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<div class="wrap hero">
<h1>Microbial Databases Guide</h1>
<p class="lede">A practical, family-friendly guide to the major databases used to look up bacteria, archaea, fungi, viruses, and other microorganisms. This is organized so kids or adults can quickly jump to the right type of resource: taxonomy, genomes, strains, pathways, pathogens, fungi, viruses, or microbiome tools.</p>
<div class="pill-row">
<span class="pill">Best starting hub: NCBI</span>
<span class="pill">Best strain data: BacDive</span>
<span class="pill">Best prokaryote naming authority: LPSN</span>
<span class="pill">Best virus taxonomy: ICTV</span>
<span class="pill">Best fungal names: MycoBank / Index Fungorum</span>
</div>
</div>
</header>
<nav class="topnav">
<div class="wrap">
<a href="#quickstart">Quick Start</a>
<a href="#core">Core Hubs</a>
<a href="#taxonomy">Taxonomy & Naming</a>
<a href="#genomes">Genomes & Sequencing</a>
<a href="#function">Function & Pathways</a>
<a href="#pathogens">Pathogens</a>
<a href="#fungi">Fungi</a>
<a href="#viruses">Viruses</a>
<a href="#rrna">rRNA / Amplicon</a>
<a href="#paid">Paid / Premium</a>
<a href="#recipes">Use Recipes</a>
</div>
</nav>
<main class="wrap">
<section class="tools">
<div class="toolbox">
<h2>Find a database</h2>
<input id="searchBox" type="search" placeholder="Search by name, topic, or keyword (example: fungi, pathogen, 16S, metabolism)" />
<div class="filters">
<button class="filter-btn active" data-filter="all">All</button>
<button class="filter-btn" data-filter="free">Free</button>
<button class="filter-btn" data-filter="paid">Paid / mixed</button>
<button class="filter-btn" data-filter="taxonomy">Taxonomy</button>
<button class="filter-btn" data-filter="genome">Genomes</button>
<button class="filter-btn" data-filter="pathogen">Pathogens</button>
<button class="filter-btn" data-filter="fungi">Fungi</button>
<button class="filter-btn" data-filter="virus">Viruses</button>
<button class="filter-btn" data-filter="rrna">rRNA</button>
</div>
</div>
<div class="toolbox">
<h2>How to use this page</h2>
<p class="subtle small">Think of these databases as different kinds of encyclopedias.</p>
<ul class="small">
<li><strong>Who is it?</strong> Use taxonomy databases.</li>
<li><strong>What genes does it have?</strong> Use genome databases.</li>
<li><strong>How does it behave?</strong> Use strain / phenotype databases.</li>
<li><strong>What pathways does it use?</strong> Use KEGG or UniProt.</li>
<li><strong>Is it a pathogen?</strong> Use BV-BRC, VFDB, or NCBI pathogen resources.</li>
</ul>
</div>
</section>
<section id="quickstart" class="section">
<div class="section-head">
<div>
<h2>Quick Start</h2>
<p class="subtle">If you only want the most useful few, start here.</p>
</div>
</div>
<div class="grid">
<article class="card db-card" data-tags="core free taxonomy genome strain literature all">
<div class="meta"><span class="score">Top pick</span><span class="tag free">Free</span><span class="tag">Core hub</span></div>
<h3><a class="mainlink" href="https://www.ncbi.nlm.nih.gov/" target="_blank" rel="noopener">NCBI</a></h3>
<p>The closest thing to a universal microbe hub. It links taxonomy, genomes, sequences, genes, proteins, assemblies, literature, and pathogen resources.</p>
<ul>
<li>Best for: first stop for almost any organism</li>
<li>Strong at: breadth and cross-linking</li>
<li>Weak at: deep phenotype curation</li>
</ul>
</article>
<article class="card db-card" data-tags="core free strain phenotype taxonomy all">
<div class="meta"><span class="score">Top pick</span><span class="tag free">Free</span><span class="tag">Phenotype</span></div>
<h3><a class="mainlink" href="https://bacdive.dsmz.de/" target="_blank" rel="noopener">BacDive</a></h3>
