Conversion of HUMAnN taxonomy outputs to GTDB

Microbial community profiling HUMAnN
1

Hi,

I’m running HUMAnN v3.9 using the mpa_vJun23_CHOCOPhlAnSGB_202403 database, and I have generated output files such as:

Gene families file (genefamilies.tsv)
Reactions file (reactions.tsv)
Pathway abundance file (pathabundance.tsv)

I understand that HUMAnN relies on MetaPhlAn’s taxonomic profiling, and the taxonomy used in the stratified outputs is based on SGB (Species-level Genome Bins).

I’ve already used the sgb_to_gtdb_profile.py script (provided with MetaPhlAn 4) to convert MetaPhlAn taxonomic profiles to GTDB format.

Now, I would like to ask:

Can the same sgb_to_gtdb_profile.py script or a similar approach be applied to convert the taxonomy in the HUMAnN output files to GTDB taxonomy?
If not directly, is there a recommended workflow or mapping file that can help translate the g__Genus|s__Species labels in the HUMAnN stratified outputs to GTDB taxonomy?

Any suggestions or tools would be greatly appreciated!

Thank you.

Boram

2

The MetaPhlAn version is based on assigning GTDB taxonomy to the SGBs. HUMAnN also outputs taxonomy in terms of SGBs (more specifically, s__SPECIES.t__SGB). So you could swap the SGB-based taxonomy in the HUMAnN output for their GTDB-equivalent species names. We do not have a script for this, but the mapping file used by the MetaPhlAn conversion script could be applied for this task (manually).