Are there any HUMANN databases specifically designed for marine habitats? Also, how is the performance on protists and small micro eukaryotic organisms?
We do not have environment-specific databases for HUMAnN. Most of the HUMAnN pangenomes (as of v3.6) correspond to bacteria and archaea. Protists and small euks would still be covered during translated search if their proteins show up in UniRef; you would need to use the infer_taxonomy script to make guesses about their taxonomy in that case.