HUMAnN3 and MetaPhlAn3 output analysis with MaAsLin2

Hi community ( @franzosa ) !!!
I have two groups of samples: case and control. I have output from MetaPhlAn3 and HUMAnN3. I want to find out the differentially abundant taxa in the control and case samples from the MetaPhlAn3 output and similarly, the differentially abundant pathways and gene families in the case and control groups from the HUMAnN3 output. Can I use MaAsLin2 for both purposes? If yes, can you please guide me?

Thanks for your time,


You can absolutely use MaAsLin2 for the analysis of per feature differences from the MetaPhlAn and HUMAnN v3 output. There should be little to no difference in the background coding between using these feature tables and the one generated via v2. The tutorial is an excellent place to start to get a good idea of how to proceed:


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Hi @Kelsey_Thompson, thanks for your kind response. Metaphlan output is relative abundance out of 100 percent. It is also not normalized to library size. Can I directly use the output to MaAsLin2? Is there any option in maaslin to consider these two things and convert them accordingly and get a proper result?


Hi, would really love an update on this! I’m kind of lost on how I can explore my functional output data outside of what’s written in the tutorial.