Microbiome, Foundation, Sample technologies
Microbial or Microbiome Workflow

The Microbial and Microbiome Workflow

Essential tools for your microbiome research workflow from start to finish

Microbiome research is hard. Samples come from a multitude of origins, can be full of contaminants and contain a myriad of different organisms. This is why you need a streamlined microbiome workflow. Our kits, assays and instruments are designed to work seamlessly together from the experiment’s beginning to the data analysis. Whether it be sample disruption, nucleic acid extraction, microbiome profiling with dPCR, or NGS, statistics or bioinformatics analysis, our microbial research tools are designed for your needs: Purity, precision, reliability and ease of use.

Find the specific kits, assay, instruments and other tools you need for every step of your microbiome research below.

Our team is here to help
We invite you to ask questions about the workflow and our products.

When taking a stool sample, the nucleic acids and microbes inside react to any variation in oxygen or water content as well as the temperature. This, plus an extensive storage time before nucleic acid extraction, can lead to the rise and fall of certain species and change the microbial composition.

Hence, to get the most accurate insights into your sample, stabilising its microbes and their nucleic acids is a crucial step. Our DNA/RNA protection solutions keep your samples intact and preserve the microbial integrity.

Discover products for microbiome sample stabilization

Tissuelyzer III, Instrument

Microbial samples often contain complex mixtures of microbes, their sturdy cell walls and metabolic products as well as other biotic and abiotic molecules. All these components can be various extracellular polymers and thus highly diverse. Such complexity and robustness renders the lysis of microbial samples rather challenging.

To ensure efficient disruption, mechanical homogenization is crucial and avoids introducing bias into the analysis workflow

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.

Discover disruption and homogenization products for microbiome sample disruption

Human biomedical research, Microbiome, Foundation, Sample Technologies

Samples from different sources come with unique challenges related to their distinctive physical, chemical and microbial compositions as well as substances. This is why, our sample preparation kits for human biomedical research are optimized for specific sample types, such as gut, stool, swabs and more.

Additionally, 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 – highlights

Discover products for human microbial sample preparation

A woman interested in marine biology studies a jar containing a rock pool sample, Environmental and agricultural research, Microbiome, Foundation, Sample Technologies

Samples from the environment often contain complex mixtures of inorganic and organic material such as plant material, insects, animal faeces or microbes. This makes environmental microbial samples exceptionally difficult to lyse and work with.

To get reliable insights, our sample preparation kits for environmental and agricultural research are optimized for specific sample types, such as soil, biofilm, (waste)water, plants and more.

Additionally, 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.

Environmental and agricultural sample preparation – highlights

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Less hands on time with automated sample preparation systems

Sample preparation is a significant factor for the success of your microbial workflow and its reproducibility. When different users extract nucleic acids from samples, chances of errors from multiple manual interventions increase. This can lead to variation in nucleic acid quality like degradation, concentration or the presence of contaminants and impact your results. Hence, automating the extraction of nucleic acids is one way to ensure reproducibility. Learn more about QIAGEN’s automated solutions for standardized and reliable sample preparation.

Sample analysis

DNA isolation service from any sample type
From extraction and quantification to NGS and analysis, using advanced technologies.
Detect, identify and quantify microbial targets, antimicrobial resistance or virulence genes by dPCR, qPCR or NGS.

Whole genome and targeted sequence analysis with next generation sequencing

NGS analysis

With next generation sequencing (NGS) methods, we can simultaneously analyse thousands of species within a microbial community. Due to that, NGS has completely revolutionised how we study the human and environmental microbiome.

Reagent and primer selection play large parts in the generation of designated NGS libraries to minimize bias and maximize read depth. Our diverse kits align with various amplification and sequencing needs to achieve even coverages and high read qualities.

All-in-one WGS – from isolation to analysis with one order

Metagenomics can describe the features of an environment in beautiful resolution, painting a picture of the microbiome. But microbial samples are complex, challenging even experienced researchers and bias introduced through complicated methodology can further blur the analytical details. This is why we have developed the WGS SeqSets for fecal and soil samples. These all-in-one bundles are specifically designed to streamline the entire sequencing process, from nucleic acid extraction to library preparation and analysis.

All-in-one WGS –from isolation to analysis with one order

NGS for microbiome and microbial detection and characterization – highlights

Discover NGS products for microbiome

Microbiome profiling service for challenging samples
Next-generation sequencing and 16S/ITS region interrogation, using advanced technologies.

Detecting and quantifying microbes with digital PCR

The presence of microbial targets at low levels in challenging samples have impeded their specific detection and monitoring. That's where digital PCR comes in handy:
Not only does i ts high precision and sensitivity allow to identify a wide range of microbial targets, including bacterial, fungal, parasitic, viral, antibiotic resistance and virulence factor genes from diverse samples. But also, dPCR enables the absolute quantification of targets without the need of standard curves.

The new dPCR Microbial DNA Detection Assay portfolio:

  • Identifies >680 targets
  • Combines microbial DNA and viral RNA detection in one reaction
  • Detects up to five targets per reaction
  • Follows a simple and fast dPCR workflow in about two hours
QIAstat-Dx, QIAcuity, syndromic testing, digital PCR, dPCR, scan cartridge, Labworker handling the instrument, touch display, Julian Phillips, Amit Singh, Chaimae Safi, mask, wearing masks, labcoat
ADNA, PCR plate, qPCR, adding DNA the colored MasterMix is turning from blue to green, visual control of correct pipetting, cat. no. 208054 QuantiNova SYBR Green PCR Kits (500), cat. no.208254 QuantiNova Probe PCR Kits (500) 05/2013, (PCR, Spin/Tube/Plate, Photography, Applications DNA (ADNA))

Specific and sensitive microbial detection with real time PCR

When using realtime PCR for microbial identification and profiling, two elements are critical: sensitivity and specificity. These rely on uniform PCR efficiency and amplification conditions. Our experimentally verified microbial DNA qPCR assays enable you to detect microbial species, virulence genes or antibiotic resistance genes using a simple qPCR workflow. Furthermore, custom arrays can be designed to evaluate specific targets of interest.

Think outside the box
Making sense of complex microbial genomic data

Only well-structured and clear data help you understand what is going on and allow you to take action. However, the volume and complexity of the data can be quite overwhelming.

This is why, QIAGEN CLC Genomics Workbench Premium is an easy and intuitive bioinformatics platform. It offers various tools and customizable workflows to make that leap from big data to characterizing your microbe of interest.

Discover digital insights for microbiome analysis

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.