Microbiome and gut health

ANTIBIOTIC – antibiotics, or antibacterials, are a type of antimicrobial used to target bacteria, and are often used in medical treatment of bacterial infections. They can either kill or inhibit the growth of bacteria.

DYSBIOSIS – also called dysbacteriosis, this refers to microbial imbalance on or inside the body. Dysbiosis is most commonly reported as a condition in the digestive tract.

FERMENTATION – a chemical process that converts sugar and carbohydrates into acids, gases, and/or alcohol. It occurs in yeast and bacteria, but also in oxygen-starved muscle cells, as in the case of lactic acid fermentation. Humans use fermentation to produce food and beverages.

PROBIOTIC – live microorganisms that, when administered in adequate amounts, confer a health benefit on the host. The term derives from the Latin preposition pro (“for”) and the Greek adjective βιωτικός (biotic), the latter deriving from the noun βίος (bios, “life”).

PREBIOTIC – generally refers to compounds (food ingredients) that induce the growth and/or activity of commensal microorganisms (eg bacteria and fungi) that contribute to the wellbeing of their host. A prebiotic is a selectively fermented ingredient that results in specific changes in the composition and/or activity of the gastrointestinal microbiota, thus conferring benefit(s) upon the host’s health.

SYMBIOSIS – interaction between two or more different biological species.

MICROBE – an organism that is microscopic.

MICROORGANISM – a microscopic living organism, single- or multiple-celled. Microorganisms include bacteria, archaea, protozoa and some fungi and algae. Viruses are also sometimes classified as microorganisms.

MICROBIOTA – sometimes called microflora; a community of symbiotic, commensal and pathogenic microorganisms inhabiting either the surface of the body or its different cavities: the skin, mouth, ears, vagina and gastrointestinal tract, among others.

GUT MICROBIOTA – microorganisms residing in the gastrointestinal tract (GI tract).

MICROBIOME – the collective genomes of the microorganisms that reside in an environmental niche, such as a gut microbiome referring to microbial genomes found in the gut.

GASTROINTESTINAL TRACT/DIGESTIVE SYSTEMan organ system responsible for consuming and digesting foodstuffs, absorbing nutrients, and expelling waste.

Microbiome and gut health
Healthy gut tips

Few words healthy gut tips

Tip #1 What to look for when choosing a probiotic supplement:

  • Choose a reputable brand
  • Select products specifying probiotics by genus, species and strain, such as Lactobacillus acidophilus DDS- Look for strains that occur naturally in human gut microbiota, and that have been clinically tested
  • CFU (Colony Forming Units). The number of live microorganisms in each serving or dose through the expiration date should be mentioned
  • Recommended dosage should be indicated
  • Choose age/condition-appropriate products
  • Ignore meaningless claims about health benefits. If they sound too good to be true, choose another brand
  • Proper storage conditions. Some probiotic products should be refrigerated and others stored at room temperature
  • Corporate contact information should be provided
  • the expiration date and the batch number should be mentioned on product packaging
  • select products with fewer or no additives

Tip #2 Probiotics during and after antibiotics:

  • Follow the recommendations of your health care professional
  • Follow manufacturers’ recommendations for dosage and frequency if taking probiotic supplements
  • Generally, take probiotic food/supplements 1-3 hours after taking antibiotics, and continue for at least 2-4 weeks after the antibiotic course
  • It is important to consume prebiotic food as it stimulates the growth of beneficial bacteria
  • Consume nourishing foods that will boost your immune system and help to balance your gut microbes
Patients taking antibiotics may suffer from digestive upset and are at risk of antibiotic-associated diarrhea, thrush, and Clostridium difficile infection.

Tip #3 How to increase the microbial gut diversity:

Why should you increase the microbial gut diversity? Microorganisms residing in our gut contribute to our wellbeing and to the way our body functions. Researchers study extensively their role in health and in disease. The westernized lifestyle and diet reduce our microbial diversity, consequently contributing to many inflammatory non-communicable diseases. There is still a lot to be learnt but we currently know that the microbial gut diversity increases resilience, stimulates our immune system and strengthens the ability to fight off specific diseases.

The more microbial diversity the better our health foundation! Tips:
  • Go for a healthy, balanced and diverse diet, for example add to your cuisine washed raw vegetables and fruits, fermented vegetables, fermented dairy products, and foods rich in soluble fiber. Raw foods and fermented foods harbor environmental microbes, whereas fiber rich foods promote growth of beneficial bacteria
  • Avoid or reduce consumption of sugars (sugars serve as food for “bad” bacteria and stimulate the growth of yeast such as Candida albicans)
  • Breastfeed your infant if possible, components of breast milk nourish not only the infant but also friendly bacteria present in mother milk and in the infant’s gut. Microbes present in breast milk and in the gut contribute to the development of the infant’s immune system
  • Avoid unnecessary antibiotics and other medications (hormones) as their use have a negative effect on your microbial diversity
  • Avoid unnecessary medical interventions, such as plastic surgeries or C-sections out of convenience. If a C-section is medically necessary, consider swabbing the newborn with mother’s vaginal microorganisms
  • Reduce the use of hand sanitizers and wash your hands with water and soap
  • Get dirty, have contact with nature, farm animals and pets (contact with animals is microbiologically beneficial especially at the young age)
  • Consider taking probiotic supplements (see tips #1 on how to select a probiotic supplement)
  • Go back to the basics and think of foods, environments and activities our grandparents were brought up with! Simple, unprocessed foods and contact with nature!

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Microbiome and gut health
Probiotics and prebiotics


PROBIOTICS – live microorganisms that, when administered in adequate amounts, confer a health benefit on the host. The term probiotic was first used in 1954 and derives from the Latin preposition pro (“for”) and the Greek adjective βιωτικός (biotic), the latter deriving from the noun βίος (bios, “life”).

Probiotic organisms can be found in numerous products, such as foods or supplements. Different probiotic strains may confer different benefits on their host, thus not all probiotics are the same. Lactobacillus and Bifidobacterium species are commonly used bacterial probiotic strains, and Saccharomyces species is commonly used as yeast probiotics. In general, probiotic organisms act by i) interfering with growth of pathogens ii) contributing in the metabolic activities of their host iii) improving mucosal barrier function and mucosal immune system iv) having effect on the systemic immune system and function of other organs such as the brain.

Probiotics can support digestive health and/or immune function, for example by reducing antibiotic-associated diarrhea, by reducing digestive symptoms, strengthening the ability to fight off colds, promoting healthy vaginal and urinary tracts, and improving digestion of lactose. In addition, studies with infants show that probiotics can reduce the risk of eczema, symptoms of colic and necrotizing enterocolitis.

Fermented foods and undefined microbial populations such as fecal microbiota transplant are defined as not probiotic live cultures.

Probiotic foods and dietary supplements are considered to be safe for the generally healthy population. Individuals with compromised immune systems, pregnant women or infants should, however, consult a physician or the manufacturer prior use.


