Brands

<h2>What are microbial and environmental DNA isolation kits?</h2>
&nbsp;
Microbial and environmental DNA isolation kits purify DNA from soil, sediment, freshwater, marine water, feces, and other complex environmental matrices using lysis and purification chemistry designed to remove humic acids, metal compounds, and other inhibitors that interfere with PCR and sequencing, supporting 16S/18S rRNA amplicon profiling and shotgun metagenomic sequencing. Related entities include "kitome" and "splashome" contamination controls, alpha diversity and microbial community composition analysis, and compatibility with both short-read (Illumina) and long-read (Oxford Nanopore) sequencing platforms. Choose a kit validated for your specific sample matrix (soil, sediment, water, or feces), since benchmarking studies consistently show kit performance varies by matrix rather than one kit being universally best.
&nbsp;
<h2 dir="ltr">What you will find:</h2>
&nbsp;
<ul>
<li dir="ltr" role="presentation">Spin-column fungal and bacterial kits for rapid DNA purification using rapid silica-membrane technology&nbsp;</li>
<li dir="ltr" role="presentation">Parallel extraction of soil, fecal, and environmental samples using high-throughput 96-well microplates&nbsp;</li>
<li dir="ltr" role="presentation">Automated&nbsp; purification of complex microbial and environmental specimens using Magnetic bead isolation systems</li>
<li dir="ltr" role="presentation">Scalable microprep and midiprep columns tailored for concentrated low-volume elution demands and diverse sample inputs</li>
</ul>
&nbsp;
<h2>How to choose a microbial and environmental DNA isolation kit</h2>
&nbsp;
Matrix-specific kit performance
Benchmarking studies comparing multiple commercial kits across sediment, water, soil, oyster gut microbiome, and mammalian feces have found that the best-performing kit varies by matrix - kits ranked highly for sediment did not necessarily perform best for water or host-associated samples. Rather than assuming a single "universal" kit, match your kit choice to published benchmarking results for your primary sample type where available.
Inhibitor removal for downstream PCR and sequencing
Environmental samples, especially sediments and soils, contain organic and metal compounds that inhibit PCR amplification if not removed during extraction; kits designed for these matrices integrate inhibitor-removal steps as part of the standard protocol. If your samples have historically produced low PCR amplification efficiency with general-purpose kits, an environmental-matrix-specific kit with built-in inhibitor removal is the first thing to evaluate.
Short-read vs. long-read sequencing compatibility
For long-read metagenomic sequencing, DNA fragment length and integrity from the extraction kit directly affect achievable read lengths, though longer extracted fragments don't always translate consistently into longer sequencing reads - kit choice affects both fragment length and downstream classification rate and reproducibility. If long-read metagenomics is your goal, prioritize kits with published long-read benchmarking data over kits validated only for short-read amplicon work.
Contamination control (kitome/splashome)
Kit-derived contamination ("kitome") and cross-sample contamination during processing ("splashome") can affect microbial community composition results, particularly for low-biomass samples; benchmarking studies evaluate kits specifically for these contamination sources alongside yield and diversity metrics. For low-biomass environmental samples, prioritize kits with documented low kitome contamination in published comparisons.
&nbsp;
<h2>Specifications context</h2>
&nbsp;
The key specs for microbial and environmental DNA isolation are matrix-specific validation (soil vs. sediment vs. water vs. feces), built-in inhibitor removal for PCR-ready output, and fragment length/integrity for long-read sequencing compatibility where relevant. Since benchmarking studies repeatedly show no single kit performs best across all matrices, identifying your primary sample type before selecting a kit is the most impactful decision. Labs running metagenomic surveys across multiple matrices (e.g., soil and water from the same field site) often need separate matrix-optimized kits rather than a single universal kit. The parent <a href="https://mbpinc.net/reagents/molecular-biology/nucleic-acid-extraction-kits/dna-extraction-kits/genomic-dna">genomic DNA extraction kits hub</a>&nbsp;links to related sample-type categories, including&nbsp;<a href="https://mbpinc.net/reagents/molecular-biology/nucleic-acid-extraction-kits/dna-extraction-kits/genomic-dna/insect">insect genomic DNA kits</a>&nbsp;and&nbsp;<a href="https://mbpinc.net/reagents/molecular-biology/nucleic-acid-extraction-kits/dna-extraction-kits/genomic-dna/plant">plant genomic DNA kits</a>&nbsp;for organism-associated environmental work, and&nbsp;<a href="https://mbpinc.net/reagents/molecular-biology/nucleic-acid-extraction-kits/dna-extraction-kits/high-molecular-weight-dna">high molecular weight DNA kits</a>&nbsp;for long-read metagenomics requiring larger fragment sizes. For cell-free DNA in environmental water samples (eDNA detection), see&nbsp;<a href="https://mbpinc.net/reagents/molecular-biology/nucleic-acid-extraction-kits/dna-extraction-kits/cell-free-dna">cell-free DNA kits</a>.&nbsp;
<section class="mbp-contact-cta">
&nbsp;
MBP's specialist team can help match kit chemistry, format, and throughput to your sample type and downstream application.&nbsp;<a href="https://mbpinc.net/contact-us">Contact the MBP team</a> for personalized guidance.
</section>

