Microbiomics

<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.

Microbial Standards & Controls

DataSheet

MSDS

Protocol

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.

Biosafety

Impurity level

Reference genomes and 16S&18S rRNA genes

Relative-abundance deviation in average

Storage solution

Total cell concentration

Manufacturer

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.

Impurity Level

Source

Storage Solution

Characterization

Concentration

Stability

Total DNA Content

Total RNA Content

Total Cell Concentration

Sample Storage

Relative-abundance Deviation

Reference Genomes

Shipping Condition

Storage Condition

ZymoBIOMICS™ Spike-in Control II (Low Microbial Load) (25 Preps.)

ZymoBIOMICS™ Spike-in Control II (Low Microbial Load) (250 Preps.)

<h2>What are PCR and molecular assays for microbiomics?</h2>
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PCR and molecular assays in this category use quantitative PCR (qPCR) or digital PCR to measure the copy number of a defined DNA target, most often the 16S rRNA gene, to determine total bacterial load in a sample, or a specific pathogen or functional gene target for detection purposes. Unlike 16S or shotgun sequencing, which characterize the full taxonomic or functional composition of a community, these molecular assays provide a faster, more targeted quantitative or presence/absence readout for a specific question.
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<h2 dir="ltr">What you will discover:</h2>
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Femto&trade; Quantification Kits: Highly sensitive systems engineered for the detection of human, bacterial, or fungal DNA at the femtogram level with negligible sequence bias.
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High-Fidelity qPCR Premixes: Tailored master mixes designed for effective amplification and enhanced nuclear signal localization in low-biomass samples.
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Certified DNA Standards: Reference materials tested for reproducibility and No Template Controls (NTC) designed to calibrate the linear dynamic range and avert background contamination.
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ZymoTaq&trade; Specialized Polymerases: Enzymes that are heat-activated and free of nucleases, crafted to minimize non-specific amplification and guarantee high specificity in workflows associated with CRISPR.
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<h2>How to choose PCR and molecular assays</h2>
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Use total bacterial load qPCR to screen samples before sequencing
A qPCR assay targeting the 16S rRNA gene quantifies total bacterial content in a sample, providing a useful pre-sequencing check for low-biomass samples likely to produce poor amplification or unreliable sequencing results if processed without this screening step.
Decide between qPCR and digital PCR based on sensitivity needs
Digital PCR can offer higher sensitivity and more accurate quantification than standard qPCR, particularly for low-biomass samples at the limit of detection, though at the cost of longer processing time, generally a meaningful tradeoff only when standard qPCR proves insufficient.
Confirm your qPCR assay design addresses known technical pitfalls
Well-designed 16S qPCR assays address known issues like self-priming or mispriming of unintended targets, amplification bias from non-optimal primer coverage, and amplicon size constraints for compatibility with clinical or high-throughput qPCR platforms.
Use pathogen-specific or functional gene qPCR for targeted detection
Beyond total bacterial load, qPCR can target a specific pathogen's single-copy gene or a functional gene of interest, such as an antibiotic resistance gene, providing a faster, more targeted answer than waiting for full sequencing and bioinformatic analysis.
Plan for known PCR limitations in environmental and clinical samples
Standard qPCR can be limited by reliance on standard reference materials for quantification and is prone to inhibition from substances naturally present in environmental or clinical samples, such as heavy metals or organic matter, which digital PCR can sometimes overcome with improved robustness.
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<h2>Specifications context</h2>
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A PCR-based total bacterial quantification assay can provide an exact calculation of bacterial abundance useful for assessing whether a sample is likely to yield positive amplification before committing it to full sequencing, helping avoid wasted sequencing runs on low-biomass samples. As of 2026, digital PCR continues to see increased adoption over standard qPCR specifically for low-biomass, environmental, or inhibitor-prone sample types, where its improved sensitivity and accuracy can outweigh its longer processing time.
<a href="https://mbpinc.net/contact-us">Reach out to the expert team at MBP Inc.</a> now to ask for a quote on the appropriate PCR and molecular assays for your laboratory.

PCR & Molecular Assays

ZymoTaq qPCR Premix

E2054 by Zymo Research is a 2x hot-start qPCR premix with SYTO® 9 intercalating dye, optimized for real-time amplification of bisulfite-converted DNA. Also suitable for general real-time PCR and HRM analysis. 50 reactions in suggested 50 µL format; 200-reaction format available as E2055.