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Microbiome

Sample to Insight workflow

Build your complete microbiome research workflow

Microbiome research calls for the analysis of diverse samples. Getting results you can trust and meaningful insights can be challenging. Make the most of your precious samples by employing unique solutions from QIAGEN for your complete workflow, from nucleic acid isolation to data analysis and interpretation. To help you navigate your way through the wide range of solutions and applications, we have designed a step-by-step guide for your entire workflow.

Our team is here to help

We invite you to ask questions about the workflow and our products.

Sample disruption

Microbiome samples are challenging because they are difficult to lyse. Microbes may contain a tough extracellular matrix. Incomplete lysis of a microbial community results in an inaccurate representation of the microbial content of the sample.

Mechanical homogenization is recommended to avoid introducing bias during the cell lysis process. QIAGEN’s sample disruption solutions ensure fast, powerful and efficient homogenization, which is a prerequisite for reproducible results.

Microbial samples in 96-well plates

How do you lyse difficult samples in a 96-well plate? How should you remove excess beads and seal the plates to avoid leakage and cross contamination? Watch the video to find out.

PowerBead Pro plates are part of QIAGEN’s new Pro kit technology. With an improved bead-beating process for the TissueLyser II, they provide a high-throughput and efficient way to lyse bacteria and fungi. For isolation of microbial genomic DNA from all soil and stool types, they’re included in the DNeasy 96 PowerSoil Pro Kit.

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Sample preparation (HBR)

For human biomedical research

Different sources of materials present diverse challenges for isolating DNA and RNA. QIAGEN kits for human biomedical research are optimized for specific sample types, such as gut, stool, swabs and more. The patented Inhibitor Removal Technology® (IRT) removes inhibitors during the purification process. This results in high yields of pure nucleic acids ready to use even in demanding downstream applications.

Human biomedical sample preparation
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highlights

Purify DNA from stool samples
The QIAamp PowerFecal Pro DNA Kit removes tough inhibitors and provides clean, ready-to-use DNA for any downstream application. DNA preparation can be done either manually or automated on QIAcube Connect.
Automate DNA purification from stool on QIAsymphony
The QIAsymphony PowerFecal Pro DNA Kit allows automated, time-saving, standardized extraction of inhibitor-free DNA from stool and soil samples. The kit is designed for 192 samples with continuous loading of 24-sample batches on QIAsymphony.
Automate DNA purification stool samples on QIAcube HT
The DNeasy 96 PowerSoil Pro QIAcube HT Kit provides simple, fully automated purification of high-quality genomic DNA from stool samples using QIAcube HT for simultaneous processing of 24–96 samples.
Purify DNA from swabs and body fluids
The QIAamp DNA Microbiome Kit facilitates the effective depletion of host DNA during the purification process and maximizes bacterial DNA coverage in NGS analysis.
Purify DNA from biofilm samples
By pairing chemical and mechanical lysis techniques with Inhibitor Removal Technology (IRT), the DNeasy PowerBiofilm Kit overcomes inefficient cell lysis in the most challenging biofilms. Purification of DNA with this kit can be automated on QIAcube Connect.
Purify RNA from biofilm samples
Overcome inefficient cell lysis with the RNeasy PowerBiofilm Kit. Mechanical and chemical lysis are combined with Inhibitor Removal Technology to isolate pure, inhibitor-free RNA. The resulting RNA is then ready for further analysis with downstream applications.
Purify DNA and RNA from stool samples
The AllPrep PowerFecal DNA/RNA Kit protocol enables the simultaneous isolation of DNA and RNA in separate eluates from one sample. The kit is optimized for metagenomic and metatranscriptomic analyses using next-generation sequencing (NGS).
Purify viral or bacterial DNA and RNA from stool samples
The AllPrep PowerViral DNA/RNA Kit is designed for fast and easy purification of viral and bacterial total nucleic acids, even from samples high in PCR inhibitors. The result is DNA and RNA from virus and bacteria ready to use in the most demanding downstream applications.
Purify RNA from stool and gut material
Designed for purification of total RNA from stool, dried feces, gut material, contaminated buccal swabs and secretions, the RNeasy PowerMicrobiome Kit isolates RNA ready for use in demanding downstream applications.

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Sample preparation (ENV/AGR)

For environmental and agricultural research

Different sources of materials present different challenges for isolating DNA and RNA. QIAGEN kits for environmental and agricultural research have been optimized or specific sample types, such as soil, water, biofilm, plants and more. Patented Inhibitor Removal Technology (IRT) removes inhibitors during the purification process. This results in high yields of high-quality, pure nucleic acids ready to use even in the most demanding downstream applications.

Environmental and agricultural sample preparation
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highlights