Microbial & Environmental DNA Isolation

DataSheet

D4302/D4308 (US) - MSDS

D4306 (US) - MSDS

D4302-E/D4308-E (EU) - MSDS

D4306-E (EU) - MSDS

D4302/D4306/D4308-Protocol

D4302-E/D4306-E/D4308-E-Protocol

D4302-Optimized Lysis Protocols

D4302-App Note-Hamilton

ZymoBIOMICS 96 MagBead DNA Kit

D4302 by Zymo Research — ZymoBIOMICS 96 MagBead DNA Kit with BashingBead™ Lysis Rack; 2 × 96 preps; processes feces, soil, water, swabs, and body fluids; ≥37.5 µL elution; up to 10 µg DNA; ~90 min for 96 samples; inhibitor-free for 16S and NGS.

Applicable For

Elution Volume

Equipment

Processing Volume

Purity

Sample Source

Sample Storage

Size Range

Type

Yield

Manufacturer

Shipping Condition

Storage Condition

ZymoBIOMICS™-96 MagBead Kit (2 x 96 Preps.)(Lysis Rack)

ZymoBIOMICS™-96 MagBead Kit (2 x 96 Preps.) CE-IVD (Lysis Rack)

ZymoBIOMICS™-96 MagBead DNA Kit (2 x 96 Preps.) (Lysis Tubes)

ZymoBIOMICS™-96 MagBead DNA Kit (2 x 96 Preps.) CE-IVD (Lysis Tubes)

ZymoBIOMICS™-96 Magbead DNA Kit (2 x 96 Preps.) (No Lysis Matrix)

ZymoBIOMICS™-96 Magbead DNA Kit (2 x 96 Preps.) CE-IVD (No Lysis Matrix)

