Question

Why do every atom in the universe vibrating? What causes this vibration?

Answer 1

First of all we should consider what do we exactly understand under “atom vibration”.
The solid matter such as a pice of a rock is a set of regularly arranged atoms. The members in such an arrangement are bind together by a force, which acts like a small string connecting two neighbor elements. Due to the fact that every molecule or a piece of material in the universe is ( or was ) a subject to the influence of some field or force this strings were forced out of equilibrium leading to some vibration. Although we cannot measure the energy of this vibration for a particular atom, we can measure the average energy for the group of atoms and we call the value proportional to this energy Temperature.
On the other hand a single atom of helium traveling in vacuum in deep space has only kinetic energy, and no vibrational energy (it is a system of one atom).
On the other hand every atom is a system of a core and electrons, which, in a classical interpretation, are moving in circles around the core. A circular motion is periodic, so it can also be called a vibration.
In the quantum mechanical interpretation, atomic core and the electrons are waves of density of probability propagating in space.