I’m preparing the results of an experiment using mothur and just wanted to make sure I’m going to be analysing the data the correct way. The experiment consists of a series of antibiotic treatments on a parrot our lab is interested in, and whether the treatment has long-term influence on the gut microbiota.
Having gone through the Schloss SOP, I’m certain I should be using an OTU-based analysis as the loss of particular OTUs (or gain of others) would be the expected result of antibiotic treatment. This seems to me to be fairly analogous to the context of the test data given for the SOP, so I’m really just checking that this is the correct way to approach the data. By contrast, the phylogeny-based approach would be used for evolutionary questions of the samples.
Thanks for your time.