Revisiting the Role of Carnitine in Heart Disease Through the Lens of the Gut Microbiota JCI l Carnitine in omnivorous diets induces an atherogenic gut microbial pathway in humans Stabilizing the enzyme in fish odor syndrome Microbiota and MalodorEtiology and Management Did You Know? Some people report a fishy smell after supplementing with L carnitine. This happens because certain gut bacteria convert carnitine to trimethylamine, a malodorous compound found in rotting fish. A recurring fishy odor could indicate a larger medical problem.