Looking at the link between red meat, eggs, and heart disease

Two recent papers about heart disease from the Cleveland Clinic are making the rounds. The studies report that red meat and eggs cause heart disease because our gut bacteria converts carnitine and choline into Trimethylamine N-oxide (TMAO), a heart disease trigger.

At Huffington Post, Chris Kresser has questions about the papers:

[W]hile at first glance the papers from Dr. Hazen's group might appear to be the final nail in the coffin for the omnivorous among us, a closer inspection of their data reveals some troubling questions. First, a study back in 1999 found that seafood generates much higher levels of TMAO than red meat, eggs, or any of the other 46 foods tested. One species of fish, halibut, produced 107 times as much TMAO as beef, and 53 times as much TMAO as eggs. If high TMAO levels cause cardiovascular disease, and eating fish increases TMAO more than any other food, we'd expect to see high rates of heart disease in people who eat the most fish. Yet that is the opposite of what research shows. In fact, some studies have found eating more fish (particularly cold-water, fatty fish like salmon) reduces the risk of heart attack by a greater margin than statin drugs!
In fact, whole grains could play a role in elevating TMAO levels:
In their second paper, Dr. Hazen's team raises the possibility that the foods we eat aren't the primary driving force behind our TMAO levels, because most people are able to excrete excess TMAO that accumulates in the blood via the urine. This suggests that something else may be to blame for high TMAO. What could that be? One possibility, which the researchers themselves demonstrated in the first paper, is that differences in our gut bacteria could account for the higher TMAO levels observed in some people. They showed that those with greater amounts of a type of bacteria called Prevotella in their gut generated more TMAO after eating carnitine. And what might lead to a higher concentration of Prevotella in the gut? Ironically, previous research has shown that the people who eat large amounts of whole grains are the most likely to fit this pattern. This would suggest that a diet high in whole grains -- and not red meat or eggs -- could increase the risk of heart disease by elevating TMAO in the blood.
Red Meat and Eggs on Trial Again, But Jury Is Still Out