Many years ago, in 460 BC, a man named Hippocrates came forward with a bold statement:

“All disease begins in the gut.”

Wow. Is that really true? Can the gut have that much of an impact on the body and health in general? Since the turn of the century, the floodgates have been opened to this “new” notion that most, if not all disease, in fact can begin in the gut. Unreal you say? Read on!

When I say “gut”, I’m describing an intricate network of intestines, immune cells, bacteria, and stomach. When you think about it, our gut is really just one loooong tube from our mouth to our other end. While many people think of the gut solely as a receptacle for chips, candy bars and cookies, the human gut is of profound importance, and actually very fascinating.

Did you know?

  • Humans have over 100 trillion bacteria in their bodies
  • Bacterial cells outnumber human cells 10:1
  • You don’t have to have constipation, diarrhea, or bloating to have a gut problem
  • Humans have about 3 pounds of bacteria in their gut at any given time
  • There are anywhere from 500-1000 different species of bacteria in the gut
  • The first 3 years of your life ‘sets’ your microbiome.

Jobs your gut has:

Break down and utilize food for energy

digestive tract

The most widely-known job of our gut is to break down, absorb, and utilize food that we put into our mouth. This process is actually quite complicated and many things can go wrong along the process. Our stomach as very acidic (pH of 1.5-3.5), and it is so in order to break down food particles (especially proteins) so they can be better absorbed in the small intestine. Another reason for stomach acid is to protect the gut and our bodies from invading organisms like H. pylori, parasites, and other bad bugs.

Once the food is broken down in the stomach, the food moves along to the small intestine, where the gallbladder releases bile from the liver, and the pancreas releases enzymes in order to change the pH of the food (bring it back to a pH of about 6). This is where food is absorbed into the body, taken off into cells and used for energy or for storage. What is left behind will follow the trail into the large intestine, and eventually exiting in a bowel movement.

Produce vitamins and short chain fatty acids

Studies have shown that gut bacteria can actually synthesize vitamins, such as Vitamin K, B12, biotin, folic acid, and thiamine. These are important vitamins utilized by the body and will falter if gut health is poor.

Gut bacteria will also produce short chain fatty acids, which are an important source of energy in the body. The bacteria feeds off of fiber in our diets.

Immune function

About 70-80% of the immune system is located in the gut. Remember, the gut is really one long tube from one end to the other; so our immune system must protect us from what we are exposed to. We have an army that is constantly monitoring the body, waiting for invaders. This is our immune system, and it includes different players like B cells and T cells.

Balance blood sugar

Blood sugar fluctuations are one of the biggest stressors on the body. If out of control, high blood glucose can lead to insulin resistance and eventually diabetes. Interesting new studies show that each person’s response to sugar is different, and may be based on their gut flora. In one study, adding fermentable fibers in a treatment plan reduced blood sugar levels.

Genetic expression

Believe it or not, our genes don’t control our destiny! In fact, the large majority of health is due to our environment. This includes things like diet, exercise frequency, amount of stress, sleep, relationships, and toxic exposure. With good environmental choices, good genes can be expressed, and vice versa poor food choices, stress, and low sleep can activate ‘bad’ genes.


Have you ever had a ‘gut feeling’? You should listen to it! The gut is sometimes called the second brain, because it has more neurons than the brain and spinal cord, and has its own nervous system, called the enteric nervous system. Most neurotransmitters, like serotonin and dopamine are actually made in the gut. Many brain disorders such as anxiety, depression, and even Parkinson’s  and dementia have gut-related issues.

So now we know how important the gut is for optimal health. Many times, we harm our gut unknowingly.

So what can cause damage to the gut?


As a newborn baby passes through the vaginal canal, he or she is bathed in the mother’s bacteria. This bacteria is the initial “inoculation” and will help build the baby’s microbiome for life. Although common (1/3 of babies in America are born via C-section), missing out on the microbiome inoculation can lead to major health challenges later in life. In a giant study, those who were born via C-section had significantly increased risk for asthma, juvenile arthritis, IBD, immune deficiencies, and leukemia.


