16S Microbiome Analysis | Ingenio Diagnostics

<!doctype html> <html lang="en"> <head> <meta charset="utf-8"> <meta name="viewport" content="width=device-width"> <title>16S Microbiome Analysis | Ingenio Diagnostics</title> <meta name="Description" content="Ingenio Diagnostics."> <link rel="apple-touch-icon" sizes="180x180" href="https://www.ingeniodiagnostics.com/images/favicons/apple-touch-icon.png"> <link rel="icon" type="image/png" sizes="32x32" href="https://www.ingeniodiagnostics.com/images/favicons/favicon-32x32.png"> <link rel="icon" type="image/png" sizes="16x16" href="https://www.ingeniodiagnostics.com/images/favicons/favicon-16x16.png"> <link rel="manifest" href="https://www.ingeniodiagnostics.com/images/favicons/site.webmanifest"> <link rel="mask-icon" href="https://www.ingeniodiagnostics.com/images/favicons/safari-pinned-tab.svg" color=""> <meta name="msapplication-TileColor" content="#"> <meta name="theme-color" content=""> <link rel="stylesheet" href="https://www.ingeniodiagnostics.com/css/style.css?v=1717704863"> <link rel="stylesheet" href="https://www.ingeniodiagnostics.com/css/interior.css?v=1717700687"> <link rel="stylesheet" href="https://www.genesisglobalgrp.com/mods/css/global_head.css"> <script>var $site = "https://www.ingeniodiagnostics.com", $page = "16s-microbiome-analysis", $template = "services", $mods = "https://www.genesisglobalgrp.com/mods/";</script> <script type="module">var body=document.querySelector("body");function show(b,c,a){document.querySelector(b).classList.toggle(c),null!==a&&a()}function lazyLoadImages(){for(var b=document.querySelectorAll(".preload"),c=new IntersectionObserver(function(d){for(var b=0;b<d.length;b++)if(!0===d[b].isIntersecting){var a=d[b].target,e=a.getAttribute("data-src"),f=a.getAttribute("data-srcset");null!==e&&(a.src=e),null!==f&&(a.srcset=f),a.classList.add("loaded"),c.unobserve(a)}}),a=0;a<b.length;a++)c.observe(b[a])}window.addEventListener("load",function(){body.classList.add("loaded"),window.show=show}),document.addEventListener("DOMContentLoaded",lazyLoadImages,!1);var inView=new IntersectionObserver(function(a){for(i=0;i<a.length;i++)!0===a[i].isIntersecting&&a[i].target.parentNode.classList.add("in-view")},{threshold:[1]});setTimeout(function(){Array.prototype.forEach.call(document.querySelectorAll(".viewBox"),function(a,b){inView.observe(a)})},500)</script> <script src="https://www.ingeniodiagnostics.com/js/tableData.js?v=1715113179" defer></script> <script src="https://www.ingeniodiagnostics.com/js/site.js?v=1715113179" defer></script> <script src="https://www.genesisglobalgrp.com/mods/js/global_head.js" defer></script> <script src="https://www.genesisglobalgrp.com/mods/cros/js/main.js" defer></script> <script src="https://js.hs-scripts.com/7155805.js" defer></script>  <script async src="https://www.googletagmanager.com/gtag/js?id=G-6X7K9PEFTF"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag("js", new Date()); gtag("config", "G-6X7K9PEFTF"); gtag("config", "UA-18558117-41"); </script> </head> <body class="page-16s-microbiome-analysis temp-services spring" style="--mainColor: #0e76bc; --subColor: #d5a829;"> <header class="ggg"> <div class="fixed"> <a href="https://www.genesisglobalgrp.com" class="parent_link"> <img class="mxHeight" src="https://www.genesisglobalgrp.com/mods/images/logo_ggg_member.png" alt="Genesis Global Group" width="359" height="36"> </a> <button class="show_divisions" onClick="showEle('#ggg_connect', 'expand', event)"> <span id="connect" class="social connect"></span> <span class="txt"></span> </button> </div> </header> <div id="ggg_connect" class=""> <div class="gc_top"> <div class="gc_select"> <button class="dlvl one" data-value="ggg_10">Investment Properties</button><button class="dlvl one" data-value="ggg_2">Hospitality</button><button class="dlvl one" data-value="ggg_3">Biotechnology</button><button class="dlvl one" data-value="ggg_4">Health</button><button class="dlvl one" data-value="ggg_5">Manufacturing & Distribution</button> </div> <span class="bg_circle"></span> </div> <div id="ggg_10" class="ggg_companies splide"> <div class="splide__track"> <ul class="splide__list div_comps"> <li class="splide__slide"> <a href="https://www.genesis-ip.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_gip.png" alt="Genesis Investment Properties"> </a> </li> </ul> </div> </div> <div id="ggg_2" class="ggg_companies splide"> <div class="splide__track"> <ul class="splide__list div_comps"> <li class="splide__slide"> <a href="https://www.genesis-hospitality.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_genesis_hospitality.png" alt="Genesis Hospitality"> </a> </li> <li class="splide__slide"> <a href="https://www.peacockinn.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_peacockinn.png" alt="The Peacock Inn"> </a> </li> <li class="splide__slide"> <a href="https://www.peacockinn.com/restaurant/" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_perch.png" alt="The Perch"> </a> </li> <li class="splide__slide"> <a href="https://www.washingtoncrossinginn.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_wci.png" alt="Washington Crossing Inn"> </a> </li> <li class="splide__slide"> <a href="https://www.lambertvillestation.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_lsi.png" alt="Lambertville Station Restaurant and Inn"> </a> </li> <li class="splide__slide"> <a href="https://www.yardleyinn.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_yardley_inn.png" alt="The Yardley Inn"> </a> </li> <li class="splide__slide"> <a href="https://www.chezalicecafe.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_chez_alice.png" alt="Chez Alice Patisserie"> </a> </li> <li class="splide__slide"> <a href="https://www.bread-boutique.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_bread_boutique.svg" alt="Bread Boutique"> </a> </li> <li class="splide__slide"> <a href="https://www.proofpizzeria.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_proof.png" alt="Proof"> </a> </li> <li class="splide__slide"> <a href="https://www.nassaudiner.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_nassau_diner.png" alt="Nassau Diner"> </a> </li> </ul> </div> </div> <div id="ggg_3" class="ggg_companies splide"> <div class="splide__track"> <ul class="splide__list div_comps"> <li class="splide__slide"> <a href="https://www.genesisbiotechgroup.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_gbg.png" alt="Genesis Biotechnology Group"> </a> </li> <li class="splide__slide"> <a href="https://www.oncoveda.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_oncoveda.png" alt="Oncoveda"> </a> </li> <li class="splide__slide"> <a href="https://www.institute-metabolic-disorders.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_imd.png" alt="Institute of Metabolic Disorders"> </a> </li> <li class="splide__slide"> <a href="https://www.ibr-genetics.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_ibr.png" alt="Institute for Biomarker Research"> </a> </li> <li class="splide__slide"> <a href="https://www.immunoveda.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_immunoveda.png" alt="Immunoveda"> </a> </li> <li class="splide__slide"> <a href="https://www.gd3services.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_gd3.png" alt="Genesis Drug Discovery & Development"> </a> </li> <li class="splide__slide"> <a href="https://www.venenumbiodesign.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_venenum.png" alt="VENENUM Biodesign"> </a> </li> <li class="splide__slide"> <a href="https://www.nedp.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_nedp.png" alt="New England Discovery Partners"> </a> </li> <li class="splide__slide"> <a href="https://www.bioblocks.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_bioblocks.png" alt="BioBlocks"> </a> </li> <li class="splide__slide"> <a href="https://www.organochem.net" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_organochem.png" alt="Organochem"> </a> </li> <li class="splide__slide"> <a href="https://www.ianalytical.net" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_ias.png" alt="Integrated Analytical Solutions, Inc."> </a> </li> <li class="splide__slide"> <a href="https://www.pharmoptima.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_pharmoptima.png" alt="PharmOptima"> </a> </li> <li class="splide__slide"> <a href="https://www.ingeniodiagnostics.