It is a combination of the dead and live bacteria and the natural tree response to microorganisms within the tree that gums up the open vessels.
The bacteria produce a mucilage that is gummy/scummy (like what is in the bottom of sap tanks) which does affect flow to some degree.
Interestingly, in terms of the tree response it doesn't matter much if the bacteria are dead or alive. The tree "senses" bacteria in the taphole, and moves substances into that area to plug off the affected vessels. This is done to prevent the "infection" from spreading throughout the tree.
Tim P.
UVM PMRC