I am preparing a metagenomics experiment from the soil sample. I will use Oxford Nanopore technology, which has only limited throughput (approx. 8 GB), so I need to discard all eukaryotic cells before the sequencing (because their genomes are really large, and would saturate the device quickly). So I am interested in the simple and reliable method, how to obtain only the prokaryotic and viral species. Is it a good idea to use some syringe filters? E.g. with the pore size 1 micron? So the eukaryotic cells will be stuck on the filter surface, and bacteria, archaea, and viruses will go through?
Thanks for all suggestions,
Martin
My start point would be something like adding sterile saline in a test tube and treating in an ultrasonic cleaning bath to release microbes from the soil. Perhaps then very short centrifugation to take down larger eukaryotic cells. Then maybe filtration above 0.45 micron. However, check if there are standard kits out there now. As I recall there are kits to remove DNA from soil as it can bind strongly. Can’t remember the name of the kit, sorry - was quite a while ago.
Filter sterilization
0.45 μm for cyanobacteria, 0.22 μm for Bacteria, 0.1μm for mycoplasma
For details of the possible methods to use, the article suggested hereunder refers. Article Selective isolation of bacteria for metagenomic analysis: Im...
Jim C Philp , Manoj Wijesekara , thanks for your suggestions, but 0.45 μm seems really small pore size to me ... typical prokaryotic cells range from 0.1 to 5.0 μm in diameter, eukaryotic cells are usually 10 to 100 μm (?)
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