The Standard American Diet leads to a less diverse gut microbiome, and intestinal inflammation. Foods like hydrogenated fats, omega-6 loaded fats like vegetable oils, refined grains, sugar, gluten, and dairy are staples in America. Yet all of these can harm the gut. This can lead to immune related problems, weight gain, and brain issues like anxiety and depression.


Breastfeeding is the infant’s second opportunity to acquire the mom’s good bacteria. This boosts the baby’s immune system and sets the tone for their immune system for life. Therefore, missing out can limit gut microbes that could have developed.

Low fiber diet

Fiber helps feed the good bacteria in our gut. Historically, hunter-gatherers ate more fiber than in our diets today. Although some researchers and doctors recommend over 50 grams of fiber per day, most Americans only consume 14 grams a day.

Conventional  meat

The large majority of antibiotics in use today are used on livestock. In fact, 80% of antibiotics are used on livestock. Consuming meat can alter gut bacteria.


When eating modern gluten, a substance called zonulin is falsely triggered to release. Zonulin opens up spaces for nutrients to get through cells. The problem with zonulin  is that is causes intestinal permeability (leaky gut) in humans, even those without celiac disease.

Pesticides and herbicides

Glyphosate, better known as Round-Up, is a known carcinogen that is used widely on conventional crops all over the US. Many European countries have banned Glyphosate due to its dangers. Recently, a judge ruled that California can require Monsanto to label Round Up as a carcinogen. (Source)

BT is a pesticide used by Monsanto on crops, especially corn. When an insect attempts to eat the crop, the BT physically breaks open their stomach and they die. What do you think happens to humans who eat these crops?

Antibiotic use

Profound and rapid loss of diversity of microbiome.


When we are stressed, the body releases cortisol, which is a protective mechanism, to keep us safe from impending danger. If we are constantly stressed (school, work, bills, kids, phones, etc.), cortisol production continues to  increase. When this happens, the defense mechanism of the intestinal immune system, secretory IgA is decreased. Besides, why would the body worry about protecting us from invaders in our gut when we have an outside invader? Also, cortisol decreases the body’s production of enzymes and hydrochloric acid; both which are needed to break down and absorb food.


Certain medication like NSAIDs (Advil, Ibuprofen) can cause serious intestinal lining damage. Also medications like birth control and antacids cause a leaky gut.

Leaky gut


Certain times, infections can make a home in the gut. These can include H. pylori, parasites, and candida. When this happens, the immune system is activated, trying to eradicate the infection. If this goes on for months and years, the immune system is called upon too much, leading to many conditions.


Alcohol consumption leads to alteration in the gut bacteria, Small Intestinal Bacterial Overgrowth (SIBO), mucosal damage, and increased gut permeability.

If you haven’t noticed, our gut is extremely important for our overall health. When damaged, the gut bacteria can grow out of balance, the gut lining can become leaky, and the immune system can be activated. This can lead to a whole host of issues.

What issues can be caused by leaky gut?


The bacteria in our gut (good or bad) can dictate whether we store fat or burn fat. For example, there are two certain groups of bacteria in the gut that have been shown to control this lever: If the Firmicutes family is considerably more prevalent than the Bacteroidetes family, one will tend to put on weight.


Inflammation is actually a defense mechanism perpetuated by the immune system. When under attack from a foreign invader (yeast, parasite, bacteria, food), the immune system can activate its troops by sending out inflammatory molecules. If the gut lining is damaged and permeable, the immune system will react quicker and with more force, leading to widespread chronic inflammation.

Autoimmune diseases

Because 70-80% of the immune system resides in the gut, it only makes sense that immune-related problems can start there. Dr. Alessio Fassano, renowned celiac, multiple Sclerosis, and Type 1 diabetes researcher states that,“Besides genetic and environmental factors, loss of intestinal barrier function is necessary to develop autoimmunity.”

In simple terms, this means that a leaky gut is a must for someone to develop an autoimmune disease.