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_ingenio.png" alt="Ingenio Diagnostics"> </a> </li> <li class="splide__slide"> <a href="https://www.nexuspharm.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_nexuspharma.png" alt="NexusPharma"> </a> </li> <li class="splide__slide"> <a href="https://www.invivotek.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_invivotek.png" alt="Invivotek"> </a> </li> <li class="splide__slide"> <a href="https://www.compbio.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_cbi.png" alt="Comparative Biosciences, Inc."> </a> </li> <li class="splide__slide"> <a href="https://www.statkingconsulting.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_statking.png" alt="STATKING Clinical Services"> </a> </li> <li class="splide__slide"> <a href="https://www.jssresearch.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_jss.png" alt="JSS Medical Research"> </a> </li> <li class="splide__slide"> <a href="https://www.mdlab.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_mdl.png" alt="Medical Diagnostic Laboratories"> </a> </li> <li class="splide__slide"> <a href="https://www.sunpathmdl.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_sunpath.png" alt="SunPath-MDL"> </a> </li> <li class="splide__slide"> <a href="https://www.4path.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_4path.png" alt="4path, Ltd."> </a> </li> </ul> </div> </div> <div id="ggg_4" class="ggg_companies splide"> <div class="splide__track"> <ul class="splide__list div_comps"> <li class="splide__slide"> <a href="https://www.montclairbreastcenter.com/partnership/" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_genesis_health.png" alt="Genesis Health"> </a> </li> <li class="splide__slide"> <a href="https://www.montclairbreastcenter.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_mbc.png" alt="Montclair Breast Center"> </a> </li> </ul> </div> </div> <div id="ggg_5" class="ggg_companies splide"> <div class="splide__track"> <ul class="splide__list div_comps"> <li class="splide__slide"> <a href="https://www.wwmponline.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_manufacturing.png" alt="Genesis Manufacturing & Distribution"> </a> </li> <li class="splide__slide"> <a href="https://www.wwmponline.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_wwls.png" alt="WorldWide Life Sciences Division"> </a> </li> <li class="splide__slide"> <a href="https://www.bioplastmfg.com" target="_blank"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_bioplast.png" alt="Bioplast Manufacturing, L.L.C."> </a> </li> </ul> </div> </div> </div> <header class="header"> <a class="header_sublogo" href="https://www.gd3services.com/"> <div class="header_sublogo_wrap"> <img class="header_sublogo_img" alt="GD3 Services Logo" src="https://www.genesisglobalgrp.com/mods/images/logo_gd3.png" /> </div> </a> <a id="logo" class="header_logo" href="https://www.ingeniodiagnostics.com"> <img class="header_logo_img" alt="Pharm Optima Logo" src="https://www.genesisglobalgrp.com/mods/images/logo_ingenio.png" /> </a> <div id="menu" class="nav_wrap"> <ul class="nav_menu nav_menu"> <li class=" parent"> <a href="https://www.ingeniodiagnostics.com/about/" class="nav_link"> <strong>About</strong> </a> <ul class="submenu"> <li class=""> <a href="https://www.ingeniodiagnostics.com/about/facilities/" class="sub_nav_link"> <strong>Facilities</strong> </a> <li class=""> <a href="https://www.ingeniodiagnostics.com/about/leadership/" class="sub_nav_link"> <strong>Leadership</strong> </a> <li class=""> <a href="https://www.ingeniodiagnostics.com/about/partnering/" class="sub_nav_link"> <strong>Partnering</strong> </a> </li> </ul> <li class=" parent active-parent"> <a href="https://www.ingeniodiagnostics.com/services/lab/" class="nav_link"> <strong>Services</strong> </a> <ul class="submenu"> <li class=""> <a href="https://www.ingeniodiagnostics.com/services/lab/" class="sub_nav_link"> <strong>Clinical Laboratory</strong> </a> <li class=" parent"> <a href="https://www.ingeniodiagnostics.com/services/anatomic-pathology/" class="sub_nav_link"> <strong>Anatomic Pathology</strong> </a> <ul class="submenuEX"> <li class=""> <a href="https://www.ingeniodiagnostics.com/services/anatomic-pathology/histology/" class="sub_nav_link"> <strong>Histology</strong> </a> <li class=""> <a href="https://www.ingeniodiagnostics.com/services/anatomic-pathology/digital-pathology/" class="sub_nav_link"> <strong>Digital Pathology</strong> </a> </ul> <li class=" parent active-parent"> <a href="https://www.ingeniodiagnostics.com/services/next-gen-sequencing/" class="sub_nav_link"> <strong>Next-Gen Sequencing</strong> </a> <ul class="submenuEX"> <li class=""> <a href="https://www.ingeniodiagnostics.com/services/next-gen-sequencing/rna-seq/" class="sub_nav_link"> <strong>RNA Seq</strong> </a> <li class="active-page "> <a href="https://www.ingeniodiagnostics.com/services/next-gen-sequencing/16s-microbiome-analysis/" class="sub_nav_link"> <strong>16S Microbiome Analysis</strong> </a> </ul> <li class=""> <a href="https://www.ingeniodiagnostics.com/services/molecular-diagnostics/" class="sub_nav_link"> <strong>Molecular Diagnostics</strong> </a> <li class=""> <a href="https://www.ingeniodiagnostics.com/services/immunoassays/" class="sub_nav_link"> <strong>Immunoassays</strong> </a> <li class=""> <a href="https://www.ingeniodiagnostics.com/services/sample-procurement/" class="sub_nav_link"> <strong>Sample Procurement</strong> </a> <li class=""> <a href="https://www.ingeniodiagnostics.com/services/case-studies/" class="sub_nav_link"> <strong>Case Studies</strong> </a> </li> </ul> <li class=" parent"> <a href="https://www.ingeniodiagnostics.com/news/" class="nav_link"> <strong>News</strong> </a> <ul class="submenu"> <li class=""> <a href="https://www.ingeniodiagnostics.com/news/publications/" class="sub_nav_link"> <strong>Publications</strong> </a> </li> </ul> <li class=" parent"> <a href="https://us241.dayforcehcm.com/CandidatePortal/en-US/ggg/SITE/IngenioDiagnosticsCareerSite" class="nav_link"> <strong>Careers</strong> </a> <ul class="submenu"> <li class=""> <a href="https://www.ingeniodiagnostics.com/careers/culture/" class="sub_nav_link"> <strong>Culture</strong> </a> <li class=""> <a href="https://www.ingeniodiagnostics.com/careers/benefits/" class="sub_nav_link"> <strong>Benefits</strong> </a> <li class=""> <a href="https://www.ingeniodiagnostics.com/careers/internships/" class="sub_nav_link"> <strong>Internships</strong> </a> </li> </ul> <li class=""> <a href="https://www.ingeniodiagnostics.com/contact/" class="nav_link"> <strong>Contact</strong> </a> </li> </ul> <a href="https://login.ingeniodiagnostics.com/" class="login_btn "> <svg version="1.2" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 25 27" width="25" height="27" fill="currentColor"> <path fill-rule="evenodd" class="a" d="m17.4 15.9q0.1 0 0.1 0 0.2-0.2 0.4-0.3 0.2-0.2 0.4-0.3 0 0 0-0.1 0.2-0.1 0.4-0.2 0-0.1 0-0.1 0.1-0.1 0.3-0.2 0-0.1 0-0.1 0.2-0.1 0.3-0.3 0 0 0.1-0.1 0.1-0.1 0.2-0.3 0 0 0.1-0.1 0-0.1 0.1-0.2 0.1 0 0.1-0.1 0.1-0.1 0.2-0.3 0-0.1 0.1-0.1 0-0.1 0.1-0.2 0-0.2 0.1-0.3 0-0.1 0.1-0.2 0-0.1 0-0.2 0.6-1.4 0.6-3.2c0-2.9-0.9-5.1-2.6-6.7-2.1-1.9-4.8-2.2-6-2.3q-0.1 0-0.3 0-0.3 0-0.3 0c-1.2 0.1-4 0.4-6.1 2.3-1.7 1.6-2.6 3.8-2.6 6.7 0 2.3 0.7 4.2 2.1 5.6 1.3-0.6 2.6-1 3.8-1.4-1.5-0.9-2.4-2.1-2.4-4.2q0-2.8 1.5-4.2c1.4-1.3 3.5-1.4 4-1.4 0.6 0 2.5 0.2 3.9 1.4q1.5 1.4 1.5 4.2c0 1.2-0.3 2.2-0.9 3q0 0 0 0-0.2 0.2-0.4 0.4 0 0.1-0.1 0.1-0.2 0.2-0.5 0.4 0 0 0 0-0.3 0.2-0.6 0.4 0 0 0 0-0.4 0.2-0.7 0.4 0 0-0.1 0-0.1 0.1-0.3 0.1 0 0 0 0.1-0.2 0-0.4 0.1 0 0-0.1 0-0.1 0.1-0.3 0.2 0 0-0.1 0-0.2 0.1-0.4 0.1 0 0.1-0.1 0.1-0.1 0-0.3 0.1 0 0-0.1 0-0.7 0.3-1.5 0.5c-1.1 0.4-2.3 0.7-3.4 1.2q-0.2 0.1-0.5 0.2 0 0 0 0-0.2 0.1-0.4 0.2-0.1 0-0.1 0-0.2 0.1-0.4 0.2 0 0-0.1 0-0.1 0.1-0.3 0.2-0.1 0-0.1 0.1-0.2 0.1-0.4 0.2 0 0-0.1 0-0.1 0.1-0.3 0.2-0.1 0.1-0.1 0.1-0.2 0.1-0.3 0.2-0.1 0.1-0.1 0.1-0.3 0.2-0.5 0.3c-2.4 2-3.6 4.7-3.6 8.4h3.5c0-5.5 3.1-6.7 8.3-8.3 1.8-0.6 3.6-1.2 5.2-2.1q0.2-0.2 0.4-0.3zm3.3 2.3q-0.7-0.5-1.4-0.9 0 0 0 0c-1.2 0.9-2.4 1.5-3.7 2 3.3 1.3 5.2 3 5.2 7.3h3.5c0-3.7-1.2-6.4-3.6-8.4z" /> </svg>Login or register </a> </div> <button type="button" id="toggle-mob-search" class="search_topics"></button> <button type="button" id="menu_open" class="nav_mob_menu_open" onclick="toggleAttr('#menu', 