How do we know that the base of entire universe is the proton (hydrogen) and not the antiproton? It may be that the base of a part of the world is anti-proton,  We've always been on the planet Earth and the Milky Way.
how do we know that the base of entire universe is proton (hydrogen atom)?
 A: There are two parts to this question.  One is a question of naming conditions.  If matter and anti-matter were created with equal probability (as they are in many processes) then it would just be a matter of convention as to which way we name them (meaning there wouldn't be a truly natural way to distinguish a proton from an anti-proton).  
However, as it is not always true that matter and anti-matter production is identical in all processes,  this leads to the second part of the question, why is there a preference of matter over anti-matter (where we use the standard convention for names).  Charge Parity violation (CP violation) was predicted and observed in certain weak processes that lead to a "handedness" to the universe, which helps explain some of the imbalance, but not enough of it.  In order to explain the imbalance seen in the universe, there should be CP violation observed in the interactions governed by the strong force.  However, it has not been seen to date, although it might just mean that we have not yet probed to high enough energies to see it.
note: this is just a self reminder to revisit and reword 
A: First of all one has to define "universe".
Let us assume that the universe contains all that we can detect with our astronomical detectors. Then, other "universes" could exist but we would only be able to hypothesize about them.
Our observations tell us that the universe, stars and galaxies and maybe galactic clusters consist of matter as we know it around us in the limit of our detection abilities. We have not detected antimatter. This because if an antimatter galaxy existed at the boundary in space between matter and antimatter, where there is a lot of space dust the annihilation of matter on antimatter would be detectable, with specific energies coming out.
Also, in the accepted cosmology model of the BIg Bang the annihilation of antimatter would affect the observed microwave background radiation in specific ways which are not seen.
We can say with assurance that our universe is mainly matter and keep on searching for isolated, undetected instances of antimatter galaxies with better and better instruments. The page of AMS.
So the answer is : by observation up to now.
As @Hal Swyers says in his answer we need a lot more CP violation in order to explain the asymmetry observed and scientists  at LHC are working hard on the question , as can be seen here in this article by John Ellis, which answers your question thoroughly.