<p>Excellent strain-level information for bacteria and archaea, especially morphology, physiology, culture conditions, and isolation sources.</p>
<ul>
<li>Best for: “What is this strain like in real life?”</li>
<li>Strong at: curated phenotype data</li>
<li>Weak at: viruses and broader eukaryotic microbes</li>
</ul>
</article>
<article class="card db-card" data-tags="core free taxonomy nomenclature bacteria archaea all taxonomy">
<div class="meta"><span class="score">Authority</span><span class="tag free">Free</span><span class="tag">Naming</span></div>
<h3><a class="mainlink" href="https://lpsn.dsmz.de/" target="_blank" rel="noopener">LPSN</a></h3>
<p>The main nomenclature authority for prokaryotes. Use it to confirm official names, synonyms, type strains, and classification status.</p>
<ul>
<li>Best for: checking the correct bacterial or archaeal name</li>
<li>Strong at: valid names and taxonomic standing</li>
</ul>
</article>
</div>
</section>
<section id="core" class="section">
<div class="section-head"><div><h2>Core Hubs</h2><p class="subtle">These are the biggest “hub” databases.</p></div></div>
<div class="grid">
<article class="card db-card" data-tags="core free taxonomy genome literature all">
<div class="meta"><span class="tag free">Free</span><span class="tag">Hub</span></div>
<h3><a class="mainlink" href="https://www.ncbi.nlm.nih.gov/" target="_blank" rel="noopener">NCBI</a></h3>
<p>Broadest general portal for microbes, sequences, genomes, taxonomy, proteins, assemblies, and papers.</p>
</article>
<article class="card db-card" data-tags="core free taxonomy genome metagenome all genome">
<div class="meta"><span class="tag free">Free</span><span class="tag">Genome hub</span></div>
<h3><a class="mainlink" href="https://img.jgi.doe.gov/" target="_blank" rel="noopener">IMG/M</a></h3>
<p>Integrated Microbial Genomes & Microbiomes from JGI. Strong for comparative genomics and microbiome dataset analysis.</p>
</article>
<article class="card db-card" data-tags="core free project metadata genome all genome">
<div class="meta"><span class="tag free">Free</span><span class="tag">Project tracker</span></div>
<h3><a class="mainlink" href="https://gold.jgi.doe.gov/" target="_blank" rel="noopener">GOLD</a></h3>
<p>Genomes OnLine Database. Best for sequencing project metadata, environmental source metadata, and project tracking.</p>
</article>
</div>
</section>
<section id="taxonomy" class="section">
<div class="section-head"><div><h2>Taxonomy & Naming</h2><p class="subtle">Use these to identify the correct scientific name and classification.</p></div></div>
<div class="grid">
<article class="card db-card" data-tags="taxonomy free bacteria archaea nomenclature all">
<div class="meta"><span class="tag free">Free</span><span class="tag">Prokaryote names</span></div>
<h3><a class="mainlink" href="https://lpsn.dsmz.de/" target="_blank" rel="noopener">LPSN</a></h3>
<p>Definitive nomenclature guide for prokaryotic names with standing in nomenclature.</p>
</article>
<article class="card db-card" data-tags="taxonomy free bacteria archaea genome all taxonomy genome">
<div class="meta"><span class="tag free">Free</span><span class="tag">Genome taxonomy</span></div>
<h3><a class="mainlink" href="https://gtdb.ecogenomic.org/" target="_blank" rel="noopener">GTDB</a></h3>
<p>Genome Taxonomy Database. Excellent for genome-based prokaryote classification and modern phylogenetic taxonomy.</p>
</article>
<article class="card db-card" data-tags="taxonomy free all">
<div class="meta"><span class="tag free">Free</span><span class="tag">Broad taxonomy</span></div>
<h3><a class="mainlink" href="https://www.ncbi.nlm.nih.gov/taxonomy" target="_blank" rel="noopener">NCBI Taxonomy</a></h3>
<p>Curated classification for organisms represented in public sequence databases. Very useful as a general framework.</p>
</article>
<article class="card db-card" data-tags="taxonomy free fungi all fungi">