'visible');toggleAttr('#menu_open', 'cross');toggleAttr('#logo', 'hide')"> <span></span> <span></span> <span></span> </button> </header> <main id="content" > <div class="search_gd3_bar"> <div class="search_pill"> <div class="topic_dropdown"> <button type="button" id="topics_btn" onclick="show_element('topics_dd', 'show')"> <span>Topics</span> </button> <ul id="topics_dd" class="drop_down toggle" onclick="show_element('topics_dd', 'show')"> <li> <button type="button"> <span class="drop_down_span">ADC</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">ADC Purification</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">ADC Synthesis</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Antibody Drug Conjugate</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Antibody Drug Conjugates</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">BRCA</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Bioanalytical Services</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Bioconjugation</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Biosimilars</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Bladder Cancer</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Breast Cancer</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">CAR-T</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Cancer Treatment</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Clinical Trial Management Ind</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Colon Cancer</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Companion Diagnostics</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Custom Synthesis</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">DMPK</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Diabetes</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Diabetes Animal Model</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Efficacy</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Fatty Liver</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Fibrosis</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">HBOC</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">IHC</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Immunofluorescence</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Immunohistochemistry</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Immunohistochemisty</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Linker Payload</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Lymphoma</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Lynch Syndrome</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Medicinal Chemistry</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">NASH</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Organic Synthesis</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">PK/PD</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Pharmacodynamics</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Pharmacogenomics</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Pharmacokinetics</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Pharmacokinetics/Pharmacodynamics</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Prostate Cancer</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Radiopharmaceutical</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Rare Diseases</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Retinopathy</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">STZ</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Small Molecule Synthesis</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Small Molecules</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Special Staining</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Streptozotocin</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Syngeneic</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">TCR</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Tissue Cross Reactivity</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Tool Compound Synthesis</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Toxicology</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Xenograft</span> </button> </li> <li> <button type="button"> <span class="drop_down_span">Xenograft Mouse Tumor Model</span> </button> </li> </ul> </div> <div class="search_field"> <input type="search" id="search_gd3_field" placeholder="Search GD3 Services" value=""> </div> <button type="button" id="gd3_search" class="search_topics"></button> </div> <div id="gd3_overlay"> <section class="gd3o_box"> <div class="logo_tunnel"> <img src="https://www.genesisglobalgrp.com/mods/images/logo_ingenio.png" alt="Ingenio Diagnostics" class="current_site"> <div class="tunnel_tie"> <span></span> <span></span> <span></span> </div> <img src="https://www.genesisglobalgrp.com/mods/images/logo_gd3.png" alt="GD3" width="109" height="65" class="target_site"> </div> <h4>You will now be redirected to the GD<sup>3</sup> website</h4> <p>Ingenio Diagnostics is a proud member of Genesis Drug Discovery & Development (GD3), a fully integrated CRO providing services to support drug discovery programs of our clients from target discovery through IND filing and managing Phase I-III clinical trials.</p> <a href="https://www.gd3services.com/members/" target="_blank" class="about_gd3">Learn more about GD<sup>3</sup></a> <div class="gd3o_btns"> <button type="button" id="gd3_search_cancel" onClick="show_element('gd3_overlay', 'show')"> <span>Cancel</span> </button> <a href="https://gd3services.com/search?site=Ingenio Diagnostics" class="gd3_link btn"> <strong>Search</strong> </a> </div> </section> </div> <style type="text/css"> .learn_gd3 { display: block; text-align: center; padding-top: .5em; } .learn_gd3 img { display:inline-block; vertical-align: middle; margin-left: .3em; } .learn_gd3 span { vertical-align: middle; } #gd3_overlay { position: fixed; left:0; top:0; height: 100vh; width: 100%; background: rgba(0,0,0,.5); z-index: 10000; display: flex; justify-content: center; align-items: center; opacity: 0; pointer-events: none; transition: opacity .3s linear; -webkit-backdrop-filter: blur(3px); backdrop-filter: blur(3px); } #gd3_overlay.show { opacity: 1; pointer-events: all;} .gd3o_box { background: #fff; border-radius: 1em; padding: 1.5em 3%; max-width: 50em; text-align: center; box-shadow: 0 0 2em rgba(0,0,0,.15); transform: scale(.3); transition: transform .4s; } .show > .gd3o_box { transform: scale(1); transition-delay: .1s; } .logo_tunnel { display: flex; justify-content: center; align-items: center; padding-bottom: 2em; } .gd3o_box h4 { color: #101010; font-size: 1.4em; padding-bottom: 1em; margin: 0; } .gd3o_box p { font-size: .813em; margin: 0 auto 1.5em; color: #2f2f2f; line-height: 1.5em; max-width: 34em; text-align: justify; } .gd3o_btns { display: flex; justify-content: space-around; flex-wrap: wrap; padding: 2em 0 0; } .about_gd3 { text-decoration: underline; color: var(--mainColor);} .current_site { max-width: 12em; max-height: 4.5em; margin-right: 1.5em; animation: logos 2s linear infinite} .target_site { margin-left: .5em; animation: logos 2s .6s linear infinite} .tunnel_tie { display: flex; } .tunnel_tie > span { border-radius: 50%; width: .6em; height: .6em; margin: 0 1em 0 0; animation: circle_line 2s .2s steps(5) infinite} .tunnel_tie > span:nth-child(2) { animation-delay: .4s;} .tunnel_tie > span:last-child{ animation-delay: .6s;} @keyframes circle_line { 0% { background: var(--mainColor); } 25%, 50%, 75%, 100% { background: #c8c8c8; } } @keyframes logos { 0%, 20% { filter:grayscale(0%)} 22%, 100% {filter:grayscale(100%) } } #gd3_search_cancel { border: 2px solid #c8c8c8; border-radius: 2em; height: 3em; padding: 0 2em; color: #101010; background: #fff; } #gd3_search_cancel:hover { color: var(--mainColor); } .btn.gd3_link { margin: 0; } </style> <script> window.addEventListener("load", function(){ var btn = document.getElementById('gd3_search'), topics_btn = document.getElementById('topics_btn'), sfield = document.getElementById('search_gd3_field'), gd3_link = document.querySelector('.gd3_link'); //add overlay to body let overlay_html = document.getElementById('gd3_overlay'), fragment = document.createDocumentFragment(); //add overlay to temp fragment fragment.appendChild(overlay_html); //add to body document.querySelector('body').prepend(overlay_html); btn.addEventListener('click', function(){ //searchGD3(); overlay_html.classList.add('show'); }); gd3_link.addEventListener('click', function(){ searchGD3(); }); sfield.addEventListener('keypress', function (e) { if (e.key === 'Enter') { overlay_html.classList.add('show'); } }); function searchGD3(){ var href = gd3_link.getAttribute('href'); event.preventDefault(); if(sfield !