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Health & Nutrition
Dimitar Marinov
Senior Product Researcher MD, PhD, Assistant Professor

The Essentials of Gut Health

The human digestive system, hosting hundreds of bacteria strains, contributes significantly to overall health. An imbalance in gut bacteria can lead to health problems including irritable bowel syndrome (IBS) and autoimmune conditions. Improving gut health involves mindful eating, quality sleep, reducing stress, and dietary adjustments like reducing FODMAPs. Consuming gut-healthy foods and probiotics can support a balanced gut microflora.


Some of us never think about our digestive system, and how it affects our overall health in ways we cannot imagine.

Scientists know that they are home to anywhere between 300-1000 different strains of bacteria, most of which are vital for human health and form the so-called gut microbiome.

The lower gastrointestinal system even has a separate nervous system, produces 90% of your serotonin levels, and houses 70% of your immune system cells.

These findings have uncovered links between poor gut health and chronic disease.

Having a healthy gut is imperative to feeling happy and healthy. If you are looking for a way to improve your digestive health, keep reading to discover the most effective methods for reducing indigestion and restoring the balance of your gut bacteria.



What is the gut microbiome?

The gut microbiome is made up of a host of intestinal microbiota that includes healthy gut bacteria, harmful bacteria, and digestive enzymes, among other gut flora. They can be found mainly in the terminal parts of your small intestine and your colon.

The bacteria are the most well-studied part of the human gut microbiota. In any given individual, the number of bacterial strains can vary between 300 and 1000, but the average is about 500. The total number of gut bacteria can reach 100 trillion (1).

The exact composition of your gut microbiome depends on several factors, including genetics and lifestyle. According to research, environmental factors such as lifestyle and diet play a more significant role in shaping the human microbiome (2).

The gut bacteria are essential for the function of a healthy digestive system, and they act similarly to an organ that’s responsible for various metabolic processes.

These functions include biotransformation of bile acids, fermentation of non-digestible carbohydrates, and synthesizing amino acids, short-chain fatty acids, vitamin B12, vitamin K, and others.

The microbiota also interacts with many other organs and systems, especially your central nervous system. They are connected in the so-called microbiota-gut-brain axis.

For example, the molecules produced by gut bacteria can affect your autonomic nervous system (3). The system regulates your involuntary responses such as fight-or-flight and rest-and-digest.

Studies also report that the gut microbiome can even affect the functions of your brain, such as memory and learning processes (4, 5). 

Furthermore, the gut bacteria that generally inhabit your digestive system regulate serotonin’s production and release, which is an essential neurotransmitter for the brain (6, 7). 

If the balance between the different gut bacteria in your intestines is disturbed, it leads to dysbiosis. Dysbiosis may occur due to various infections, dietary changes, antibiotics, alcohol, etc. 

The condition may increase your risk for numerous gut health problems, ranging from gastrointestinal disturbances to gut inflammation.


Common gut health issues

Your digestive system can be split into the upper and lower gastrointestinal tracts. The lower gastrointestinal tract includes your small and large intestines. 

The most common lower gastrointestinal symptoms which could indicate an unhealthy gut are bloating, pain, diarrhea, and constipation. They can be accompanied by upper gastrointestinal symptoms such as nausea and reflux.

Experiencing these once in a blue moon shouldn't be a cause for concern, but if your complaints are persistent, it might be a sign of a medical problem. 

The ones that primarily affect your intestines include irritable bowel syndrome (IBS), food hypersensitivity, and autoimmune conditions such as inflammatory bowel diseases (IBD).

IBS is surprisingly common, and according to The American Journal of Gastroenterology, it affects about 7% to 10% of the population worldwide (8, 9). It is a chronic recurring condition characterized mainly by pain or discomfort in the abdominal region and changes in bowel habits for at least three months. 

IBS is a functional disorder which means that there aren't pathological changes in the gastrointestinal that explain the symptoms. The cause is unknown, but scientists suspect a problem in the interaction between the gut and the central nervous system, aka the microbiota-gut-brain axis.

