Metaphlan 4 using with Humann3.9

Microbial community profiling HUMAnN
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Are you considering the below strategy ?

  1. Environment A (The Latest Taxonomy): Running the newest MetaPhlAn (4.2.2+) to get the most accurate, up-to-date taxonomic resolution and using that output for all your alpha/beta diversity analyses and abundance bar plots.

  2. Environment B (The Functional Silo): Running HUMAnN 3.9 tied to an older, compatible MetaPhlAn 4 (with the Jun23 markers) strictly to generate the gene family and pathway abundance files.

If you use this strategy, the taxonomic profiles that drive your functional pathways in Environment B will be slightly different from the standalone taxonomic profiles you generated in Environment A. When writing your methodology for a manuscript, you simply have to be transparent about this. You would state that taxonomy and diversity metrics were calculated using MetaPhlAn v4.2.2 (database Jan25), while functional potential was profiled using HUMAnN v3.9 and its corresponding MetaPhlAn marker database (Jun23). Other parts, MetaPhlAn 4. as the developer (franzosa) mentioned, HUMAnN 3.9 is compatible with MetaPhlAn 4, but only with a specific, older database (the Jun23 markers). It is completely incompatible with the newest MetaPhlAn 4 versions (like 4.2.2 with the Jan25 markers). Because the Biobakery team maps the functional databases (ChocoPhlAn) directly to the taxonomic markers. This is my opinion

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