<h2>What are Magnetic Bead Bacterial and Fungal RNA Extraction Kits?</h2>
&nbsp;
Magnetic bead bacterial and fungal RNA extraction kits isolate total RNA from Gram-positive and Gram-negative bacteria, yeasts, filamentous fungi, algae, and protozoa by combining mechanical bead-beating lysis with paramagnetic silica-bead RNA purification in a 96-well format. After disrupting cell walls with BashingBeads in a ZymoBIOMICS lysis buffer, the clarified lysate is added to paramagnetic beads that bind RNA under chaotropic conditions; a magnetic field captures the bead-RNA complex during wash steps, eliminating centrifugation for the purification phase. Choose the magnetic bead format for bacterial/fungal RNA when processing more than 48 samples per session, when diverse microbial community samples require unbiased lysis, or when your lab has compatible automation infrastructure.
&nbsp;
<h2 dir="ltr">What you will find:</h2>
&nbsp;
<ul>
<li data-section-id="1xshhha" data-start="0" data-end="127">ZymoBIOMICS&trade; 96 MagBead RNA Kit for high-throughput isolation of total RNA from complex microbiome and environmental samples.</li>
<li data-section-id="1lfygkt" data-start="128" data-end="253">Ultra-dense magnetic bead technology designed to maximize RNA recovery from difficult matrices with high inhibitor content.</li>
<li data-section-id="hclgjn" data-start="254" data-end="354">96-well magnetic bead workflows that enable efficient parallel processing of large sample batches.</li>
<li data-section-id="mefpx5" data-start="355" data-end="477">Inhibitor-free RNA purification solutions suitable for downstream RT-qPCR, RNA sequencing, and gene expression analysis.</li>
<li data-section-id="9ywux8" data-start="478" data-end="625" data-is-last-node="">Automation-friendly RNA extraction systems compatible with high-throughput microbiome, metatranscriptomics, and environmental research workflows.</li>
</ul>
&nbsp;
<h2>How to Choose a Magnetic Bead Bacterial/Fungal RNA Kit</h2>
&nbsp;
Unbiased Lysis Confirmation
For community samples containing mixed Gram-positive and Gram-negative bacteria and fungi, verify the kit is validated for unbiased lysis of all organism types. The ZymoBIOMICS MagBead DNA/RNA kit uses a lysis buffer system designed to eliminate the bias toward Gram-negative recovery that affects kits relying solely on enzymatic or detergent lysis. Run the ZymoBIOMICS Microbial Community RNA Standard alongside samples to confirm balanced recovery.
DNA/RNA Co-Extraction
For microbiome studies requiring both 16S rRNA amplicon sequencing (DNA) and metatranscriptomic RNA-seq (RNA) from the same sample, select a kit explicitly validated for co-extraction. The ZymoBIOMICS MagBead DNA/RNA kit delivers both analytes from one extraction, conserving sample and reducing per-analyte processing time.
Automation Platform
Confirm validated automation scripts before purchase. ZymoBIOMICS MagBead kits provide scripts for KingFisher Flex, Apex, Accuris IsoPure 96, and AllSheng AutoPure 96; Thermo Fisher MagMAX Microbiome Ultra kit is validated on KingFisher instruments. Generic magnetic bead kits without platform-specific protocols require in-house development.
Sample Type and Stabilization
Environmental samples (stool, soil, water, biofilms, swabs) benefit from DNA/RNA Shield for ambient-temperature stabilization during collection and transport. Confirm the kit accepts Shield-preserved samples directly, which eliminates a centrifugation and resuspension step.
DNase I Treatment
For RNA-seq and RT-qPCR, include DNase I to remove co-purified genomic DNA. Bacterial DNA-to-RNA ratios are high; confirm whether the kit includes on-bead DNase digestion or requires a post-extraction treatment step.
&nbsp;
<h2>Specifications Context</h2>
&nbsp;
Performance benchmarks for magnetic bead microbial RNA kits: A260/A280 &gt;= 1.8, A260/A230 &gt;= 1.5, and &gt;=70% recovery of representative Gram-positive and Gram-negative reference targets by RT-qPCR relative to a known input standard. Unbiased lysis is measured by even recovery of Gram-positive organisms such as Enterococcus faecalis and Gram-negative species such as E. coli from a mixed community; a &gt;=50% ratio between Gram-positive and Gram-negative recovery indicates acceptable extraction performance. ZymoBIOMICS workflows are used as reference extraction methods in NIH Human Microbiome Project follow-on studies and are cited in peer-reviewed metatranscriptomic methods papers. DNA/RNA Shield-stabilized samples remain stable at room temperature for 30 days, enabling field collection and shipment to centralized extraction facilities without cold-chain requirements.
<section class="mbp-contact-cta"></section>
&nbsp;
<a href="https://mbpinc.net/contact-us">Contact the expert team </a>at MBP today and get downstream-ready mag bead systems for your lab.

Mag Beads

Bacterial/Fungal RNA/Mag Beads

MSDS

Protocol

ZymoBIOMICS 96 MagBead RNA Kit

ZymoBIOMICS 96 MagBead RNA Kit (R2137) by Zymo Research is a high-throughput magnetic bead-based kit for total RNA isolation (≥17 nt) from diverse microbial and environmental samples in 96-well format. Binds up to 15 µg RNA per 30 µl beads, elutes in 50 µl, and is compatible with Tecan, Hamilton, KingFisher, and other automated platforms. Available in 96-prep and 4 × 96-prep formats.

Binding Capacity

Equipment Needed

Recommended Materials

Sample Preservation

Sample Types

Size Limits

Storage

ZymoBIOMICS™ 96 MagBead RNA Kit (96 Preps.)

ZymoBIOMICS™ 96 MagBead RNA Kit (4 x 96 Preps.)

