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Healthy Gut, Healthy You

by Dr. Michael Ruscio
Home/Blog/Protect Your Mental Wellbeing During the COVID-19 Pandemic

You may have heard the quote Hippocrates made over 2000 thousand years ago: “All disease begins in the gut.” But what does that really mean?

Get a Gut Health Checkup Even If You Don’t Have Digestive Symptoms

Are you on a Paleo diet but still suffering from autoimmune diseases such as hypothyroidism, or symptoms such as fatigue or weight gain? Find yourself chasing allergy symptoms, hormone imbalances, adrenal fatigue, or other chronic health problems?

If so, it is time to evaluate the health of your gut.Often people and practitioners make the mistake of looking for the cause of the problem within the same system that is expressing symptoms, while missing the cause of the problem — the gut. The root cause of all of these woes may be an unhealthy gut, even though you might not be experiencing any digestive symptoms. 

In functional medicine, we understand symptoms that show up in one part of our body may be caused by imbalances in a completely different location. Our bodies communicate as an entire ecosystem — a community of interacting organisms — and it is said, we are more bacteria than we are human cells. A new study by the Weizmann Institute in Israel I., estimates that we have 30 to 50 trillion bacteria cells making up our diverse system. More importantly, our gut walls are home to 70 percent of the cells that make up our immune system. Our diverse digestive system is home to both good and bad bacteria. The good bacteria help us digest, eliminate wastes, and regulate and promote proper metabolism and immune function.

You might not be thinking of digestive problems if you are suffering from things such as autoimmune disease, acne, weight gain, or depression, but many symptoms and diseases are manifested by gut imbalances. Evaluating your intestinal health and your ability to digest and absorb vital nutrients is the most important step you can take for your overall health.

What Can Cause Imbalanced Gut Health?

We all know a healthy Paleo diet and lifestyle is a foundation to general well-being and gut health. But what other items can be damaging our gut and thwarting our health?

While counterintuitive, some people are inadvertently eating too much fiber and prebiotic-rich foods. Even though foods high in fiber and prebiotics are healthy and Paleo-friendly, these foods can be problematic for individuals with gut imbalances such as SIBO (Small Intestine Bacterial Overgrowth). Other factors can also diminish gut health, such as fungal infections or even parasites. If you have one of these, you may not be getting the most out of your diet. A healthy diet simply cannot be fully assimilated by an unhealthy gut. This might be why you’re eating healthy but not feeling well.

Common Gut Infections and Imbalances


The largest density of immune cells in our bodies reside in the small intestines, whose other main function is to absorb our essential nutrients. Our colon also has large amounts of bacteria that are essential for breaking down indigestible foods. When too many large intestinal bacteria migrate into our small intestine, it is called SIBO. If this excess of bacteria in the small intestine is not removed, the bacteria begin to feed on our vital nutrients, causing a vast array of food intolerance, nutrient deficiencies, and autoimmune disorders. Resolving SIBO not only helps with annoying digestive symptoms of gas, bloating, diarrhea, and constipation but can also help improve metabolism. Follow this link to learn more about the connection.

Inflammatory Bowel Disease (IBD)

There are many different faces of IBD, which is a name for a group of bowel disorders in which the immune system reacts with the healthy bacteria in your intestines. Crohn’s disease and ulcerative colitis are the most widely recognized. Some people have subclinical IBD, which causes nagging bloating and loose stools. The travesty here is that high-fiber Paleo-type diets can make these issues worse. You may need a modified Paleo diet if you have this condition.

Check out my video to learn more: “Gut that just won’t improve? Could it be IBD?”

Irritable Bowel Syndrome (IBS)

IBS is a broad term that refers to chronic swelling and inflammation of the intestines that results in gas, bloating, alternating bowel habits, and abdominal pain. Although most symptoms of IBD and SIBO overlap with IBS, IBS is not classified as a true disease but instead as a functional disorder. IBS is often labeled as a “diagnosis of exclusion.” One clinical study showed that up to 84% of IBS suffers would test positive for SIBO. V.


