ribosome">ribosome</a> subunits</div></th></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="/wiki/Archaea" title="Archaea">Archaea</a><br />(70<a href="/wiki/Svedberg" title="Svedberg">S</a>)</th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"><a href="/wiki/LSU_rRNA" title="LSU rRNA">Large</a> (<a href="/wiki/50S#Archaea" class="mw-redirect" title="50S">50S</a>): <div class="hlist inline"><ul><li><a href="/wiki/5S_ribosomal_RNA#Archaea" title="5S ribosomal RNA">5S</a></li><li><a href="/wiki/23S_ribosomal_RNA#Archaea" title="23S ribosomal RNA">23S</a></li></ul></div><br /><a href="/wiki/SSU_rRNA" title="SSU rRNA">Small</a> (<a href="/wiki/30S#Archaea" class="mw-redirect" title="30S">30S</a>): <div class="hlist inline"><ul><li><a class="mw-selflink-fragment" href="#Archaea">16S</a></li></ul></div></div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="/wiki/Bacteria" title="Bacteria">Bacteria</a><br />(70<a href="/wiki/Svedberg" title="Svedberg">S</a>)</th><td class="navbox-list-with-group navbox-list navbox-even hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"><a href="/wiki/LSU_rRNA" title="LSU rRNA">Large</a> (<a href="/wiki/50S" class="mw-redirect" title="50S">50S</a>): <div class="hlist inline"><ul><li><a href="/wiki/5S_ribosomal_RNA" title="5S ribosomal RNA">5S</a></li><li><a href="/wiki/23S_ribosomal_RNA" title="23S ribosomal RNA">23S</a></li></ul></div><br /><a href="/wiki/SSU_rRNA" title="SSU rRNA">Small</a> (<a href="/wiki/30S" class="mw-redirect" title="30S">30S</a>): <div class="hlist inline"><ul><li><a class="mw-selflink selflink">16S</a></li></ul></div></div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="/wiki/Eukaryote" title="Eukaryote">Eukaryotes</a></th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"></div><table class="nowraplinks navbox-subgroup" style="border-spacing:0"><tbody><tr><th scope="row" class="navbox-group" style="width:1%"><a href="/wiki/Eukaryotic_ribosome" title="Eukaryotic ribosome">Cytoplasmic</a> (80<a href="/wiki/Svedberg" title="Svedberg">S</a>)</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"><a href="/wiki/LSU_rRNA" title="LSU rRNA">Large</a> (<a href="/wiki/60S" class="mw-redirect" title="60S">60S</a>): <div class="hlist inline"><ul><li><a href="/wiki/5S_ribosomal_RNA" title="5S ribosomal RNA">5S</a></li><li><a href="/wiki/5.8S_ribosomal_RNA" title="5.8S ribosomal RNA">5.8S</a></li><li><a href="/wiki/28S_ribosomal_RNA" title="28S ribosomal RNA">28S</a></li></ul></div><br /><a href="/wiki/SSU_rRNA" title="SSU rRNA">Small</a> (<a href="/wiki/40S" class="mw-redirect" title="40S">40S</a>): <div class="hlist inline"><ul><li><a href="/wiki/18S_ribosomal_RNA" title="18S ribosomal RNA">18S</a></li></ul></div></div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="/wiki/Mitochondrial_ribosome" title="Mitochondrial ribosome">Mitochondrial</a> (55S)</th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em"><a href="/wiki/LSU_rRNA" title="LSU rRNA">Large</a> (28S): <div class="hlist inline"><ul><li><a href="/wiki/MT-RNR2" title="MT-RNR2">MT-RNR2, 16S</a></li><li><a href="/wiki/MT-TV_(mitochondrial)" title="MT-TV (mitochondrial)">MT-tRNA<sup>Val</sup></a></li></ul></div><br /><a href="/wiki/SSU_rRNA" title="SSU rRNA">Small</a> (39S): <div class="hlist inline"><ul><li><a href="/wiki/MT-RNR1" title="MT-RNR1">MT-RNR1, 12S</a></li></ul></div></div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="/wiki/Chloroplast#Chloroplast_ribosomes" title="Chloroplast">Chloroplast</a> (70S)</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"><a href="/wiki/LSU_rRNA" title="LSU rRNA">Large</a> (<a href="/wiki/50S#Plastid" class="mw-redirect" title="50S">50S</a>): <div class="hlist inline"><ul><li><a href="/wiki/5S_ribosomal_RNA#Plastid" title="5S ribosomal RNA">5S</a></li><li><a href="/wiki/23S_ribosomal_RNA#Plastid" title="23S ribosomal RNA">4.5S</a></li><li><a href="/wiki/23S_ribosomal_RNA#Plastid" title="23S ribosomal RNA">23S</a></li></ul></div><br /><a href="/wiki/SSU_rRNA" title="SSU rRNA">Small</a> (<a href="/wiki/30S#Plastid" class="mw-redirect" title="30S">30S</a>): <div class="hlist inline"><ul><li><a class="mw-selflink-fragment" href="#Plastid">16S</a></li></ul></div></div></td></tr></tbody></table><div></div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="/wiki/Ribosomal_protein" title="Ribosomal protein">Ribosomal proteins</a></th><td class="navbox-list-with-group navbox-list navbox-even hlist" 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