Columns, Plastics & Accessories

ZymoBIOMICS BashingBead Lysis Rack (0.5 mm & 0.1 mm)

The ZymoBIOMICS™ BashingBead Lysis Rack by Zymo Research is a 96-tube rack (12 strips × 8 tubes) for high-throughput mechanical disruption of tough-to-lyse samples. Each 1.1 ml tube contains 0.5 ml dry volume of 0.5 mm and 0.1 mm BashingBead Lysis Matrix. Compatible with bead homogenizers; strip caps and rack cover included. Also available with heat-sealing foils.

ZymoBIOMICS BashingBead Lysis Rack (0.5 mm & 0.1 mm) (1 Rack)

ZymoBIOMICS BashingBead Lysis Rack (0.5 mm & 0.1 mm) (1 Rack) with Heat Sealing Foil (2 Pack)

<h2>What Are Zymo Research Buffers?</h2>
Zymo Research buffers are formulation-specific reagents used at defined steps &mdash; lysis, binding, wash, and elution &mdash; in Zymo-Spin column-based purification protocols for DNA, RNA, and bisulfite-converted DNA. Each buffer is optimized for a specific kit family: DNA Wash Buffer concentrate (requires ethanol addition before use) removes salts and contaminants before elution from Zymo-Spin silica columns; DNA Elution Buffer (10 mM Tris, pH 8.5, 0.1 mM EDTA) releases purified DNA from the matrix; RNA Wash Buffer supports RNA extraction kits including Quick-RNA and Direct-zol lines; M-Elution Buffer is designed for eluting bisulfite-converted DNA in EZ DNA Methylation kits. Researchers typically order these separately when a single buffer component runs out before the rest of the kit, or when scaling up a protocol beyond the volume included.
TL;DR: Order Zymo buffers individually to replenish a specific step in your existing Zymo workflow without replacing the full kit.
<h2>How to Choose Zymo Research Buffers</h2>
<h3>Match the buffer to your kit family</h3>
Every Zymo buffer is paired to a specific kit line. DNA Wash Buffer and DNA/RNA Wash Buffer concentrate are used in DNA Clean &amp; Concentrator, Quick-DNA, and Zymoclean Gel DNA Recovery kits. RNA Wash Buffer pairs with Quick-RNA kits. ZymoBIOMICS DNA Wash Buffer 1 and Wash Buffer 2 are specific to the ZymoBIOMICS microbiomics line. Substituting a buffer from a different kit family can compromise yield or purity.
<h3>Confirm ethanol addition requirements before use</h3>
Several Zymo wash buffer concentrates require addition of 96-100% ethanol to the bottle before first use &mdash; the label states the exact volume. DNA Wash Buffer concentrate, DNA/RNA Wash Buffer concentrate, and Urine DNA Wash Buffer concentrate all require this step. Pre-made (non-concentrate) versions such as RNA Wash Buffer are supplied ready to use.
<h3>Select the right volume for your throughput</h3>
Zymo buffers are available in sizes from 6 ml (single-experiment replenishment) up to 500 ml (Buffer P1 Red, for high-volume plasmid prep labs). For labs processing more than 50 samples per week, ordering the largest available size reduces per-sample cost and the frequency of reordering.
<h3>Choose elution buffer chemistry based on downstream application</h3>
