Method about comparing metacyc pathway

I would like to compare the metacyc pathway of microbiome in two groups by using human intestinal bacterial samples.
I have obtained "path_abun_unstrat_descrip.tsv" using picrust2, but I am not sure how to compare the two groups.
I have used STAMP and LEfSe, but there is a difference in the metabolic pathways obtained. Some say STAMP is outdated, so I would like to know which one I should trust or if there is another better comparing method.(ALDEx2 etc?)