biom convert -i matrix_counts.txt -o matrix_counts.biom --table-type="OTU table" --to-hdf5
where matrix_counts.txt is the name of your counts file from MED and matrix_counts.biom is the name you want to give the biom-formatted version of this info.
Note, however, that you won't have taxonomic info in this biom table, which will cause problems if you try to perform downstream analyses based on taxonomy such as summarizing taxa in core_diversity_analyses.py .
Best,
Amanda