I recently came up with a crude but working solution for creating a Bugbase compatible OTU table right within QIIME2 and thought might be useful to others. Since BugBase utilizes PICRUSt under the hood, that means this solution also works for PICRUSt. Note that there is a newer version of PICRUSt, which also has a Qiime2 plugin, q2-picrust2, which users should consider if their end goal is not to use BugBase.
There are other posts on this forum that have dealt with this issue in the past as well, this is just my version. Hope it works and PRs welcome.
Is there a tutorial for q2-picrust2?