<div class="meta"><span class="tag free">Free</span><span class="tag">Fungal names</span></div>
<h3><a class="mainlink" href="https://www.mycobank.org/" target="_blank" rel="noopener">MycoBank</a></h3>
<p>Key resource for fungal nomenclature, naming novelties, and taxonomic information.</p>
</article>
<article class="card db-card" data-tags="taxonomy free fungi all fungi">
<div class="meta"><span class="tag free">Free</span><span class="tag">Fungal names</span></div>
<h3><a class="mainlink" href="https://www.indexfungorum.org/" target="_blank" rel="noopener">Index Fungorum</a></h3>
<p>Global nomenclatural reference for fungal names, including yeasts and lichens.</p>
</article>
<article class="card db-card" data-tags="taxonomy free virus all">
<div class="meta"><span class="tag free">Free</span><span class="tag">Virus taxonomy</span></div>
<h3><a class="mainlink" href="https://ictv.global/taxonomy" target="_blank" rel="noopener">ICTV Taxonomy Browser</a></h3>
<p>Official taxonomy source for viruses, maintained by the International Committee on Taxonomy of Viruses.</p>
</article>
</div>
</section>
<section id="genomes" class="section">
<div class="section-head"><div><h2>Genomes & Sequencing</h2><p class="subtle">Use these when you want assemblies, comparative genomics, or sequencing project metadata.</p></div></div>
<div class="grid">
<article class="card db-card" data-tags="genome free all">
<div class="meta"><span class="tag free">Free</span><span class="tag">Assemblies</span></div>
<h3><a class="mainlink" href="https://www.ncbi.nlm.nih.gov/genome/" target="_blank" rel="noopener">NCBI Genome</a></h3>
<p>Genome portal spanning assemblies, annotation, and links out to genes, proteins, and sequence records.</p>
</article>
<article class="card db-card" data-tags="genome free bacteria archaea metagenome all">
<div class="meta"><span class="tag free">Free</span><span class="tag">Comparative genomics</span></div>
<h3><a class="mainlink" href="https://img.jgi.doe.gov/" target="_blank" rel="noopener">IMG/M</a></h3>
<p>Strong for comparing isolates, single-cell genomes, MAGs, and microbiome datasets.</p>
</article>
<article class="card db-card" data-tags="genome free metadata project all">
<div class="meta"><span class="tag free">Free</span><span class="tag">Metadata</span></div>
<h3><a class="mainlink" href="https://gold.jgi.doe.gov/" target="_blank" rel="noopener">GOLD</a></h3>
<p>Very useful for sample context, ecosystem classification, sequencing center tracking, and project metadata.</p>
</article>
<article class="card db-card" data-tags="genome free bacteria archaea taxonomy all">
<div class="meta"><span class="tag free">Free</span><span class="tag">Genome taxonomy</span></div>
<h3><a class="mainlink" href="https://gtdb.ecogenomic.org/" target="_blank" rel="noopener">GTDB</a></h3>
<p>Best for classifying prokaryotic genomes in a phylogenetically consistent way.</p>
</article>
<article class="card db-card" data-tags="genome free bacteria archaea all">
<div class="meta"><span class="tag free">Free</span><span class="tag">Genome browser</span></div>
<h3><a class="mainlink" href="https://bacteria.ensembl.org/" target="_blank" rel="noopener">Ensembl Bacteria</a></h3>
<p>Convenient browser for bacterial and archaeal genomes assembled from INSDC sources.</p>
</article>
<article class="card db-card" data-tags="genome paid bacteria archaea identification all">
<div class="meta"><span class="tag paid">Paid / mixed</span><span class="tag">Clinical ID</span></div>
<h3><a class="mainlink" href="https://www.ezbiocloud.net/" target="_blank" rel="noopener">EzBioCloud</a></h3>
<p>Microbiology platform with bacterial identification and genomics tools; often useful in applied or clinical workflows.</p>
</article>
</div>
</section>
<section id="function" class="section">
