Hello,
Will qiime2 include plugins in the future to do association analysis, such as MaAsLin, to link changes in taxa to other metadata collected from the same study?
Researchers are now more interested to learn the associations between microbiota and physiological precesses than just characterizing the intestinal microbiota.
Hi @yanxianl,
Absolutely. The future is now. There is not yet an implementation of maaslin or a similar tool, but sample-classifier and gneiss are examples of current plugins that find associations between many taxa and an individual metadata category. Other plugins (e.g., composition, longitudinal) test associations between individual taxa and one or more metadata categories. Other plugins and actions will be added in the future as QIIME2 grows — don't forget that this is a new method still in its infancy. It is far from reaching its full potential. 
Of course — and so it has been forever. QIIME2 (and QIIME1 before it) does much more than characterize microbial composition in samples. Other methods like maaslin may be supported in the future, but for now it should be fairly straightforward to export the data (or download from the visualizations provided by various plugins) and input those data directly into maaslin, R, or other software for downstream analysis.
Happy QIIMEING. 
