The power of the unknown
You didn’t expect to be out after dark. Work ran long, your train was canceled; one of a million everyday circumstances caused a delay. Now you make your way through the nighttime city. People pass, faces hidden in shadow. Your phone vibrates, and you stop to check it. A car passes, and when it’s gone, there are footsteps in the alley next to you. You look up, but flash-blind from the headlights, the way is completely black. Your heart quickens. The hairs on your arms stand, and you want to run.
This is the power of the unknown. And in research, unknowns are everywhere.
Light in the darkness
Scientists explore the dark alleyways of our world, shedding light upon the unknown. The proper equipment (say a 20,000-lumen flashlight instead of a matchbook) can ease the task and provide better resolution. However, in microbiology and microbiome research, there is a huge variety of samples and sample types and many different methods with which to analyze them. In episode 3 of Q-rious (What’s bugging you? Microbial secrets revealed; now available on-demand), we discussed many of these methods, including soil DNA/RNA extractions, working with water filters, microbiome sequencing, dPCR and automation. But even in this 60-minute episode, we weren’t able to cover everything, and the audience let us know that they had questions.
Which kit is the best for my sample type?
Among the most common questions during Q-rious were the following: “I work with sample X. What is the best kit to extract microbial DNA or RNA?” Sample X is, of course, a stand-in for the many different microbiome sample types (such as soil, stool, skin swabs or water) and the many different types of microbes (such as viruses, bacteria or fungus). In other words, most people wanted to know what is the proper tool to elucidate the mysteries of Sample X, that stranger in the darkness.
So, which kit is best for your sample type? Sometimes you can tell by the name. Did you know that all kits with “Power” in the name contain Inhibitor Removal Technology® (IRT) and kits with both “Power” and “Pro” have second-generation IRT, which is performed in a single step? For instance, the RNeasy PowerMax Soil Pro Kit is designed to extract RNA from soil samples, specifically from larger sample masses (“Max”), and it contains second-generation IRT (“Power Pro”).
If you need more specifics, we have several resources to help you find the perfect kit to extract pure, high-quality microbial nucleic acids. These include the free-to-download microbiome interactive booklet, the human microbiome selection guide and the environmental microbiome selection guide. In addition, please find the answers to many Sample X questions from Q-rious below:
Human samples
- Saliva sample DNA: The PowerFecal Pro is effective for these samples, as is the QIAamp DNA Microbiome kit if host DNA removal is required.
- Dental calculus DNA: We have no in-house data on dental plaques. However, the DNeasy PowerBiofilm Kit with around a 50 mg sample may be a good starting point, and some of our customers process these samples using the DNeasy PowerSoil Pro 96 QIAcube HT kit.
- Skin Swab microbial DNA: The QIAamp DNA Microbiome Kit integrates a step for the removal of mammalian DNA and should be suitable for this purpose.
- Sputum sample RNA: The AllPrep PowerFecal Pro DNA/RNA Kit should isolate viral, bacterial and eukaryotic nucleic acids. ®
Environmental samples
- DNA from 0.22 µm water filters: The DNeasy PowerWater Kit can be used with common filter membrane types including 0.45 µm and 0.22 µm filter funnels.
- Manure DNA: The QIAamp PowerFecal Pro Kit or the QIAsymphony PowerFecal Pro DNA Kit (for automated isolation of nucleic acids).
- Removing humic acid from soil DNA samples: All kits with ‘power’ in their name will be able to remove humic acids from soil, in particular any of the DNeasy PowerSoil Pro kit variants, such as the standard spin kit, the QIAcube HT kit or the 96-well plate. For large starting amounts of soil, the DNeasy PowerMax Soil kit is recommended.
- Freshwater protists in biofilm DNA: The DNeasy PowerBiofilm Kit pairs chemical and mechanical lysis techniques and should work well for this sample.
- Fermented plant product microbiome DNA: The DNeasy PowerSoil Pro Kit should be a good fit for this extraction.
- Viral DNA from wastewater: The DNeasy PowerWater Kit or the DNeasy PowerWater Sterivex could both be suitable for these samples if starting from filtered wastewater. For other concentration methods, such as centrifugation, the AllPrep PowerViral or AllPrep PowerFecal Pro DNA/RNA are ideal.
- Low biomass soil DNA or RNA: There are two kits specifically designed to isolate DNA or RNA from low biomass (or normal biomass) soil samples. The DNeasy PowerMax Soil Kit and the RNeasy PowerMax Soil Pro Kit contain 50 mL high-capacity tubes designed to handle up to 10 g (in the case of DNA) or 15 g (in the case of RNA) of soil.