== ''){ window.location = href + '&search=' + sfield.value; } } //topics var topics = document.querySelectorAll('#topics_dd button'); Array.prototype.forEach.call(topics, function(el, i){ el.addEventListener('click', function(){ var searchTerm = el.querySelector('span').innerHTML; document.getElementById('search_gd3_field').setAttribute('value', searchTerm); }); }); }); function show_element(ele, cla){ var el = document.getElementById(ele); el.classList.toggle(cla); } </script> </div> <div class="spacer"></div> <section class="main"> <div class="container_wide"> <div class="page_heading_wrap"> <h1 class="page_heading">SERVICES</h1> </div> <section class="info info-nav-wrapper"> <div class="info-nav_wrap"> <button class="info-nav_btn _left"></button> <ul class="info-nav"> <li class="info-nav_link "> <a href="https://www.ingeniodiagnostics.com/services/lab/">Clinical Laboratory</a> </li> <li class="info-nav_link "> <a href="https://www.ingeniodiagnostics.com/services/anatomic-pathology/">Anatomic Pathology</a> </li> <li class="info-nav_link _active"> <a href="https://www.ingeniodiagnostics.com/services/next-gen-sequencing/">Next-Gen Sequencing</a> </li> <li class="info-nav_link "> <a href="https://www.ingeniodiagnostics.com/services/molecular-diagnostics/">Molecular Diagnostics</a> </li> <li class="info-nav_link "> <a href="https://www.ingeniodiagnostics.com/services/immunoassays/">Immunoassays</a> </li> <li class="info-nav_link "> <a href="https://www.ingeniodiagnostics.com/services/sample-procurement/">Sample Procurement</a> </li> <li class="info-nav_link "> <a href="https://www.ingeniodiagnostics.com/services/case-studies/">Case Studies</a> </li> </ul> <button class="info-nav_btn _right"></button> </div> <div class="info_bg_wrap"> <div class="info_bg"></div> <div class="info_bg"></div> </div> </section> <section class="info info-nav-wrapper secondary"> <div class="info-nav_wrap"> <button class="info-nav_btn _left"></button> <ul class="info-nav"> <li class="info-nav_link "> <a href="https://www.ingeniodiagnostics.com/services/next-gen-sequencing/rna-seq/">RNA Seq</a> </li> <li class="info-nav_link _active"> <a href="https://www.ingeniodiagnostics.com/services/next-gen-sequencing/16s-microbiome-analysis/">16S Microbiome Analysis</a> </li> </ul> <button class="info-nav_btn _right"></button> </div> </section> <div class="cta_wrapper"> <div class="cta"> <a href="https://www.ingeniodiagnostics.com/contact/" class="cta_btn"> <img class="cta_img" src="https://www.genesisglobalgrp.com/mods/cros/images/callout-img.png"> <div class="cta_main"> <div class="cta_text">Contact our Experts</div> </div> <div class="cta_dec"> <span></span> </div> </a> </div> </div> <section class="info overview _16s"> <div class="overview_body"> <div class="overview_col"> <h2 class="info_title">Diversity Assessment</h2> <p class="info_text">High-throughput sequencing and taxonomic classification are essential for microbiome research projects. Our complete 16S microbiome analysis includes 16S sequencing, taxonomic classification of organisms, sample diversity statistics, and the option to assess the beta diversity between groups of samples (e.g. populations, treatments, sites). Project-specific analyses are available upon request.</p> <p class="info_text"><strong>We currently offer amplicon based 16S sequencing for V1-2, V3, V4, and V6. A custom mix of variable regions can be ordered as well.</strong></p> <btn onclick="toggleAttr('#mouse-run-report', 'visible')" class="btn">View a typical 16S Microbiome Analysis report</btn> </div> <div class="overview_col"> <img src="https://www.ingeniodiagnostics.com/images/16s-microbiome.png?v=1710947945" class="info_img" alt="16S Microbiome Sample"> </div> </div> </section> <div id="mouse-run-report" class="content-modal"> <div class="content-modal_body"> <div class="content-modal_header"> <h3 class="info_title">Ingenio NGS Differential Expression Analysis Report</h3> <button onclick="toggleAttr('#mouse-run-report', 'visible')" class="content-modal_close"> <span></span> <span></span> </button> </div> <div class="content-modal_info"> <div class="info_row"> <div class="info_col"> <h4 class="info_title _secondary">Mouse Run Report</h4> <p class="info_text">Report generated on November 10, 2021</p> <h4 class="info_title">Submitted Samples</h4> <p class="info_text">Sample names and analysis groups were taken directly from the submission form. The table was created with the kableExtra R package<sup><span class="citation">[<a href="#ref-zhu2021" role="doc-biblioref">1</a>]</span></sup></p> <p class="info_text">Number of Samples Submitted: <strong>10</strong></p> <figure id="submittedSamples" class="table-container"></figure> <h4 class="info_title">Run Report</h4> <p class="info_text">Sequencer Used: <strong>Illumina MiniSeq</strong> <br> NGS Sequencing Method: <strong>Paired-End Amplicon Sequencing</strong> <br> Bacterial Region Sequenced: <strong>16S (V3, V4, and V6)</strong> <br> Amplicon Size: <strong>160-300bp</strong> <br> Mock Communities Used: <strong>BEI Mock Even and Mock Staggered Communities for 16S</strong> <br> <br> Total Reads: <strong>7,871,350</strong> <br> Total Paired Reads: <strong>3,935,675</strong> <br> Minimum Paired Read Count: <strong>237,641</strong> <br> Maximum Paired Read Count: <strong>410,966</strong> <br> Average Read Size: <strong>128 bases</strong> <br> <br></p> <h4 class="info_title _secondary">Read Counts Per Sample</h4> <p class="info_text">Raw paired-end reads from each sample are reported in the following bar graph and corresponding table. All samples must pass this threshold for successful reporting of low abundant bacterial organisms. The submitted samples are labeled with the user-provided IDs from the submission form. Submitted samples are listed alphabetically, and duplicates are denoted with an underscore and numbered sequentially. The bar graph was generated with the ggplot2 and plotly R packages<sup><span class="citation">[<a href="#ref-wickham2016" role="doc-biblioref">2</a>, <a href="#ref-sievert2020" role="doc-biblioref">3</a>]</span></sup>, and the table was created with the kableExtra R package<sup><span class="citation">[<a href="#ref-zhu2021" role="doc-biblioref">1</a>]</span></sup></p> <div class="tabs"> <div class="tabs_header"> <button class="tabs_tab _active">Bar Graph</button> <button class="tabs_tab">Table</button> </div> <div class="tabs_content"> <div class="_active"> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/paired-read-counts.png?v=1710947958" alt="Paired Read Counts Per Sample Graph"> </figure> </div> <div> <figure id="pairedReadCounts" class="table-container"></figure> </div> </div> </div> <h4 class="info_title _secondary">Read Counts After Filtering</h4> <p class="info_text">Paired-end reads were filtered with Fastp<sup><span class="citation">[<a href="#ref-10.1093/bioinformatics/bty560" role="doc-biblioref">4</a>]</span></sup> and new FastQ files were generated with the passing reads. To ensure proper alignments and classification, reads with ambigous bases in the forward or reverse reads were removed from the read count. Additionally, reads with less than 50 bases in either direction were filtered out. The resulting read counts after Fastp filtering are shown in the bar graph and table below. Raw read counts are shown as a blue bar and read counts following Fastp filtering are shown as a yellow bar on the graph. The percentages of passing paired-reads after Fastp filtering are reported in the table. The bar graph was generated with the ggplot2 and plotly R packages<sup><span class="citation">[<a href="#ref-wickham2016" role="doc-biblioref">2</a>, <a href="#ref-sievert2020" role="doc-biblioref">3</a>]</span></sup>, and the table was created with the kableExtra R package<sup><span class="citation">[<a href="#ref-zhu2021" role="doc-biblioref">1</a>]</span></sup></p> <div class="tabs"> <div class="tabs_header"> <button class="tabs_tab _active">Bar Graph</button> <button