I've listened again and it is definitely weird. 

The fact you feel a vibration points to something going on in the subfloor. While it's very possible for sound to transfer along pipes, I'd be surprised if a (quiet) noise would also produce a vibration in the floor over any distance. Also pointing to the subfloor is that you can't hear it from outside. The fact it's not metallic or sharp would tend to point away from pipes banging. I might have guessed some kind of water hammer going on, but the noise is independent of running water.

What sort of insulation do you have (if any) in the subfloor? Expol makes a hollow that might account for changing the noise to the sort of harmonic sound? But totally guessing here.

In terms of who you would get to investigate further, I would start with a builder. Plumbers (and plumber rates) would only be relevant if pipes were involved.