Ground with different power supply and microcontroller
You have several ground loops.

1) from the 12 volt supply thru the GROUND wire to the STM board, then out the other GROUND wire thru the anti-aliasing filter to the microphone and on to the 5 volt supply and its AC power wiring (capacitive coupling between primary and secondary of the isolation transformer)

2) from the 12 volt supply thru the GROUND wire to the STM board, then along the USB cable to the PC USB

3) from the 5 volt supply thru the GROUND wire to the STM board, then along the USB cable to the PC USB

4) the wiring in the wall or in any power cords (the fields of the "hot" wire in the cord is only partly captured by the "return" wire), coupling onto any of your circuits thru the air, and then taking all possible paths back to your local 50/60 Hertz 10,000 watt power transformer

5) the presence of any black brick battery chargers, with fast edges in the brick's switching power supplies (200 volts in 200 nanoseconds) that couple thru the air onto any of your circuit and then take all possible paths back to the switching power supply