class="tabs_tab">Table</button> </div> <div class="tabs_content"> <div class="_active"> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/filtered-read-counts.png?v=1710947950" alt="Filtered Read Counts Per Sample Graph"> </figure> </div> <div> <figure id="filteredReadCounts" class="table-container"></figure> </div> </div> </div> <h4 class="info_title _secondary">Read Counts After Mothur Filtering</h4> <p class="info_text">Read alignment and taxonomic classification were done using the Mothur pipeline for 16S data<sup><span class="citation">[<a href="#ref-10.1128/AEM.01541-09" role="doc-biblioref">5</a>]</span></sup>. Paired-end reads were used to generate a Fasta file that was used for 16S analysis. The Fasta sequences were aligned to the reference 16S V4 region obtained from the SILVA database<sup><span class="citation">[<a href="#ref-10.1093/nar/gks1219" role="doc-biblioref">6</a>–<a href="#ref-GLOCKNER2017169" role="doc-biblioref">8</a>]</span></sup>. Aligned sequences were then classified using the RDP database<sup><span class="citation">[<a href="#ref-10.1093/nar/gkt1244" role="doc-biblioref">9</a>]</span></sup>. Classified reads were filtered to remove sequences outside of the 16S region, sequences with non-bacterial classification, and poor quality sequences. The remaining read counts are reported in the following graph and table. The percentages of passing reads after Mothur filtering are listed in the table. The bar graph was generated with the ggplot2 and plotly R packages<sup><span class="citation">[<a href="#ref-wickham2016" role="doc-biblioref">2</a>, <a href="#ref-sievert2020" role="doc-biblioref">3</a>]</span></sup>, and the table was created with the kableExtra R package<sup><span class="citation">[<a href="#ref-zhu2021" role="doc-biblioref">1</a>]</span></sup></p> <div class="tabs"> <div class="tabs_header"> <button class="tabs_tab _active">Bar Graph</button> <button class="tabs_tab">Table</button> </div> <div class="tabs_content"> <div class="_active"> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/mothur-read-counts.png?v=1710947958" alt="Mothur Filtered Read Counts Per Sample Graph"> </figure> </div> <div> <figure id="mothurReadCounts" class="table-container"></figure> </div> </div> </div> <h4 class="info_title">Group Diversity</h4> <p class="info_text">The sequences were divide into organizational taxonomic units (OTUs) based on their taxonomic classifications. Group diversity (beta diversity) metrics assess the similarity and dissimilarity of OTU composition between groups of samples. Due to varying read counts between samples, all read counts were normalized to match the sample with the lowest read count, via subsampling without replacement, prior to statistical analysis. Diversity heatmaps and bar charts were generated using the total read count per sample.</p> <h4 class="info_title _secondary">Principal Component Analysis</h4> <p class="info_text">Principal Component Analysis (PCA) was done using normalized read counts as described above. Groups were predefined on the sample submission form, and colored accordingly. Mock samples were also included for this analysis and separated as an independent group. A PCA was done to reduce the dimensions of the final OTU table, and the first two principal components (PC1 and PC2) are plotted below using the plotly R package<sup><span class="citation">[<a href="#ref-sievert2020" role="doc-biblioref">3</a>]</span></sup>.</p> <div class="tabs"> <div class="tabs_header"> <button class="tabs_tab _active">V3 PCOA</button> <button class="tabs_tab">V4 PCOA</button> <button class="tabs_tab">V6 PCOA</button> </div> <div class="tabs_content"> <div class="_active"> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v3-pcoa.png?v=1710947973" alt="V3 PCOA Graph"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v4-pcoa.png?v=1710947979" alt="V4 PCOA Graph"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v6-pcoa.png?v=1710947987" alt="V6 PCOA Graph"> </figure> </div> </div> </div> <h4 class="info_title _secondary">Phylum Level OTU Heatmap</h4> <p class="info_text">Samples were clustered based on phylum level OTUs and the heatmap is shown below. OTU read counts were log10 .transformed and infinite values were set to zero. The sample and OTU dendrograms were ordered using optimal leaf ordering (OLO) from the heatmaply R package<sup><span class="citation">[<a href="#ref-galili-tal2017" role="doc-biblioref">10</a>]</span></sup> and the heatmap was visualized using the plotly R package<sup><span class="citation">[<a href="#ref-sievert2020" role="doc-biblioref">3</a>]</span></sup>. Values are shown as log10(total reads) and infinite values were set to zero.</p> <div class="tabs"> <div class="tabs_header"> <button class="tabs_tab _active">V3 Heatmap</button> <button class="tabs_tab">V4 Heatmap</button> <button class="tabs_tab">V6 Heatmap</button> </div> <div class="tabs_content"> <div class="_active"> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v3-heatmap.png?v=1710947969" alt="V3 heatmap Graph"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v4-heatmap.png?v=1710947976" alt="V4 heatmap Graph"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v6-heatmap.png?v=1710947982" alt="V6 heatmap Graph"> </figure> </div> </div> </div> <h4 class="info_title _secondary">AMOVA</h4> <p class="info_text">A Statistics section will only be included if there is more than one group for the project.</p> <p class="info_text">The <strong>Analysis of Molecular Variance (AMOVA)</strong> is used to detect the variance of molecular markers between two groups. The groups used for these analyses have been predefined on the sample submission form. Normalized read counts from genus level OTUs were used for this section. Mothur uses an asterisk to denote significance (p-Value < 0.01). All the tables in this section were generated using the kableExtra R package<sup><span class="citation">[<a href="#ref-zhu2021" role="doc-biblioref">1</a>]</span></sup>.</p> <figure id="amova" class="table-container"></figure> <h4 class="info_title _secondary">Bar Charts</h4> <p class="info_text">Visualization of group diversity and taxonomic classification with bar charts. The Mock Communities were assessed for accurate classification and compared to the expected read counts from the BEI data sheet. The phylum level composition and the genus level composition are provided for all submitted samples. All bar graphs were generated using the ggplot2 and plotly R packages<sup><span class="citation">[<a href="#ref-wickham2016" role="doc-biblioref">2</a>, <a href="#ref-sievert2020" role="doc-biblioref">3</a>]</span></sup>.</p> <h4 class="info_title _secondary">V3 Composition</h4> <div class="tabs"> <div class="tabs_header"> <button class="tabs_tab _active">Mock Communities</button> <button class="tabs_tab">Samples (Genera)</button> <button class="tabs_tab">Samples (Phyla)</button> </div> <div class="tabs_content"> <div class="_active"> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v3-mock.png?v=1710947973" alt="V3 Mock Graph"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v3-genera.png?v=1710947969" alt="V3 Genera Graph"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v3-phyla.png?v=1710947973" alt="V3 Phyla Graph"> </figure> </div> </div> </div> <h4 class="info_title _secondary">V4 Composition</h4> <div class="tabs"> <div class="tabs_header"> <button class="tabs_tab _active">Mock Communities</button> <button class="tabs_tab">Samples (Genera)</button> <button class="tabs_tab">Samples (Phyla)</button> </div> <div class="tabs_content"> <div class="_active"> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v4-mock.png?v=1710947979" alt="V4 Mock Graph"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v4-genera.png?v=1710947976" alt="V4 Genera Graph"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v4-phyla.png?v=1710947980" alt="V4 Phyla Graph"> </figure> </div> </div> </div> <h4 class="info_title _secondary">V6 Composition</h4> <div class="tabs"> <div class="tabs_header"> <button class="tabs_tab _active">Mock Communities</button> <button class="tabs_tab">Samples (Genera)</button> <button class="tabs_tab">Samples (Phyla)</button> </div> <div class="tabs_content"> <div class="_active"> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v6-mock.png?v=1710947986" alt="V6 Mock Graph"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v6-genera.png?v=1710947982" alt="V6 Genera Graph"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v6-phyla.png?v=1710947987" alt="V6 Phyla Graph"> </figure> </div> </div> </div> <h4 class="info_title">Sample Diversity</h4> <p class="info_text">Sample Diversity (alpha diversity) summarizes the composition of the microbial community within a sample using measurements for its richness (number of taxonomic groups) and/or evenness (distribution of abundances of the groups). The calculations for Sample Diversity were done using normalized read counts as described in the Group Diversity section.