I have personally only run into this twice, and neither time was with someone I was in a relationship with. One was a girl...I went down on her, but not for long xD I didn't say anything, I just used my hands and kissed her other places. Once was with a guy...I knew before I even got down there that there was a funky smell afoot...so I just never even attempted it, let alone mentioned it.
I don't like to hurt peoples' feelings..
However, if it was my partner, I would suggest he take a shower ("You just got off work, why don't you shower before we get in bed?"), or that we both take a shower...or IF it was something going on for a while and really bothering me, I would just tell him as gently as possible.