DNA Elution Buffer (10 mM Tris pH 8.5, 0.1 mM EDTA) is the standard for most PCR and sequencing applications. For applications sensitive to EDTA &mdash; such as some restriction enzyme digests or direct use with divalent cation-dependent enzymes &mdash; eluting in molecular-grade water or a Tris-only buffer is preferable. M-Elution Buffer is specifically formulated for bisulfite-converted DNA and should not be substituted with standard elution buffer in methylation workflows.
<h3>Verify research-use-only status</h3>
All Zymo Research buffers sold through MBP are for research use only (RUO). They are not cleared for in vitro diagnostic use. For clinical or diagnostic laboratory applications, confirm regulatory status with your institutional compliance officer before use.
<h2>Compare Zymo Buffer Types</h2>
<table>
<thead>
<tr>
<th>Buffer Type</th>
<th>Primary Application</th>
<th>Kit Family</th>
<th>Format Available</th>
</tr>
</thead>
<tbody>
<tr>
<td>DNA Wash Buffer (concentrate)</td>
<td>Salt removal before DNA elution</td>
<td>DNA Clean &amp; Concentrator, Quick-DNA</td>
<td>6 ml &ndash; 200 ml</td>
</tr>
<tr>
<td>DNA/RNA Wash Buffer (concentrate)</td>
<td>Salt removal for dual DNA/RNA preps</td>
<td>Quick-DNA/RNA kits</td>
<td>6 ml &ndash; 200 ml</td>
</tr>
<tr>
<td>DNA Elution Buffer (10 mM Tris pH 8.5, 0.1 mM EDTA)</td>
<td>DNA release from silica column</td>
<td>All Zymo DNA purification</td>
<td>16 ml &ndash; available sizes vary</td>
</tr>
<tr>
<td>RNA Wash Buffer</td>
<td>RNA purification wash step</td>
<td>Quick-RNA kits</td>
<td>Ready-to-use</td>
</tr>
<tr>
<td>M-Elution Buffer</td>
<td>Elution of bisulfite-converted DNA</td>
<td>EZ DNA Methylation kit families</td>
<td>Small volume</td>
</tr>
<tr>
<td>ZymoBIOMICS DNA Wash Buffer 2</td>
<td>Metagenomic/microbiomic DNA cleanup</td>
<td>ZymoBIOMICS DNA kits</td>
<td>Sold separately</td>
</tr>
<tr>
<td>Buffer P1 Red</td>
<td>Alkaline lysis resuspension (plasmid prep)</td>
<td>Zyppy Plasmid Miniprep</td>
<td>10 ml &ndash; 500 ml</td>
</tr>
</tbody>
</table>
<h2>Specifications Context</h2>
Zymo wash buffer concentrates are supplied at a defined fold-concentration (commonly 4x or 6x) and require ethanol addition to reach working strength &mdash; the exact ratio is printed on the bottle and in the kit protocol. Elution buffer volumes for Zymo-Spin columns typically range from 6 to 100 &micro;l per elution; larger elution volumes improve total yield at the cost of DNA concentration. For DNA elution from Zymo-Spin columns, the protocol recommends a minimum 1-minute contact time between elution buffer and the silica matrix to maximize recovery of fragments 10 kb and above. As of 2025, Zymo Research tests all buffer lots for performance consistency, with integrity guaranteed for up to one year from purchase date.
Browse the full <a href="https://www.notion.so/reagents">Zymo Research reagents collection at MBP</a> for kits and columns that use these buffers, or visit our <a href="https://www.notion.so/reagents/buffers">reagent buffers category</a> for non-Zymo buffer options including ABM and other brands. For volume orders or purchase orders, use the <a href="https://www.notion.so/quickorder">Quick Order</a> tool or <a href="https://www.notion.so/contact-us">contact us</a> directly &mdash; MBP is a registered vendor for institutional procurement systems.
Last updated: June 2025
&nbsp;

