Clarification on HUMAnN taxonomy assignment beyond MetaPhlAn

Microbial community profiling HUMAnN
1

Hello,

I would like to confirm whether HUMAnN performs additional taxonomic assignment beyond what is provided by MetaPhlAn. My understanding was that MetaPhlAn is responsible for taxonomic profiling, while HUMAnN focuses on functional annotation. However, I have observed taxa (e.g., p__Streptophyta) in HUMAnN’s output that are not present in the corresponding MetaPhlAn profile.

Could you confirm whether HUMAnN can assign taxonomy independently of MetaPhlAn, for example, through the use of UniRef annotations?

Additionally, I am using the following command to infer taxonomy from gene families:

humann_infer_taxonomy -l "Phylum" -d uniref90-tol-lca -i humann_genefamilies.tsv -o Phylum/humann_genefamilies.tsv"

Can this method retrieve taxonomic assignments that were not originally present in the MetaPhlAn profile?

Thank you for your help!

Best,
Jérémy

2

Yes, the infer_taxonomy method can make taxonomic assignments that were not made by MetaPhlAn, although they are less reliable. infer_taxonomy is simply looking at the LCA of the species that contributed to each detected UniRef90 family (as annotated in UniProt) and then assigning the UniRef90 to 1) that taxon or 2) one of its ancestor taxa (depending on the rank at which you ran the script, e.g. Phylum).

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