PREBIOTIC – a selectively fermented ingredient that allows specific changes, both in the composition and/or activity in the gastrointestinal microbiota (microorganisms), and confers benefits upon the host’s well-being and health.

Dietary prebiotics, typically non-digestible fiber compounds, act as food to stimulate the growth and/or activity of beneficial bacteria (such as Bifidobacteria or Lactobacillus). Natural dietary sources of prebiotic compounds include fiber rich foods such as vegetables, fruits, legumes, and unrefined grains (bran). As a functional component, prebiotics are often added to foods such as cereals, biscuits, breads, table spreads, drinks, and yoghurts. The most common prebiotic compounds include inulin, fructooligosaccharides (FOS) and galactooligosaccharides (GOS). It has been shown that certain prebiotics, consumed in adequate amounts, can improve digestion, prevent constipation, inhibit growth of pathogenic bacteria, improve insulin and lipid metabolism, and improve absorption of certain minerals such as calcium.





There are a lot of clinical studies being conducted these days to investigate the effect of probiotics in healthy individuals and in individuals with various conditions. Based on the current findings, I list below selected probiotic strains and their (potential) effect in humans.

Please note that not all probiotics are the same, different probiotic strains can have different effects on their host. The benefits of probiotics are strain specific.

Microbial species are classified and named by genus, species and strain, such as Lactobacillus acidophilus DDS-1. Lactobacillus refers to genus, acidophilus refers to species, and DDS-1 to strain. Lactobacillus Species

Lactobacillus species belong to the lactic acid bacteria group and they reside typically in the small intestine, the vagina, and the urinary tract. They produce an enzyme, lactase, which breaks down lactose and other carbohydrates to lactic acid. Lactic acid creates acidic environment and helps keeping pathogens in check, also it increases absorption of calcium, iron, copper, and magnesium.

Lactobacillus species Bifidobacterium Species

Bifidobacterium species in humans colonize the gastrointestinal tract, the vagina, and mouth. Bifidobacteria, similarly to Lactobacillus species, break down lactose and other carbohydrates to lactic acid. Bifidobacterium species produce vitamin K and B-complex vitamins and they facilitate absorption of minerals in the gut. Bifidobacteria improve the intestinal mucosal lining and can inhibit or reduce the colonization of pathogens.

Bifidobacterium species

Relevant reading:

Microbiome and gut health
how to supercharge imunity
Information provided below is meant for educational purposes only, and does not constitute medical or nutritional advice or act as a substitute for seeking such advice from a qualified health professional. 


You may have some questions now. Why do some of us get sick more often than the others? What makes some people more susceptible to get sick? Is it possible to, by supporting your immune system, become almost resistant to colds, flu and other infections? And if you do catch something, can you bounce back to feeling well within 1-2 days? There are many factors that influence the condition of our immune system, some of them are genetically determined and some are determined by our environment, lifestyle, diet (the so-called epigenetics). So by and large, we can take actions to support our immunity. Lifestyle factors that compromise our immune system in adulthood include poor diet (resulting in a suboptimal nutritional status), chronic stress (physical and psychological), sleep disturbances, alcohol overuse, cigarette smoke, pollution, prolonged and excessive exercise. As I am writing this blog, we are facing a coronavirus COVID-19 pandemic. Catching a coronavirus may manifest from mild to severe symptoms (severe especially in elderly and those with health issues). What determines how you experience an infection is the virulence (pathogenicity) of a given virus, bacteria and the efficiency of your immune system. “Compromised immune function increases the risk of infection” The immune system evolved as a defense mechanism against infectious disease. The immune system is a collection of various cells and molecules present in our bloodstream, tissues and organs.  They defend our body against foreign bodies (antigens), such as bacteria, viruses and cancerous cells. There are many molecules involved in an immune response, such as lymphocytes, antibodies, dendritic cells, mast cells, macrophages, NK cells.  It’s important to realize that to support your immune system and to have long-term results, it’s not something you do overnight, it’s a process. The more you do to positively stimulate your immunity (like eating healthy foods and having restorative sleep) and the less you do to undermine it (like eating junk foods, excess sugar, or having poor sleep), the stronger your immune system will be. In addition to building immune resilience, you can also improve, and even reverse, many health issues. Below I have put together essential and powerful tips to make your immune system resilient. It’s all about having a good foundation. There is NO shortcut or a miracle pill and the reality is that the safest, most robust interventions include lifestyle interventions. It's worth the daily investments in your diet and lifestyle.


Get quality sleep. Sleep is one of the best immune superpowers. Sleep deficit promotes release of pro-inflammatory cytokines (more inflammation) and can lead to chronic, systemic low-grade inflammation. Studies show that sleep deprived people (common among parents of young children) are more prone to catch a flu virus, and when sick they have more symptoms and longer recovery than people who sleep well and enough. During sleep you make a hormone, a powerful anti-oxidant, melatonin. Preliminary findings indicate that melatonin could be helpful in the management of COVID-19 infections. Also, no surprise why we need more sleep when we are sick, it helps us to mobilize our immune defences. Tip: invest in a relaxing evening routine (taking Epsom salt bath, reading a book) to promote quality sleep, avoid alcohol and caffeine in the afternoon.  Nourish your body and feed your good gut microbes.  Healthy immune system components need good and regular nourishment. Scientists have long recognized that people who live in poverty and are malnourished are more vulnerable to infectious diseases. Healthy foods provide us with nutrients and help our beneficial gut microbes (microbiota) thrive, on the contrary junk foods and sugary foods deprive us from nutrients and result in compromised microbiota. Gut microbes teach our immune system to generate appropriate immune response and competes with pathogens for nutrients. Gut health is essential to immune health and how we respond to viruses and other pathogens. Therefore, the quality (not quantity) of foods you eat is essential. Research indicates that brightly colored vegetables and fruits boost immunity better than most supplements. Tip: have a diversity of healthy foods, strive for colors and quality. Eat high amounts of vegetables and fruits, have healthy fats and adequate protein. Avoid sugar, alcohol and processed foods. Minimize stress. Scientists are actively studying the relationship between stress and immune function and there is still a lot to learn as stress is perceptive and difficult to define. But what we know now is that short-term stress can actually boost your immunity and is adaptive, however chronic stress is maladaptive, it weakens our immune system and can result in Th2 dominance (Th2 cells are helper T cells producing various interleukins) resulting in an immunological shift, imbalance. When we’re stressed, the immune system’s ability to fight off antigens is reduced. That is why we are more susceptible to infections. For example, prolonged stress and elevated cortisol levels can suppress the effectiveness of the immune system (lowers lymphocytes). Luckily, humans have the capability to modify what they perceive as stressful and how they respond to it. It’s all in our hands, whether we manage stress or stress manages us. Tip: some successful stress management strategies include meditation, mindfulness, psychotherapy, physical activities, social connection, breathing, hobbies, humor, keeping a perspective in life. Do what works for you. Stay hydrated. Proper hydration helps us to feel better, to function better and it’s key to our overall health. Water is our building block, solvent, lubricant, medium for biochemical reactions, transport medium, thermo-regulator, and shock absorber. Water facilitates countless number of processes in our body so if we have too little of it, these processes will be impaired, impaired at the cellular level. If you are chronically dehydrated, at some point you may start experiencing certain symptoms like constipation, headaches, or dryness. Your optimal water intake is affected by physical activity, exercise, metabolism, diet, health status, humidity and ambient temperature. If you sport and sweat you obviously need to drink more water. Tip: the average recommendation for adult females is about 2,5 liter daily, for adult males about 3-3,5 liter daily. Exercise moderately. Regular physical activity of moderate intensity is one of the pillars of healthy living. It improves cardiovascular health, helps control body weight, and protects against a variety of diseases. Just like a healthy diet, exercise can contribute to general good health and therefore to a healthy immune system. Exercise, by promoting good circulation, can allow the cells and immune system molecules to move through the body freely and do their job efficiently, and therefore be helpful in reducing inflammation, maintaining the proper immune response, enhancing immunosurveillance, and reducing psychological stress. Be positive. Your mindset influences not only how you perceive the world but also how you feel and how your immune system is working. Positive thinking creates positive results and more optimistic individuals are less likely to suffer from chronic diseases and stress burden. Also, being surrounded by loving and positive people helps us to stay positive. Tip: by telling yourself “I am strong”, “I am healthy”, “I am resilient”, “I have a supercharged immune system” you are telling yourself how you should feel. It literally can make you feel better. And it’s not about curing a disease by positive thinking but about creating health promoting thoughts in contrast to disease promoting thought (“I am weak”, “I am sick”). You can “program” yourself to a certain degree. Your mind believes what you are saying, whether it’s good or bad. So let’s keep it positive.