</p> <h5 class="info_title _secondary">Rarefaction Curves</h5> <p class="info_text">Rarefaction and rarefaction curves are used to measure OTU richness within a sample. The number of OTUs are plotted against the number of sequences and the resulting curves suggest the richness of each sample. Sequences were subsampled 100 times to generate the rarefaction curves below. Rarefaction curves typically flatten after a steep incline for samples that have been sufficiently sequenced. Low diversity samples will reach their peak and flatten out much earlier. Very high diversity samples or samples that have not been sequenced completely will continue to rise without flattening.</p> <div class="tabs"> <div class="tabs_header"> <button class="tabs_tab _active">V3</button> <button class="tabs_tab">V4</button> <button class="tabs_tab">V6</button> </div> <div class="tabs_content"> <div class="_active"> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v3-rarefaction.png?v=1710947974" alt="V3 Rarefaction Graph"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v4-rarefaction.png?v=1710947980" alt="V4 Rarefaction Graph"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v6-rarefaction.png?v=1710947987" alt="V6 Rarefaction Graph"> </figure> </div> </div> </div> <h5 class="info_title _secondary">Diversity Index</h5> <p class="info_text">Sample diversity can also be assessed using the Simpson’s Diversity Index and the Shannon’s Diversity Index. <strong>Simpson’s Diversity Index</strong> measures the probability that any two individuals drawn at random from a community belong to different species/OTUs (dominance and richness). <strong>Shannon’s Diversity Index</strong> describes the diversity and species/OTU richness of a sample in one metric. All the tables in this section were generated using the kableExtra R package<sup><span class="citation">[<a href="#ref-zhu2021" role="doc-biblioref">1</a>]</span></sup>.</p> <div class="tabs"> <div class="tabs_header"> <button class="tabs_tab _active">Simpson’s Diversity Index</button> <button class="tabs_tab">Shannon’s Diversity Index</button> </div> <div class="tabs_content"> <div class="_active"> <figure id="simpson" class="table-container"></figure> </div> <div> <figure id="shannon" class="table-container"></figure> </div> </div> </div> <h4 class="info_title">Taxonomic Classification</h4> <h5 class="info_title _secondary">Sunburst Plots</h5> <p class="info_text">The sunburst plots for the groups and individual samples were generated using the plotly R package<sup><span class="citation">[<a href="#ref-sievert2020" role="doc-biblioref">3</a>]</span></sup>.</p> <h5 class="info_title _secondary">V3 Classification</h5> <div class="tabs"> <div class="tabs_header"> <button class="tabs_tab _active">Mock Group</button> <button class="tabs_tab">Mock Even</button> <button class="tabs_tab">Mock Staggered</button> <button class="tabs_tab">JAX Group</button> <button class="tabs_tab">JAX 1</button> <button class="tabs_tab">JAX 2</button> <button class="tabs_tab">JAX 3</button> <button class="tabs_tab">JAX 4</button> <button class="tabs_tab">JAX 5</button> <button class="tabs_tab">TAC Group</button> <button class="tabs_tab">TAC 1</button> <button class="tabs_tab">TAC 2</button> <button class="tabs_tab">TAC 3</button> <button class="tabs_tab">TAC 4</button> </div> <div class="tabs_content"> <div class="_active"> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v3-mock-group.png?v=1710947972" alt="V3 Mock Group"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v3-mock-even.png?v=1710947972" alt="V3 Mock Even"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v3-mock-staggered.png?v=1710947973" alt="V3 Mock Staggered"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v3-jax-group.png?v=1710947972" alt="V3 JAX Group"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v3-jax-1.png?v=1710947970" alt="V3 JAX 1"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v3-jax-2.png?v=1710947970" alt="V3 JAX 2"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v3-jax-3.png?v=1710947971" alt="V3 JAX 3"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v3-jax-4.png?v=1710947971" alt="V3 JAX 4"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v3-jax-5.png?v=1710947971" alt="V3 JAX 5"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v3-tac-group.png?v=1710947975" alt="V3 TAC Group"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v3-tac-1.png?v=1710947974" alt="V3 TAC 1"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v3-tac-2.png?v=1710947974" alt="V3 TAC 2"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v3-tac-3.png?v=1710947975" alt="V3 TAC 3"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v3-tac-4.png?v=1710947975" alt="V3 TAC 4"> </figure> </div> </div> </div> <h5 class="info_title _secondary">V4 Classification</h5> <div class="tabs"> <div class="tabs_header"> <button class="tabs_tab _active">Mock Group</button> <button class="tabs_tab">Mock Even</button> <button class="tabs_tab">Mock Staggered</button> <button class="tabs_tab">JAX Group</button> <button class="tabs_tab">JAX 1</button> <button class="tabs_tab">JAX 2</button> <button class="tabs_tab">JAX 3</button> <button class="tabs_tab">JAX 4</button> <button class="tabs_tab">JAX 5</button> <button class="tabs_tab">TAC Group</button> <button class="tabs_tab">TAC 1</button> <button class="tabs_tab">TAC 2</button> <button class="tabs_tab">TAC 3</button> <button class="tabs_tab">TAC 4</button> </div> <div class="tabs_content"> <div class="_active"> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v4-mock-group.png?v=1710947979" alt="V4 Mock Group"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v4-mock-even.png?v=1710947978" alt="V4 Mock Even"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v4-mock-staggered.png?v=1710947979" alt="V4 Mock Staggered"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v4-jax-group.png?v=1710947978" alt="V4 JAX Group"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v4-jax-1.png?v=1710947976" alt="V4 JAX 1"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v4-jax-2.png?v=1710947977" alt="V4 JAX 2"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v4-jax-3.png?v=1710947977" alt="V4 JAX 3"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v4-jax-4.png?v=1710947977" alt="V4 JAX 4"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v4-jax-5.png?v=1710947978" alt="V4 JAX 5"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v4-tac-group.png?v=1710947982" alt="V4 TAC Group"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v4-tac-1.png?v=1710947980" alt="V4 TAC 1"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v4-tac-2.png?v=1710947981" alt="V4 TAC 2"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v4-tac-3.png?v=1710947981" alt="V4 TAC 3"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v4-tac-4.png?v=1710947981" alt="V4 TAC 4"> </figure> </div> </div> </div> <h5 class="info_title _secondary">V6 Classification</h5> <div class="tabs"> <div class="tabs_header"> <button class="tabs_tab _active">Mock Group</button> <button class="tabs_tab">Mock Even</button> <button class="tabs_tab">Mock Staggered</button> <button class="tabs_tab">JAX Group</button> <button class="tabs_tab">JAX 1</button> <button class="tabs_tab">JAX 2</button> <button class="tabs_tab">JAX 3</button> <button class="tabs_tab">JAX 4</button> <button class="tabs_tab">JAX 5</button> <button class="tabs_tab">TAC Group</button> <button class="tabs_tab">TAC 1</button> <button class="tabs_tab">TAC 2</button> <button class="tabs_tab">TAC 3</button> <button class="tabs_tab">TAC 4</button> </div> <div class="tabs_content"> <div class="_active"> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v6-mock-group.png?v=1710947986" alt="V6 