I’m very new to Qiime2 and any sort of bioinformatics work so I apologize in advance for my lack of understanding.
I’m using Qiime2 to look at diversity of Fungi in environmental DNA samples I’ve processed.
I’ve followed the Moving Picture Tutorials and created feature tables of my data and even used the taxa collapse option to generate a table containing my taxa in column one, and the reads per sample in all other columns.
The example feature table you gave looks a little odd, but I think more or less what is described in this tutorial:
Otherwise you may want to get in touch with the FUNGuild developers to troubleshoot, since they would know their format best.
Note: qiime 1 used biom format in all but the earliest releases… what you describe (a txt document containing an OTU table) is what became known as “classic” OTU tables in qiime 1. The tutorial link above describes how to make a “classic” OTU table.