Micronutrient (vitamins, minerals) deficiencies can impair immune function. Therefore, malnourished individuals are more prone to infections and may have a more challenging time to recover. Micronutrients with most vital immune support include vitamins C and D and zinc. Also, vitamin A, B12, B6, E, folate, selenium, iron, and copper are essential to ensure the proper integrity of immune barriers and proper function of immune cells. These micronutrients are involved at every stage, via various mechanisms, of the immune response. Noteworthy, foods contain many nutrients we can never get in supplements, yet foods alone will not always meet all of our needs for micronutrients. Thus, sometimes micronutrient supplementation is beneficial to support immune function and/or reduce the risk of infection. A word of caution about supplementation, more supplements or higher dosages do not necessairly create better results, on the contrary - over dosing can even create unwanted results! It is about having enough of what our body needs. Micronutrients can challenge your immune system when you have too little and too much. They are also not helpful if they are in the wrong chemical form or in poor proportions. For example, there is a tendency to take very high amounts of vitamin D3 without any assessment of a baseline vitamin D levels. I discourage taking mega doses of any individual vitamin or mineral, unless recommended by a health care professional.  You may consider taking daily:
  • A high-quality Multi-Vitamin & Mineral Supplement
  • A high-quality omega-3 supplement (DHA, EPA), especially for individuals with a low intake of fatty fish
In a period of an increased infection risk and/or lower immunity:
  • Zinc - 15-45 mg daily (zinc glycinate, zinc methionine, zinc gluconate, zinc citrate or zinc sulfate), best divided in 3-4 doses taken through the day. If you supplement with zinc daily for a longer period of time, take copper supplement as well. Aim to get 1-3 milligrams of copper per day. Aim for 15-to-1 zinc to copper ratio to provide 1 milligram of copper per 15 mg of zinc.
  • Vitamin D: 1,000 – 5,000 IU daily (in case of a deficiency the dosage might be adjusted). Of note, sunshine is where most of our vitamin D comes from. Resonable sun exposure can elevate your vitamin D levels without a need of supplementation. 
  • Vitamin A: 3,000 - 10,000 IU daily (in case of a deficiency the dosage might be adjusted)
  • Vitamin C (with bioflavonoids): 500 - 3,000 mg daily
  • Elderberry extract: 500 - 2,000 mg daily
  • Echinacea extract: 500 - 2,000 mg daily
I do not recommend supplementation with high doses of individual vitamins and minerals for a longer period of time.  Other immunomodulating compounds: Astragalus, medicianal mushrooms (like Reishi, Turkey Tail), antioxidants (like glutathione, resveratrol, flavonoids, vitamin E, selenium, melatonin, quercetin)


