MetaPhlan V 4.0.4
I have been testing MetaPhlan4 for taxonomy of bacteria from metagenomic reads. I have been comparing the outcomes to that of a known control and to the outcomes of Kraken2. In my opinion MetaPlan produces a much more accurate estimation of taxonomical abundance, however it does not consider Acidobacteria at all. This is the only reason I will not use the tool because a major group of bacteria is excluded from taxonomy.
Am I missing some setting to include this group of bacteria to the database or has it not been added?
The latest version of the metaphlan 4 database (Oct22) contains 131 SGBs from the phylum Acidobacteria, you can have a look at the taxa included in the following file: http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_vOct22_CHOCOPhlAnSGB_202212_species.txt.bz2
If that is the case then could you provide an explanation as to why Acidobacteria is not being assigned at all when compared to known standards?
Could you share the results and the known control community you are using to better investigate what might be the problem?