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  • simpsoncl
    Junior Member
    • Sep 2016
    • 1
    #1

    Metagenomic DNA/RNA from human tissue samples

    Hi,

    Is anyone extracting microbial DNA/RNA from human (or animal) tissue? I've got some kidney biopsies that I want to look at the microbiome but I'm not having much luck in finding a protocol to isolate the nucleic acids. Any advice, kit recommendations etc would be gratefully received.

    Thanks,

    Claire
    Tags: biopsy, kidney, microbiome, tissue
  • nucacidhunter
    Jafar Jabbari
    • Jan 2013
    • 1250
    #2
    NEBNext microbiome DNA enrichment kit

    Comment

    • fanli
      Senior Member
      • Jul 2014
      • 197
      #3
      Do you mean extraction or enrichment of microbial DNA/RNA? For extraction, we've been using the AllPrep kit from Qiagen with reasonable success.

      @nucacidhunter, how much enrichment do you see using the NEBNext? We've had pretty limited success (~20-40%), depending on sample.

      Enrichment of microbial RNA seems trickier - I haven't heard of anything besides the theoretical "you can use an array to pull out human RNA".

      Comment

      • nucacidhunter
        Jafar Jabbari
        • Jan 2013
        • 1250
        #4
        I have not used them but following paper has compared NEBNext Microbiome DNA Enrichment Kit and the Molzym MolYsis Basic kit. They use different strategies for DNA enrichment.

        Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing - PubMed
        http://www.ncbi.nlm.nih.gov/pubmed/27237775
        Metagenomic whole genome sequencing for detection of pathogens in clinical samples is an exciting new area for discovery and clinical testing. A major barrier to this approach is the overwhelming ratio of human to pathogen DNA in samples with low pathogen abundance, which is typical of most clinical …

        Comment

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