I think this is a problem not of language but of particle physics. You know what 'matter' means, but it's not so easy to grasp the concepts of Antimatter - Wikipedia, the free encyclopedia and Dark matter; - Wikipedia, the free encyclopedia. I can't, for example. The sentence refers to 'the physical Universe of matter' - that is, things and their relationships; this doesn't refer to the whole Universe - so I think the use of 'Universe' (especially the capital U) is not helpful; it would be clearer if it were reworded like this:b
In fact, the Universe as a whole largely consists of stuff we don't know about; physical matter represents only a very small percentage of it."
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