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Do I extract RNA or DNA from gut microbiome (stool samples) if want to do 16s rRNA sequencing?

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    $\begingroup$ Genomic DNA, see Illumina's own protocol. $\endgroup$ – CKM May 4 '17 at 21:07
  • $\begingroup$ More correctly: you are sequencing 16s rDNA, the gene coding for the 16S rRNA. $\endgroup$ – skymningen May 5 '17 at 10:12
  • $\begingroup$ Well, it depends on what you want to know. If you want to find who is there, then DNA, if you want to know who is there and their functionality, then RNA. Though if you have a lot of samples and limited budget, 16S rRNA is a cheap reliable option. $\endgroup$ – aLbAc Mar 8 at 15:16
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In general, you extract DNA, then PCR out the 16rRNA coding regions and finally sequence them. Here some links

http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/16s/

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0068739

https://support.illumina.com/content/dam/illumina-marketing/documents/products/other/16s-metagenomics-faq-1270-2014-003.pdf

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