Gut Microbiome, Made Simple
The human gut microbiome represents the most widely studied topic in the field of microbiomics, as it provides a non-invasive and relatively easy way to study the microbial communities residing in the human gastrointestinal tract. Zymo Research offers effective solutions to address several challenges associated with collecting and processing fecal samples to streamline fecal microbiome research.
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A Comprehensive Workflow for Gut Microbiome Research
The field’s only complete, end-to-end microbiome research solutions
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Microbiome Standards & Controls
Take control of your research
The microbial composition of the ZymoBIOMICS® Gut Microbiome Standard (D6331) measured by NGS shotgun sequencing as compared to the defined composition. The microbial composition of the standard was confirmed using Illumina® shotgun sequencing. Genomic DNA was extracted using the ZymoBIOMICS® DNA Miniprep Kit. Library preparation was performed using an in-house protocol. Shotgun sequencing was performed using Illumina MiSeq™. Microbial abundance was estimated based on the number of reads that were mapped to reference genomes of the organisms.A study is only as good as its controls, and this is especially true for microbiome research. With so many potential sources of bias, it is important to use controls that address all of these challenges, and more. The ZymoBIOMICS® Microbial Community Standard contains 8 bacteria and 2 yeasts, representing a wide range of genome sizes, G/C content, and lysis difficulties, making it the ideal positive extraction control, as well as an invaluable tool for workflow validation. The ZymoBIOMICS® Gut Microbiome Standard takes things a step further by providing 21 commensal and pathogenic strains of human gut microbes, in the form of bacteria, archaea, and yeast, allowing for benchmarking of both cross-kingdom detection as well as strain-level resolution. Finally, the ZymoBIOMICS® Fecal Reference with TruMatrix™ Technology offers 2 million identical preps of a composite fecal sample for the truest test of any metagenomics pipeline in the form of real sample composition and diversity.Microbiome Standards Products Cat. No. ZymoBIOMICS® Microbial Community Standard D6300 ZymoBIOMICS® Gut Microbiome Standard D6331 ZymoBIOMICS® Fecal Reference w/ TruMatrix™ Technology D6323 -
Sample Collection Devices
Just a Wipe (or Swab) Away
Collecting fecal samples can be logistically challenging, especially in large-scale studies. Proper collection and preservation methods are crucial to maintain the integrity of the sample during transportation and storage. DNA/RNA Shield™ addresses these issues by preserving the sample at ambient temperature, removing the need for cold chain during shipping, and chemically inactivating microbes, making them both safer and easier to work with.
For added convenience, DNA/RNA Shield™ is provided in a variety of pre-filled collection devices. The Bunny Wipe with DNA/RNA Shield™ Fecal Collection Tube goes one step further by pairing pre-filled collection tubes with an easy-to-use fecal collection wipe. Similarly, DNA/RNA Shield™ SafeCollect Swab Collection Kit allows for simple swab collection into spill-proof DNA/RNA Shield tubes.
Microbiome Standards Products Cat. No. DNA/RNA Shield™ R1100 DNA/RNA Shield™ Fecal Collection Tube R1101 DNA/RNA Shield™ Fecal Collection Tube (with Beads) R1137 Bunny Wipe w/ DNA/RNA Shield™ Fecal Collection Tube R1138 DNA/RNA Shield™ SafeCollect™ Swab Collection Kit R1160 -
DNA & RNA Extraction Kits
Get the Most Out of Your Sample
The ZymoBIOMICS® DNA Miniprep Kit provides unbiased representation of the organisms extracted from the ZymoBIOMICS® Microbial Community Standard. DNA was extracted from ZymoBIOMICS® Microbial Community Standard using four different DNA extraction methods (ZymoBIOMICS® DNA Miniprep Kit, Human Microbiome Project Protocol, Supplier Q1, and Supplier Q2) and analyzed using 16S rRNA gene sequencing.Make certain that you aren't missing anything, by using the only extraction kits validated for unbiased lysis against our ZymoBIOMICS® microbial standards. The ZymoBIOMICS® DNA Miniprep Kit utilizes BashingBead™ technology to ensure complete recovery of Gram-positive and negative bacteria, archaea, and yeast. This comes coupled with certified low bioburden reagents and robust inhibitor removal technology to provide the best sequencing results possible. Looking to automate? The ZymoBIOMICS® 96 MagBead DNA Kit offers all of the same features, in an automation-ready format, with scripts for most common platforms readily available. Interested in metatranscriptomic as well? The ZymoBIOMICS® DNA/RNA Miniprep Kit can be used to capture both DNA and RNA as separate fractions from the same sample source.Microbiome Standards Products Cat. No. ZymoBIOMICS® DNA Miniprep Kit D4300 ZymoBIOMICS® 96 MagBead DNA Kit (Lysis Rack) D4302 ZymoBIOMICS® 96 MagBead DNA Kit (Lysis Tubes) D4308 ZymoBIOMICS® DNA/RNA Miniprep Kit R2002 ZymoBIOMICS® MagBead DNA/RNA Kit R2135 -
