16S/ITS NGS Library Preparation Kits

<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.

MSDS

Protocol

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

Manufacturer

Shipping Condition

Storage Condition

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

DataSheet

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.

Equipment Needed (user provided)

Index Sequences

V4 Primer Sequences (adapters not included)

Quick-16S Plus NGS Library Prep Kit (V4) (96 preps) with Index Primer Set 1

Quick-16S Plus NGS Library Prep Kit (V4) (96 preps) with Index Primer Set 2

Quick-16S Plus NGS Library Prep Kit (V4) (96 preps) with Index Primer Set 3

Quick-16S Plus NGS Library Prep Kit (V4) (96 preps) with Index Primer Set 4

Quick Protocol -  High Microbial

Quick Protocol - Low Microbial

Quick Protocol - Non-Quant PCR

Guide For > 96 Samples

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.

Equipment

Preparing > 96 Samples

Recommended RT PCR System

Sequencing Compatibility

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.