Purify DNA from all soil types
The DNeasy PowerSoil Pro isolates high yields of pure microbial DNA from all soil types, including compost, clay and topsoil. The extraction of DNA using the DNeasy PowerSoil Pro Kit can be automated on QIAcube Connect.
Purify DNA from soil on QIAcube HT
The DNeasy 96 PowerSoil Pro QIAcube HT kit provides simple, fully automated purification of high-quality genomic DNA from soil samples. With QIAcube HT 24–96 samples are processed simultaneously.
Purify DNA from water
The DNeasy PowerWater Kit isolates genomic DNA from filtered water samples, free from salts, metals, humic substances and other organic materials. The kit can isolate high-quality DNA even from water containing high levels of contaminants. Purification can be automated on QIAcube Connect.
Purify DNA from biofilm samples
By pairing chemical and mechanical lysis techniques with patented Inhibitor Removal Technology (IRT), the DNeasy PowerBiofilm Kit overcomes inefficient cell lysis in the most challenging biofilms. Purification of DNA using this kit can be automated on QIAcube Connect.
Purify DNA from plant cells, tissues and seeds
The DNeasy Plant Pro Kit has several innovative features to enable recovery of high-quality DNA from the toughest sample types, including strawberry leaf, grapevine leaf, pine needles and various seed types. The kit can be automated on the QIAcube Connect.
Purifying RNA from soil samples
Isolation of total RNA from up to 2 grams of soil is easy with the RNeasy PowerSoil Total RNA Kit. While the kit works with all soil types, it excels with samples with a high humic substance content such as manure, sediment, or compost.
Purify RNA from filtered water samples
RNA isolation from all microbes present in environmental water samples using the RNeasy PowerWater Kit. The kit isolates RNA from bacteria (Gram +/-), algae and fungi. Resulting RNA can then be used in RT-PCR, qPCR, RNA-seq and other downstream applications.
Purify RNA from biofilm samples
Power up your RNA isolation with RNeasy PowerBiofilm Kit. Mechanical and chemical lysis are combined with Inhibitor Removal Technology for efficient lysis resulting in the isolation of pure RNA free from the inhibitors typical of biofilms. The resulting RNA is then ready for further analysis with downstream applications.
Purify DNA from any sample type with our DNA isolation service
With QIAGEN DNA isolation service, you can be sure that decades of expertise are applied to your sample purification. We will select the kit that is best suited to your downstream application. DNA quantification and purity data can be provided.

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DNA isolation service from any sample type

From extraction and quantification to NGS and analysis, using advanced technologies.

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NGS analysis

Next-generation sequencing (NGS) methods have revolutionized the study of the microbiome. NGS enables the simultaneous analysis of thousands of species within a microbial community.

Reagent and primer selection plays a large part in the generation of a proper NGS library, one that minimizes bias and maximizes read depth. QIAGEN offers diverse kits to align with various amplification and sequencing needs to achieve even coverage and high-read quality.

NGS for microbiome
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highlights

Differentiation of host vs. Microbial DNA
The UCP SYBR® Green PCR and UCP Probe PCR kits enable quantification of microbial DNA versus host DNA, prior to NGS library preparation from swabs or body fluids. For more information on the entire UCP product group, please click here.
Shotgun metagenomic sequencing
The QIAseq FX DNA Library Prep Kit is a complete, all-enzymatic NGS library preparation for high-complexity DNA sequencing application with low GC bias, superior coverage distribution and lower duplication rate.
16S/ITS profiling
The QIAseq 16S/ITS Region Panels and QIAseq 16S/ITS Screening Panel provide comprehensive and robust profiling of bacterial and fungal communities with the flexibility to interrogate any combination of bacterial 16S variable regions and fungal ITS regions on Illumina platforms using phased primers.
Targeted sequencing
The UCP Multiplex PCR Kit enables bias-free preamplification for targeted sequencing using your own primer sets. The UCP HiFidelity PCR Kit provides superior fidelity for error-free NGS analysis. For library preparation, choose the QIAseq 1-Step Amplicon Library Kit to achieve high yields of library DNA with uniform coverage distribution.
5S/16S/23S rRNA removal + Metatranscriptomics
The QIAseq FastSelect –5S/16S/23S Kits remove highly abundant bacterial 5S/16S/23S rRNA from your RNA-seq library. They have been designed for complex community microbial samples. QIAseq Stranded RNA Library Kits provide a superior method for generating Illumina-compatible RNA-seq libraries from total RNA or mRNA enriched samples.
Genomic services for comprehensive profiling of bacterial and fungal communities
Let us do the work for you. With 16S/ITS microbiome profiling services, you can move quickly and confidently from challenging samples to insights. Any combination of 16S variable regions and ITS regions can be interrogated.

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Microbiome profiling service for challenging samples

Next-generation sequencing and 16S/ITS region interrogation, using advanced technologies.

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Digital insights

An excellent software suite goes a long way in turning metagenomics data interpretation from a chore to a joy. Tools and features to cover all of your needs, from taxonomy to polymorphism analysis, enable gaining valuable insights from complex data. QIAGEN’s bioinformatics solutions for microbiome are easy-to-use. With an intuitive interface, they help researchers focus on what really matters.

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QIAGEN CLC Genomics Workbench Professional
For microbial profiling, pathogen typing and outbreak analysis using state-of-the-art bioinformatics
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QIAGEN CLC Genomics Workbench
For analyzing, comparing, and visualizing next-generation sequencing data
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FAQs about microbiome research methods

What are 16S and ITS rRNA sequencing?

The most common method used for profiling microbial communities is sequencing the 16S ribosomal RNA (rRNA) gene and Internal Transcribed Spacer (ITS) regions for bacteria and fungi, respectively. Due to their universal distribution and conserved nature, the 16S rRNA and ITS genes are well-established genetic markers used for bacterial and fungal identification and classification.

The 16S rRNA gene consists of both highly conserved and hypervariable regions. The conserved regions serve as primer binding sites for PCR amplification of the variable regions and the variable regions contain sequences that can be used for bacterial identification and classification.

What is Shotgun Metagenomic Sequencing?

In contrast to 16S rRNA and ITS sequencing, shotgun metagenomic sequencing covers the entire genome of all organisms present in a sample.

Shotgun metagenomic sequencing covers all genetic information in a sample; therefore, the data can be used for various analyses, e.g., metagenomic assembly and binning, metabolic function profiling and antibiotic resistance gene profiling.

What is Metatranscriptomics?

Metatranscriptomics studies the entire gene expression profile of microbial communities in natural living environments. It enables the quantification of gene expression levels and their changes in response to different conditions, e.g. physiological vs. pathological conditions in an organism.