16s rRNA Sequencing From Gut Microbiome (stool)
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