How to Fix Your Health by Fixing Your Gut

Did you know that your body’s overall health depends on the bacteria in your gut? It’s true! We have more bacteria in our GI tract than we have cells in our bodies. Collectively, these colonies of gut bacteria are called the microbiome. Scientists estimate the average person has 100 trillion micro-organisms in their gut. About 500 different species have been identified, but only 20 types make up 75% of the total.

bacteriaMany of these bacteria are beneficial, but we can have bad bacteria too. Good bacteria are protective. They help us break down food, absorb nutrients, and guard our immune system. On the other hand, bad bacteria produce toxins that wreak havoc in the body.

Optimum health depends on minimizing bad bacteria. We do this by encouraging more good bacteria to grow, so they crowd out the bad kind. And also, by eliminating the things that damage our gut and feed bad bacteria.

Fermented Foods Promote a Healthy Microbiome

To improve the health of our microbiome, we first need to protect the good bacteria we already have by eating foods that help good bacteria flourish. These include foods that contain prebiotics, which is a type of soluble fiber found in certain plant foods like garlic, onions, and asparagus. Our microbiome also thrives on probiotics, which are living bacteria found in fermented foods like sauerkraut, kimchi, yogurt, and even dark chocolate.


Homemade Kimchi is a superfood packed with healthy nutrients, beneficial bacteria, and fiber.

WonderMill Junior Deluxe

A grain mill like our WonderMill Junior Deluxe makes quick work of grinding dehydrated sprouted grains and legumes into nutritious flour.

Since ancient times, people from the Middle Eastern and Asian cultures have known about the health-promoting properties of fermented foods. Scientists have since discovered that preparing grains and legumes the traditional way—by soaking, sprouting, and fermenting—greatly reduces (and sometimes completely eliminates) certain compounds that interfere with nutrient absorption. Grains and legumes that have been soaked and sprouted can be dehydrated and ground into more nutritious flours.

As part of the fermenting process, we add an appropriate starter culture to inoculate the food with beneficial bacteria that will grow as the food ferments. When making fermented vegetables, for example, we add a veggie fermenting starter culture that contains several strains of healthy bacteria. Similarly, we add special powdered yogurt cultures, kefir starter, and cheese cultures to milk when making fermented dairy products. Adding a mushroom-like kombucha culture (SCOBY) to sugar-sweetened kombucha tea a delicious, fizzy, probiotic drink.

Straining Yogurt

Make Greek yogurt or yogurt cheese by straining off the whey.

As these foods ferment, the healthy bacteria in the culture feed on the food and grow in number. During this process, compounds that are hard to digest—like lactose (the sugar naturally found in milk)—are consumed by the bacteria. So, in a way, fermenting is like predigesting your food. Fermented foods are especially healthy because they feed our gut with both pre-biotics (from the fiber) and pro-biotics (from the living bacterial culture).

Beware of commercially “fermented” foods, however. They don’t have the same health-promoting properties as the naturally fermented foods we make at home the old fashioned way. Foods like pickles are sour because they are preserved in vinegar. Instead of fermenting foods before putting them foods in jars or cans, manufacturers run them through a lactobacterial slurry. When foods like sauerkraut are canned, any living bacteria cultures they might have contained are destroyed by exposure to high heat during canning process.

Our Gut Is the Backbone of Our Immune System

For a long time, it was thought that the purpose of our digestive system was to process and eliminate the food we eat. However, modern research has shown that our microbiome plays a vital role in immunity. For example, good bacteria manufacture Vitamin K, which is important for immune function, and produce important B-Complex vitamins. Good bacteria also protect our immune system by warding off infection, combatting food poisoning, and manufacturing natural antibiotics  like acidophilin, which fights staph and strep.

Good Brain Function Depends on a Healthy Microbiome

Recently, scientists have begun referring to our gut as our second brain. Emeran Mayer, MD, a professor at UCLA, says, “The system is way too complicated to have evolved only to make sure things move out of your colon. A big part of our emotions are probably influenced by the nerves in our gut.” With more than 100 million nerves in our digestive tract, is it any wonder we sometimes experience “gut feelings” or “butterflies in the stomach”?

The micro-organisms in our gut secrete an immense number of chemicals, and some of them are used by our brain. These brain chemicals (called neurotransmitters) enable communication between nerve cells in our brain (neurons). Until recently, scientists believed neurotransmitters like serotonin and dopamine were manufactured in our brain; however, modern research has proven 95% of the body’s serotonin is made in our gut.

Certain Gut Bacteria Act Like Psychiatric Drugs


Our gut manufactures brain chemicals that act like prescription anti-depressants.

A certain class of psychiatric medications, called Selective Serotonin Reuptake Inhibitors (or SSRI’s), is used to treat major depression and panic attacks. These include commonly prescribed drugs, like Prozac and Zoloft. Now that we know about the brain-gut connection, it makes sense why SSRI’s are associated with side-effects like upset stomach, loss of appetite, nausea, vomiting, and diarrhea.

Cutting-edge science has begun to unlock the mysteries of the human microbiome and its complex impact on our overall well-being. A rapidly emerging field of research suggests our gut bacteria affect our mood, and that an unhealthy diet is a major risk factor for depression. Researchers are finding more proof certain gut microbes make chemicals that act like psychiatric drugs. And now that a link has been established between the gut and the brain, researchers are studying the role of the microbiome in mental illness and various brain disorders in children, such as autism and hyperactivity.

Currently, scientists are experimenting with fecal transplants to correct microbiome deficiencies in unhealthy animals. By transferring feces from healthy animals into the intestines of sick animals, researchers have succeeded in reversing conditions like anxiety and depression.