Zymo Buffers

ZymoBIOMICS DNase/RNase Free Water

ZymoBIOMICS DNase/RNase Free Water (D4302-5) by Zymo Research — certified DNase-free and RNase-free nuclease-free water for ZymoBIOMICS purification kits and molecular biology workflows. Available in 1 ml, 10 ml, 30 ml, and 50 ml. Research use only. Made in the USA.

ZymoBIOMICS™ DNase/RNase-free Water (1 ml)

ZymoBIOMICS™ DNAse/RNAse Free Water (10 ml)

ZymoBIOMICS™ DNase/RNase Free Water (30 ml)

ZymoBIOMICS™ DNase/RNase Free Water (50 ml)

<h2>What are Magnetic Bead Microbial DNA/RNA Co-Extraction Kits?</h2>
&nbsp;
Magnetic bead microbial DNA/RNA co-extraction kits purify both genomic DNA and total RNA, including small RNAs &gt;=17 nt, from microbial community samples - stool, soil, water, biofilm, swabs, and body fluids using BashingBead mechanical lysis in a 96-deep-well plate followed by binding of nucleic acids to paramagnetic silica-coated beads, magnetic separation during successive wash steps to remove PCR inhibitors, and elution in &gt;=50 ul of ZymoBIOMICS DNase/RNase-Free Water. The entire purification phase requires no centrifugation and integrates directly with KingFisher Flex, Accuris IsoPure 96, and AllSheng AutoPure 96 liquid-handling platforms. Choose the magnetic bead format for microbial DNA/RNA co-extraction when processing 48+ community samples per session, when a compatible automation platform is available, or when reproducibility across hundreds of samples is required for a human microbiome cohort, environmental monitoring, or clinical trial.
&nbsp;
<h2 dir="ltr">What you will find:</h2>
&nbsp;
<ul>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" aria-level="1">
Quick-DNA/RNA HT Kit for high-throughput isolation of total nucleic acids from liquid clinical and biological specimens using a magnetic bead&ndash;based extraction system.
</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" aria-level="1">
ZymoBIOMICS MagBead DNA/RNA Kit for unbiased recovery of microbiome DNA and RNA without chemical bias, featuring an innovative lysis system.
</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" aria-level="1">
Quick-DNA/RNA Pathogen MagBead Kit for rapid isolation of viral, bacterial, and protozoan nucleic acids from challenging vector samples using an optimized buffer
</li>
</ul>
&nbsp;
<h2>How to Choose a Magnetic Bead Microbial DNA/RNA Co-Extraction Kit</h2>
&nbsp;
Automation Script Availability
Confirm the kit manufacturer provides a validated, instrument-specific script for your platform before purchase. Zymo Research provides automation scripts for KingFisher Flex, KingFisher Apex, Accuris IsoPure 96, and AllSheng AutoPure 96; Tecan Fluent and Hamilton STAR scripts require adaptation. Script development and validation add 2-4 weeks; factor this into project timelines.
Combined vs. Separate Analyte Fractions
The ZymoBIOMICS MagBead DNA/RNA kit elutes a combined total nucleic acid fraction. For studies requiring separate DNA and RNA fractions from the same extraction (parallel metagenomics and metatranscriptomics), apply post-extraction enzymatic depletion (DNase I on the RNA aliquot, RNase A on the DNA aliquot) or use the ZymoBIOMICS DNA/RNA Miniprep kit, which uses column-switching architecture for native separation.
96-Well Bead-Beating Setup
The lysis step requires a 96-well bead mill compatible with ZR-96 BashingBead Lysis Racks. Validated instruments include GenoGrinder 2000, Retsch MM400 with a 96-tube rack adapter, and Bertin Precellys. The bead-beating step is the primary manual step in an otherwise automated workflow; confirm the lab has a compatible bead mill before adopting the kit.
Inhibitor Load by Sample Type
Stool samples have moderate inhibitor loads (bile salts, starch metabolites) that ZymoBIOMICS wash steps reliably remove. Soil samples -- especially high-humic tropical or peat soils - carry heavier inhibitor loads that may require reducing input mass to 10-50 mg per well and validating A260/A230 &gt;= 1.5 on initial test extractions. If A260/A230 remains below 1.5, apply an additional cleanup step with Zymo OneStep PCR Inhibitor Removal Columns before library preparation.
DNA/RNA Shield Sample Collection
For multi-site human microbiome cohort studies, use DNA/RNA Shield fecal collection tubes (Zymo R1101) as the collection device. Samples stabilized at room temperature for up to 30 days in Shield are directly loadable into the ZR-96 BashingBead Rack, streamlining the pre-extraction workflow and enabling consistent RNA preservation across diverse collection sites.
&nbsp;
<h2>Specifications Context</h2>
&nbsp;
ZymoBIOMICS MagBead DNA/RNA kit produces total nucleic acid eluted into &gt;=50 ul with A260/A280 &gt;= 1.8, A260/A230 &gt;= 1.5, and DNA fragment sizes suitable for 16S rRNA amplicon sequencing and shotgun metagenomics. Input specification: approximately 2 &times; 10^8 bacterial cells, 2 &times; 10^7 yeast cells, or ~40 mg human stool per well. A published 2024 high-throughput fecal microbiome DNA extraction study demonstrated that bead-beating at &gt;=3,000xg significantly improves detection of hard-to-lyse Gram-positive genera - Blautia, Bifidobacterium, and Ruminococcus compared with no bead-beating, confirming that mechanical lysis is non-negotiable for unbiased community co-extraction. ZymoBIOMICS MagBead workflows are used in NIH-funded human microbiome research and are the standard extraction approach for multi-site gut microbiome cohort studies at institutions registered with MBP, including Howard Hughes Medical Institute and MD Anderson Cancer Center.
&nbsp;
<a href="https://mbpinc.net/contact-us">Contact the MBP team</a> and get high-yield mag bead systems for your high-throughput extraction workflows.

