Microbiomics

<h2>What are 16S/ITS NGS library preparation kits?</h2>
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16S/ITS NGS library preparation kits convert extracted microbial DNA into a sequencing-ready library by amplifying a targeted hypervariable region: the 16S ribosomal RNA gene for bacterial and archaeal community profiling, or the ITS (internal transcribed spacer) region for fungal community profiling. Both genes contain conserved flanking sequences that serve as universal PCR primer binding sites, allowing amplification of the variable region in between, which is then sequenced and compared against a reference database for taxonomic classification.
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<h2 dir="ltr">What you will discover:</h2>
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Quick-16S&trade; Plus Kits (V1&ndash;V4): Enhanced systems for targeted amplification of bacterial 16S rRNA, incorporating validated reagents for accurate classification.
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Quick-ITS&trade; Plus Library Prep: Sensitive kits for fungal detection, employing specialized chemistry to capture ITS regions while preserving genomic integrity at its best.
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UDI Indexing Integration: Sophisticated indexing methods to avoid barcode hopping and guarantee precise demultiplexing during simultaneous processing.
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Accelerated Workflows: Nuclease-free procedures that reduce manual effort while ensuring transfection-grade purity for delicate sequencing systems.
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<h2>How to choose a 16S/ITS library preparation kit</h2>
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Confirm which hypervariable region(s) your kit targets
16S library prep kits commonly target specific hypervariable regions such as V3-V4, and primer sets re-designed against an updated 16S reference database can meaningfully improve taxonomic coverage compared with older primer designs that may underrepresent certain taxa.
Decide between single-region and full-length amplicon coverage
Short-read sequencing of a single hypervariable region, or a small number of regions, is the standard, cost-effective approach, while long-read platforms can sequence the full-length 16S gene, providing improved species- and strain-level resolution at a different cost and throughput tradeoff.
Plan for PCR chimera formation as a known amplicon sequencing challenge
PCR chimeras, artificial sequences formed from recombination of multiple templates during amplification, are a recognized challenge in amplicon library prep, and kits using real-time PCR to control amplification cycle number can help keep chimera abundance to a low, well-controlled percentage of total reads.
Confirm fungal ITS coverage if your study includes fungal community profiling
Some 16S kits can be run alongside a separate ITS-targeted protocol, or as a combined workflow, to capture both bacterial and fungal community composition from the same sample set, which matters for studies where fungi are a relevant part of the community.
Check hands-on time and workflow complexity for your sample throughput
Some 16S library prep kits are designed for a single-tube, single-reaction workflow with simultaneous indexing and amplification, substantially reducing hands-on time and contamination risk compared with multi-step protocols, which matters for higher-throughput sample sets.
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<h2>Specifications context</h2>
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16S rRNA sequencing requires less input DNA and is less impacted by the presence of host DNA than shotgun metagenomic sequencing, which is part of why it remains the more accessible default for routine bacterial community composition profiling across many labs and sample types. As of 2026, single-tube, real-time-PCR-controlled 16S library prep workflows continue to reduce hands-on time for high-throughput studies while keeping PCR chimera formation to a low, well-controlled percentage of total reads.
<a href="https://mbpinc.net/contact-us">Reach out to the MBP Inc. team</a> today to inquire about a quote for your NGS library preparation requirements.

16S/ITS NGS Library Preparation Kits

DataSheet

MSDS

Protocol

Quick Protocol -  High Microbial

Quick Protocol - Low Microbial

Quick Protocol - Non-Quant PCR

Guide For > 96 Samples

Plate Setup Guide

Quick-16S™ NGS Library Prep Kit

D6400 by Zymo Research converts purified microbial DNA from up to 96 samples into Illumina MiSeq-ready 16S amplicon libraries targeting V1–V2 (~486 bp) or V3–V4 (~596 bp) hypervariable regions. Input is 2 µL of DNA at 5–20 ng/µL; dual barcoding supports 96-plex sequencing. Compatible with standard and low-biomass microbiome protocols.

Amplicon Size

Barcode Sequences

Equipment

Index Primers

Preparing > 96 Samples

Recommended RT PCR System

Sample Input

Sequencing Compatibility

Manufacturer

Shipping Condition

Storage Condition

Quick-16S™ NGS Library Prep Kit (96 Rxns.)

Quick-16S™ Primer Set V1-V2 (400 µl)

Quick-16S™ Primer Set V3-V4 (400 µl)

ITS Guide

Quick-ITS Plus NGS Library Prep Kit (UDI) (96 preps) with Primer

The Quick-ITS Plus NGS Library Prep Kit UDI D6425-PS1 by Zymo Research delivers 96-prep fungal ITS2 amplicon sequencing with Unique Dual Indexing, ~30 min hands-on time, up to 70% fewer chimeras, and compatibility with Illumina MiSeq and NextSeq platforms.

