Part 1

The Digestive System and Gut Microbiome

Functional medicine takes the view that all body systems are connected. When patients come to me with hormonal imbalances, autoimmune disease, mental health concerns, or various symptoms, I always think about the gut. 

Over 2000 years ago, Hippocrates, the father of medicine said, “all disease begins in the gut.” Today, modern science supports this connection. When we take a root cause approach, we can’t overlook digestive health and the microbiome. It’s one of the most important places to look. 

Over 2000 years ago, Hippocrates, the father of medicine said, “all disease begins in the gut.” Today, modern science supports this connection. When we take a root cause approach, we can’t overlook digestive health and the microbiome. It’s one of the most important places to look. 

In this two-part series, I’m going to explore the basics of the GI tract and microbiome and talk about how we can encourage a healthy, robust microbiome by what we choose to eat, our relationship with food, and many lifestyle factors. 

Let’s get started with the basics:

• Digestion and the GI tract 
• The microbiome

What Is Digestion? What Makes Up the Digestive System?

Digestion is the mechanical and chemical process of transforming the food we eat into nutrients that are absorbed into the body. It takes large molecules and breaks them up into the smallest possible components. Digestion also involves water balance and other functions of the microbiome, which I’ll discuss shortly. 

The digestive system includes the gastrointestinal tract, or GI tract, and the liver, gallbladder, and pancreas. The GI tract is the hollow tube that extends from the mouth to the anus. Technically what is inside the tube is outside the body! 

Here’s a roadmap through the digestive system:

• The first phase of digestion, called the cephalic phase, occurs before food enters your mouth. The sight and smell and even thought of food leads to the release of saliva and digestive secretions that prime your GI tract to receive the food. 

• In the mouth, chewing breaks the food into smaller pieces and mixes them with saliva. Saliva contains amylase, an enzyme that breaks down carbohydrates. 

• When you swallow, the food travels through the esophagus into the stomach. Smooth muscle contractions called peristalsis helps move the food through the GI tract.

• The stomach muscles mix the food with stomach acid and digestive enzymes to further break down food molecules. 

• When the food mixture leaves the stomach, it’s called chyme and enters the small intestine, which has three parts: the duodenum, jejunum, and ileum. In the small intestine, proteins, fats, and carbohydrates break down into their smallest components, and most nutrients are absorbed here. The pancreas releases digestive enzymes into the small intestine. The cells that line the small intestine also produce digestive enzymes. The liver makes bile, which is stored in the gallbladder and released into the small intestine to aid fat absorption. 

• What’s left of the chyme, fiber, and other undigestible components, move to the large intestine, where most of the gut microbiome lives. The gut microbiome ferments fiber and other prebiotics, producing nutrients and metabolites. The colon helps with water balance and regularity. The microbiome also plays a role in the phase 3 detoxification of estrogen and toxins, helping to remove them from the body. 

• When you have a bowel movement, all waste products, including fiber, toxins, hormones, and dead bacteria are excreted. 

When the digestive system isn’t working correctly, you may experience:

• Food sensitivities
• Acid reflux
• GI symptoms: gas, bloating, changes in bowel movements
• SIBO: small intestinal bacterial overgrowth (add link to SIBO article)
• Dysbiosis 

Dysbiosis is an imbalance in the gut microbiome, which may look like low levels of beneficial bacteria, overgrowths of bacteria, yeast, or other organisms, or infections like H. pylori. 

What Is The Microbiome? 

The microbiome is the collection of over 100 trillion organisms, including bacteria, fungi, viruses, protozoa, archaea, and their DNA, that live in and on our bodies. Within the overall microbiome, we have subsets that share common characteristics but are also distinct. These include:

• The oral microbiome
• The gut microbiome
• The vaginal microbiome
• The lung microbiome
• The eye microbiome
• The skin microbiome

The microbiome begins to develop in the mother’s womb and is influenced by delivery, breastfeeding, diet, the physical environment, exposure to toxins, medications, and a host of lifestyle factors. Your microbiome is unique to you but also has a large capacity to change and adapt to changing inputs. This is where our sense of empowerment comes in!

The notion that we have control to influence our outcome is key because gut microbiome plays a critical role in overall health. The health of the microbiome influences:

• Digestive health
• Immunity
• Metabolism
• Hormone balance
• Brain health and cognition 
• Nutrient status
• Epigenetics, or gene expression
• Behavior
• And more! 

It’s truly remarkable to understand that we share our bodies with various organisms, each relying on the other for survival and health. Working to optimize the microbiome is a critical root cause to approach when healing from symptoms or disease. In Part 2, I’ll cover the many tools we have to bring the gut microbiome back into balance. 

References

1. Boland M. (2016). Human digestion--a processing perspective. Journal of the science of food and agriculture, 96(7), 2275–2283. 
2. NIH – National Institute of Diabetes and Digestive and Kidney Diseases. Your Digestive System and How it Works. Accessed 7/12/22. 
3. Dominguez-Bello, M. G., Godoy-Vitorino, F., Knight, R., & Blaser, M. J. (2019). Role of the microbiome in human development. Gut, 68(6), 1108–1114. 
4. Barko, P. C., McMichael, M. A., Swanson, K. S., & Williams, D. A. (2018). The Gastrointestinal Microbiome: A Review. Journal of veterinary internal medicine, 32(1), 9–25. 

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