Using MetaPhlAn4 & HUMAnN 3.0 for mouse gut microbiome


I wanted to inquire about the viability of using MetaPhlAn4 & HUMAnN 3.0 to study mouse gut microbiome? or are they more optimized for human?


We did some evaluations of MetaPhlAn 3 + HUMAnN 3 on murine gut metagenomes from CAMI as part of the publication for those methods. You can see the results here:

MetaPhlAn 4 will further improve upon this result by also considering MAGs reconstructed from published mouse metagenomes.