I want to share the blog post from the "American Gut" project - the ones who are actually studying the microbiome. This explanation is the most lucid I have seen on this whole issue yet.
From Meat to Microbes to Main street: is it time to trade in your George Foreman Grill? - Human Food Project
The bacteria responsible for increased TMAO levels are actually ones that thrive on a diet of whole grains ... um...
THe issue is FAR from clear, and this post really illuminates the major issues that are still unresolved.
Worth a read.