In addition to what’s mentioned above, there are few measures specific for the COVID-19 situation, such as: #1 Avoid exposure. The key is prevention. One of the best strategies is to isolate to prevent contracting a virus. People can be contagious days before they have any symptoms at all. If you have any possible options for staying away from all others, please do so. Avoid touching your eyes, nose, and mouth. #2 Realize it’s temporal. There is panic and stress around coronavirus situation, but it’s important to realize that it will pass. You need to use your mind to stay calm and remind yourself that it’s a temporal situation. #3 Wash your hands well and regularly, disinfect and clean surfaces. #4 Cover your mouth when coughing. #3 Include following herbs, extracts and foods in your diet for protection: oregano, turmeric, ginger, citrus peel, tickberry leaves, orange peel, garlic (stabilized allicin), onion, green tea, wild berries, pomegranates, seaweeds, mushrooms, cat's claw tea, lemon balm tea, elderberry, and grapefruit seed extract. #5 Sore throats: Try salt water gargles, sage tea gargles, hot teas and lozenges containing slippery elm, lozenges with zinc for fighting infection and soothing irritated sore throats. #6 Respiratory congestion & congested sinuses. Nasal irrigation using a neti pot (with saline solution) can be very helpful, as well as nasal sprays (with saline solution, xylitol) and sinus drainage massage. Saline solution (water + salt) is easy to make or can be purchased. You can also use a humidifier, vaporizers, or steam inhalers, or spend time in steamy baths or showers. Vaporizers and inhalers can also be used with decongestants or essential oils such as eucalyptus, menthol, peppermint, or frankincense. #4 Be careful with anti-inflammatory medications like Ibuprofen and Aspirin. It's unclear at the moment but there was a suspicion that they may raise the risk of COVID-19 complications. #6 Be careful with high doses of vitamin D3 and vitamin A. Vitamins A and D are very important to ensure a proper function of our immune system. However, there is a hypothesis that over-supplementing with these vitamins may potentially make us more vulnerable to COVID-19 infection. Why? Because the coronavirus uses the receptor ACE2 (angiotensin-converting enzyme 2), mainly in the respiratory tract, to get inside our cells. And these two vitamins are helping us to make ACE2 and therefore it’s thought that possibly the more ACE2, the higher risk of virus invasion. We are still learning about the impact and the best management of COVID-19, therefore the recommendations can change overtime as new research emerges. Last but not least, if you are feeling unwell, watch out for the typical symptoms associated with the COVID-19 infection. Most of those who contract COVID-19 will have less or more severe symptoms. While having no symptoms is possible, if you have COVID-19 you are likely to experience: fever, cough, impaired breathing, fatigue and a small population of patients may have gastrointestinal complaints like diarrhea. References: https://www.ncbi.nlm.nih.gov/pubmed/31747581 https://www.ncbi.nlm.nih.gov/pubmed/31216461 https://www.ncbi.nlm.nih.gov/pubmed/30920354 https://www.ncbi.nlm.nih.gov/pubmed/30920354 https://www.ncbi.nlm.nih.gov/pubmed/25061767 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5911985/ https://www.ncbi.nlm.nih.gov/pubmed/26477922 https://www.ncbi.nlm.nih.gov/pubmed/23688939 https://www.ncbi.nlm.nih.gov/pubmed/19172691 https://www.ncbi.nlm.nih.gov/pubmed/31963293 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7019735/ https://www.ncbi.nlm.nih.gov/pubmed/30336639 https://www.ncbi.nlm.nih.gov/pubmed/32169119
Microbiome and gut health
unhappy gut tips
If want to feel better and don’t know where to start, begin by healing your gut as the saying goes “When in doubt, begin in the gut”. Healing tips for an unhappy gut   When your gut is out of balance and digestive system is weak, it is often the best to go back to basics by eating simple and restorative foods to accelerate healing. Below I provide some basic tips to consider when dealing with an unhappy gut:
  • Have (warm) cooked/steamed/baked foods, they are easier to digest than raw and cold foods
  • Eat frequently and in small amounts, it’s easier on your digestion than big portions at once
  • Have proteins as they are needed to heal, include bone broths, vegetable broths, mushroom broths, soups and stews, well-cooked pastured meats, bone marrow, organic eggs, optionally high quality dairy (sheep, goat, coconut) and protein powder (green pea, hemp, whey)
  • Have healthy fats to nourish and soothe your immune system, consider coconut oil, butter, ghee, olive oil, hemp seed, avocados, flax seed, coconut milk and coconut water. If you tolerate nuts and seeds you may eat them in small amounts, preferably soaked at first
  • Have various (cooked) vegetables – at least half of what’s on your plate ought to be vegetables. Cabbage-family foods are high in glutamine, a healing nutrient that helps repair the gut
  • Have preferably non-gluten containing grains such as quinoa, amaranth, buckwheat, millet and rice. Soaked in water for few hours before cooking, it makes them easier to digest
  • Have gentle fruits, such as ripe or cooked fruits
  • Have enough liquids such as water, water with lemon, water with raw apple cider vinegar, mint tea, fennel tea, ginger tea, green tea, rooibos tea, broths (bone broths are rich in glutamine), or some fresh vegetable juice (carrot, ginger, beet, kale, parsley, cabbage or sauerkraut)
  • Have herbs and spices such as salt, peper, basil, oregano, dill, fennel, cumin, coriander, cinnamon, nutmeg. Try to avoid hot spices such as cayenne and chili
  • Supplementation with licorice (in a form of deglycyrrhizinated licorice DGL), glutamine, or quercetin can quench inflammation and help gut healing
  • Get unstressed – stress is a very common contributor to digestive complains
  • If you feel like you overreact to almost all foods, go low on lectins. Check the shopping list of Dr. Gundry for foods low/high in lectins. Lectins can aggravate inflammation
If above strategies do not help or you think you need a more targeted approach, seek some professional help. Common causes of digestive issues:
  • Chronic stress
  • Poor diet and low dietary fiber intake
  • Infections
  • Low stomach hydrochloric acid
  • Medications, prescribed and over the counter
  • Alcohol, drugs and cigarette smoking
  • Genetics
  • Lack of exercise
  • Environmental toxins, irritants, heavy metals
“P-foods” for good gut health Your gut likes real foods but here I want to focus specifically on three gut healthful P’s: prebiotics, probiotics and polyphenols. 3 x P rich foods for heathy gut and for healthy you: #1 Prebiotic rich foods = serve as food (dietary fiber) for beneficial microbes. Prebiotics are non-living, non-digestible by human ingredients (carbohydrates) that feed trillions of microbial mouths in your gut and helping them to bloom. They are microbiome superfoods that naturally occur in plant foods (vegetables, fruits, grains) such as chicory root, Jerusalem artichoke, onion, leek, garlic, raw oats, banana, broccoli, carrots, or fruit skin. Dietary fiber aids digestion, bowel movement and assists the removal of toxins from the body. #2 Probiotic rich foods = contain beneficial microbes such as bacteria or yeast. They are present in certain foods containing live cultures such as yoghurt, kefir, aged cheese, kombucha, kimichi, sauerkraut, and miso. Probiotic rich foods may support digestion and immunity. #3 Polyphenol rich foods = polyphenols are plants’ powerful nutrients that to become active undergo diverse intestinal transformations thanks to the action of human digestive enzymes and microbial metabolism. They include flavonoids, tannins, chlorogenic acids, anthocyanidins. They have antiviral, antibacterial, and anti-parasitic properties. Vegetables, fruits, herbs are rich in polyphenols: onion, apples, grapefruit, plums, broccoli, citrus fruits, tomatoes, green thee, cocoa, banana, berries, chickpeas, beans, soy, parsley, thyme, celery, walnuts, grapes, flaxseed, apricots, coffee seeds, and peaches. If you want to know more how to create a healthy plate for you, for your gut and your gut microbes, check my blog on “How to create your healthy plate”. Keep in mind that everyone is different and some foods that are great for one person will not necessarily be healthful for the other person.
Microbiome and gut health
gut essentials
Healthy Diet promotes Healthy Gut - Healthy Gut promotes Heathy You! The wisdom of Hippocrates (460-370 BC) with regards to the importance of gut health finds its place today. Hippocrates has stated ages ago that “All Diseases Begin in the Gut”. Recent scientific and clinical findings support his statement. If you want to invest in your wellbeing one of the elements you want to give a special attention to is your gut heath. I am here to take the gut health under the loop and to have a gut talk. Why is healthy digestion essential for optimal health?  Healthy gut is one of the prerequisites of staying healthy. Digestive health promotes overall health as digestive system communicates with your immune system, it runs your metabolism, it chops up the food to usable nutrients, and communicates with other cells in your body. By nourishing your gut you nourish every cell of our body. In a perfect world, the foods you eat are properly digested, their digestion products are absorbed, assimilated and used as a fuel, building blocks and materials for various biochemical reactions within our body. Digestive system brings nutrients to your body. When these nutrients are deficient or do not get where they are needed, you feel tired, have concentration problems and over time you develop more symptoms. Conditions not obviously associated with gut such as skin conditions (eczema, psoriasis, acne) are actually often linked to dysfunctional gut. The take-home-message: thrive to have a properly functioning digestive system. Two brains in one body Our digestive system is often called the “second brain”, it’s connected with our brain via the vagus nerve forming the enteric nervous system (ENS) and the communication system – the so called gut-brain axis. Importantly, most of your neurotransmitters such as serotonin and dopamine is manufactured in the gut and not in the brain. If these neurotransmitters are out of balance you may experience mood swings or mood disorder. Another factor that makes your gut so vital is that about 70-75% of your immune cells reside in the gut. So the first thing to do if you want to boost your immunity, you need to take care of your gut. Think of