Dear Nicholas,
Thank you very much for the answers. After your explanation its pretty clear the advantage of a unique OTU ID instead of an arbitrary number.
Regarding the Biom convertion, I was following the "Moving Pictures" tutorial and have combined the sequence variant ID with the taxonomy, following a post of the forum (How to make classic otu table with QIIME2?). I got stuck on the final step when converting the biom format to txt.
The code is the following:
qiime tools export table.qza --output-dir exported
qiime tools export taxonomy.qza --output-dir exported
#####Change the first line of biom-taxonomy.tsv (i.e. the header) to this:
#OTUID
taxonomy
#confidence
biom add-metadata -i exported/feature-table.biom -o table-with-taxonomy.biom --observation-metadata-fp exported/biom-taxonomy.tsv --sc-separated taxonomy
#convert to classic table
biom convert -i table-with-taxonomy.biom -o OTU_Table.txt --to-tsv --header-key taxonomy