Symptoms of parasitic infections include diarrhea, constipation, fatigue, stomach cramps, nausea, and vomiting. Researchers have discovered that infections from a number of bacteria can lead to IBS. The most common infections are Campylobacter, Salmonella, Shigella, and amoeba, giardia, and Cryptosporidium parasites. Learn more from this conversation with one of my patients about intestinal worms causing weight gain, stress, food allergies, constipation, and insomnia.

Blastocystis Hominis

This parasite infection can cause fatigue, loss of appetite, hives, nausea, diarrhea, abdominal cramps, bloating, and gas. Another example of the gut connection to autoimmunity has been documented by a case study where treating Blasto improved thyroid autoimmunity and thyroid hormone levels. Get more information on Blastocystis Hominis infections linked to hypothyroidism here.


This bacteria resides predominately in the stomach and can cause stomach pain, ulcers, reflux, and heartburn. An interesting study looked at 10 patients with Hashimoto’s thyroid disease who also had H. pylori infections. Half of the patients were treated for the infection and the other half were not. Those that were treated for H. pylori saw a decrease in thyroid autoimmunity.


We have certain types of microorganisms that naturally live in different mucosa areas of our body. We are supposed to have a certain amount of fungus in the body, but an overgrowth of fungus or candida can become a health concern. Some common causes are stress, lack of probiotic-rich foods, a high-carbohydrate diet, or overuse of antibiotics. This increase of fungus or candida can cause a whole host of symptoms, including food sensitivities, autoimmune issues, and weight gain.

For a more detailed explanation, view my video on candida, weight gain and brain fog, or this one on candida biofilm treatment for weight loss.

Leaky Gut, or Intestinal Permeability

According to research, leaky gut, or intestinal permeability, may be the cause of many chronic conditions, including food allergies, joint pain and inflammation, lack of energy, depression, skin issues, and autoimmune diseases. When the lining of your small intestine becomes inflamed, your intestinal barrier allows large particles of protein, toxins, and microorganisms to leak into your bloodstream. Once these foreign invaders are in the bloodstream, they trigger an immune response that causes systematic inflammation. By addressing the above gut infections and imbalances, you can heal leaky gut once and for all.

Putting It All Together

Whether you are suffering with digestive issues or not, addressing the health of your gut and treating any gut infections or imbalances can help with a variety of symptoms and reduce or eliminate autoimmune disease.

How do you address all of this?

At this year’s Paleo f(x)™, I will be doing a talk with my good friend Melissa Hartwig of The Whole30 on how to get started with functional medicine so you can get healthy and get back to your life. Don’t miss it!



I. Ron Sender, Shai Fuchs, Ron Milo. Revised estimates for the number of human and bacteria cells in the body.

II. Durgan DJ1Ganesh BP2Cope JL2Ajami NJ2Phillips SC2Petrosino JF2Hollister EB2Bryan RM Jr2Role of the gut microbiome in obstructive sleep apnea-Induced hypertension.

III. G Sigthorsson, J Tibble, J Hayllar, I Menzies, A Macpherson, R Moots, D Scott, M J Gumpel, I Bjarnason, Intestinal permeability and inflammation in patients on NSAIDs.

IV. Bertalot GMontresor GTampieri MSpasiano APedroni MMilanesi BFavret MManca NNegrini RDecrease in thyroid autoantibodies after eradication of Helicobacter pylori infection.

V. Mark Pimentel, Evelyn J Chow and Henry C Lin, The American Journal of Gastroenterology 98, 412-419 (February 2003) | doi:10.1111/j.1572-0241.2003.07234.x

Microbiome photo licensed under the Creative Commons.


The Paleo movement incorporates several different optimizing perspectives for helping you improve your health, all based on the latest science. Everyone is different. We want to support you in understanding your unique genetic makeup, symptoms and health goals so you can choose the path that is right for you.

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Dr. Michael Ruscio

Michael Ruscio is a doctor, clinical researcher, author, and health enthusiast. Dr. Ruscio practices Functional Medicine and is currently performing two clinical trials in the treatment of digestive conditions.