A “Leaky Gut” Can Cause Serious Illness

Imbalances in our gut bacteria can also cause conditions like arthritis, asthma, autoimmune diseases, fibromyalgia, psoriasis, and cancers of the breast and colon. Researchers are finding that these serious illnesses often go away by themselves when bacterial balance is restored. Many psychiatric symptoms, too, seem to clear up with gut bacteria are balanced.

junk food

Junk food upsets bacterial balance in the gut.

Poor food choices and lack of fiber are major causes of bacterial imbalance. As convenience foods have gained popularity, people are eating even fewer fruits and vegetables than they did as recently as ten years ago. Fruits and vegetables contain plenty of soluble and insoluble fiber. Soluble fiber bulks up the stool by attracting water and forming a spongy, jelly-like material. It helps slow things down in the stomach so our body can extract the nutrients we need from our food.

Insoluble fiber has a laxative affect that helps with elimination. Without these healthy fibers, food sits in our digestive system and rots, creating toxicity and irritating our intestines. For this reason, many natural health doctors recommend eating at least 40 grams of fiber a day.

Bad bacteria aren’t the only underlying cause of gut problems. The worst offender is probably stress.


Alcohol is harmful to the digestive tract and can cause serious disease.

Also, our digestive tract can get damaged when we ingest certain medications, including antibiotics, antacids, contraceptives, and pain pills, such as ibuprofen. Alcohol is also very harmful, too, as are GMO foods, and the additives and chemicals found in processed foods. Some people have food intolerances to common foods that contain allergens like eggs, dairy, gluten, peanuts, or soy. For those folks, food intolerances can cause major gut problems.

Dr. David Perlmutter is one of several modern researchers who believes grains, in general, have a detrimental effect on the microbiome. For many patients, eliminating all grains from the diet has resulted in a complete remission of symptoms. In particular, removing grains from the diet of psychiatric patients has been shown to reverse mental illnesses like schizophrenia.

The latest research also suggests that sensitivity to a milk protein called casein could be a culprit in weight loss resistance. When patients continue to have difficulty losing weight even after eliminating grains, many progressive doctors now recommend eliminating dairy products also. A trial period of three weeks is usually enough time to determine if a casein sensitivity exists.


Artificial sweeteners damage the microbiome and promote glucose intolerance, which can lead to disease.

Sugar and artificial sweeteners are especially destructive to the gut. One study, published in the 9 October 2014 issue of the international science journal Nature, concluded that artificial sweeteners induce glucose intolerance by altering the gut microbiota. Taken together, all the above wreak havoc and cause a condition called leaky gut syndrome.

The cells of a healthy intestine are tightly packed. However, when the intestines become damaged, the intestinal lining becomes permeable. These little holes allow microscopic particles of poorly digested food to leak out into the bloodstream. Microbes leak out too, as do the waste and toxins they produce. This puts the body’s immune system on high alert as it begins to attack these foreign substances. To neutralize the threat, the body releases a flood of chemicals that cause inflammation, which further damages the intestinal lining. Over time, it becomes more difficult to absorb nutrients from our food. But the trouble does not end there.

Our immune system wraps the microscopic particles that leak out in specific antibodies, forming larger molecules called immune complexes. These circulate throughout our entire body and get deposited in various places where they cause localized inflammation. Inflamed tissue can manifest as joint pain, headaches, fatigue, rashes and other symptoms of systemic illness. But the trouble doesn’t end there, either.


An unhealthy microbiome can lead to obesity.

The antibodies our immune system creates to protect us are like an army of soldiers that go around looking for foreign invaders to kill. They circulate throughout our body in a constant search for harmful particles to annihilate. When the supply of these particles runs short, the army doesn’t retreat. Instead, our body begins to crave the very foods that make us sick, just so the army of antibodies can have a continuous supply of harmful particles to attack. This sets up a vicious cycle of inflammation and weight gain that’s hard to break.

How to Heal a Leaky Gut

red onion

Red onion is one of the healthiest foods for healing leaky gut.

We can begin to heal a leaky gut with specific foods and nutrients. Besides fermented foods, some of the best foods for healing the gut are ginger, aloe vera juice, red onions, cold water fish, apples, and freshly ground flax seeds. Natural health practitioners often recommend certain nutritional supplements like oregano, aged garlic extract, and cod liver oil.

Equally important is that we eliminate the foods other substances that harm the digestive system. In many cases, gentle herbal remedies can be just as effective as pharmaceutical medications. Anti-inflammatory herbs like turmeric and ginger are especially powerful.

turmeric ginger

Turmeric and ginger are powerful anti-inflammatory herbs that promote gut health.

Natural health practitioners often recommend an elimination diet to pinpoint any food intolerances. The most common allergenic foods are completely eliminated for a period of time, and then reintroduced one by one to see which, if any, cause symptoms to reappear. And, of course, eating a clean diet devoid of GMO’s, chemically laden processed foods, and alcohol is absolutely essential to healthy gut function.


Do you eat fermented foods on a regular basis? If so, have you noticed any improvement in your health as a result? Please share your experiences in the comments below.


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This article is for educational use only and is NOT intended as medical advice. The information presented herein is based on the opinions of the author, unless otherwise noted. Any statements or claims about the possible health benefits conferred by any foods or supplements have not been evaluated by the Food & Drug Administration (FDA ) and are NOT intended to diagnose, treat, prevent or cure any disease or condition. We encourage you to do your own research and consult a qualified health professional before making any health-related changes.

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All rights reserved ©2016 Anna Paige