Our gut microbiome can highly influence our brain function through chemicals messengers, neuronal signals, and inflammation. Many postulate that depression is actually an inflammatory disorder, where the glial cells (immune cells) in the brain are activated and unable to shut off. Also feel-good neurotransmitters like dopamine and serotonin are made mostly in the gut.

A research team at McMaster University, showed that mice with little or no gut microbes could change personalities when inoculated with another mouse’s gut flora. Naturally timid mice became daring and outgoing.


Mazmanian and Hsiao performed a study which experimented with giving a microbe called Bacteroides fragilis, known for anti-inflammatory properties, to animals. This microbe also protects mice from experimentally induced colitis. Findings demonstrated that the treatment healed intestinal leaks and restored a more normal microbiota. It also diminished the propensity toward repetitive behavior and minimized communication. Mazmanian succeedingly found that B. fragilis reverses MIA deficits, even in adult mice. “So, at least in this mouse model, it suggests features of autism aren’t hardwired—they’re reversible—and that’s a huge advance,” he says.

“What I see in the families of autistic children is that 100 percent of moms of autistic children have abnormal gut flora and health problems related to that.”

Dr. Natasha Campbell-McBride

For good gut health:

Bone broth/ fermented veggies

Bone broth provides vitally healing nutrients that heal and seal the gut wall. Bone broth contains electrolytes, collagen proteins, and glucosamine, all of which can either speed recovery or maintain gut integrity.

Anti-inflammatory diet

Certain foods can irritate the gut mucosa, leading to immune activation and maldigestion. Avoiding foods like gluten and sugar is important, while adding in foods like green leafy vegetables, berries, coconut oil and olive oil, wild caught fish, and grass fed meats can aid in gut health.


Be mindful and find ways to destress, like meditation, deep breathing, yoga or pilates, and walking outside. All of these have been shown to decrease stress, turn off inflammation, and decrease aging.

Boost your fiber

Bulk up your diet and feed your good bacteria- they will thank you! Load up with chia seeds, flax seeds, berries, starchy vegetables like sweet potato and yucca.


Getting enough sleep can dampen inflammation, balance hormones, stabilize blood sugar, and much more! Shoot for 8 hours per night for optimal health.

Healing herbs and nutrients:


Zinc supplementation has been shown to decrease intestinal permeability and aid in balancing the immune system.


When under stress, our body will use up more glutamine to heal and repair tissues and for energy production. Glutamine is an essential amino acid used as fuel for the enterocytes (gut cells).

Turmeric (curcumin)

The most famous and potent anti-inflammatory. This can dampen intestinal inflammation and be soothing on the gut lining.


Ginger is an anti-inflammatory and can aid gut motility, meaning that the bowels can move along easier.


Probiotics help replenish and feed gut bacteria. Look for probiotics with different strains of bacteria and billions of colony forming units.


Pancreatic enzymes aid in the breakdown and digestion of food in the small intestine. Hydrochloric acid can aid the stomach in breakdown of food, especially protein. I would advise speaking with your functional medicine doctor prior to beginning an enzyme regimen.

Vitamins  A, D, E, K

These fat-soluble vitamins are critical for the integrity of the gut lining and strength of the immune system.

Why Functional Medicine tops all for gut health:

Functional Medicine shines in finding the root cause of health challenges. Because the gut can affect the entire body, it is important to find and fix any problems that arise. Testing to see gut bacteria levels, inflammation, digestibility, and looking for infections is important. The typical functional medicine protocol to fix the gut could look something like this:


Giving nutrients to heal, seal, and soothe the damaged gut lining. This can help in food absorption, calm inflammation, and correct the immune system.


Once there is an identified pathogenic bacteria or infection, eradicating it is a high priority. Using natural therapies such as herbs are common.


Replacing enzymes or hydrochloric acid, even for a short while, can help the gut digest essential nutrients.


Rebalancing the gut microbiome is usually the last step, but a very important step, in returning to optimal health. Replenishing with certain strains of bacteria and fuel for the bacteria are used.

If you have any questions or concerns regarding your gut health, please feel free to contact me!