<div class="section-head"><div><h2>Function, Proteins & Pathways</h2><p class="subtle">Use these when you want to know what a microbe can do.</p></div></div>
<div class="grid">
<article class="card db-card" data-tags="function free metabolism genome all">
<div class="meta"><span class="tag free">Free</span><span class="tag">Pathways</span></div>
<h3><a class="mainlink" href="https://www.kegg.jp/" target="_blank" rel="noopener">KEGG</a></h3>
<p>Classic pathway and metabolism resource. Excellent for understanding genes in the context of pathways and functions.</p>
</article>
<article class="card db-card" data-tags="function free protein annotation all">
<div class="meta"><span class="tag free">Free</span><span class="tag">Proteins</span></div>
<h3><a class="mainlink" href="https://www.uniprot.org/" target="_blank" rel="noopener">UniProt</a></h3>
<p>Highly useful protein knowledgebase with curated annotation, domains, function, and links to taxa and genomes.</p>
</article>
<article class="card db-card" data-tags="function free strain phenotype all">
<div class="meta"><span class="tag free">Free</span><span class="tag">Phenotypes</span></div>
<h3><a class="mainlink" href="https://bacdive.dsmz.de/" target="_blank" rel="noopener">BacDive</a></h3>
<p>Best place to understand morphology, growth conditions, oxygen use, salt tolerance, and culture traits.</p>
</article>
</div>
</section>
<section id="pathogens" class="section">
<div class="section-head"><div><h2>Pathogens & Clinical / Infectious Disease Tools</h2><p class="subtle">Use these if the organism is medically important or you care about virulence, outbreaks, or infectious disease analysis.</p></div></div>
<div class="grid">
<article class="card db-card" data-tags="pathogen free bacteria virus all">
<div class="meta"><span class="tag free">Free</span><span class="tag">Infectious disease</span></div>
<h3><a class="mainlink" href="https://bv-brc.org/" target="_blank" rel="noopener">BV-BRC</a></h3>
<p>Bacterial and Viral Bioinformatics Resource Center. Strong for pathogen genomes, tools, workflows, trees, and comparative analysis.</p>
</article>
<article class="card db-card" data-tags="pathogen free bacteria fungi all">
<div class="meta"><span class="tag free">Free</span><span class="tag">Surveillance</span></div>
<h3><a class="mainlink" href="https://www.nlm.nih.gov/ncbi/resource-lists/pathogen-resources.html" target="_blank" rel="noopener">NCBI Pathogen Resources</a></h3>
<p>NIH / NCBI hub for pathogen-related data, including pathogen detection resources and surveillance-linked genomes.</p>
</article>
<article class="card db-card" data-tags="pathogen free bacteria virulence all">
<div class="meta"><span class="tag free">Free</span><span class="tag">Virulence</span></div>
<h3><a class="mainlink" href="http://www.mgc.ac.cn/VFs/" target="_blank" rel="noopener">VFDB</a></h3>
<p>Virulence Factor Database. A classic specialist database for bacterial virulence genes.</p>
</article>
</div>
</section>
<section id="fungi" class="section">
<div class="section-head"><div><h2>Fungi & Yeasts</h2><p class="subtle">The bacterial world has different authorities than the fungal world, so these are worth bookmarking separately.</p></div></div>
<div class="grid">
<article class="card db-card" data-tags="fungi free taxonomy all">
<div class="meta"><span class="tag free">Free</span><span class="tag">Fungal names</span></div>
<h3><a class="mainlink" href="https://www.mycobank.org/" target="_blank" rel="noopener">MycoBank</a></h3>
<p>Important fungal nomenclature and taxonomic resource with registration features for new names.</p>
</article>
<article class="card db-card" data-tags="fungi free taxonomy all">
<div class="meta"><span class="tag free">Free</span><span class="tag">Fungal names</span></div>
<h3><a class="mainlink" href="https://www.indexfungorum.org/" target="_blank" rel="noopener">Index Fungorum</a></h3>
