When you consider that the human colon houses many trillions of bacteria, you have to wonder at the immune system’s complexity. The intestinal lining houses the gut-associated lymphoid tissue (GALT), which makes up the majority of your immune system. And yet, even though the only separation between these bacteria and the immune system is a one-cell thick layer called the epithelial lining, there remains a mutual agreement between them, at least in a healthy gut.

Normally, the immune system is programmed to recognize bacteria as foreign and mounts an inflammatory response against the invader as a way to protect the body from infection. But the bacteria in the intestines enjoy protection from this inflammation. Scientists believe that this protection comes, at least in part, by way of the effects of the short-chain fatty acids butyrate, propionate, and acetate produced by beneficial gut bacteria.

Butyrate in particular is well known for its beneficial effects on the cells that line the colon. Butyrate nourishes the intestinal lining, providing energy to the cells so that they remain intact and replicate appropriately. Butyrate is also known to protect these cells from turning cancerous, and quells inflammation in the colon. Propionate is known to lower lipogenesis (the production of fats), serum cholesterol levels, and carcinogenesis (the production of cancer cells).1

Gut bacteria in the colon have been found to call forth a particular cell receptor—known as Slc5a8—to the epithelial lining.2 When that happens, butyrate and propionate enter the cell through the receptor and get into dendritic cells. Dendritic cells are found underneath the epithelial lining and are able to extend an appendage between the epithelial cells in order to grab certain contents in the colon and then present them to the immune system. Once butyrate and propionate are grabbed by a dendritic cell, they are able to reprogram genes within the cell to prevent the dendritic cells from upregulating immunity and triggering inflammation.

The biochemistry of this research is complex, but it paints a beautiful picture of the intricate goings on inside the vast ecosystem that is our gut. The bottom line from this research is that if you do not eat enough fiber in your diet then your beneficial gut bacteria won’t have enough fiber. As a result, your gut bacteria will not produce enough protective SCFAs and may become inflamed as your immune system inappropriately responds to your gut microbes.



  1. Hosseini E, Grootaert C, Verstraete W, et al., “Propionate as a health-promoting microbial metabolite in the human gut.” Nutr Rev. 2011 May;69(5):245-58.
  2. Singh N, Thangarajou N, Prasad PD, et al., “Blockade of dendritic cell development by bacterial fermentation products butyrate and propionate through a transporter (Slc5a8)-dependent inhibition of histone deacetylases.” J Biol Chem. 2010 Sep 3;285(36):27601-8.