Microbiomics

<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

MSDS

Bacterial DNA Standards and No Template Control (#1-8)

E2006-2 by Zymo Research is a set of 8 ready-to-use bacterial DNA standards (50 µL each) spanning 20 ng to 0.00002 ng per well in a 10-fold serial dilution series, plus a no-template control. Used to generate qPCR standard curves with the Femto™ Bacterial DNA Quantification Kit (E2006). Compatible with any real-time qPCR instrument. Store at −20°C.

Manufacturer

Shipping Condition

Storage Condition

Protocol

DataSheet

Femto™ Bacterial DNA Quantification Kit (100 Rxns.)

E2006 by Zymo Research — Femto™ Bacterial DNA Quantification Kit, 100 reactions, qPCR detection 20 fg to 20 ng bacterial DNA from 1 µL sample. 16S rRNA primers; selective in mixed non-bacterial backgrounds. Store at −20°C.

Detection Range

Equipment

Sample Source

Femto™ Bacterial qPCR Premix (1.8 ml)

Femto™ Bacterial qPCR Premix (E2006-1) by Zymo Research — 1.8 mL, 100 reactions, targets 16S rRNA gene, detects as few as 20 fg bacterial DNA (5 copies E. coli), 20 fg–20 ng quantification range. Includes bacterial DNA standards 1–7 and NTC.

Femto™ Fungal DNA Quantification Kit (100 Rxns.)

E2007 by Zymo Research is the Femto™ Fungal DNA Quantification Kit (100 rxns) — detects as little as 20 fg of fungal DNA per reaction using SYTO® 9 and ITS1-F/ITS2-R primers. Detection range 20 fg to 20 ng. S. cerevisiae-derived 7-point standard curve. High fungal specificity; no cross-reactivity with bacterial, plant, or animal DNA.

Femto™ Fungal qPCR Premix (1.8 ml)

E2007-1 by Zymo Research — Femto Fungal qPCR Premix; 1.8 mL 2× premix; ITS-targeting primers; 20 fg–20 ng detection range; ≥2 copies S. cerevisiae; compatible with any qPCR instrument; store at –20°C.

Femto™ Human DNA Quantification Kit (100 Rxns.)

E2005 by Zymo Research is the Femto™ Human DNA Quantification Kit (100 rxns) — detects as little as 20 femtograms of human DNA per reaction using SYTO® 9 and LINE-1 primers. Detection range 20 fg to 20 ng. HeLa-derived 7-point standard curve. High specificity; no cross-reactivity with non-human DNA.

Femto™ Human qPCR Premix (1.8 ml)

E2005-1 by Zymo Research: 1.8 ml 2× qPCR premix for human DNA quantification from 20 fg to 20 ng per reaction (&lt;1 copy of human genomic DNA). Targets LINE-1 on SYBR Green channel. Compatible with any real-time qPCR instrument. Store at −20°C.

Fungal DNA Standards and No Template Control (#1-8)

E2007-2 by Zymo Research is the Fungal DNA Standards and No Template Control replacement set for the Femto™ Fungal DNA Quantification Kit (E2007). Contains 8 tubes × 50 µL: seven 10-fold serial dilution standards (20 ng to 0.00002 ng fungal DNA) plus a No Template Control for contamination detection.

Human DNA Standards and No Template Control (#1-8)

E2005-2 by Zymo Research is the Human DNA Standards and No Template Control replacement set for the Femto™ Human DNA Quantification Kit (E2005). Contains 8 tubes × 50 µl: seven HeLa-derived standards (20 ng to 0.00002 ng, 10-fold serial dilution) plus a No Template Control.

<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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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

Quick-16S Plus NGS Library Prep Kit (V1-V2)

Quick-16S™ Plus NGS Library Prep Kit V1-V2 (D6434-PS1) by Zymo Research — 96-reaction single-PCR kit targeting the V1-V2 region with 30 min hands-on time. Compatible with Illumina MiSeq and NextSeq 1000/2000. No normalization required.

16s V1-V2 Primer Sequences (adapters not included)

Amplicon Size

Barcode Sequences

Index Primers

Required Equipment

Sample Input

Sequencing Platform

Quick-16S Plus NGS Library Prep Kit (V1-V2) with Primer Set 1

Quick-16S Plus NGS Library Prep Kit (V1-V3) with Primer Set 1

Guide for Preparing More Than 96 Samples

Plate Setup Guide

Quick-16S Plus NGS Library Prep Kit (V3-V4, UDI)

The D6421-PS1 by Zymo Research is a 96-reaction Quick-16S Plus NGS Library Prep Kit for V3-V4 16S rRNA amplicon sequencing, using a single qPCR/PCR step with Unique Dual Index (UDI) 10-bp barcodes to prepare 96 samples in ~30 minutes hands-on time, with no normalization or gel analysis required. Primer Set 1 (341f/806r) covers 84.2% bacteria and 75.8% archaea; compatible with Illumina MiSeq and NextSeq 2000. Made in the USA.

16S V3-V4 Primer Sequences (adapters not included)

Primer Coverage

Quick-16S Plus NGS Library Prep Kit (V3-V4, UDI) with Primer Set 1

Quick-16S Plus NGS Library Prep Kit (V3-V4, UDI) with Primer Set 2

Quick-16S Plus NGS Library Prep Kit (V3-V4, UDI) with Primer Set 3

Quick-16S Plus NGS Library Prep Kit (V3-V4, UDI) with Primer Set 4

Quick-16S Plus NGS Library Prep Kit (V3-V4, UDI) with Primer Set 5

Quick-16S Plus NGS Library Prep Kit (V3-V4, UDI) with Primer Set 6

Quick-16S Plus NGS Library Prep Kit (V3-V4, UDI) with Primer Set 7

Quick-16S Plus NGS Library Prep Kit (V3-V4, UDI) with Primer Set 8

Protocol - D6430

Protocol - D6432

Guide for Preparing More than 96 Samples

Quick-16S Plus NGS Library Prep Kit (V4)

D6430-PS1 Quick-16S Plus NGS Library Prep Kit (V4) by Zymo Research prepares 96 indexed Illumina-compatible 16S libraries targeting the V4 region (515–806) using EMP primers, with 30 min hands-on time and MagBead cleanup.