ZymoBIOMICS MagBead DNA/RNA

R2135 by Zymo Research is the ZymoBIOMICS&#8482; MagBead DNA/RNA kit for simultaneous co-purification of DNA and total RNA from complex microbiome samples in a 96-well magnetic bead format. With a binding capacity of 15 µg DNA/RNA per 30 µl beads and elution in 50 µl, R2135 delivers NGS-ready nucleic acids (A260/A280 &gt;1.8) from fecal, soil, water, biofilm, and swab samples, with compatibility for automated liquid handling platforms and robotic processors.

Sample types

ZymoBIOMICS™ 96 MagBead DNA/RNA Kit (96 Preps.)

ZymoBIOMICS™ 96 MagBead DNA/RNA Kit (4 x 96 Preps.)

ZymoBIOMICS MagBinding Beads

D4302-6 by Zymo Research is the ZymoBIOMICS™ MagBinding Beads—a magnetic bead suspension for use in ZymoBIOMICS magnetic bead-based DNA purification kits for high-throughput microbiome and metagenomic DNA extraction from fecal, soil, water, and biofilm samples in 96-well automation formats. Available as 6 mL or 12 mL standalone bottles for bead replenishment.

ZymoBIOMICS™ MagBinding Beads (12 ml)

ZymoBIOMICS™ MagBinding Beads (6 ml)

<h2>What are microbiome standards and controls?</h2>
&nbsp;
Microbiome standards and controls are defined reference materials, ranging from a single microbial DNA standard to a complex mock community containing multiple known bacterial, fungal, or archaeal species at defined relative abundances, used to validate that an extraction, library preparation, and sequencing pipeline is performing as expected. Running a standard alongside real samples provides a specific, customized control for confirming reproducibility and enables meaningful comparison of results generated in different laboratories or at different times.
&nbsp;
<h2 dir="ltr">What you will discover:</h2>
&nbsp;
<ul>
<li dir="ltr" aria-level="1">
ZymoBIOMICS&trade; Community Standards: Mock communities tested for reproducibility with specific microbial ratios to assess taxonomic profiling and ensure accuracy across sequencing platforms.
</li>
<li dir="ltr" aria-level="1">
Log-Distributed DNA Standards: Customized genomic blends created to assess the limit of detection (LOD) and linear dynamic range for identifying rare taxa.
</li>
<li dir="ltr" aria-level="1">
Microbial Spike-in Controls: Internal standards with high and low loads for precise cell quantification and normalization of data across various matrices in simultaneous processing.
</li>
<li dir="ltr" aria-level="1">
Site-Targeted Reference Materials: Specialized standards for gut, oral, and fecal analysis, employing TruMatrix&trade; technology to replicate authentic spatial transcriptomics environments.
</li>
<li dir="ltr" aria-level="1">
High Molecular Weight (HMW) DNA: Ultra-pure, elongated templates designed explicitly to standardize long-read sequencing systems and verify assembly efficacy.
</li>
</ul>
&nbsp;
<h2>How to choose microbiome standards and controls</h2>
&nbsp;
Match standard complexity to your validation goal
A single-species microbial DNA or inactivated bacteria standard is sufficient for confirming basic assay sensitivity or specificity, while a multi-species mock community standard with defined relative abundances is needed to evaluate extraction and amplification bias across an entire workflow.
Use a standard to benchmark a new extraction or library prep protocol
Running a known mock community through a new or modified extraction and library preparation protocol, then comparing the resulting sequencing output against the standard's defined composition, reveals whether the new protocol introduces meaningful bias compared with an established method.
Confirm whether your standard supports both DNA-based and RNA-based workflows
Some standards are formulated specifically for DNA-based 16S or shotgun metagenomic workflows, while others, or specific lots, are validated for RNA extraction and metatranscriptomic workflows as well, a distinction worth checking against your specific application.
Include a standard when comparing results across different laboratories
Because microbiome sequencing results can be sensitive to differences in extraction method, primer choice, and sequencing platform between labs, including the same reference standard across collaborating sites supports more reliable comparison of results generated independently.
Confirm standard storage and stability before long-term use
Microbial community standards typically have documented stability windows and storage temperature requirements, and confirming these align with your intended use timeline helps avoid degraded standard material producing misleading validation results.
&nbsp;
<h2>Specifications context</h2>
&nbsp;
Individual microbial DNA and inactivated bacteria standards add value specifically by providing a specific, customized control, supporting both microbiomics and metagenomics workflows by increasing reproducibility and allowing reliable comparison of results from different laboratories. As of 2026, defined mock community standards remain a standard tool for benchmarking new extraction or library preparation protocols against established methods before adopting a new workflow for real sample processing.
<a href="https://mbpinc.net/contact-us">Reach out to the expert team at MBP Inc.</a> now to obtain a quote for the appropriate microbial standards for your lab.

