We have observed that DNA size and quality does affect the microbiome DNA
separation, as does the overall quantity of CpG methylated dinucleotides. For
example, normal human fibroblast DNA (IMR-90) is methylated at 4–5% of the
genome and is effectively separated by this technique (90% of human DNA is
removed). Cancer DNA (HeLa, Jurkat) is less methylated globally at 3%, and
enrichment is less efficient. Likewise, if the DNA fragment size is less than
15 Kb, enrichment will be less efficient. The larger and more CpG methylated
the host DNA, the better the separation will be.
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