Metaphlan4 species not included in Humann3.5 output?

Hi! I noticed that in the Humann3.5 pathway abundance output, only a subset of the Metaphlan4 species are present as contributors to pathway abundance (i.e. SGB species and some others are missing in the pathway file). Is this supposed to be the case? If so, is the Humann3.5 output not representative of all the species present based on the Metaphlan4 genomes?

Thank you,
Brandi

That’s right - HUMAnN 3.5 will profile the subset of species that it recognizes from MetaPhlAn 4.0 output, but species that are new to MetaPhlAn 4.0 (especially uSGBs) will be skipped. HUMAnN 4.0 is in development and will again fully cover the MetaPhlAn species, but we released HUMAnN 3.5 in the interim to maximize compatibility between the software versions.

Hi,
We are also interested in running Humann on metaphlan 4 output. Can Humann 3.6 be run directly on the metaphlan 4 mpa_vJan21_CHOCOPhlAnSGB_202103 db?
Is the development version of Humann 4 available?
Can you share a time estimate for Humann 4 official release?
Thank you,
Ilya.

HUMAnN 3.6 can be run with MetaPhlAn 4 databases - it will match as many of the SGBs as it can based on their species-level taxonomy. A development version of HUMAnN 4 is close - I would expect to see it in the next couple of months.