Macronutrients
How Macronutrients affect the Gut Microbiome - Dr. Tom Fabian (video transcript).
When we think of food influences on the gut microbiome we mainly think of fiber but recent research shows many other macronutrients and micronutrients have an influence.
Carbohydrates:
- Primary source of energy for most gut microbes. Most beneficial microbes can break down carbs (saccharolytic). Some do not (asaccharolytic/proteolytic)
- Microbes produce many more types of carbohydrate-digesting enzymes than humans
- Carbohydrate fermentation is most prevalent in the ascending colon
Products of carbohydrate fermentation:
- Short chain fatty acids (acetate, propionate, butyrate)
- Organic acids & other compounds (lactate, succinate, formate, ethanol)
- Gases (hydrogen, methane, carbon dioxide)
Proteins
- Small Intestine: Microbial activities related to food antigens, proteins are the main source of food antigens such as gluten and many other types of foods.
- Large Intestine: Protein fermentation which is prevalent in the descending colon (also where colon cancer tends to be prevalent).



There's an antagonist relationship between dietary carb and protein fermentation. Carbs fermented in proximal colon, proteins fermented in distal colon. In a healthy situation, carbohydrate fermentation occurs almost throughout the length of the large intestine.
Fats
The best studied effects on the microbiome are those of carbohydrates and proteins. TLR4 - Toll-Like Receptor 4 is a receptor for LPS. Saturated fatty acids can trigger that same receptor. It can be counteracted by DHA. Some of the best studied effects of fats on the microbiome have to do with bile acids that fats in the diet tend to stimulate. These effects can be beneficial or harmful depending on the kinds of microbes present.