What are these glowing orbs?
That is BFG-9000 ammo. It took me a while to realize this as well, probably because I didn't have the BFG yet, or my BFG ammo was full when I first encountered one, and so couldn't pick it up.
Do you have the BFG-9000 yet? Once you have it, and need ammo, you can pick these up for it.