The way microorganisms are named affect the final results of lefse

Hey, I encountered an issue: I was working on Galaxy and trying to run lefse but the output files were different when I changed the way microorganisms are named.
The lef_usual.txt is the input file whose microorganisms are named like “Clostridium_sp_DL_VIII”. Underscore is the only special character in the input file.
lef_usual.txt (423.5 KB)
The result is uploaded here.


Then I cleaned up the data to the most basic of formats like “ClostridiumspDLVIII” and ran it again. The input file named lef_basic.txt is uploaded here.
lef_basic.txt (423.4 KB)
The new result is uploaded here and it is different from the first one.

The relevant parameters of the two tasks are the same, and only the naming method of the first column of the input file has changed.

So, why does just changing the way microorganisms are named affect the final results? Do we need to turn the data into the most basic way like “ClostridiumspDLVIII” to get the most correct results? If so, cleaning up to the most basic of formats like “ClostridiumspDLVIII” is hard to read and it is also difficult to search “ClostridiumspDLVIII” on the Internet. So, can Galaxy solve this problem thoroughly? Can the program of Lefse analysis be optimized?