One hundred trillion

That’s approximately how many cells are inside your microbiome, the colony of flora that dwells within your gut. That’s about two or three fold more cells than the human body has, and with a much greater amount of genetic diversity. The microbiome can weigh up to three to five pounds in a healthy adult human being.

Are we more bacteria than human?

If we’re just counting cells that conclusion could potentially be drawn. But by sheer mass we are much more human than bacteria. If anything it is a true symbiotic relationship — whereas humans could not exist without our microbiome and our microbiome could not exist without us.

A microscopic-level photo of gut flora and partially digested food particles.

There are also a several other organisms in our gut outside of bacteria, including viruses, yeast and in some cases parasites.

What are they all doing down there?

When we eat food there are several stages of digestion. Most digestion starts with chewing. The more food is chewed, the easier it is for the stomach and its acid to further break down the food. The overall goal being that food enters the small intestine in as small of particles as possible.

Microscopic-level shot of the epithelial wall in the small intestine.

Once partially digested food particles make it to the small intestine, they reach the microscopically thin cellular epithelial layer that facilitates the absorption of nutrients in to the bloodstream.

Mr. Glutenochov, tear down this wall!

Many individuals have varying degrees of epithelial wall permeability. This permeability leads to larger particles entering the blood stream, such as proteins (wheat gluten an especially well known epithelial antagonist) and fats, which can then trigger an autoimmune response because the body is not accustomed to seeing these particles in the blood stream

Immune system “super” cells.

Once the autoimmune response is triggered, the body begins to train its defense force of T-cells to identify these partially digested food particles as hostile invaders and wages a costly war. Because one of the components of an immunological response is the production of pro-inflammatory proteins, like tumor necrosis factor alpha (TNFa), when the autoimmune response kicks in to high gear, so may a whole host of other issues.

It is now thought with a reasonable degree of scientific certainty that most autoimmune disorders originate with a permeable epithelial wall setting forth this immune reaction. While individual sensitivities and genetic predispositions vary from person to person, many advanced manifestations of autoimmune disorders are likely related to permeability. In fact, in some situations there may also be a compounding factor: overgrowth of gram negative bacteria and yeast in the small intestine further exacerbating the situation and complicating recovery.

What about the gut?

As food progresses further down the digestive tract it reaches the large intestine and colon, which are largely colonized by gram positive bacteria such as Lactobacillus and Bifidus. These helpful bacteria largely feed on soluble fiber and excrete short chain fatty acids (SCFA). The short chain fatty acids act as a source of nourishment for other healthy gut bacteria. Soluble fiber and SCFAs are also very important for controlling inflammation and maintaining a healthy epithelial wall.


One of those SCFAs is called L-Butyrate. Think of the immune system as having something that is the inverse of a fire alarm. A sort of “everything is OK” alarm, if you will. It’s always running to tell the body that things are OK. Until it isn’t and that’s when there is an outsize autoimmune response.

L-Butyrate is the SCFA that is in essence the signal that tells the autoimmune system that everything is OK. No need to panic. Don’t start attacking healthy tissue or cells!

How much soluble fiber is needed?

Ancestral human societies eat up to 150 grams of soluble fiber per day. It’s an almost unimaginable amount. To contrast that, Americans get about 10-15 grams of combined insoluble and soluble fiber content per day.

Mmm, soluble fiber-rich foods.

While the US FDA lumps all fiber together on the nutritional metrics table, there are two different kinds of fiber and they act quite a bit different.

Insoluble fiber acts as bulk. If you think of your bowels moving down a highway, the bulk of insoluble fiber is metaphorically additional traffic. It does not feed the microbiome’s ideal population.

Soluble fiber on the other hand acts as a source of nutrients for the microbiome’s ideal population of gram positive bacteria. Recent studies suggest having at least 30 grams and in upwards of 50 grams of soluble fiber per day to optimize overall health — and to feed our one hundred trillion friends.