The last version of Akismet 2.5.1 or maybe even the previous one won't clean up the comment meta details in DB after deleting a comment.
I woke up one morning and after checking my DB I realized that it is doubled in size. I started to rewind my thoughts on what I recently did and of course, after every WordPress update, Akismet was rolling out update too.
I quick glance at the DB and I realized that commentmeta table was enormous. Akismet should store comment details there until they're deleted or approved but in my case it was failing to do so. The records were remaining there.
I've deactivated and deleted Aksimet and reinstall it again, but the problem stayed.
So I had to manually delete around 25.000 records from my commentmeta table in the DB.