a link between your gut– brain– immune system. The forgotten organ: gut microbiota You may have not realized that about 500-1000 microbial species (bacteria, yeast, protozoa, and viruses) live in your gut, weighting up to 1,5-2 kg. This gastrointestinal community of microorganisms is called gut microbiota (microflora). It comprises of commensal (coexisting, acquired during and after birth, from breastmilk and from environment) and transitional (just passing through, contracted through food and drinks) microorganisms. They can be beneficial, opportunistic (potentially harmful) or pathogenic (harmful). Your body has much more microbial cells than your own human cells. Your gut microbiome (genomes of the gut microbiome) contains about 150 times more genes than your human genome. Our gut microbes coevolved with us, playing an essential role in various processes within our body, such as food digestion, immunity or neuro-psychological functions. The condition of our gut ecosystem has a significant effect on our health. Beneficial microbes help to keep “bad” microbes in balance as a results to keep a balance between inflammation and healing. For example, an imbalance (dysbiosis) of microorganisms (either in number or type) inhabiting your gut can affect digestion and even contribute to the pathogenesis of some diseases including asthma, eczema, obesity, or rheumatoid arthritis. The take-home message: thrive to have a balanced gut microbiota. Quality matters more than quantity Imagine building or repairing your house using poor quality materials, will it last long and in good condition? Probably not because of poor foundation, the same counts for your health. The same counts for your body, the quality of materials (foods and drinks) you consume every day is very important. Your body recognizes real foods and gets confused with highly processed foods. Too much and too frequent consumption of processed foods will cause the “fire” (inflammation, dysbiosis and more) in the gut and as a result it may affect other parts of your body - including brain. Food is your best medicine so thrive to consume real foods and avoid processed foods.  Real foods contain information (proteins, fats, carbohydrates, vitamins, minerals and phytonutrients, water) that our bodies utilize to run and optimize countless number of processes. A handful of candies can’t be compared with a handful of wild blackberries, the first one has no nutritional value and undermines our health whereas the second one is laden with nutrients and promotes our health. Highly processed foods disrupt our biology, the flow of information and are devastating to our health. Remember that foods best for you come as mother nature designed them: naked and not packed, not labeled and not processed. For drinking, water should be your number one drink. If you are craving sweets, please read my blog on “combating your sweet tooth”. Also, if you want to learn more about sneaky sugars in our wester diet, have a look at the piece I wrote on “sugar essentials” for SugarSkills, which is a sugar awareness initiative. The take-home message: nourish your body by eating real foods. Healthy gut: good digestion + balanced microbiota + intake of real foods + stress management If want to feel better and don’t know where to start, begin by healing your gut as the saying goes “When in doubt, begin in the gut”.  If your gut is unhappy, try tips provided here.
Microbiome and gut health
Know your poop, it can tell you a lot
It’s time for a poop talk. I always ask my clients about their bowel movement. I realize it’s not the most comfortable question but poop can be an important marker of health or disease. It can tell you a lot. Is it soft, hard, smelly, yellowish, back, fatty, with mucus, with blood or with undigested foods? Next time you poop, pay attention to what comes out! We can observe our body, our body fluids (blood) and our body secretions (urine, feces, saliva) for signs of dysfunction. Some parameters can only be measured by a laboratory but you can also be your own detective and learn how to distinguish a healthy bowel movement from an unhealthy one. What you need to look at in terms of poop? Color, consistency and smell are the key parameters. Normal, healthy poop is brown (from light brow to dark brown), well-formed (sausage like) and has no repelling smell. What’s your poop color like? Healthy human feces is brown. The color can change after eating some foods (red beets, spinach), after taking certain medications (iron for example) or it can also be an indication of a health issue. - Black or a very dark color can be related to the use of certain medications, supplements (iron, activated charcoal), foods (black barriers, red wine). It can also indicate a blood loss from stomach or (small) intestine, or can be a sign of inflammation, ulcer, polyps, or cancer. Constipation may promote darker stools. A black stool with a very strong abdominal pain can indicate an internal bleeding. - Red, eating red beets can color your stool red. - Green, if you eat a lot of green vegetables your poop can turn green. - Grey – light color, can indicate that there is no bilirubin (color compound) present in a bile or/and too high fat intake. It can be caused by impaired bile production/storage, intestinal infection, reactivity to foods, pancreas problems, low gastric acid, resulting in impaired digestion. Noteworthy, if you suddenly change your diet by for example following a low carb diet and will be eating more fat, your stool may have lighter color especially in the beginning. It’s related to the fact that if you eat more fat - your body needs more bile and sometimes it needs some time to adjust and to produce more bile. - Bloody, most of the time caused by rectal/anal bleeding such as hemorrhoids. - Yellow, often occurs together with a soft stool/diarrhea and intense smell. It can be related to a quick intestinal passage, lack of bile. Bile contains bilirubin which turns your feces brown. Possible causes of yellow stool include gluten intolerance, infection (Salmonella/Clostridium), use of medicines, alcohol consumption, liver and/or bile dysfunction, bile stones. Quick intestinal passage can promote nutrient malabsorption. Babies may have yellow poops. What’s your poop smell like? Normal fecal matter can smell as a result of intestinal bacterial fermentation and the presence of dead intestinal microbes. However when the smell of your poop is very intense – it stinks – or it has other than a regular smell it should raise a red flag. It can be a sign of intestinal infection (parasites bacteria), impaired digestion (specially of proteins), intestinal inflammation, food allergy or food intolerance. Sour smell can indicate a low fecal pH, yeast overgrowth and/or overconsumption of starch. If you let stinky gases, of rotten eggs, then think of putrefaction and sulphur release. If your stool stinks and has a “pap-like” consistency – it may indicate a medical condition. What’s your poop consistency like? Normal feces has a sausage like shape and the consistency which is not too hard and not too soft – just right. If this description does not fit your poop, please read on. Note, that some people may experience changing stool consistency from too soft to too hard. *Chronically “Pap-like”, your poop is soft and not well formed. It can stick to the toilet and you need to use a lot of toilet paper to wipe yourself well. The pieces of the feces can float. The most common causes of a “pap-like” stool include parasitic infection (such as Dientoamoeba fragilis), intestinal dysbiosis for example after antibiotic use (candida overgrowth), food intolerance (histamine, lactose, gluten), low gastric acid, pancreatic issues, or medicine use. *Chronically too hard, a slow bowel movement with a sausage-like but lumpy stool, or separate hard lumps like nuts. For constipation the frequency can be once in 3 days or less. Often there is a feeling of pressure to go to the toilet yet you can’t poop. Hard feces and constipation is more prevalent in women and in overweight individuals. Constipation can be related to a slow intestinal passage which can be a result of holding the stool for too long, for example children and teachers at schools, car drivers may have this tendency. Overweight, intestinal parasites, food allergy, pregnancy, underactive thyroid, gluten intolerance, medicine (codeine, anti-depressives, anti-histamine) use, supplements (iron), genetic predisposition, intestinal physiology, sometimes dehydration and too little dietary fiber (fruits and vegetables) can contribute to constipation and hard stools. *Chronically too watery, diarrhea. Diarrhea is watery, unformed feces that you can’t keep in. You can have acute or chronic diarrhea. With acute diarrhea complaints should resolve by itself within few days. Chronic diarrhea takes more than 3 weeks. Chronic diarrhea can be accompanied with fecal mucus and blood. Chronic diarrhea can also alternate with the episodes of normally formed stools or constipation and hard stools. Chronic diarrhea increases the risk of dehydration and loss of electrolytes, therefore remember to drink adequate amount of water if you suffer from chronic diarrhea. Chronic diarrhea can be caused by a chronic bacterial infection or a post-infectious syndrome, parasites, food intolerance (gluten, histamine, lactose, fructose), food allergies, intestinal inflammation, auto-immune disease, pancreatic and bile problems, nickel or latex allergy, intestinal dysbiosis (after antibiotic), additives to foods, or cancer. Fatty poop? Normal feces contains fat, about 0-4 gram fat per 100 gram poop. If there is more fat or you can’t digest fat properly, your stool will be fatty, shiny and will stick to the toilet surface. Fatty stool can also stink more or has a lighter color. If your stool is fatty consider following issues: low gastric acid, impaired pancreatic function, bile or liver issues, celiac disease, alcoholism, bacterial or parasitic infection, intestinal inflammation (Crohn disease, Colitis ulcerosa), or over consumption of nuts. Fat malabsorption can cause malabsorption of fat soluble vitamins such as vitamin D, E, A or K. Mucus? Fecal mucus comes from intestinal mucosal membranes. Normal and well-formed feces contains no visible mucus. If you do see mucus around your stool or within it, it may indicate inflammation or irritation of the intestinal lining. Bloody mucus will indicate inflammation. With constipation and inflammatory bowel diseases there may be more mucus formation/secretion. If your feces is off and you can’t identify the reason, do a fecal analysis to begin with.
Microbiome and gut health
How gut bacteria can contribute to the extra weight

