Microbial Standards & Controls

<h2>What are microbiome standards and controls?</h2>
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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.
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<h2 dir="ltr">What you will discover:</h2>
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ZymoBIOMICS&trade; Community Standards: Mock communities tested for reproducibility with specific microbial ratios to assess taxonomic profiling and ensure accuracy across sequencing platforms.
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Log-Distributed DNA Standards: Customized genomic blends created to assess the limit of detection (LOD) and linear dynamic range for identifying rare taxa.
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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.
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Site-Targeted Reference Materials: Specialized standards for gut, oral, and fecal analysis, employing TruMatrix&trade; technology to replicate authentic spatial transcriptomics environments.
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High Molecular Weight (HMW) DNA: Ultra-pure, elongated templates designed explicitly to standardize long-read sequencing systems and verify assembly efficacy.
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<h2>How to choose microbiome standards and controls</h2>
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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.
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<h2>Specifications context</h2>
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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.

DataSheet

MSDS

Protocol

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.

Applicable For

Purity

Sample Source

Processing Volume

Yield

Sample Storage

Manufacturer

Shipping Condition

Storage Condition

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.)

MSDS (EU)

MSDS (US)

ZymoBIOMICS™ Fecal reference with TruMatrix Tech (1 ml)

The D6323 by Zymo Research is a 1 mL human fecal reference material with TruMatrix Technology, containing ~10 mg feces/mL, ~6 µg DNA/mL, and ~11 µg RNA/mL from a single homogenized batch of over 2 million identical preparations. Stored in DNA/RNA Shield with fully inactivated pathogens, D6323 serves as a reproducible positive control for 16S amplicon sequencing, metagenomics, and metatranscriptomics workflows.

Characterization

Concentration

Stability

Total DNA Content

Total RNA Content

ZymoBIOMICS™ Gut Microbiome Standard (750 µl)

ZymoBIOMICS Gut Microbiome Standard (D6331) by Zymo Research — 750 µl (10 preps), 21 microbial strains (Bacteria, Fungi, Archaea), ~3.94 × 10⁹ cells/ml, &lt;15% abundance deviation. BSL 1 inactivated. For gut microbiome NGS workflow validation. Stored in 2× DNA/RNA Shield. Made in the USA.

Biosafey

Relative-abundance Deviation

Total Cell Concentration

ZymoBIOMICS™ HMW DNA Standard (50 µl)

D6322 by Zymo Research is a high-molecular-weight (&gt;50 kb) DNA standard containing 5000 ng of genomic DNA from seven bacterial species and one yeast strain at defined theoretical proportions, designed to benchmark third-generation long-read sequencing workflows including Oxford Nanopore and PacBio platforms.

Source

ZymoBIOMICS™ Microbial Community Standard (10 Preps.)

D6300 by Zymo Research is the ZymoBIOMICS™ Microbial Community Standard (10 preps, 0.75 ml each), containing 8 fully inactivated bacteria and 2 yeasts at ~1.4 × 1010 cells/ml with cross-validated theoretical composition and <0.01% foreign microbial DNA. Use it to benchmark 16S, ITS, and shotgun metagenomics workflows, or to detect bias in DNA isolation protocols. Store at -80°C. MBP is a registered vendor for Howard Hughes Medical Institute, Vanderbilt University, MD Anderson Cancer Center, Eurofins, and many other institutes across the USA.

ZymoBIOMICS™ Microbial Community Standard II (Log Distribution) (750 µl)

The ZymoBIOMICS™ Microbial Community Standard II (D6310) by Zymo Research is a 750 µl (10 × 75 µl) whole-cell mock community with log-distributed abundance spanning 10 organisms across six orders of magnitude — 89.1% L. monocytogenes down to 0.000089% S. aureus (~100 cells/prep). Composition independently verified; &lt;0.01% foreign microbial DNA. For detection-limit benchmarking in 16S/metagenomics workflows.

ZymoBIOMICS™ Oral Microbiome Standard (750 µl)

D6332 by Zymo Research — ZymoBIOMICS Oral Microbiome Standard; 12 inactivated bacterial strains; ~1.3 × 10⁹ cells/mL in DNA/RNA Shield™; &lt;0.01% foreign DNA; 10 preps × 750 µL; positive control for 16S and NGS microbiome workflows.

Impurity level

Reference genomes and 16S&18S rRNA genes

Relative-abundance deviation in average

Storage solution

Total cell concentration

ZymoBIOMICS™ Spike-in Control II (Low Microbial Load)

D6321 by Zymo Research is the ZymoBIOMICS™ Spike-in Control II (Low Microbial Load). Whole-cell spike-in control with 3 bacterial strains (10³–10⁵ cells, log distribution): Truepera radiovictrix, Imtechella halotolerans, Allobacillus halotolerans. Foreign microbial DNA <0.01%. Preserved in DNA/RNA Shield™. Store at −80°C.