The Microbial and Microbiome Workflow

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.

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.

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.

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.

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

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.

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.