Linking the gut microbiota to obesity and diabetes

Have you ever envied skinny people who eat a lot of unhealthy foods yet remain slim-figured? People often say it’s because of genes or better metabolism, but that’s not the whole story! Whose metabolism are they talking about? The person’s metabolism or the metabolism of their gut microbes?

INTERESTED? First, let me explain that our intestinal microorganisms coevolved with us to support our physiology and our metabolism. Our body constantly communicates and cooperates with them. When our microbes, the so-called “internal garden,” are in a state of balance and when operate at peak efficiency, so do we and our metabolism. When things get out of balance and we suffer from microbial gut dysbiosis, it directly affects our health and our weight. To achieve and maintain a healthy weight it is essential to take care of our microbial selves. You may have, for example, difficulties in losing weight. Until you address your microbiome, you may be trapped in a vicious circle of dieting because you are missing an important player in a game — the gut microbiome. Let’s see how these microbes may contribute to weight control.

Gut microbes affect our energy harvest and storage

shutterstock_252994213Recent studies indicate that gut microbes contribute to our energy harvest, storage, and spending. This process is optimal when the amount of energy extracted from the diet equals the amount used, maintaining equilibrium. Over the course of evolution, animals have developed a smart strategy to protect energy reservoirs by forming fatty adipose tissue. However, once energy-dense foods erupted in western countries, we began to over-accumulate and over-stimulate this energy, which can result in obesity. It has been found that multiple factors, such as genetics, diet, sedentary lifestyle, or hormonal imbalance, may contribute to the development of and progression of obesity. In addition, recent scientific findings bring to light the role of the gut microbiota and its influence on fat storage, glucose blood levels, or hormonal expression. Obesity and type 2 diabetes are characterized, among other features, by low-grade inflammation and alterations in intestinal permeability, called leaky gut. Inflammation is considered a significant obesity component.

Some obesity facts to digest

World Health Organization (WHO) recognizes the problem of a global obesity epidemic. Though once associated with high-income countries, it is now found across low- and middle-income populations. It strikes young and old, wealthy and poor. Overweight children are at higher risk to become obese adults and develop diabetes.

According to WHO (from January 2015):

  • worldwide obesity has more than doubled since 1980
  • in 2014, more than 1.9 billion adults, 18 years and older, were overweight, of which over 600 million were obese
  • 39% of adults aged 18 years and over were overweight in 2014, and 13% were obese
  • Most of the world's population lives in countries where being overweight kills more people than being underweight
  • 42 million children under the age of 5 were overweight or obese in 2013
  • 1 in 3 children at the age of 11 is overweight or obese

As a consequence, there is a worldwide increase in the prevalence of obesity-associated diseases, such as insulin resistance, hypertension, type 2 diabetes, cardiovascular disease, end-stage renal disease, and non-alcoholic fatty liver disease. Diabetes mellitus (DM) affects about 347 million people worldwide.

An interplay between obesity and inflammation

Inflammation is a key component of obesity-associated diseases. Higher levels of certain inflammatory markers have been found in obese individuals. Some of the inflammatory markers include C-reactive protein, erythrocyte sedimentation rate, inflammatory cytokines, and plasminogen-activator inhibitor 1. However, connecting the dots between obesity, inflammation and the risk of disease remains to be unknown. Scientists are trying to put the obesity puzzle pieces together by studying the complex network of gut microbiota (microorganisms), the intestinal lining (mucosa), and the gut-associated lymphoid tissue. Below you will find the latest findings in this field of research.