<p>Global nomenclatural reference covering fungi, yeasts, lichens, and related fungal-like groups.</p>
</article>
<article class="card db-card" data-tags="fungi free genome all">
<div class="meta"><span class="tag free">Free</span><span class="tag">Fungal genomics</span></div>
<h3><a class="mainlink" href="https://mycocosm.jgi.doe.gov/mycocosm/home" target="_blank" rel="noopener">MycoCosm</a></h3>
<p>JGI comparative genomics portal focused on fungi. Strong for genome browsing and comparative analysis.</p>
</article>
<article class="card db-card" data-tags="fungi free agriculture all">
<div class="meta"><span class="tag free">Free</span><span class="tag">Host/location data</span></div>
<h3><a class="mainlink" href="https://fungi.ars.usda.gov/" target="_blank" rel="noopener">USDA Fungal Databases</a></h3>
<p>Useful especially for agriculturally important fungi, host associations, and location-linked information.</p>
</article>
</div>
</section>
<section id="viruses" class="section">
<div class="section-head"><div><h2>Viruses</h2><p class="subtle">Viruses have their own official taxonomy system, separate from bacteria and fungi.</p></div></div>
<div class="grid">
<article class="card db-card" data-tags="virus free taxonomy all">
<div class="meta"><span class="tag free">Free</span><span class="tag">Official taxonomy</span></div>
<h3><a class="mainlink" href="https://ictv.global/taxonomy" target="_blank" rel="noopener">ICTV Taxonomy Browser</a></h3>
<p>The official current taxonomy browser for viruses.</p>
</article>
<article class="card db-card" data-tags="virus free taxonomy all">
<div class="meta"><span class="tag free">Free</span><span class="tag">Downloadable taxonomy</span></div>
<h3><a class="mainlink" href="https://ictv.global/msl" target="_blank" rel="noopener">ICTV Master Species List (MSL)</a></h3>
<p>Downloadable spreadsheet of the current complete ICTV taxonomy. Great when you want the whole taxonomy in one file.</p>
</article>
<article class="card db-card" data-tags="virus free pathogen all">
<div class="meta"><span class="tag free">Free</span><span class="tag">Infectious disease</span></div>
<h3><a class="mainlink" href="https://bv-brc.org/" target="_blank" rel="noopener">BV-BRC</a></h3>
<p>Very useful for viral infectious disease datasets and analysis tools.</p>
</article>
</div>
</section>
<section id="rrna" class="section">
<div class="section-head"><div><h2>rRNA / Amplicon / Microbiome Identification</h2><p class="subtle">These help with 16S, 18S, and ribosomal RNA-based classification.</p></div></div>
<div class="grid">
<article class="card db-card" data-tags="rrna free bacteria archaea euk taxonomy all">
<div class="meta"><span class="tag free">Free</span><span class="tag">rRNA reference</span></div>
<h3><a class="mainlink" href="https://www.arb-silva.de/" target="_blank" rel="noopener">SILVA</a></h3>
<p>Major aligned rRNA sequence resource covering Bacteria, Archaea, and Eukarya.</p>
</article>
<article class="card db-card" data-tags="rrna paid bacteria archaea identification all">
<div class="meta"><span class="tag paid">Paid / mixed</span><span class="tag">Identification</span></div>
<h3><a class="mainlink" href="https://www.ezbiocloud.net/" target="_blank" rel="noopener">EzBioCloud</a></h3>
<p>Useful for bacterial identification and curated type/reference strain sequence matching.</p>
</article>
<article class="card db-card" data-tags="rrna free legacy bacteria archaea fungi all">
<div class="meta"><span class="tag free">Free / legacy</span><span class="tag">Historic toolset</span></div>
<h3><a class="mainlink" href="https://www.canr.msu.edu/cme/resources" target="_blank" rel="noopener">RDP status page</a></h3>
<p>The classic Ribosomal Database Project website is no longer available, but it remains important historically and some classifier tools still circulate offline.</p>
