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  • Alexandra Joachim, M.S

Meet the Gut: Gastrointestinal Biochemistry 101

Updated: Feb 17, 2019


Over half of Americans today suffer from a chronic health condition. While the rate of chronic illness has reached an all-time high, emerging research has shined a light on your belly. What do heartburn, GERD, migraines, chronic fatigue, depression, anxiety, autoimmune disease, irritable bowel syndrome and autism have in common?


One thing: the gut.


Within the last decade, the gut has become a newfound priority in the world of scientific health research. The National Institute of Health set aside $115 million in 2008 to begin learning more about the gut’s microbiome.


So what exactly is the gut and the microbiome?

The gut refers to the gastrointestinal tract, which is comprised of the esophagus, stomach, small intestine, colon, and accessory organs including the pancreas, liver, and gallbladder. Within the gut are over 100 trillion microbial cells, referred to as the microbiome.


The gut and its microbiome are responsible for processing food, sending and receiving neurotransmitter signals, absorbing nutrients, maintaining hormones, stabilizing immunity, and balancing inflammation.


The microbiome facilitates thousands of chemical messengers to the brain, including serotonin, a mood-regulating neurotransmitter, and melatonin, a hormone regulating the sleep-wake-cycle. The trillions of gut microbes in the microbiome act as intermediaries to communicate directly with the brain. This pathway of biochemical communication is referred to as the gut-brain axis. For this reason, the gut has been referred to as the second brain in scientific literature.


What is the gut’s role in food digestion, and how does this relate to chronic illness?


Let’s break it down in three steps.


Step 1: Eating & Digestion

The minute you put food into your mouth, the digestion process begins.


Salivary enzymes in the mouth begin breaking down carbohydrate macromolecules into smaller molecules which can later be easily absorbed. The food is chewed up and subsequently sent directly into the stomach via the throat’s esophagus. Once the food reaches the stomach, the highly acidic gastric environment (1.5 – 3.5 pH) facilitates further enzymatic breakdown of proteins and fats. The liver, gallbladder, and pancreas also begin supporting the breakdown of food by supplying bile, insulin, and other enzymes.


The takeaways: Various enzymes coupled with the highly acidic stomach environment make it possible for your body to start breaking down and digesting food.


Our dietary and lifestyle habits can easily hamper the body's ability to break down food during this first phase. A diet high in refined carbohydrates and processed foods (think breads, pastas, food-dyes, snack packs, bars, sweeteners, preservatives), can promote growth of pathogenic gut microbes, which increase our gastric pH and therefore weaken our enzymes. Alcohol, stress, and lack of sleep all worsen these effects leading to a highly inflammatory gastrointestinal environment.


When our microbiome becomes disrupted due to imbalanced diet and lifestyle habits, our gastric juices and enzymes become less effective. This disrupts digestion, and leads to further problems in the digestion journey.


Step 2: Absorption & Microbial Communication

After the food enters the stomach, the next stop in the assembly line is the small intestine, a 23-foot long folded tube situated directly below your stomach (think of a folded water hose).


The food you just ate is now separated into 1) nutrients that the intestines can absorb, and 2) toxic byproducts that need to be eventually be eliminated through stool. The intestinal barrier-wall is made up of thousands of finger-like projections called villi, which are home to millions of enterocyte cells. The villi and enterocytes are responsible for absorbing helpful nutrients, and also keeping the toxic byproducts confined inside the intestines, for eventual elimination through stool.


The villi and enterocytes are only able to do their job of absorbing nutrients and keeping the toxins confined if the neighboring gut microbes are healthy. If the microbiome is not healthy due to imbalanced diet and lifestyle, nutrients aren't absorbed as efficiently, and toxins can "leak" into the body which causes systemic inflammation.


The takeaways: The small intestine is supposed to only absorb nutritious material into the bloodstream and keep the toxic material confined so that it can eventually be eliminated from the body. Inflammatory foods, stress, medications, alcohol, smoking, poor diet, and hidden gut infections caused by these things can disrupt the microbiome balance and weaken the intestinal villi.


Microbiome disruption and villi weakening causes the following to happen:



  • A phenomenon called “leaky gut” where the intestinal cells become permeable, permitting undigested food particles, toxins, and bacteria to leak into the bloodstream. This causes systemic inflammation and underlies chronic disease.

  • Early fermentation of the food, which causes bloating, also known as “the food baby”.

  • Neurotransmitter deficiencies, commonly linked to depression, anxiety, and insomnia.

  • Tip: Nearly all pharmaceutical drugs for depression are aimed at boosting serotonin levels. Given that 80% of the body’s serotonin is manufactured in the gut, and gut peptides are directly responsible for mood-regulating neurotransmitters, getting to the root cause of depression involves healing the gut.

  • Nutrient insufficiencies or deficiencies.

All of these downstream effects cause the body’s defense mechanisms to be on overdrive, leading to systemic inflammation. Inflammation underlies chronic conditions including fatigue, brain fog, depression, anxiety, autism, degenerative disease, and autoimmune disease.


Step 3: Elimination

Once the food passes through the small intestine, the last stop is large intestine, also known as the colon. The colon is another hose-like tube that is 5-feet long and has its own microflora (which is part of the overarching microbiome). Like the small intestine, the colon is responsible for synthesizing and absorbing certain nutrients.


During this phase, fiber, a type of healthy carbohydrate from plants, beans, and grains, delivers important short chain fatty acids to the body. Lack of fiber in the diet and the consumption of processed foods and meats correlate with a depleted short-chain fatty acid profile. This is linked to colon cancer, crohns disease, and irritable bowel syndrome.


Importantly, fiber promotes the formation of stool. To put it simply, fiber helps us poop, and pooping is required in order to remove dangerous toxins from the body.


Putting it all together: In order for the colon to produce the healthy short-chain fatty acids and healthy microflora, the first few steps of the digestion and absorption process must go off without a hitch. If your diet and lifestyle are affecting your body’s ability to break down food, or to absorb food, then your colon will inherently suffer because it’s the last step in the assembly line. This can result in chronic constipation (toxic buildup), diarrhea, irritable bowel syndrome, or irritable bowel disease.



In conclusion, your gut is often at the center of your wellness or your illness. Diet and lifestyle play a major factor, in addition to genetic predispositions in some cases. Because of these important gut-derived processes, 80% of the immune system is dictated by the gastrointestinal tract.


How to keep your gut healthy:

  • If you are suffering from a chronic health condition, chances are that you can optimize your food intake to promote gut healing. Treat your gut with respect by cutting out processed foods and emphasizing a whole-food nutrient dense diet.

  • Take note of the food you eat and how it makes you feel. Start a food diary. You shouldn't have to suffer from a "food baby", or feel super fatgued after you eat!

  • Work a nutritionist or health coach to plan an elimination diet to cut out the foods that might be making you sick.

  • Work with a nutritionist or health coach to add high-quality probiotics and supplements to your routine, to rebalance gut microflora and replenish nutrient deficiencies.

  • Embrace exercise and mindfulness practices such as mediation and yoga


#GutGuardian #FunctionalMedicine #GutHealth #FunctionalNutrition #LeakyGut #HealtheGut #Inflammation


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