Obesity and the intestinal microbiota

Our intestinal tract harbors between 500 — 1000 microbial species and this microbial population is commonly called the gut microbiota. There are three dominant bacterial phyla; Bacteroidetes ( eg. Bacteriodes spp), Firmicutes (eg, Bacillus and Clostridium spp), and Actinobacteria (eg. Bifidobacterium spp). These gut microbes are involved in energy metabolism and therefore are important to consider when talking about obesity. Very interesting results were found from animal studies, with germ-free mice having lower body mass and body fat in comparison to germ-inhabited, or “normal” mice. Moreover, transplantation of “normal” microbiota to germ-free mice led to normal bodyweight found in germ-inhabited mice. Even more interesting were the findings of the microbial transplant performed from obese mice to germ-free mice; for whom an increased fat mass was recorded. Further animal studies indicated that the bodyweight can be partly determined by the gut microbiota as well as by the diet.

shutterstock_117645061Human studies looking at the gut microorganisms of obese and lean individuals reveal that lean humans and animals have different microbial gut composition than the obese ones, with a lower microbial diversity in obese subjects. More specifically, some obese individuals, in comparison to lean individuals, were shown to have higher relative abundance of bacterial Firmicutes species with lower relative abundance of Bactoroidetes bacteria. Contrary to obese people, lean people tend to have higher diversity of microbial species in their gut and are often found to have more microbial life of Bacteroidetes bacteria, which utilize plant polysaccharides as a source of energy. Other studies, however, showed conflicting results or no significant difference in the microbial gut composition, but did show greater diversity in lean individuals. There is some controversy around the Firmicutes/Bacteroidetes ratio as an obesity or obesity-risk indicator. For example, my gut microbial fingerprint (sample analysis done by uBiome) showed relative high abundance of Firmicutes, characteristic for obese individuals, but I am a lean person. We know however, that the composition, such as low diversity, of the gut microbiota early in life may predict the subsequent development of obesity or being overweight. Interestingly, there is a bacterium called Akkermansia muciniphila that resides in mucus layer of human intestinal lining which tends to be less abundant in obese individuals. Several studies have indicated its potential in reducing inflammation and therefore possibly protecting against the development of obesity and type 2 diabetes.

Our food shapes the composition of our microbial gut companions

shutterstock_214341322There are studies looking at the effect of diet on the microbial gut fingerprint. For example, increased daily caloric intake (2400 kcal vs 3400 kcal with similar macronutrient intake ratios) resulted, after only 3 days, in greater abundance of Firmicutes and lower abundance of Bacteriodetes. Another study investigating the impact of high-fat diet recorded the gut microbiome changes as early as one day after a new diet initiation. Low- or high-carbohydrate, high-protein, plant- or animal-based, high- or low-fat — all different diets influence and modulate, in  a more or less favorable way, the gut microbiome.

The appetite regulation by a hunger stimulating hormone, ghrelin, has been shown to be influenced by presence or absence of Helicobacter pylori. Some studies indicated that H. pylori eradication was linked to increased ghrelin levels, which could perhaps explain increased appetite and weight gain following H. pylori eradication. Western populations have largely eradicated this bacterium from their lives — could this also contribute to obesity? And what about the effect of antibiotic use on weight gain in humans and livestock? It should not be underestimated when facing a global obesity epidemic.

Endotoxin – an important player in metabolic inflammation

Let's talk for a moment about the intestinal permeability (leaky gut) and short-chain fatty acids. Although their role in obesity specifically is not yet entirely clear, they certainly are of importance. For more information about the intestinal permeability, please check my article on a leaky gut. Noteworthy, when dealing with a leaky gut, gut-derived metabolic endotoxaemia may occur, which can increase the risks of obesity associated-diseases, such as cardiovascular disease or type 2 diabetes. Metabolic endotoxaemia, also called circulating endotoxin, takes place when increased concentrations of bacterial (Gram-negative) endotoxin, also called lipopolysaccharides (LPS), enter the blood as a result of impaired epithelial tight junctions with an increased intestinal permeability (leaky gut). LPS also circulates, at low concentrations, in the blood of healthy individuals. Chronic bacterial translocation, resulting in circulating LPS due to increased intestinal permeability, may trigger inflammation and an immune response, causing a persistent low-grade inflammation typically found in obese individuals. In animals and humans, consumption of high-fat foods was shown to result in increased levels of endotoxins (LPS) in the blood and an altered composition of the gut microbiota.

Picture1A few words about short-chain fatty acids (butyrate, acetate, and propionate): they are produced by bacterial fermentation of non-digestible dietary fiber, largely in our colon. They, mainly butyrate, support the intestinal lining integrity, serve as the energy source for colon epithelial cells, increase fluid and electrolyte uptake, promote blood flow and the secretion of gut hormones, stimulate mucin release, and exert profound immunometabolic effects. For example, butyrate-producing bacteria, Roseburia intestinalis and Faecalibacterium prausnitzii, are present at lower concentrations in individuals with type 2 diabetes than in healthy individuals.

What about the Fecal Microbial Transplantation (FMT)?

More and more fecal microbial transplants are performed, typically in individuals suffering from Clostridium difficile infection. A small-scale fecal microbial transplant study was conducted with lean male donor in insulin-resistant males with metabolic syndrome. As a result, there was a significant improvement in insulin sensitivity and increased intestinal microbial diversity, with more butyrate-producing bacterial strains, such as Roseburia. These results are promising, but we need more studies to have a better understanding of the ability to control the process and avoid possible unwanted effects of FMT.

Metabolic diseases are caused by multiple factors, such as high consumption of energy-rich foods, limited physical activity, age, or genetic factors. There is a growing array of interesting findings regarding the gut microbiota in obesity and obesity-related diseases. Yet, the controversy persists as to what degree gut microorganisms contribute to obesity. I think the complexity of the microbiota and its interaction with its host makes it very challenging to get clear answers. However, there is certainly an interplay between the gut microbiota, intestinal permeability, diet, and the immune system that shapes the development and progression of obesity and obesity-associated diseases, including type 2 diabetes. Manipulation of the intestinal microbes, by dietary changes, prebiotics, probiotics, or the more radical methods of fecal microbial transplant (FMT) or Roux-en-Y gastric bypass may serve as supportive avenues to obesity management.



“Obesity, Inflammation, and the Gut Microbiota.” Cox at el., Lancet Diabetes Endocrinal 2015; 3: 207-215.

“Impact of the Gut Microbiota on the Development of Obesity: Current Concepts.” DiBiase et al, Am J Gastroenterol Suppl 2012; 1:22-27.

“Microbiota and Diabetes: an Evolving Relationship.” Tilg H and Moschen A, Gut 2014; 63: 1513-1521.

“Insights into the Role of the Microbiome in Obesity and Type 2 Diabetes.” Hartstra et al, Diabetes Care 2015; 38: 159-165.

“10 Facts on Obesity.” World Health Organization, 2015 January.

Suggested readings:

“The Microbiome Diet.” Kellman R, 2014.

“The Good Gut.” Sonnenburg J & Sonnenburg E. 2015.

Microbiome and gut health
Is your gut leaky?

Lets face it: exposure to certain factors makes our gut leak!

Scientists all over the world are working hard to unravel the puzzles on the growing incidence of many diseases, particularly in Western countries. It will take time before we get all the pieces together, but what we already know is that many diseases are linked to poor diet, gut dysbiosis, pollution, and stress, to name a few. Our Western diet has changed over the last two to three decades, from simple and unprocessed foods to highly processed foods with high sugar content. Coincidently, as we eat more processed foods, there is also a growing number of diseases, including autoimmune diseases. So the primary question arises: What’s the link between a poor diet and how our Westernized diet make us sick? Multiple factors are often involved, such as genetics, environment, lifestyle, and diet. They determine why some people get sick while others do not. Diet is undoubtedly a very important factor in our well-being. As Hippocrates stated “Let food be thy medicine and medicine be thy food.” Diet choice may have a profound effect on our health. Actually, a poor diet is one of the factors that has been linked to a leaky gut and consequently to diseases. Let’s find out what a so-called leaky gut is.