ITS Primer Sequences (adapters not shown)

Sequencing Platform

Required Equipment

Quick-ITS Plus NGS Library Prep Kit (UDI) (96 preps) with Primer Set 1

Quick-ITS Plus NGS Library Prep Kit (UDI) (96 preps) with Primer Set 2

Quick-ITS Plus NGS Library Prep Kit (UDI) (96 preps) with Primer Set 3

Quick-ITS Plus NGS Library Prep Kit (UDI) (96 preps) with Primer Set 4

<h2>What are RNA-seq accessories?</h2>
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RNA-seq accessories are the supporting consumables used alongside a core metatranscriptomic library preparation kit, including rRNA depletion reagents that reduce the ribosomal RNA dominating most total RNA extracts, magnetic bead-based reagents for library cleanup and size selection between preparation steps, and quantification or fragment-size quality-control tools used to confirm a library's concentration and integrity before committing it to a sequencing run.
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<h2 dir="ltr">What you will find:</h2>
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Dual-Indexed UDI Primer Sets: High-purity Unique Dual Index (UDI) primers designed to eliminate index hopping and ensure accurate demultiplexing during high-throughput NGS library preparation.
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96-Index Primer Plates: Nuclease-free, high-diversity primer configurations optimized for scalable parallel processing and the detection of rare microbial transcripts with maximum precision.
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<h2>How to choose RNA-seq accessories</h2>
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Match your rRNA depletion reagent to your sample's species complexity
A depletion reagent validated for human and common bacterial species works well for many host-associated samples, while a depletion kit specifically designed for mixed, complex bacterial populations is needed for more diverse environmental or microbiome community samples.
Use magnetic bead cleanup for size selection between library prep steps
Magnetic bead-based cleanup reagents remove unwanted small fragments and reaction components between enzymatic steps in library preparation, and the bead-to-sample ratio used can be adjusted to select for a specific fragment size range appropriate to your sequencing platform.
Confirm library quantification method matches your downstream platform requirements
A fluorometric or fragment-analysis-based quantification method provides the library concentration data needed to pool multiple samples accurately for multiplexed sequencing, and using a method appropriate to your specific library type avoids over- or under-loading the sequencer.
Check fragment size distribution before sequencing to catch problems early
Running a quality-control check of library fragment size distribution, using an instrument like a Bioanalyzer or similar fragment analyzer, helps catch a library prep problem, such as adapter dimer contamination, before committing the sample to a full sequencing run.
Plan for accessory compatibility with degraded or low-input RNA samples
Some accessories and protocols accommodate degraded RNA with low RNA integrity number (RIN) scores, such as RNA from challenging sample types, though performance may be somewhat reduced compared with high-quality, intact RNA input.
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<h2>Specifications context</h2>
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A streamlined rRNA depletion accessory can effectively deplete multiple rRNA species in a single-tube reaction, reducing the hands-on accessory steps needed compared with older multi-step depletion protocols, while still requiring downstream library cleanup and quantification accessories regardless of which depletion method is used. As of 2026, fragment analyzer and similar QC instrumentation remain a standard accessory-stage check before sequencing, helping confirm library quality issues are caught and addressed prior to committing limited sequencing capacity to a problematic sample.
<a href="https://mbpinc.net/contact-us">Contact the helpful team at MBP Inc.</a> today to request a quote for your RNA-Seq accessory needs.

RNA-seq accessories

Zymo-Seq UDI Primer Plate (Indexes 1-96)

D3096 by Zymo Research provides 96 unique dual-index (UDI) primer pairs — indexes 1–96 — in a pre-formatted 96-well plate for multiplexed Illumina® NGS library preparation. Each well delivers 10 µL at 5 µM total primer concentration, compatible with TruSeq® adapter-based kits including Zymo-Seq RiboFree® and SwitchFree™. Store at -80°C.

Zymo-Seq UDI Primer Set (Indexes 1-12)

D3008 by Zymo Research is the Zymo-Seq UDI Primer Set (Indexes 1–12)—12 unique dual-index primer pairs, each pre-mixed at 5 µM total (2.5 µM i5 + 2.5 µM i7) in individual 1.5 mL tubes. Compatible with the Zymo-Seq RiboFree® Total RNA and SwitchFree 3′ mRNA library kits and any Illumina TruSeq® adapter-based library kit, enabling unambiguous multiplexing of up to 12 samples on any Illumina sequencer.

<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

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

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.

United States

Texas

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