Hi @danielsebas,
If you want to perform a differential abundance test, you can use qiime composition ancom (see the tutorials at qiime2.org for examples, e.g., the "moving pictures" or "parkinson's mouse" tutorials both use ANCOM).
There is also a new differential abundance plugin that joined the QIIME 2 family ():
LEfSe is not part of QIIME 2 — if you want to use LEfSe you should check out the appropriate manual or post to the LEfSe forum to learn more about formatting for that method.