Hello everybody,
--just a brief intro about the background of my question--
I have to analyse the gut microbiome of a marine fish through whole metagenome sequencing. Going through literature, I have noticed that one of the major problems in studies carrying out whole metagenome sequencing is that more than the 90% of raw sequences belong to the host's DNA and not from the microbial community. Therefore all the downstream analysis are going to be one on a minimum part of the raw sequences.
I have found out that is possible to deplete the host DNA either before or after extracting DNA through different methods (Benzonase, MoIYsis kits, NEBNext® Microbiome DNA Enrichment kit) and I would like to try a few of them out in order to see which one would deplete more host DNA without impacting the microbial DNA load too much.
Some of these methods use selective lysis of eukaryotic cells before the activation of a nuclease aimed to eliminate extracellular DNA.
Here comes my question: In order to test the efficiency of different storage methods, I will have samples stored either in Ethanol or RNAlater and then frozen at -20°C or directly frozen at -20°C, do you think it would be possible to carry out selective lysis in samples stored in these conditions? (I am mainly concern about the ethanol and RNAlater).
In case of a positive response which method/solution/buffer could I use?
Thank you all!
Ginevra
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