| Technology | Magnetic beads |
| Format | 96-well, supports automation |
| Sample material | 50–200 mg soil, stool, biofilm (including swabs) |
| Typical yield | 1–30 μg DNA (depending on sample type) |
| Elution volume | 50–200 μl |
| Preparation time | Approx. 140 min/plate |
Tech Note
Automated extraction of high-quality microbiome DNA on the Eppendorf epMOTION 5075t/5073t
Microbiome and metagenomics research relies on the extraction of high-quality DNA representative of all species present within a sample. NucleoMag DNA Microbiome is designed to purify DNA from a variety of sample inputs for downstream microbiome and metagenomic analysis. Features of the kit include:
- Reproducible and consistent DNA recovery
- Suitable for a variety of samples including soil, stool, water, and biofilm (swab)
- Unique, patented inhibitor removal technology to ensure success in downstream applications
- Easy magnetic bead-based isolation
- Automation friendly for high-throughput workflows
We used the NucleoMag DNA Microbiome kit on the epMotion 5073t or 5075t liquid handler to purify high-quality DNA from human stool samples and soil samples. To ensure efficient, unbiased lysis from hard-to-lyse organisms often present in microbiome samples, we combined the NucleoMag DNA Microbiome kit with mechanical homogenization by bead beating using MN Bead Tubes Type A. For soil samples, the addition of Enhancer SX ensures optimal conditions to bind the DNA. Sample disruption was performed on a MN Bead Tube Holder in combination with a Vortex-Genie 2 for 4–5 minutes operating at full speed. A subsequent precipitation step ensures that contaminants and inhibitors are removed very efficiently from the samples. All downstream DNA purification steps were performed on the epMotion 5073t or 5075t without the need for user intervention.
At-a-glance
Application data: human stool samples
Stool samples are often used to study the gut microbiome and its effect on human health, but also as clinical specimens for a variety of purposes, including identification of numerous disease-causing bacteria and for biomarker detection. Often, large numbers of samples need to be processed in a clinical setting. The NucleoMag DNA Microbiome kit in combination with the epMotion 5073t automation system purifies high-quality DNA from stool samples suitable for downstream applications in a high-throughput manner.
Figure 1. High-quality DNA obtained from human fecal samples. DNA was purified from six individual human stool samples using the NucleoMag DNA Microbiome kit on the epMotion 5073t system. The purity of each sample was determined by UV spectroscopy (A260/A280).
Figure 2. High DNA integrity and reliable qPCR performance from human stool samples. Panel A. DNA was purified from a spatula tip from six individual human stool samples using the NucleoMag DNA Microbiome kit on the epMotion 5073t system. Integrity of genomic DNA was visualized via gel electrophoresis (10 μl per lane; 1% TAE gel). Panel B. Equal volumes of purified DNA and primers detecting gram +/– bacteria (top graph) or E. coli specifically (bottom graph) were used for qPCR analysis. qPCR was performed using SensiFAST SYBR Lo-ROX qPCR assays from Bioline on an Applied Biosystems 7500 Real-Time PCR System.
Application data: soil samples
A gram of soil contains about 100 million microorganisms, including bacteria, fungi, viruses, and archaea. Understanding the microbial composition of the soil is essential for assessing soil health and agricultural sustainability. The NucleoMag DNA Microbiome kit has been optimized for purifying microbial nucleic acids from a variety of soil types, including agricultural soil, pine forest soil, and heathland soil. We show that the superior inhibitor removal and efficient lysis with Enhancer SX allows for purification of high-quality DNA from a variety of soil microbial communities.
Figure 3. High-quality and reliable DNA yields obtained from various soil samples. Panel A. DNA was purified from 200 mg of samples of agricultural soil, pine forest soil, heathland soil, and bog forest soil using the NucleoMag DNA Microbiome kit on the epMotion 5075t system. Integrity of genomic DNA was visualized via gel electrophoresis on a 1% TAE gel. Panel B. DNA yields recovered after processing each replicate on the epMotion 5075t liquid handling system with the NucleoMag DNA Microbiome kit.
Figure 4. Reliable qPCR performance from DNA purified from various soil samples. DNA was purified from four different soil types using the NucleoMag DNA Microbiome kit on the epMotion 5075t system. qPCR analysis for the bacterial 16s rRNA gene was performed with the SensiFAST SYBR Lo-ROX qPCR assay from Bioline on an Applied Biosystems 7500 Real-Time PCR System.
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