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.
Think you could benefit from this webinar, but missed it? You can now watch it on demand at a time that suits you.
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.
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.
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.
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.
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.
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.
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.
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.
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>>