If my bioinformatic core uses a different tool than qiime2, can I combine their results with the ones I compute in qiime2? Or all analyses should be done using the same tool?
Welcome to the forum @Javi!
The short answer is that yes mothur, QIIME 2, and related tools should in theory be able to arrive at fairly similar answers, but there are many different ways (methods) to arrive at those answers (process your data). So unless if you very carefully control the internal methods that you are using, you may receive different results for even the same sample.
It sounds like you are trying to do an analysis where you pool samples from two or more studies for comparison. You should ALWAYS process the data in exactly the same way… i.e., do not attempt to combine QIIME 2 and mothur results in a pooled analysis, otherwise differences you see are very likely to be due to methodological differences rather than biological differences!
I hope that helps!