Mock Group"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v6-mock-even.png?v=1710947986" alt="V6 Mock Even"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v6-mock-staggered.png?v=1710947986" alt="V6 Mock Staggered"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v6-jax-group.png?v=1710947985" alt="V6 JAX Group"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v6-jax-1.png?v=1710947983" alt="V6 JAX 1"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v6-jax-2.png?v=1710947983" alt="V6 JAX 2"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v6-jax-3.png?v=1710947984" alt="V6 JAX 3"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v6-jax-4.png?v=1710947984" alt="V6 JAX 4"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v6-jax-5.png?v=1710947985" alt="V6 JAX 5"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v6-tac-group.png?v=1710947989" alt="V6 TAC Group"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v6-tac-1.png?v=1710947988" alt="V6 TAC 1"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v6-tac-2.png?v=1710947988" alt="V6 TAC 2"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v6-tac-3.png?v=1710947989" alt="V6 TAC 3"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/v6-tac-4.png?v=1710947989" alt="V6 TAC 4"> </figure> </div> </div> </div> <h5 class="info_title _secondary">Phylum Level Pie Charts</h5> <p class="info_text">Pie charts showing the phylum level composition for the groups defined on the submission sheet as well as individual samples. These plots were generated using the plotly R package<sup><span class="citation">[<a href="#ref-sievert2020" role="doc-biblioref">3</a>]</span></sup>.</p> <h5 class="info_title _secondary">V3 Pie Charts</h5> <div class="tabs"> <div class="tabs_header"> <button class="tabs_tab _active">JAX Group</button> <button class="tabs_tab">JAX 1</button> <button class="tabs_tab">JAX 2</button> <button class="tabs_tab">JAX 3</button> <button class="tabs_tab">JAX 4</button> <button class="tabs_tab">JAX 5</button> <button class="tabs_tab">TAC Group</button> <button class="tabs_tab">TAC 1</button> <button class="tabs_tab">TAC 2</button> <button class="tabs_tab">TAC 3</button> <button class="tabs_tab">TAC 4</button> </div> <div class="tabs_content"> <div class="_active"> <figure class="scheme _active"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v3-jax-group.png?v=1710947960" alt="V3 JAX Group"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v3-jax-1.png?v=1710947959" alt="V3 JAX 1"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v3-jax-2.png?v=1710947959" alt="V3 JAX 2"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v3-jax-3.png?v=1710947959" alt="V3 JAX 3"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v3-jax-4.png?v=1710947960" alt="V3 JAX 4"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v3-jax-5.png?v=1710947960" alt="V3 JAX 5"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v3-tac-group.png?v=1710947961" alt="V3 TAC Group"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v3-tac-1.png?v=1710947960" alt="V3 TAC 1"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v3-tac-2.png?v=1710947961" alt="V3 TAC 2"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v3-tac-3.png?v=1710947961" alt="V3 TAC 3"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v3-tac-4.png?v=1710947961" alt="V3 TAC 4"> </figure> </div> </div> </div> <h5 class="info_title _secondary">V4 Pie Charts</h5> <div class="tabs"> <div class="tabs_header"> <button class="tabs_tab _active">JAX Group</button> <button class="tabs_tab">JAX 1</button> <button class="tabs_tab">JAX 2</button> <button class="tabs_tab">JAX 3</button> <button class="tabs_tab">JAX 4</button> <button class="tabs_tab">JAX 5</button> <button class="tabs_tab">TAC Group</button> <button class="tabs_tab">TAC 1</button> <button class="tabs_tab">TAC 2</button> <button class="tabs_tab">TAC 3</button> <button class="tabs_tab">TAC 4</button> </div> <div class="tabs_content"> <div class="_active"> <figure class="scheme _active"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v4-jax-group.png?v=1710947963" alt="V4 JAX Group"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v4-jax-1.png?v=1710947962" alt="V4 JAX 1"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v4-jax-2.png?v=1710947962" alt="V4 JAX 2"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v4-jax-3.png?v=1710947962" alt="V4 JAX 3"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v4-jax-4.png?v=1710947962" alt="V4 JAX 4"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v4-jax-5.png?v=1710947962" alt="V4 JAX 5"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v4-tac-group.png?v=1710947964" alt="V4 TAC Group"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v4-tac-1.png?v=1710947963" alt="V4 TAC 1"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v4-tac-2.png?v=1710947963" alt="V4 TAC 2"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v4-tac-3.png?v=1710947963" alt="V4 TAC 3"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v4-tac-4.png?v=1710947964" alt="V4 TAC 4"> </figure> </div> </div> </div> <h5 class="info_title _secondary">V6 Pie Charts</h5> <div class="tabs"> <div class="tabs_header"> <button class="tabs_tab _active">JAX Group</button> <button class="tabs_tab">JAX 1</button> <button class="tabs_tab">JAX 2</button> <button class="tabs_tab">JAX 3</button> <button class="tabs_tab">JAX 4</button> <button class="tabs_tab">JAX 5</button> <button class="tabs_tab">TAC Group</button> <button class="tabs_tab">TAC 1</button> <button class="tabs_tab">TAC 2</button> <button class="tabs_tab">TAC 3</button> <button class="tabs_tab">TAC 4</button> </div> <div class="tabs_content"> <div class="_active"> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v6-jax-group.png?v=1710947965" alt="V6 JAX Group"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v6-jax-1.png?v=1710947964" alt="V6 JAX 1"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v6-jax-2.png?v=1710947964" alt="V6 JAX 2"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v6-jax-3.png?v=1710947965" alt="V6 JAX 3"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v6-jax-4.png?v=1710947965" alt="V6 JAX 4"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v6-jax-5.png?v=1710947965" alt="V6 JAX 5"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v6-tac-group.png?v=1710947967" alt="V6 TAC Group"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v6-tac-1.png?v=1710947966" alt="V6 TAC 1"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v6-tac-2.png?v=1710947966" alt="V6 TAC 2"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v6-tac-3.png?v=1710947966" alt="V6 TAC 3"> </figure> </div> <div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/pie-v6-tac-4.png?v=1710947966" alt="V6 TAC 4"> </figure> </div> </div> </div> <h5 class="info_title _secondary">Differential OTUs</h5> <p class="info_text">Differntial OTU tables were generated using LEfSe. The LDA Effect Size (LEfSe) is an algorithm for High-Dimensional microbiome biomarker discovery. LEfSe uses the Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear Discriminant Analysis to find biomarkers of groups<sup><span class="citation">[<a href="#ref-pmid21702898" role="doc-biblioref">11</a>]</span></sup>.</p> <div class="tabs"> <div class="tabs_header"> <button class="tabs_tab _active">V3 OTUs (Genus Level)</button> <button class="tabs_tab">V3 OTUs (Phylum Level)</button> <button class="tabs_tab">V4 OTUs (Genus Level)</button> <button class="tabs_tab">V4 OTUs (Phylum Level)</button> <button class="tabs_tab">V6 OTUs (Genus Level)</button> <button class="tabs_tab">V6 OTUs (Phylum Level)</button> </div> <div class="tabs_content"> <div class="_active"> <figure id="v3Genus" class="table-container"></figure> </div> <div> <figure id="v3Phylum" class="table-container"></figure> </div> <div> <figure id="v4Genus" class="table-container"></figure> </div> <div> <figure id="v4Phylum" class="table-container"></figure> </div> <div> <figure id="v6Genus" class="table-container"></figure> </div> <div> <figure id="v6Phylum" class="table-container"></figure> </div> </div> </div> <figure class="scheme"> <img class="scheme_img" src="https://www.ingeniodiagnostics.com/images/mouse-feces.png?v=1710955005" alt="Mouse feces JAX"> </figure> <h4 class="info_title">Classification Table</h4> <p class="info_text">Tables with read counts and full taxonomic breakdowns. Regions are separated into tabs and the link for the csv can be found at the bottom of each table. These tables were created using the reactable R package<sup><span class="citation">[<a href="#ref-lin2020" role="doc-biblioref">12</a>]</span></sup>.