Hello,
I am interested in applying the Dirichlet multinomial mixtures (DMM) model proposed by Holmes et al. (2012, PLoS ONE 7(2): e30126) and implemented in Mothur via the get.communitytype command for an analysis I am currently working on. In the example provided by Holmes, and in Pat’s recent publication in Nature (2014 May 15;509(7500):357-60), the DMM model was applied to genus-level phylotypes, as opposed to an OTU table. In several other examples I came across (La Rosa PS et. al., 2012. PLoS ONE 7(12): e52078.), the DMM model was also applied to sequences clustered at a single taxonomic level.
I am hoping to get some feedback on what are the benefits and limitations of applying the DMM model to a table of genus-level (or other) phylotypes vs. an OTU table? Basically, I know I can fit the DMM model to an OTU table, but I am wondering if are there any good reasons as to why I shouldn’t? In particular I am thinking of tables of counts (as opposed to presence/absence).
Also, for the phylotype analyses, it seems some have chosen to “merge” sequences reads that cannot be classified at a given level (i.e. genus-level) to a single group denoted as “other”, while some have culled them from the table (if I am reading this correctly).
Thanks in advance for any thoughts on the topic!