I believe that many of the qiime2 users in this forum have published research papers that provide results based on the outputs of qiime2 pipeline. QIIME2 has certainly accelerated the pace of research in reverse ecology. However, it is important that in the race to publish, we do not overlook, ignore, misuse, misinterpret or violate the fundamentals of sequence analyses. By doing so, we not only contribute to pseudoscience but also overdo science claims. As an Editor/Reviewer of journals in this field, I come across a large number of manuscripts and also read several published articles that violate/have violated the assumptions/theories of reverse ecology and sequence analyses.
To minimize pseudoscience, we must form a team consisting of subject experts, computational biologists and data scientists to review articles that used QIIME2 pipeline but violated the assumptions underlying each q2-plugin. Publishing a commentary on the erroneous article would caution other researchers against the overuse of q2-results. Unfortunately, not all journal Editors/Reviewers who handle such erroneous manuscripts are experts in QIIME2, so they fail to detect the violations.
I urge the q2-admins and users to come forward and provide their ideas to this proposed initiative. Thanks!