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How Gut Dysbiosis Negatively Affects Hormone Regulation, Immune System Activation, and Neurotransmitter Production

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How Gut Dysbiosis Negatively Affects Hormone Regulation, Immune System Activation, and Neurotransmitter Production

We've been taught our whole lives that what we eat only plays a role in our digestion, but in reality, our gut health lays the foundation for our overall health. Today, an estimated 133 million Americans suffer from at least one chronic illness. That figure is 15 million higher than just a decade ago; by 2030, this number is expected to reach 170 million.

Chronic diseases such as heart disease, cancer, and diabetes are the leading causes of death and disability in the United States. They also drive the nation's $4.1 trillion annual health care costs.

Why do we bring these statistics up? Because many of these chronic diseases are a direct result of lifestyle and what we put on our plates.

Through many studies, we have learned the health of the gut influences more than just the gastrointestinal system. A healthy microbiome plays an important role in hormone regulation, disease prevention, and neurotransmitter production.


What is The Gut?

When we refer to the "gut," most people reference their stomach or large intestine, depending on the associated symptoms. However, digestion actually starts with our mouth, which leads to our stomach, small intestine, and large intestine, and ends at the anus. So anytime someone references their gut, they are referring to the whole GI tract.  

The length of our gut varies from person to person because of our height, but on average, here are the lengths:

  • Small intestines: approximately 9-16 feet (3-5 meters)
  • Large intestines: approximately 5 feet (1.5 meters)

Small Intestine

The small intestine is responsible for the breakdown of food and absorption of nutrients. It is separated into three sections: the duodenum, jejunum, and ileum. Digestive enzymes such as lipase, protease, and amylase, from the pancreas and bile from the liver, enter the duodenum to break down:

  • Carbs into glucose
  • Fat into fatty acids
  • Protein into amino acids

This starts the absorption process. Then the jejunum absorbs the minerals (micronutrients), glucose, fatty acids, and amino acids (macronutrients).

The ileum cleans up any leftover macronutrients and absorbs bile acids, fluid, and vitamin B-12. It also has an immune function that protects the body from harmful bacteria in the gastrointestinal tract.

Large Intestine

The large intestines contain four different sections: the ascending colon, transverse colon, descending colon, and sigmoid colon. Once the macronutrients have been absorbed, the ascending colon continues to absorb anything that was missed. This includes water, vitamins, and minerals, which are called micronutrients.

Then the muscles within the large intestinal wall continue to move forward what has not been absorbed for elimination. The waste that cannot be absorbed is called feces, which goes to the descending colon to be stored—eventually, the sigmoid colon contracts to apply pressure to move the waste into the rectum. Once the feces is in the rectum, it waits for the final step of elimination, known as defecation. It can stay in the sigmoid for seven hours or more and is usually expelled when new waste material requires entry into this region.

Digestion: How Long Does It Take?

Digestion time varies among individuals. The exact time depends on the amount and types of foods you've eaten, your metabolism, and whether you have any digestive issues that could slow down or speed up the process. Generally, food takes 24 to 72 hours to move through your digestive tract.


After you eat, it takes anywhere from 40 mins to two hours for your stomach to empty and move the food to the small intestine. The more protein or fat it has, the longer it takes to digest.

Small Intestine

Food takes around two to six hours to pass through your small intestine. If food moves slower than this time, it can lead to small intestine bacterial overgrowth (SIBO).

Large intestine

Food can take anywhere from 10-59 hours to move through the entire colon, depending on factors like hydration, thyroid health, medications, and fiber intake.

How Does Gut Health Affect The Body?


Poor gut health can also affect our mood and cause brain fog. That is because our gut produces neurotransmitters such as serotonin, dopamine, and GABA. When there are imbalances in our gut microbiome or nutrient absorption issues, this can affect the production of these neurotransmitters. For example, we need an amino acid called tryptophan to make serotonin. Studies have shown that probiotics with Lactobacillus can also help produce GABA, serotonin, and dopamine. Another study looked at how supplementing with Bifidobacterium longum reduced symptoms of depression in patients with IBS.

Immune System

About 70-80% of our immune system is located in the gut. When we eat food, we are not just ingesting and absorbing the macronutrients & micronutrients we also absorb chemicals, pesticides, and compounds, such as casein in milk or gluten in wheat, that our immune system thinks are foreign invaders. These chemicals can disrupt our hormones, and the compounds create antibodies that attack our cells, called molecular mimicry. The combination of these inflammatory products can lead to lower immunity and the possibility of autoimmune disorders.

Micronutrient Absorption

The lining of the intestinal wall is only one cell thick to allow for easy absorption of nutrients. On top of this lining is a thick mucus barrier to protect it. Because it is very thin, many things can affect this mucosa and intestinal barrier, causing it to break down and causing a "leaky gut." Nutrients are not easily absorbed if the intestinal barrier is inflamed or destroyed. This can lead to micronutrient-related malnutrition.

Thyroid Dysfunction: Gut/Thyroid Axis

The change in the microbiome of the gut can affect the function of our thyroid. The Thyroid-Gut Axis shows the link between those who have Celiac Disease or Non-celiac wheat sensitivity and hypothyroidism. When the intestinal barrier is inflamed or destroyed, antigens produced by our immune system from a wheat allergy or sensitivity pass through the barrier and activate the immune system. This can lead to autoimmune diseases such as Hashimoto's or Graves'. Small intestinal bacterial overgrowth (SIBO) can also impact thyroid function.

We also need certain nutrients to support the health of our thyroid, such as iodine, selenium, zinc, and iron. Iodine, selenium, and zinc make our thyroid hormones, T4 and T3.

