Making a Plan
It is important to first ask what your main questions are before jumping to community analyses. Very quickly you can become lost in all the various figures and graphs. It is recommended to make an outline of the questions you want to answer about your data and then sketch a work flow of various scripts that will answer these particular questions.
Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. Nature. 2012 Sep 13; 489(7415): 220–230.