</article>
</div>
</section>
<section id="paid" class="section">
<div class="section-head"><div><h2>Paid / Premium Options Worth Considering</h2><p class="subtle">Most excellent resources are free, but a few premium tools can be useful in applied or clinical settings.</p></div></div>
<div class="grid">
<article class="card db-card" data-tags="paid bacteria archaea rrna genome all">
<div class="meta"><span class="tag paid">Paid / mixed</span><span class="tag">ID + genomics</span></div>
<h3><a class="mainlink" href="https://www.ezbiocloud.net/" target="_blank" rel="noopener">EzBioCloud</a></h3>
<p>Probably the clearest premium-style option to consider if you want curated bacterial identification workflows and practical genomics tools in one place.</p>
</article>
<article class="card db-card" data-tags="paid all">
<div class="meta"><span class="tag">Note</span></div>
<h3>Do you actually need to pay?</h3>
<p>For most educational, hobby, and even a lot of research use, you can do extremely well with <strong>NCBI + BacDive + LPSN + KEGG + SILVA + ICTV + MycoBank</strong> without paying.</p>
</article>
<article class="card db-card" data-tags="paid all">
<div class="meta"><span class="tag">Best value stack</span></div>
<h3>Recommended default stack</h3>
<p><strong>General:</strong> NCBI<br><strong>Phenotype:</strong> BacDive<br><strong>Prokaryote naming:</strong> LPSN<br><strong>Pathways:</strong> KEGG<br><strong>rRNA:</strong> SILVA<br><strong>Viruses:</strong> ICTV<br><strong>Fungi:</strong> MycoBank / Index Fungorum</p>
</article>
</div>
</section>
<section id="recipes" class="section">
<div class="section-head"><div><h2>Use Recipes</h2><p class="subtle">Simple workflows for common questions.</p></div></div>
<div class="grid">
<article class="card db-card" data-tags="all">
<div class="meta"><span class="tag">Recipe</span></div>
<h3>I have a bacterial name and want to verify it</h3>
<ol>
<li>Search the name in <strong>LPSN</strong>.</li>
<li>Check whether there are synonyms or a newer accepted name.</li>
<li>Then open <strong>NCBI Taxonomy</strong> and <strong>BacDive</strong> for broader context.</li>
</ol>
</article>
<article class="card db-card" data-tags="all">
<div class="meta"><span class="tag">Recipe</span></div>
<h3>I have a sequence and want to know what it is</h3>
<ol>
<li>Use <strong>NCBI BLAST</strong> or your usual alignment workflow.</li>
<li>For ribosomal sequences, compare against <strong>SILVA</strong>.</li>
<li>For prokaryotic genome context, check <strong>GTDB</strong>.</li>
</ol>
</article>
<article class="card db-card" data-tags="all">
<div class="meta"><span class="tag">Recipe</span></div>
<h3>I want to know what a microbe does metabolically</h3>
<ol>
<li>Start with <strong>KEGG</strong> and <strong>UniProt</strong>.</li>
<li>Then compare genome context in <strong>NCBI</strong> or <strong>IMG/M</strong>.</li>
</ol>
</article>
<article class="card db-card" data-tags="all">
<div class="meta"><span class="tag">Recipe</span></div>
<h3>I want the most exhaustive practical setup</h3>
<p>Bookmark these: <strong>NCBI, BacDive, LPSN, GTDB, KEGG, SILVA, ICTV, MycoBank, Index Fungorum, IMG/M, GOLD, BV-BRC</strong>.</p>
</article>
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<h2>Notes</h2>
<p class="small">This page is a curated guide, not a claim that one database contains everything. Microbiology is split across multiple specialist resources. The practical answer is to use a small “stack” of trusted databases rather than expect one site to do it all.</p>
<p class="small">For your family website, this file is self-contained and easy to host as a single HTML page. If you want, it can be expanded later with logos, a kid-friendly glossary, or a simple “microbe detective” landing page.</p>
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