Hello,
I am using metaphlan4 for taxonomic profiling and I am getting bacteroidota and bacteroidetes as two separate phylum in the results. Was this classification done intentionally with some logic or should I consider them to be the same phylum for analysis?
Any insights will be appreciated.
Thank you
Hi @Vikas
Which version of the database are you using? Updating to the newest database (vJun23_CHOCOPhlAnSGB_202403) should give you a consistent taxonomy.
Hi, I had used vJun23_CHOCOPhlAnSGB_202307.
Sure, I will try with the updated version, thank you.
But for the time being, if I use the abundance of Bacteroidetes to be the sum of bacteroidota and bacteroidetes, it should not be a problem right?
From what I see there are no species with phylum Bacteroidetes in vJun23_202307 either. Anyway in earlier version this could have happened due to inconsistencies in NCBI taxonomy, so I think you can consider them as the same phylum.
Ok, I found the problem. I was using results from two different runs and they were profiled with different versions of CHOCOPhlAn, so I was getting this overlap.
Thank you for the clarification.