Gut Bacteria, TMAO and Whole-food, Plant-based Diets

It is well established that microbes in the intestines are essential for the breakdown of complex carbohydrates, the production of short chain fatty acids and synthesis of vitamins. More than 1000 different species have been identified. Despite the vast number of bacteria species and people, there are only two types of bacteriological ecosystems in the gut (enterotypes).

Microbiome composition changed within 24 hours of initiating a high-fat/low-fiber or low-fat/high-fiber diet. However, it takes a longer period of time to change the enterotype from one state to the other. ¹

Gut bacteria dominated by Prevotella are associated with healthier outcomes. ^{2 3 4 5 6 7}

Changes to gut bacteria change more rapidly when converting to animal-based diet than converting to a plant-based diet. Practitioner probiotics can be make the transition more rapid.

Fibre is the component of the diet that is most significantly associated with Prevotella species.

Animal-based diets are associated with an increase in bile-resistant bacteria which is due to the higher fat content. However, any high-fat diet, plant-based or animal-based, increases bile production.

Bile is produced in the liver which assists in the digestion of fats in the small intestine. It is stored in the gallbladder and released into the small intestine. Bile-resistant bacteria genus are Alistipes, Bilophila, and Bacteroides. Bilophila wadsworthia is associated with irritable bowel syndrome because it produces hydrogen sulphide – rotten egg gas. ⁸

Lactobacillus are not native to humans. These bacteria found in yogurt, cheese and other dairy products are not essential to humans. They will not multiply in the intestine.

Choline is converted by our gut bacteria into trimethylamine (TMA) which is then converted into trimethylamine N-oxide – (CH₃)₃NO – in our liver. Trimethylamine N-oxide (TMAO) is implicated in a number of detrimental outcomes. TMAO is nasty. ⁹

The choline in foods, such as eggs, can be turned by gut bacteria into TMA. However, it is only produced by the bacteria that are prevalent in high-fat, low-fibre, animal-based diets.

Carnitine is similar in structure to choline and the major food source is red meat. Unlike choline, which is an essential nutrient, we have no need to consume carnitine. It is also found in dietary supplements and carnitine-energy drinks. ¹³

The production of TMA is absent or greatly reduced in vegans. Feeding people steak or eggs can cause an increase in TMAO within a day – but only those that have a high-fat, low-fibre enterotype. ¹⁴

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Last updated on Monday 13 October 2025 at 07:48 by administrators

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