Estrogen Detoxification

The health of the gut microbiome also plays a role in Estrogen Detoxification. Specific bacteria are responsible for eliminating inactive estrogen metabolites, called the estrobolome. However, if there are not enough good bacteria, an enzyme called beta-glucuronidase gets produced. Beta-glucuronidase converts the inactive estrogen into its active form, which gets reabsorbed into the body. This can result in estrogen imbalances.

What are the Symptoms of an Unhealthy Gut?

An unhealthy gut happens when there is a disruption of the gut microbiome (dysbiosis), leading to an unbalance between good and harmful microorganisms. There are many different signs and symptoms that can indicate a state of an unhealthy gut, and they can differ widely from person to person.

Some common symptoms of dysbiosis include:

  • Bloating
  • Gas
  • Belching
  • Bad Breath
  • Nausea
  • Vomiting
  • Heartburn
  • Constipation
  • Diarrhea
  • Abdominal Discomfort
  • Crohn's
  • Ulcerative Colitis
  • Food allergies or sensitivities
  • Skin issues: Acne, Rosacea, Eczema
  • Mood disorders: Anxiety, Depression
  • Joint pain
  • Fatigue
  • Brain Fog

Root Cause Labs to Guide Individualized Treatment

Comprehensive Stool Test

A comprehensive stool test is an excellent start to assessing the gut's health. This test measures a variety of bacteria, parasites, viruses, fungi/yeast, antibiotic resistance genes, and several intestinal health markers.

For patients suffering from GI symptoms, autoimmune diseases, or any chronic illness, gut health testing may be the key to understanding the root cause of the disease.

Micronutrient Testing

Micronutrient testing is critical to assess, especially if you have any symptoms of poor gut health. If food isn't digested properly, the micronutrients won't get easily absorbed. One way to assess the status of how well you are absorbing vitamins, minerals, fats, and proteins from your food is a blood and urine test like the NutrEval by Genova Diagnostics.


If you are experiencing anxiety, depression, or other mood disorders, consider a Neurotransmitters test alongside the micronutrient and comprehensive stool test. If you are not breaking down and absorbing protein and micronutrients, you may see lower levels of specific neurotransmitters such as Serotonin, Dopamine, and Norepinephrine.


If your gut health is affecting hormone imbalances, a DUTCH Complete and Comprehensive Thyroid Test are recommended. These test can help practitioenrs individualize treatment strategies to balance hormones.

Root Cause Treatment for Imbalanced Gut


Making simple changes to your diet can help support a healthy microbiome. The Mediterranean diet is one of the most researched nutrition plans for lowering systemic inflammation and improving gut health. Increasing foods that contain fiber and resistant starches can help increase beneficial short-chain fatty acids and butyrate, which feed your healthy gut bacteria. Sources of fiber, short-chain fatty acids, and resistant starches include oats, berries, apples, pears, nuts, seeds, leafy greens, lentils, and chickpeas.

Fermented foods also contain probiotics, which are healthy gut bacteria that support a healthy microbiome in the short and long term. They should be considered an essential element of the human diet. Sources of fermented foods include sauerkraut, kimchi, pickled vegetables, yogurt, and kombucha.

Herbs and Supplements

Supplementing with probiotics can help diversify and support a healthy microbiome. Comprehensive stool testing can help personalize probiotic recommendations by evaluating what microbes are out of balance. Probiotics such as Lactobacillus and Bifidobacterium have also been shown to improve certain chronic disorders, such as:

Prebiotics are sources of fermentable fiber, such as inulin and psyllium. Fermentable fiber feeds our gut bacteria and helps regulate our bowel movements.

L-glutamine is an amino acid that has also been found to help repair intestinal permeability and reduce zonulin levels.

Curcumin is an antioxidant that is found in turmeric roots. This study shows that curcumin can help alleviate gastrointestinal symptoms and reduce systemic inflammation.

Berberine is an herb that can be used to alter the microbiome and support healthy glucose levels, especially in people with diabetes.


Supplementing with nutrients such as iodine, selenium, zinc, and iron can help support thyroid health. Other nutrients to consider supplementing that support immune health are Vitamin D and Vitamin C. Omega 3 fatty acids and amino acids are also essential for brain health.

Taking a multivitamin can provide some of these micronutrients. However, a multivitamin only provides the lowest amount of nutrients needed to maintain health. Most people will still need more nutrients than a multivitamin can provide. Therefore, a micronutrient test provides an individualized approach to replenishing deficient nutrients.


A diet high in fiber and probiotics isn't the only thing that can help our microbiome. Exercise and stress reduction are other important lifestyle factors that support our gut health.

One study shows an increase in butyrate-producing bacteria in obese individuals who participated in 6 weeks of endurance exercise. Doing at least 25 minutes of exercise three days a week is recommended.

There is a link between stress and the Gut-Brain Axis. The hypothalamic-pituitary-adrenal (HPA) axis is the body's system that helps us regulate stress. Stress negatively impacts gut health by increasing intestinal permeability and changing the microbiome. Adding in a daily practice of yoga or meditation can help reduce stress and support a healthy microbiome.


The health of our gut not just impacts the absorption and digestion of our food but influences many other systems in our body. You can take simple steps to start supporting a healthy gut by adopting a low inflammatory diet and increasing your fiber consumption and fermented foods. Maintaining a healthy lifestyle, such as regular exercise and daily stress-reducing activities, can also help support a healthy gut. If you still experience gut symptoms, or a chronic disorder, consider working with a functional medicine practitioner to help get to the root of what's happening at the cellular level.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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