Hi @Jasmine84, When I export a FeatureData[Taxonomy] artifact (e.g., as illustrated here) and want to change the header, I typically just open the resulting .tsv file in a text editor and make the change. However the following command would also work:
sed 's/Feature ID/#OTUID/g' taxonomy.tsv > biom-taxonomy.tsv
The resulting biom-taxonomy.tsv command will then have the new header. (It's usually just quicker for me to make the edit by hand in a text editor than remember how to write a sed command.)
Hope this helps!