Expert Insight: Optimize your microbiome research workflow with a gold standard sample prep solution

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Véronique Karsten, Molecular Biology Product Manager at MP Biomedicals

Microorganisms dominate the biosphere and carry out the majority of biochemical activity on the planet. Diverse and complex communities of bacteria, archaea, fungi, and viruses inhabit Earth’s many environments, from the human body to plants, as well as soil, oceans and even the atmosphere.

These microbiomes maintain the healthy function of the ecosystems they inhabit and their dysfunction is often associated with human disease, crop failure, and environmental disaster. Despite the variety of microorganisms out there, most of them have not yet been identified, and our understanding of the composition and function of microbiomes is still in its infancy. As a result, advancing microbiome research has become a major focus for many life sciences, environmental, and clinical researchers.

In this on-demand SelectScience webinar, Véronique Karsten, Molecular Biology Product Manager, MP Biomedicals, explores a series of case studies that illustrate how to optimize sample preparation for a range of complex microbiome samples and discusses how the FastPrep System and FastDNA SPIN Kit for Soil are designed to enhance these methods.

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Q: When comparing the FastDNA Spin Kit for Soil with other commercial kits, what are the main differences between these kits? And is the FastDNA Spin Kit for Soil a gold standard for microbiome research?

VK: The major difference between the FastDNA Spin Kit for Soil and other kits is the grinding bead-beating step. The FastDNA SPIN Kit for Soil includes Lysing Matrix tubes containing a mix of three types of beads, and this is the specificity. These three types of beads will guarantee the lysis of any cells, even the most difficult ones. So, a high percentage of cell lysis, meaning a high yield of DNA. Moreover, reagents included in the kit are optimized to remove PCR inhibitors and organic contaminants such as humic acid more efficiently. This is a guarantee of a better purity of the DNA isolated with the FastDNA SPIN Kit for Soil that is thus suitable for any downstream application.

Q: Can I use the FastDNA Spin Kit for Soil if I would like to purify DNA from large amounts of soil or sediment samples, for example, 1 to 5 grams?

VK: Yes. The FastDNA Spin Kit for Soil has been developed in two versions, so, a 2-milliliter version and a 50-milliliter version where up to 10 grams of soil environmental samples can be processed. So, for large samples, a different kit with larger tubes and larger spin filters.

Q: For someone who doesn’t have a fast prep instrument in his lab but would like to use the FastDNA Spin Kit for Soil with another bead-beating homogenizer. Is this possible?

VK: Yes. The Lysing Matrix tubes included in the FastDNA Spin Kit for Soil, have the advantage of being compatible with any high-speed bead-beating homogenizer.

Q: Is the kit standardized for extraction of gDNA for shrimps?

VK: Yes. The FastDNA Spin Kit for Soil has been used with shellfish and with oysters. There are publications mentioning that kit for that kind of sample.

Q: What are the optimal conditions for the sample prep of rodent feces? If the feces has been sampled in metabolic cages, are they suitable for genomic analysis?

VK: Yes. For rodent feces, the best thing to do is grind samples two times 40 seconds at speed 6 with the FastPrep instrument. Then for samples that are coming from metabolic cages, it is suitable as well for this genomic analysis.

Q: Do you recommend for gram-positive bacteria a pre-lysis step before following the DNA isolation protocol and what is the most efficient way to separate the sample from the beads after homogenization?

VK: For gram-positive bacteria, no, a pre-lysis step is not needed. Using the standard conditions of the protocol will lyse efficiently any gram-positive bacteria. To separate the beads from the homogenate, the best practice is to centrifuge the tubes after the homogenization and even best is to do it for 10 to15 minutes in order to remove all the cell debris and the bead that will be pelleted as well. After that, the supernatant can be collected for the purification step.

Q: For low biomass samples, could you include any additional steps to produce a higher DNA yield?

VK: No. There is no additional step that will improve the yields. For the purity, if there is a high level of humic acid, for example, it is possible to add an additional wash step. But to get high yields, the standard protocol is perfect.

Q: What are the major differences between your MPure-12 and FastDNA Spin Kit for Soil?

VK: The MPure-12 is an automated purification system and is supplied with different kits for the purification. But the technology is completely different from the FastDNA Spin Kit for Soil. 

Q: Are you aware of any protocols for extracting DNA and RNA from rock samples such as limestone or sandstone? Would this require an additional grinding step?

VK: Yes, I think this application can be compared to the building material publication. For rocks, I think an extending bead-beating step will be required. But afterwards, for the purification protocol, the same standard protocol can be used.

Q: What would you advise for soil and for fecal samples, if you have a kit for feces?

VK: The FastDNA Spin Kit for Soil and FastDNA Spin Kit for feces are very similar. There is a washing step added in the fecal kit, but a lot of researchers are also using the FastDNA Spin Kit for Soil for that application and get very good results. So, both are suitable and can be tested to give similar results, but definitely the soil kit can be used as well with fecal samples.

This webinar is part of the SelectScience Advances in Microbiology Webinar Series >>

SelectScience runs more than 10 webinars a month across various scientific topics, discover more of our upcoming webinars>>