Metagenomic DNA/RNA from human tissue samples

simpsoncl · 09-20-2016, 01:39 PM

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

nucacidhunter · 09-20-2016, 02:35 PM

NEBNext microbiome DNA enrichment kit

fanli · 09-20-2016, 03:39 PM

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".

nucacidhunter · 09-20-2016, 07:35 PM

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.

http://www.ncbi.nlm.nih.gov/pubmed/27237775

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09-20-2016, 01:39 PM	#1
simpsoncl Junior Member Location: Memphis, TN Join Date: Sep 2016 Posts: 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

09-20-2016, 02:35 PM	#2
nucacidhunter Jafar Jabbari Location: Melbourne Join Date: Jan 2013 Posts: 1,238	NEBNext microbiome DNA enrichment kit

09-20-2016, 03:39 PM	#3
fanli Senior Member Location: California Join Date: Jul 2014 Posts: 198	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".

09-20-2016, 07:35 PM	#4
nucacidhunter Jafar Jabbari Location: Melbourne Join Date: Jan 2013 Posts: 1,238	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. http://www.ncbi.nlm.nih.gov/pubmed/27237775