Found that the rattle comes rear left door. Knocking on the door, I could hear something was loose inside the door. So I proceeded to remove the door panel and check
Removed the foam insulation carefully
The culprit was that top metal piece which has become loose
Used some silicone to hold it in place. I applied silicone along the whole length of this metal piece.
Since everything was opened. Cleaned and re-greased the hinges. Also cleaned up and re-greased all necessary moving parts inside the door
Door Hinge looking much better after being cleaned
After cleaning everything, refitted the door panel and the rattle is gone. The door closes with a solid thud once again.