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.

The industry’s most-cited standards and controls for microbiome research
Certified unbiased microbial lysis and robust nucleic acid purification technologies
The fastest NGS library prep kits and microbiome sequencing services

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    A Comprehensive Workflow for Gut Microbiome Research

    The field’s only complete, end-to-end microbiome research solutions

    1. 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.
    2. 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.

    3. 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.
    4. 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.
    5. Microbiome Standards & Controls

      Take control of your research

      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

    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
    $1,500 $2,321 Save $821
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