We are hoping to assay the microbiome of a small mammal (16S RNA) from frozen whole intestines (cecum, large, and small intestine).
We are wondering what is the best way to collect the DNA?
We have seen intestinal flushing/scraping in a few papers but no specific methodological protocol. Possibly swabs? Some studies just homogenize the entire intestine but would host DNA clog the columns (we'll be using MoBio's Powerfecal DNA extraction kit)?
There are different and very detailed assessments. Please see:
http://www.colorado.edu/eeb/EEBprojects/FiererLab/Lauber_etal_FEMS_2010.pdf
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0034605
http://bmcmicrobiol.biomedcentral.com/articles/10.1186/1471-2180-12-158
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0088982
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0046953
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0036934
http://link.springer.com/article/10.1007/s00253-010-2838-2#/page-1
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0070460
Thanks Howard! Some useful info on storage the Bai paper on swabs will be helpful.
If anyone else has experience with collection methods in particular I'd appreciate any insight you may have!
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