The 4 Most Common Gut Issues & How to Fix Them

By Dr. Justin Marchegiani

Gluten Intolerance

Gluten sensitivities, like Celiac disease and gluten intolerance, have become an object of public interest in recent years. 

Gluten is a protein found in grains such as wheat, barley and rye. One thing to be conscious of is the fact that although gluten isn’t found in many ancient grains like oats, quinoa, rice, or corn, these foods are often cross-contaminated. If you are gluten sensitive, it’s best to avoid any gluten-containing or cross-reactive foods.

Celiac disease and true gluten allergy are rarer than gluten intolerance. Gluten allergy symptoms include malnutrition, stunted growth, cancer, severe and neurological illnesses.

Much more common is gluten intolerance and sensitivity, which has been dubbed non-celiac gluten sensitivity (NCGS). Those with NCGS feel and perform noticeably better when they stay away from gluten. When they do consume gluten, symptoms include:

  • Digestive problems including:  IBS, abdominal pain, cramping, bloating, constipation, diarrhea
  • Brain fog, headaches, concentration and memory problems
  • Skin issues such as: dermatitis, eczema, rosacea, and rashes
  • Nutritional deficiencies
  • Mood imbalances like anxiety and depression
  • Reproductive problems and infertility
  • Higher risk for learning disabilities and neurological diseases, including autism, ADHD, dementia and Alzheimer’s. 
  • Chronic fatigue, low energy levels
  • Muscle and joint pain, or numbness in the limbs

Because gluten opens the door to so many health issues, I recommend cutting gluten regardless. A gluten molecule looks similar to the thyroid tissue, the body can mistakenly start an attack on healthy body parts, driving autoimmunity. If you don’t want to do testing, you can try an elimination diet to see how you feel when you cut out gluten. There are so many healthier alternatives!

Leaky Gut

Leaky gut occurs when the intestinal lining becomes inflamed, which can be caused by infections, a poor microbiome, and the consumption of gluten, sugar, or other foods you are sensitive to. The inflamed gut lining opens the tight junctions of the gut, which allows food particles and other toxins to slip through into the bloodstream, creating more inflammation and driving autoimmunity. 

More and more research is starting to show that the gut microbiome plays a pivotal role in the prevention and healing of leaky gut. Probiotics can help reverse leaky gut by enhancing production of the proteins which form the tight junctions that keep the gut barrier sealed. Antibiotics, on the other hand, disrupt the balance of the gut microbiome and can weaken junctions, letting pathogens into the bloodstream. To heal leaky gut, you need to remove foods that cause inflammation along with any foods you have a sensitivity to. I recommend removing sugar, dairy, gluten, processed foods, and alcohol to allow your body to recover. You will also want to supplement with enzymes, acids, and bile salts; and finally repair the gut with healing nutrients and probiotics.

Gut Dysbiosis

We all have around two pounds of microbes living in and on our bodies; the majority of which lives in our gut! Breakthroughs in science are discovering how the gut is a kind of ‘second brain’ and the trillions of bacteria in our gut communicate with the neurons in our gut lining. Poor gut health is tied to many health issues and diseases, including:

  • Asthma and allergies
  • Autoimmune diseases (arthritis, IBS)
  • Cognitive decline (Alzheimer’s, dementia)
  • Fatigue and brain fog
  • Fungal overgrowth
  • Gluten sensitivity and other food allergies and intolerances
  • Infertility
  • Learning disabilities (ADHD)
  • Mood disorders (anxiety, depression)
  • Parasitic infections
  • Small intestinal bacterial overgrowth (SIBO)

Click here if you are suffering from digestive issues to consult with a functional medicine doctor and start feeling better today!

Just as bad bacteria negatively affect your health, good bacteria have a positive influence on your health! Good gut flora assists in the following ways:

  • Better nutrient absorption and storage
  • Strong intestinal lining and prevents leaky gut
  • Stronger immune system and lower inflammation
  • And, avoiding the negative symptoms associated with poor gut health, like brain fog and digestive distress

Here are some tips to keep your gut bacteria strong:

  • Avoid antibiotics, which deplete good gut bacteria. Be cautious of prescription drugs, which can do the same.
  • Reduce your sugar intake: Bad bacteria love sugar!
  • Avoid inflammatory foods, which can reduce good bacteria and also create leaky gut.
  • Eat vegetables with every meal: If you can fill half your plate with vegetables and plant-based foods, your good bacteria will have plenty of fiber and nutrition to feast on and use to boost your health!
  • Choose organic: Not only are GMOs and toxic pesticides are bad for our microbiome, they also affect the soil they’re grown in, and our gut bacteria and the bacteria in the soil are related.
  • Incorporate fermented foods into your diet: Sauerkraut, kombucha, kefir, and pickles are all delicious fermented foods.
  • Take prebiotics and probiotics: The use of pre- and probiotics feed the good bacteria that keep your gut healthy.
  • Take steps to lower your stress: Studies have shown that stress can actually negatively affect the composition of your gut flora!

Parasites and Infections

Symptoms of Parasite Infections Include:

  • Brain fog, Mood problems like anxiety and depression
  • Sweet cravings
  • Skin issues like acne and eczema
  • Nutrient deficiencies like anemia
  • Allergies
  • Fatigue
  • Digestive problems like: Bloating, Gas, Indigestion, Diarrhea, Constipation, GERD or acid reflux, IBS, Crohn’s Disease, Ulcerative colitis

A parasite infection will not only rob you of energy and nutrition, they also produce other biotoxins that can disrupt digestion. These toxins are a product of parasitic defecation and debris of dead parasites.

  • Parasites include larger worms: hookworms, roundworms, pinworms, tapeworms, nematodes, and protozoa.
  • As well as small, microscopic parasites like: Giardia, Entamoeba histolytica, Blastocystis hominis, Cryptosporidium, Dientamoeba fragilis, Entamoeba coli, Yersinia enterocolitica, Entamoeba hartmanni, and Toxoplasma.

70–80% of my patients dealing with health problems have a parasite infection, and aren’t even aware of it! Chronic infections steal your nutrients and energy while deplete your body’s ability to produce regenerative hormones.

To test for a parasite infection, click here!

Everyday Habits to Keep Your Gut Healthy

A gluten-free, paleo-inspired diet rich in grass fed meats, butter, pastured eggs, and bountiful organic product is one of the best ways to support a healthy gut and healthy digestion. You may also incorporate fermented foods like sauerkraut and kombucha, or a quality probiotic supplement to help your good gut bacteria rebuild!


The entire contents of this website are based upon the opinions of Dr. Justin Marchegiani unless otherwise noted. Individual articles are based upon the opinions of the respective author, who retains copyright as marked. The information on this website is not intended to replace a one-on-one relationship with a qualified health care professional and is not intended as medical advice. It is intended as a sharing of knowledge and information from the research and experience of Dr. Justin and his community. Dr. Justin encourages you to make your own health care decisions based upon your research and in partnership with a qualified healthcare professional. These statements have not been evaluated by the Food and Drug Administration. Dr. Marchegiani’s products are not intended to diagnose, treat, cure or prevent any disease. If you are pregnant, nursing, taking medication, or have a medical condition, consult your physician before using any products.