The results of both experiments, in short, showed the C. botulinum survived the glyphosate, but the protozoa and helpful bacteria much less so.
The protozoa are mostly ciliates, identified with a stain and high power light microscope. They disappeared at low glyphosate additions. In the rumen, these protists are essential to breaking down the coarse cellulose in grass and leaves into food materials the other bacteria can use.
So we can see that without these ciliates, removed by the lowest glyphosate levels, the rumen food chain cannot get started, and a cow could become very sick from herbicide-mediated dysbiosis.
In the second experiment, C botulinum spores grew well, and were found at all levels of glyphosate addition, but BoNT was only found in the mix at the highest level, 1000 micrograms/milliliter. I take this to mean that until the normal bacteria (Enterococcus, Lactobacillus, etc.) were all diminished, their bacteriocines and or proteolytic enzymes degraded the actual toxin.