NGS Library Prep Kits
Sample to Result, In a Flash
Tired of lengthy library prep protocols that require tedious normalization of each sample? Looking to avoid complicated workflows or turn around high sample volumes in a short amount of time? The Quick-16S™ Plus NGS Library Prep Kit (V3-V4) and Quick-ITS™ Plus NGS Library Prep Kit (ITS2) utilize novel Equalase™ technology to amplify sample inputs as little as 100 femtograms without the need for manual normalization; simply pool by equal volume and go. This, combined with pre-aliquoted qPCR Premix Plates, and only a single amplification and clean-up required, reduces hands-on times to as little as 30 minutes to prepare 96 sequencing-ready libraries. The Quick-16S™ Plus NGS Library Prep Kit (V4) pairs this same workflow with custom sequencing primers to allow for V4 amplicon sequencing with 300-cycle kits, opening the possibility of targeted sequencing applications on all Illumina platforms.Microbiome Standards Products Cat. No. Quick-16S™ Plus NGS Library Prep Kit (V3-V4, UDI) D6421 Quick-ITS™ Plus NGS Library Prep Kit (ITS2) D6425 Quick-16S™ Plus NGS Library Prep Kit (V4) D6430 -
NGS Analysis
Become your own bioinformatician, or let us do it for you
![16S/ITS Amplicon Sequencing]()
16S/ITS Amplicon Sequencing
![Full Read 16S]()
Full-Length 16S Sequencing
![Shotgun Metagenomic Sequencing]()
Shotgun Metagenomic Sequencing
![Magnifying class over microbes]()
Metatranscriptomic Sequencing
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Custom Solutions for Industry Partners
![Long-Read Metagenome Sequencing & Assembly]()
Long-Read Metagenome Sequencing & Assembly
Long-Read Bacterial Whole Genome Assembly
Looking to simplify the complexities of microbiome data analysis while gaining access to the most comprehensive resources available? The MGscan™ Bioinformatics Analysis Suite offers an end-to-end solution for processing, analyzing, and visualizing NGS microbiome data, delivering rapid, publication-ready insights without the need for custom coding or extensive computational expertise. Pair this with the Orion Microbiome™ Database, a platform designed to eliminate common bottlenecks in microbiome research by compiling a large collection of curated public microbiome data and research cohorts. For those seeking a complete sequencing solution, Zymo Research's Microbiome Sequencing Services provide streamlined, sample-to-report workflows, combining industry-leading library prep methods, robust quality controls, and powerful downstream analysis for both 16S and shotgun metagenomics. Together, these resources empower scientists to focus on making new discoveries rather than problem solving.
Build Your Custom Workflow Today
Everything You Need for Gut Microbiome Research
Save 36% with the all-in-one bundle
D4300 x 2
Key Benefits of the Gut Microbiome Research Bundle:
- All necessary sample prep steps covered
- Optimized workflow integrates seamlessly
- Smart Value – Bundle and save 36% off the full price
Gut Microbiome Resources
Everybody Poops: How to Extract DNA from Feces
Tips & Tricks for Fecal DNA Extraction
The number of human microbiome studies has exploded in the past decade with a majority analyzing fecal samples. While not the most pleasant sample to work with, there is a lot for us to learn about human health and biology that can be found in stool.
The Microbiome of Fermented Foods
Inside the Microbiome of Kimchi & Sauerkraut
Fermentation is a naturally occurring process that has been used for culinary purposes, from brewing beer to leavening bread. Prior to the age of refrigeration, fermentation was primarily used for thousands of years as a means for preserving perishable foods.
Getting the Whole Picture
Microbiome Whole-cell Spike-ins for Absolute Quantification
The field of metagenomics has progressed by leaps and bounds over the past decade and even more so with the recent adoption of microbiomics-grade sample collection and unbiased nucleic acid purification techniques.
From Gut Instinct to Gold Standard
Efforts to explore the clinical impact of the human gut microbiome
Efforts to explore the clinical impact of the human gut microbiome are confounded by the complexity of microbiome measurements, compounded by biases and errors at each step.
