Hi, I've run Humann2 (using default settings and the chocophlan database) on human gut shotgun metagenomic samples that has been quality trimmed and dehosted (mapped against hg38) but I still find mammalian pathways with high abundance, eg.
A biosynthesis II (mammalian)|
LYSINE-DEG1-PWY: L-lysine degradation XI (mammalian)
L-tryptophan degradation XI (mammalian, via kynurenine)|
I know that Humann2 is quite conservative, but is it possible these are false positives? Or is there some alternate explanation?