I contacted Nicola Segata from Lefse team about how the input table with OTU IDs should look like and he responded me like that:
So in addition to removing the OTUs IDs in the internal leves, you have to add it in the final level of each phylotype.
LEfse adds the abundances of the internal levels (e.g. Bacteria|Bacteroidetes|Bacteroidia|Bacteroidales|Porphyromonadaceae) by summing up all abundances of OTUs at that level (as Otu001 above) and lower levels (e.g. OTUs in the Porphyromonas genus)."
Maybe you could change Mothur’s output to look like that.