Microbial Standards & Controls

ZymoBIOMICS Microbial Community DNA Standard

D6305 by Zymo Research is a microbial community DNA standard composed of genomic DNA from eight bacterial and two fungal strains at defined log-distribution proportions, with DNA fragments less than 15 kb, designed to assess bias and performance in microbiomics and metagenomics sequencing workflows.

ZymoBIOMICS™ Microbial Community DNA Standard (200 ng)

ZymoBIOMICS™ Microbial Community DNA Standard (2000 ng)

ZymoBIOMICS Microbial Community DNA Standard II (Log Distribution)

ZymoBIOMICS Microbial Community DNA Standard II Log Distribution (D6311) by Zymo Research — 220 ng/20 µl, 10 microbial strains (8 bacteria + 2 yeasts) at logarithmic abundances spanning 6 orders of magnitude. &lt;0.01% foreign DNA; detects as few as 3 DNA copies. For NGS metagenomics QC and workflow bias detection. Made in the USA.

ZymoBIOMICS Spike-in Control I (High Microbial Load)

The D6320 by Zymo Research is a ZymoBIOMICS Spike-in Control I for high microbial load samples, containing equal cell numbers of fully inactivated Imtechella halotolerans and Allobacillus halotolerans (&lt;0.01% foreign DNA impurity) stored in DNA/RNA Shield at −80°C. Added before extraction, D6320 enables absolute microbial quantification and extraction QC in 16S rRNA amplicon sequencing and metagenomic workflows.

Biosafety

Impurity Level

Reference Genomes

Storage Solution

ZymoBIOMICS™ Spike-in Control I (High Microbial Load) (25 Preps.)

ZymoBIOMICS™ Spike-in Control I (High Microbial Load) (250 Preps.)

ZymoBIOMICS™ BashingBead Buffer (150 ml)

D4302-1-150 by Zymo Research is a 150 mL bottle of ZymoBIOMICS™ BashingBead Buffer — 750 µL used per sample with ZR BashingBead Lysis Tubes (0.1/0.5 mm) for mechanical bead-beating lysis of microbial cells in fecal, soil, water, and tissue samples. For use with ZymoBIOMICS DNA and DNA/RNA extraction kits.

MSDS - D4301

Optimized Lysis Protocols

MSDS - D4305

ZymoBIOMICS™ DNA Microprep Kit

D4301 ZymoBIOMICS DNA Microprep Kit by Zymo Research — 50 preps; BashingBead lysis; 20 &micro;l elution; up to 5 &micro;g yield; 15&ndash;20 kb DNA; OneStep PCR inhibitor removal; feces, soil, swabs, cells.

ZymoBIOMICS™ DNA Microprep Kit (Lysis Tubes) (50 Preps.)

ZymoBIOMICS™ DNA Microprep Kit (No Lysis Matrix) (50 Preps.)

D4300/D4300T - MSDS

D4300-1 - MSDS

D4300-2 - MSDS

D4300-3 - MSDS

D4300-4 - MSDS

D4304 - MSDS

D4304-Protocol

D4300-Optimized Lysis Protocol

ZymoBIOMICS™ DNA Miniprep Kit

D4300 by Zymo Research: ZymoBIOMICS™ DNA Miniprep Kit, 50 preps. Extracts inhibitor-free microbial DNA from feces (≤200 mg), soil (≤250 mg), and cells (≤100 mg). Yield up to 25 µg; 15–20 kb DNA; BashingBead lysis; HRC inhibitor removal. Validated for microbiome and metagenomics. Made in USA.