Are there anyway to increase the microbial DNA concentration in a Mixed sample of Human and microbial DNA ?
Knowing that acquiring the samples was very difficult because of strict inclusion and exclusion criteria, so I can not re-sample !!!!:)
You can try the NEBNext® Microbiome DNA Enrichment Kit from New England Biolabs. This kit enhances microbial DNA in a mixed sample- a bit expensive!
I think it's a matter of sensitivity of your bac-detection to find it in the hum-DNA background. I did an assay for helicobacter pyl. on human gastric biopsies. So also much hum-DNA with little bac-DNA. The LOD of the test was about 5-10 bacs within 50-60 ng whole DNA in the PCR-tube. Maybe you can get valid results in presence of hum DNA.
If you use the appropriate 16S primers, and you use faeces or intestinal contents as sample, you must not have any problem with human DNA contamination. Only in the case of working with intestinal mucosa samples (to analyse the microbioma closely associated with mucus or with intestinal mucosa) you can obtain a significant amount of sequences related with the mitochondrial DNA depending on the 16S primer that you use.
You can try the NEBNext® Microbiome DNA Enrichment Kit from New England Biolabs. This kit enhances microbial DNA in a mixed sample- a bit expensive!
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