Yeah, I would tend to call BS on that particular statistic. Let's say the average water bottle is .5L. In that one, single water bottle that is sitting on my desk, there are 5.01*10^25 atoms. That's one hell of a number.
Now, let's pretend God has a really good magnifying glass and a really small set of tweezers, and he's removing atoms from this water bottle at a rate of 1 per second. Conservative estimates put the universe at 13.5 billion years old, which converts to 4.25*10^17 seconds.
So, since the beginning of time, God has removed 4.25*10^17 atoms from my water bottle. A lot, right? Not quit. (4.25*10^17)/(5.01*10^25)=8.00*10^-9.
Even removing an atom every second since the beginning of time, only a few trillionths are missing from my bottle of water. That's just a bottle of water, now imagine the number of atoms in the ocean, or in the sun. Something does not seem right with the "More than number of atoms in the universe" claim.