Is HUMANN3 good for finding all the nitrogen metabolism from soil samples? Including denitrification to N2O?
For working with soil samples I’d recommend running HUMAnN using the UniRef50 database rather than the default UniRef90 database to catch more remote homology. After that, you should be able to quantify nitrogen metabolism processes as represented as ECs/KOs/Pfams and GO processes assigned to individual UniRef50s. We should also be able quantify any nitrogen metabolism pathways represented in MetaCyc, e.g.: MetaCyc nitrate reduction I (denitrification).