I'm reading this as saying it is the amount of choline determining what the gut bugs do with it.
"These studies suggest we can intelligently design a heart healthy yogurt or other form of probiotic for preventing heart disease in the future. It also appears there is a need for considering the risk vs. benefits of some commonly used supplements."
The first is that gut bugs matter, though it's hard to tell if what matters is what kind they are or how much of them you have. The second conclusion is that excessive choline and other subtances can be turned into plaque-causing compounds by gut bugs, with less emphasis on the bugs' particular kind or quantity.
"I'm reading this as saying it is the amount of choline determining what the gut bugs do with it."
This article is written quite poorly and no particular metabolites of choline, TMAO, or betaine that are implicitly referenced are given. The blood conc. of these molecules is only used to indicate the probability of developing CVD. Choline metabolism by gut bugs isn't determined by choline concenttration though. This article is claiming it's the type of bug that produced the bad metabolic end products. The article abstract just says the following about excess choline...
From the Abstract: "Suppression of intestinal microflora in atherosclerosis-prone mice inhibited dietary-choline-enhanced atherosclerosis."