Understanding Digestion – The Microbiome

Whole Systems Healthcare


  • The microbiome, the community of microorganisms living in our guts, is an integral part of us.
  • They aid in digestion, regulate immunity, produce important vitamins, regulate behavior, and influence the brain.
  • Some have argued that the merging of human and microbes is what makes someone complete, and chronic health issues can result from a faulty merge.
  • The Stomach in Chinese Medicine explains and accounts for much of what we know about this microbiome.

There is an additional piece to the digestive system that needs to be discussed. If you haven’t read part 1, where I introduce the Chinese Medicine perspective of the Stomach, I recommend you start there as I will be referencing concepts explained in that first part. In part 2 I discuss a few of the more prominent gut-related hormones, and how they echo the functions of the Chinese Medicine Stomach. Part 3 is about the enteric nervous system and some of the neurotransmitters that are associated with the gastrointestinal (GI) tract. Now it is time to bring in the microbiome.

The importance of the gut microbes has been known for decades, though interest and awareness of the microbiome has increased dramatically in recent years (1). The microbes have been shown to influence many aspects of human physiology beyond the process of digestion, and are an integral part of a complete human being. Some authors refer to the the human-microbiome superorganism as the Completed Self, and suggest that incomplete integration between human and microbe at birth is responsible for a whole host of problems (2). The effects of the microbiome are encompassed by the roles of the Stomach in Chinese Medicine; understanding the gut microbes from the perspective of the Stomach gives new insights into the importance of the digestive system.

Microbiome Functions

Bacteria in the gut produce a wide range of metabolic products that effect the body in different ways. Infants have large fluctuations in their gut microbes during the first year of life, but by age 3 the population starts to resemble that of adults. There seems to be a “core” gut microbiome that is shared by healthy adults, even given the diversity of the microbiome between different individuals. These microorganisms help digest carbohydrates, regulate immune function, defend against infection, produce vitamins and amino acids, influence fat storage, regulate behavior development, and influence the brain (34).

Many of these functions can be correlated with the Stomach in Chinese Medicine. Digesting carbohydrates and fiber is a core function of the Stomach, as is providing nourishment (in this case, the production of vitamins and amino acids). The Stomach’s containing ability is key for defending against infection by not letting pathogens into the body. Fat is an important fuel source for the body and it’s production and storage is regulated by the Spleen and Stomach. Developmentally the Earth organs are incredibly important in the growth and maturation of infants and small children. The previous posts have already discussed the importance of the Stomach in regulating mood and emotions, and it’s no surprise that the microbiome also plays a part.

Microbiome and the Immune System

There is more and more evidence that the microbiome plays a significant role in modulating the immune system and controlling inflammation in the body. The gut immune system has to be tolerant of the microbes, but at the same time control their population. Different interactions between the immune system and the gut bacteria are responsible for teaching the body how to perform this delicate balance. The resident microbes help protect the body from any pathogenic, invading organisms, as well as stimulating the immune system against invaders. This immune stimulation is also key in teaching the body to regulate the growth of the microbiome. It’s a complex dance so that there is just the right amount of immune activation, but not too much (56).

An important element of this immune modulation is that exposure to the right microbial communities must begin at a young age. When humans are born their immune systems are immature, and the presence of the microbiome plays a huge role in educating the young immune system (23). Children who don’t start off with a good mix of microbes develop health issues (I’ll be taking a look at some of these in the next section).

This ability to distinguish between friend and foe, to distinguish between self and other, is a key attribute of the Stomach. The ability of the Stomach to create appropriate boundaries extends to the wall of the gut. Furthermore, this strength of the Stomach is typically developed early in life, and correlates age-wise with the development of gut-mediated immunity in infants and young children.

Microbiome and the Brain

The human microbiome effects the brain in several different ways. Gut bacteria can produce the exact same hormones and neurotransmitters that are used in the nervous system (for a brief review of a few of these substances see part 2 and part 3). Bacteria can also directly stimulate nerves in the gut that send signals to the brain. The immune system interacts with the brain, and the microbiome influences immunity tremendously. The gut microbes influence sleep, stress, mood, memory, cognition, and more (6).

All the effects of the gut microbiome on cognition and brain functions supports the understanding that the Stomach in Chinese Medicine is not only involved in digestion of food but has an intimate connection to our mental-emotional state as well. Because there is a complex interaction within the microbial communities and between the microbiome and the human body approaching disease from an integrated perspective – as represented by the Stomach – makes diagnosing and treating health issues much more straightforward.

The Completed Self

An interesting perspective about the role of the microbiome is put forward in a paper by Rodney Dietert and Janice Dietert, titled The Completed Self: An Immunological View of the Human-Microbiome Superorganism and Risk of Chronic Diseases. They assert that the human organism is incomplete at birth and that colonization with the appropriate microbes is required to complete the organism. The timing of this colonization is very important and is supposed to take place at birth, and immediately afterwards. Babies born vaginally have microbes from the mother’s vaginal canal, whereas babies born via c-section typically have microbes from the mother’s skin. The authors suggest that the immune system’s main function is not to kill, but to regulate and harmonize the superorganism, which is human and microbes combined. Problems with the integration between human and microbiome sets the stage for chronic disease later in life, something I’ll discuss in the next part of this series.

This idea of the completed self is encompassed in the concept of the Stomach in Chinese Medicine. The Stomach is involved with the creation of boundaries and the establishment of relationships, something that requires a solid sense of what is self and what is not self. It appears that the integration of the microbiome early in life could be an element of this ability. A proper integration allows the Stomach to clearly define what is inside and what is outside, whereas improper colonization creates confusion over the boundary between self and other.


  • Dr. Kye Peven, ND, DSOM, EAMP, earned a B.S. from UC Berkeley in Materials Science and Engineering, with minors in Nuclear Engineering and Energy Management, believing that applying his interest in technology would help make the world a better place. He then completed a Doctorate of Naturopathic Medicine (ND) and a second Doctorate of Science in Oriental Medicine at the National University of Natural Medicine (NUNM). Dr. Peven serves as Director of the WSHC Clinical Care Initiative and is the founder and Clinic Director of the WSHC Seattle Clinic.