From the methods I have come across, I haven't seen any that claim to be capable of purifying nucleic acid from bacterial, fungal and viral cells. Is there a commercially available method out there capable of this? Also, most methods seem to focus on blood. Are there any methods out there for sputum? Thanks for your help.
I have used Qiagen DNA easy kits for clinical samples (mouth, esophagus, stomach, duodenum, colon, skin, tonsils) - these work well for getting your bacterial DNA extracted (with some optimizations and modifications), but removing the host human DNA is very difficult. any reason you need to do this? what is your downstream application? QPCR? 16S survey? in most cases you dont need to remove host DNA.
Thanks for the great question, i planed to ask it myself :)
I have question about Qiagen DNA easy kit. I wanna look in 16s in my samples. Did you have equal success with both gram+ and gram- bacteria? another question is, is it usable with tissue samples embedded in O.C.T.?
Best regards,
Vlado
To ensure gram + and - representation, you need to add a lysozyme step before using the qiagen reagents. when done, it gives you both + and - as well as archaea. it should be compatible with OCT, but you can check their protocol for compatability.
Thanks Carlos. I am aware of commercially available kits for pathogen specific DNA isolation e.g http://www.molzym.com/products/dna-isolation-products/pathogen-dna.html . However most kits seem to be designed for bacteria in blood. My focus is microbial diagnostics of pathogens present in very low numbers in clinical samples. This includes bacteria, fungi and viruses.
DNAeasy works with tissue - we got good results from esophagus, stomach, and duodenum, that have low microbial biomass.
Hi Justin,
just in case you are still 'on' - we might have a solution for you: LOOXSTER Enrichment Kit (see http://www.analytik-jena.de/en/life-science/products/prod/cat/enrichment/prod/looxster-enrichment-kit.html).Input material for the LOOXSTER Enrichment kit is total extracted DNA (up to 300 µg). Prokaryotic DNA is bound to the magnetic particles; approx. 95 to 98% of eukaryotic - in your case human - background DNA is depleted hereby. Prokaryotic DNA is eluted finally and can be used in further downstream applications.
Best,
Ingo
Check this paper! It can give you some ideas.Article DNA extraction from primary liquid blood cultures for bloods...
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