Autoimmune conditions affecting the gut are also quite common, including inflammatory bowel disease (IBD) and celiac disease. 

Autoimmunity means that the immune system attacks its normal structures. In the case of celiac disease, the autoimmune reaction is triggered by gluten consumption, while the causes of IBD flare-ups are still unknown.

In addition, many patients suffer from food hypersensitivity, including cases of allergy or intolerance. Common food allergies include tree nuts, peanuts, milk, eggs, shellfish, fish, wheat, and soy.

As seen in lactose intolerance, food intolerance may occur due to a lack of certain digestive enzymes.


The role of the microbiome and intestinal permeability in an unhealthy gut

Conditions such as IBS, autoimmunity, and hypersensitivity have been linked to gut microbiota and intestinal permeability changes.

For example, the immune system's reaction in celiac disease leads to an increase in intestinal permeability, which weakens the intestine's barrier function.

Increased permeability further contributes to the inflammation and possibly the extraintestinal symptoms (10). In such cases restricting gluten alleviates inflammation and restores normal intestinal permeability.

Increased intestinal permeability is often called "leaky gut," although the medical community does not recognize the latter term.

Allergies, IBS, and autoimmune conditions have also been linked to specific changes in the gut microbiome and the prevalence of particular bacteria strains (11, 12).

Studies report that dysbiosis in IBS patients is around 73%. It is about 16% amongst healthy people (13, 14, 15). It is not clear if these changes in the microbiota are the causes or consequences of these diseases.


Simple ways of improving gut health

If you have any persisting complaints, consult with your doctor and ensure that they are not due to a specific medical condition.

In some cases, an unhealthy gut can be attributed to a poor diet, especially when consuming large amounts of processed food and not enough healthy food choices.

Practice mindful eating

Healthy digestion begins in the mouth. Therefore, eating too fast is a common cause of overeating and indigestion.

Instead, it would help if you tried to be more mindful about the whole process of having a meal and focus on chewing the food well.

Avoiding distractions while eating, such as eating in front of your phone, computer, and TV, can significantly improve your mindfulness and eating habits.

Avoid overeating

Overeating is a common cause of indigestion in otherwise healthy individuals. Too much protein, carbs, or fats at once can overload the digestive system and slow digestion. 

Overeating with one or several macronutrients leads to unpleasant symptoms such as bloating, nausea, flatulence, and even pain. 

Make sure to split your macronutrients evenly across your meals. Do not eat all your protein, fats, or carbohydrates for the day in one meal. Besides, eating regularly can also significantly improve your digestion and gut health.

Enough sleep

Scientists have found that sleep quality and duration are also related to your gut health. Individuals who sleep better tend to have increased diversity in their gut microflora, improved levels of healthy bacteria, and thus a healthier microbiome (16).

You can improve your sleep cycle by going to bed at the same hour every night, avoiding blue light exposure before bed, avoiding meals 2-3 hours before bed, improving your sleep environment, and taking melatonin supplements.

Lower stress

Since your microbiota, gut, and brain are all interconnected in the gut-brain axis, it is no wonder that stress can harm your digestive system. 

Nerves, such as the vagus nerve, directly link your gut to your brain and change their tonus when your body gets into fight or flight mode (17). 

During stress, your brain also releases increased amounts of corticotropin-releasing hormone. It leads to different motility changes and possible alterations affecting the gut microbiota and function(18).  

Some of the most effective methods to alleviate stress include meditation, walking, getting a massage, spending time with friends or family, decreasing the intake of stimulants, and even owning a pet. Healthy living, in general, can improve the way your digestive system functions.

Reduce FODMAPs

People with irritable bowel syndrome (IBS) may benefit from certain elimination diets, such as the low-FODMAPs diet. Some gastroenterological guidelines recommend the diet as a second-line treatment (19).

