Notation of bacterial names in LEfSe analysis

Thank you very much for your help.

I am getting different results from the LEfSe analysis of the raw data (left side of the image) and the LEfSe analysis of the data (right side of the image), which is organized in the same way as the sample in the tutorial.

There is no difference between the left and right images except for the name of the bacteria.
Is it not good that there is a line with the same bacterial name on the right side of the image?
I would appreciate it if you could tell me.

This is interesting. I was coming here to post about a similar issue. It doesn’t appear that this forum is very active though so I am not sure if it is going to get a response, so I will delay making my own post. For my situation the inconsistency is important to resolve as one of the results of the differences is a valuable result but I don’t want to report it without knowing why there is this inconsistency.

Hello, and sorry for the delay in response. I think what may be happening is that the left-hand side is interpreting the incomplete taxonomic values as specific species, since there are | denoting taxonomies down to the species level (even if the names are essentially blank), whereas the right side is treating Bacteria|TM6 for instance as the sum of all species in that phylum. Without knowing your data I’m not sure which is the correct interpretation of your data, but if Bacteria|TM6||, etc refers to the total relative abundance in that phylum, then the version on the right is what you want.
I hope that helps!