</p> <div class="tabs"> <div class="tabs_header"> <button class="tabs_tab _active">V3 Classification</button> <button class="tabs_tab">V4 Classification</button> <button class="tabs_tab">V6 Classification</button> </div> <div class="tabs_content"> <div class="_active"> <figure id="v3Class" class="table-container"></figure> </div> <div> <figure id="v4Class" class="table-container"></figure> </div> <div> <figure id="v6Class" class="table-container"></figure> </div> </div> </div> <div class="info_references"> <h4>References</h4> <ol class="reference_list"> <li id="ref-zhu2021" class="reference_list-item">Zhu H. kableExtra: Construct complex table with ’kable’ and pipe syntax. 2021. <a href="https://CRAN.R-project.org/package=kableExtra">https://CRAN.R-project.org/package=kableExtra</a>.</li> <li id="ref-wickham2016" class="reference_list-item">Wickham H. ggplot2: Elegant graphics for data analysis. Springer-Verlag New York; 2016. <a href="https://ggplot2.tidyverse.org">https://ggplot2.tidyverse.org</a>.</li> <li id="ref-sievert2020" class="reference_list-item">Sievert C. Interactive web-based data visualization with r, plotly, and shiny. Chapman; Hall/CRC; 2020. <a href="https://plotly-r.com">https://plotly-r.com</a>.</li> <li id="ref-10.1093/bioinformatics/bty560" class="reference_list-item">Chen S, Zhou Y, Chen Y, Gu J. <span class="nocase">fastp: an ultra-fast all-in-one FASTQ preprocessor</span>. Bioinformatics. 2018;34:i884–90. doi:<a href="https://doi.org/10.1093/bioinformatics/bty560">10.1093/bioinformatics/bty560</a>.</li> <li id="ref-10.1128/AEM.01541-09" class="reference_list-item">Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology. 2009;75:7537–41. doi:<a href="https://doi.org/10.1128/AEM.01541-09">10.1128/AEM.01541-09</a>.</li> <li id="ref-10.1093/nar/gks1219" class="reference_list-item">Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. <span class="nocase">The SILVA ribosomal RNA gene database project: improved data processing and web-based tools</span>. Nucleic Acids Research. 2012;41:D590–6. doi:<a href="https://doi.org/10.1093/nar/gks1219">10.1093/nar/gks1219</a>.</li> <li id="ref-10.1093/nar/gkt1209" class="reference_list-item">Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, et al. <span class="nocase">The SILVA and <span>“All-species Living Tree Project (LTP)”</span> taxonomic frameworks</span>. Nucleic Acids Research. 2013;42:D643–8. doi:<a href="https://doi.org/10.1093/nar/gkt1209">10.1093/nar/gkt1209</a>.</li> <li id="ref-GLOCKNER2017169" class="reference_list-item">Glöckner FO, Yilmaz P, Quast C, Gerken J, Beccati A, Ciuprina A, et al. 25 years of serving the community with ribosomal RNA gene reference databases and tools. Journal of Biotechnology. 2017;261:169–76. doi:<a href="https://doi.org/10.1016/j.jbiotec.2017.06.1198">https://doi.org/10.1016/j.jbiotec.2017.06.1198</a>.</li> <li id="ref-10.1093/nar/gkt1244" class="reference_list-item">Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, et al. <span class="nocase">Ribosomal Database Project: data and tools for high throughput rRNA analysis</span>. Nucleic Acids Research. 2013;42:D633–42. doi:<a href="https://doi.org/10.1093/nar/gkt1244">10.1093/nar/gkt1244</a>.</li> <li id="ref-galili-tal2017" class="reference_list-item">Galili, Tal, O’Callaghan, Alan, Sidi, Jonathan, et al. Heatmaply: An r package for creating interactive cluster heatmaps for online publishing. Bioinformatics. 2017. doi:<a href="https://doi.org/10.1093/bioinformatics/btx657">10.1093/bioinformatics/btx657</a>.</li> <li id="ref-pmid21702898" class="reference_list-item">Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, et al. <span class="nocase"><span>M</span>etagenomic biomarker discovery and explanation</span>. Genome Biol. 2011;12:R60.</li> <li id="ref-lin2020" class="reference_list-item">Lin G. Reactable: Interactive data tables based on ’react table’. 2020. <a href="https://CRAN.R-project.org/package=reactable">https://CRAN.R-project.org/package=reactable</a>.</li> </ol> </div> </div> </div> </div> </div> </div> <section class="info _has-depth _even _sample"> <div class="info_row"> <h3 class="info_title">Sample Submissions Guidelines</h3> <div class="info_col"> <h4 class="info_title _secondary">DNA for 16S Sequencing</h4> <ul class="list _cols"> <li class="list-item">Extraction via a kit designed for microbiome analysis (e.g. ZymoBIOMICS DNA Kit)</li> <li class="list-item">Optical Density (260/280): 1.8-2.0</li> <li class="list-item">No RNA contamination</li> <li class="list-item">Suspended in DNase-free water or such buffers as 10mM Tris, Qiagen EB, or TE</li> <li class="list-item">At least 10ul of DNA at a concentration of > 5 ng/ul</li> <li class="list-item">Shipped with dry ice</li> </ul> </div> <div class="info_col"> <h4 class="info_title _secondary">Stool and Soil Samples for 16S Sequencing</h4> <ul class="list _cols"> <li class="list-item">Flash freeze as soon as collected</li> <li class="list-item">A minimum of 0.5g of stool or soil</li> <li class="list-item">Stored at -80C prior to shipping</li> <li class="list-item">Shipped with dry ice</li> <li class="list-item">Alternative: collect samples with Zymo DNA/RNA Shield and ship at ambient temperature</li> </ul> </div> </div> </section> </div> </section> </main> <div id="modal">  <div id="optin-modal" class="modal_overlay"> <div class="modal _optin"> <span class="modal_icon"></span> <p class="modal_text">Before you download, please fill out some info so we can discuss our services with you</p> <div class="modal_body"> <form class="form specific" data-sth="downloads"> <div class="form_msg"> <p class="status">Thank you for your message!</p> </div> <div class="field required"> <input placeholder="Optional" class="if" type="text" name="d_name" required /> <label for="last-name">Name</label> </div> <div class="field required"> <input placeholder="Optional" class="if" type="email" name="d_email" required /> <label for="email">Email</label> </div> <div class="field"> <input placeholder="Optional" class="if" type="number" name="d_phone" /> <label for="phone">Phone</label> </div> <input type="hidden" name="link"> <input type="hidden" name="key_code" value="7305b85c2a8b34d7672ee25327887521"> <input type="hidden" class="timer" name="timer" value=""> <label style="display: block;height:0;"> <input type="text" name="catch" style="height: 100%; border:0; padding:0;"> </label> <div class="modal_row"> <button id="modal-close" type="button" class="btn">Cancel</button> <div> <a href="" class="btn _submit">Skip</a> <button type="submit" class="btn _submit">Continue</button> </div> </div> </form> </div> </div> </div> </div> <footer class="footer"> <div class="footer_bg in_view_check"> <div class="footer_content"> <div class="footer_container container"> <div class="footer_info"> <div class="footer_info_wrap"> <img class="footer_info_img" alt="Icon Map" src="https://www.genesisglobalgrp.com/mods/cros/images/icon-map.svg" /> </div> <span class="footer_info_text">2439 Kuser Road<br>Hamilton, NJ 08690</span> </div> <div class="footer_info"> <div class="footer_info_wrap"> <img class="footer_info_img" alt="Icon Phone" src="https://www.genesisglobalgrp.com/mods/cros/images/icon-phone.svg" /> </div> <span class="footer_info_text _strong"> 844-272-8234<br> </span> </div> <div class="footer_info"> <div class="footer_info_wrap"> <img class="footer_info_img" alt="Icon Fax" src="https://www.genesisglobalgrp.com/mods/cros/images/icon-fax.svg" /> </div> <span class="footer_info_text _strong">609-570-1050</span> </div> </div> </div> </div> <div class="subfooter in_view_check"> <div class="subfooter_content container"> <div class="subfooter_links"> <a class="subfooter_text" href="https://www.ingeniodiagnostics.com/terms/">Terms of Use</a> <a class="subfooter_text" href="https://www.ingeniodiagnostics.com/privacy/">Privacy Policy</a> </div> <p class="subfooter_text">©2024 Ingenio Diagnostics, All Rights Reserved.</p> </div> </div> </footer> </body> </html>

CINXE.COM

16S Microbiome Analysis | Ingenio Diagnostics