Merged abundance table to biom format

Hello researcher and developer @fbeghini.

It’s my first time to analyse shotgun and I have difficulties to communicate metaphlan output to phyloseq.

I have used but in absolute counts (code available from but when I tried to construct the otu table I obtained the following output:

I have all the taxonomic ranks mixed in the first column. Therefore, I understand that I cannot do tax_glomf function in phyloseq R package.

Therefore it will be interesting to construct 7 independent OTU tables (one for each taxonomic rank) and construct 7 phyloseq objects?

Thanks for your help,

Kind regards,