What would you suggest as the most efficient method for virus concentration in DNA extraction from soil for shotgun metagenomics assay? In a situation where you have soil and shoot samples for DNA extraction, targeted for metagenomics.
Alex Ignatov
Tangential flow (crossflow) filtration work well for virus concentration
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Bertrand Cornu
Physical separation: Physical separation techniques, such as filtration or centrifugation, can be used to separate viruses from other contaminants in the soil sample. Filters with a small pore size (e.g. 0.2-0.45 microns) can be used to capture viruses, while larger particles such as bacteria and soil debris are retained. Centrifugation can also be used to separate viruses based on their size and density. Chemical lysis: Chemical lysis techniques involve the use of detergents or enzymes to break down cell walls and release the viral DNA from the viral particles. This can be combined with physical separation techniques to increase the efficiency of virus recovery. Enrichment culture: Enrichment culture involves the growth of viruses in the presence of specific host cells, which can be used to selectively enrich for viruses in the soil sample. This method can be combined with DNA extraction and metagenomics techniques to identify and characterize the viral communities present in the sample. Tangential flow filtration can be a useful method for virus concentration in DNA extraction, as it allows for the efficient separation of viral particles from other contaminants in the sample. This can be particularly useful for soil samples, which can contain a wide range of contaminants that can interfere with downstream analysis. By concentrating the viral particles using tangential flow filtration, it may be possible to improve the sensitivity and accuracy of DNA extraction and metagenomics techniques.
There are a number of methods that can be used to concentrate viruses from soil samples for DNA extraction and shotgun metagenomics analysis. Some of the most commonly used methods include:
Overall, the most efficient method for virus concentration in DNA extraction from soil will depend on the specific goals of your study and the resources available to you.
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