FODMAPs stands for fermentable oligosaccharides, disaccharides and monosaccharides, and polyols. These are non-digestible nutrients that get fermented by your gut microflora and sometimes act as a prebiotic.

However, the fermentation process involves the production of gas. Individuals with IBS are sensitive to colon distention by gas, so increased gas production in the colon may trigger their symptoms.

Always consult with your doctor or a trained dietitian before attempting the low-FODMAPs diet.


Which are the gut healthy foods

Your food choices can significantly impact your gut microbiome. Scientists report that changes in your diet can lead to dramatic shifts in the microbial strains in your gut within just 24 hours (20).

Therefore, it is crucial to consume a healthy and well-balanced diet, which will also help maintain the balance of your gut microflora. In addition, some foods contain prebiotics, which are various compounds used by gut bacteria for energy. 

Thus, they help your healthy gut microflora grow and develop. Prebiotics are non-digestible carbohydrates such as fiber and resistant starch (21). 

Dietary sources include fresh fruits and vegetables, whole grains (oats and barley), beans, peas, and lentils. Men should aim for at least 38 grams of fiber per day, while the minimum for women is 25 grams (22).

Some scientists recommend adding antioxidants, such as polyphenols, prebiotics, and probiotics (23). They are known to improve heart health and brain function and lower blood sugar levels.

Some of the benefits of these antioxidants may even be mediated via their favorable effects on the gut microbiome. Foods rich in polyphenols are fresh fruits, seeds, vegetables, tea, and cocoa products.

The gut bacteria that normally colonize your digestive system can also be found in some foods and supplements called probiotics. 

Consuming such products is thought to help colonize your intestines with good bacteria and restore the balance between various strains.

Probiotic supplements are widely recommended for various gut health problems, especially for dysbiosis after treatment with antibiotics. According to research, probiotic foods are equally effective in colonizing the human gut after consumption (24).

Examples of probiotic fermented foods include yogurt, kefir, kombucha, sauerkraut, pickles, miso, tempeh, kimchi, sourdough bread, and some cheeses. However, if the product has been pasteurized or canned, it will not contain live bacteria.


Should you perform a colon cleanse, and how?

Your colon functions as the terminal part of your digestive system, which reabsorbs water, houses a large amount of your gut microbiome, and stores the remaining waste products from digested food fermented by the bacteria.

In some cases, people may seek to perform a colon cleansing, which can help clear out the stored waste in your large intestine. 

Yet, there are different ways to perform such a cleanse, and you should consider the advantages and disadvantages of each before making your choice.

Cleansing can be performed naturally (via drinks and supplements) or colonic irrigation (enema).

Performing colon irrigation may even be necessary in cases of severe constipation or before a medical procedure. However, regular colonic irrigation, or in chronically ill patients, is associated with severe risks and can lead to dehydration, electrolyte imbalance, and even bowel perforation. 

It may also cause dysbiosis since the irrigation can remove a large percentage of the beneficial gut bacteria found in the colon and disrupt the balance of healthy and bad bacteria. Therefore, the procedure may even harm your gut health if performed too often.

Instead, it may be better to opt for a natural cleanse, which can help you relieve constipation and improve your gut health gently without many of the risks listed above.

It usually involves drinking plenty of fluids and taking certain foods or supplements that help increase bowel movements.

The supplements usually contain laxative herbs such as senna, psyllium, and aloe vera.

When choosing a supplement for a colon cleanse, make sure that it also contains probiotics, which can help support your gut microbiome. 

Note: This article is for informational purposes only and not intended for use as medical advice. Always consult your healthcare provider before starting any dietary supplement.

Dimitar Marinov
Senior Product Researcher MD, PhD, Assistant Professor
Dr. Marinov is a licenced physician and scientist with years of experience in clinical and preventive medicine, medical research, nutrition and dietetics. His research is focused primarily on nutrition and physical activity as preventive measures to improve and preserve human health. He is passionate about creating evidence-based content about various medical topics and takes great care in referencing every statement with high-quality evidence.
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