Intestinal barrier and intestinal permeability

What exactly stands behind a “leaky gut”? A leaky gut commonly refers to an increased permeability within the intestinal wall. This condition is sometimes called a “leaky gut syndrome.” Permeability allows certain molecules and ions to pass through the (intestinal) membranes. A leaky gut can be associated with food sensitivities, cramps, gas, bloating, and/or aches, pains, and diseases. To better grasp it, let’s define first “intestinal barrier” and “intestinal permeability.

Intestinal barrier refers to a complex intestinal structure of the digestive tract that includes vascular endothelium, the epithelial cell lining with tight junctions, and the mucus layer. It anatomically separates what’s within our digestive tube (microorganisms, food particles, or drugs) from what’s outside of it (immune cells, blood vessel, smooth muscles, enteric nervous system). The intestinal barrier serves to protect us from harmful staff such as microorganisms or toxins.

Intestinal permeability on the other hand, facilitating the passage between the inside (inner host) and the outside (lumen) of the intestinal lining, allows us to selectively absorb nutrients, liquids and to respond to the triggers present within the gut. Intestinal permeability is an intestinal barrier feature that selectively lets some molecules in and others out. Factors such as microbial gut imbalance, infections, some foods, exposure to chemicals, toxins, alcohol, or stress may alter-increase the intestinal permeability, as well as possibly damage the intestinal barrier by forming tissue lesions and punctures that could lead to a leakage   a leaky gut. One of issue is it may lead to the translocation of undesired luminal gut content (microorganisms, toxins, gluten, undigested food particles) into the host (into tissues, into blood vessels), activating an immunological response. Intestinal epithelial tight junctions are another key players (proteins) keeping our intestinal barrier intact by functioning as a seal between neighboring gut cells. Disrupted epithelial tight junctions can be found in a leaky gut.

Healthy Gut vs Leaky Gut

Regulation of gut permeability: what to blame for an increased intestinal permeability?

Besides genetics, environmental factors also play an important role in keeping our intestinal barrier intact with normally functioning permeability. Possible harmful factors include nutritional factors, pathogens, toxins, too clean/sterile environment (the hygiene hypothesis), too low microbial gut diversity with impaired microbial functioning (the lifestyle hypothesis), or endogenous factors (chronic inflammation/autoimmunity).

Intestinal permeability may be influenced by:

1. The gut microbiota - dysbiosis

The gut microbiota is involved in a number of processes, such as the production of vitamins and hormones, metabolism and absorption of nutrients, and protection against pathogenic organisms. There is constant fine-tuning between the host’s immune system and the gut microbiota to maintain an equilibrium-homeostasis state and promote health. The healthy gut microbiota stimulates the synthesis of protective mucus (mucus sugars) lining by the gut epithelial cells. Some bacteria regulate the mucus layers by using the mucus components as an energy source so there is no mucus overgrowth. There is a regulation at multiple levels between the gut microbiota and the intestinal barrier. If the microbial gut ecosystem is out of balance, leading to dysbiosis and/or increased activity of pathogens, it may in turn promote inflammation, altered intestinal permeability and gut barrier damage. For example, some pathogens such as Helicobacter pylori, Salmonella eterica serovar typhimur., Clostridium difficile, or Vibrio cholera were shown to disrupt the epithelial tight junctions, increasing the intestinal permeability.

2. Diet

Diet, apart from an individual’s genetic imprint and gut microbiota, may affect to a greater or lesser extent, the gut permeability. Some studies have shown that Vitamin A deficiency may compromise the intestinal lining. Additionally, Vitamin D deficiency may potentially have a similar effect. Short chain fatty acids (SCFA), such as butyrate, produced by the gut microbiota play an important role in intestinal barrier formation and maintenance. Individuals suffering from Irritable Bowel Disease (IBD) were shown to have intestinal permeability and barrier impairment that has been linked to the deficit of butyrate, produced by the gut microbiota. In addition, A1 casein present in dairy cow products may also contribute to the problem. Let’s not forget about the negative effect of the overconsumption of alcoholic beverages. Lectins present in legumes show affinity to intestinal mucosa, which make the mucosa porous and leaky. It has also been demonstrated that commonly used food additives increase intestinal permeability, potentially leading to the gut leakage.

Lets pay some attention to food additives:

Sugars  can be found in most processed foods. Glucose is an absorption enhancer and an increased gut permeability is required for its absorption. It has been shown that the presence of glucose affects the distribution of an intestinal barrier related protein (Caco-2), which may lead to the disruption of intestinal tight junctions and consequently to the intracellular leakage.

Salt – usually overconsumed, salt has been associated with strokes, hypertension, renal diseases and obesity. About 75% of sodium intake comes from manufactured foods, such as baked goods or cereals. Recent studies indicated that increased salt consumption enhances the intestinal permeability by disrupting the functioning of claudins (2 and 15) and proteins, which are the backbone component of the intestinal tight junctions.

shutterstock_49644346Emulsifiers/surfactants there is plenty of these substances available and used in the food industry. The emulsifier market is growing worldwide. The list is long but commonly used emulsifiers include mono-and di-glycerides of fatty acids, sucrose esters of fatty acids, polyglycerols of fatty acids, lecithin, glycolipids, saponins, unsaturated and saturated/trans fatty acids. They are widely used in the bakery products, dairy, sauces, margarine, ice cream, beverages, chocolates and many other products. Many (synthetic) surfactants are shown to increase intestinal permeability. For example sucrose monoester fatty acids, which are widely used in the food industry – even in infant formula - have been shown to compromise the intestinal integrity of tight junctions.

Organic solvents - used to dissolve another substance. They need to be handled under special conditions as they are poisonous. Some commonly used organic solvents in the industry are benzene, xylene, toluene, acetone, hexane, ethanol, and some detergents. They are typically used in the process of extraction of active compounds and/or removal of unwanted substances, such as in oil production. Some are used as food additives. For example, alcohol and its metabolites were shown to breach the intestinal barrier.

Gluten – typically to be found in wheat derived products. Gliadin, one of gluten’s proteins, in known to increase the gut permeability and to contribute to intestinal damage.

Microbial transglutaminase – an enzyme of microbial origin commonly used in industry to simplify certain manufacturing processes related with economic savings. It is used to improve the texture and appearance of meat, fish, dairy products, bakery products, and sweet products, among many others. Scientists are alarmed that microbial transglutaminase may increase intestinal permeability by affecting/cross-linking certain amino acids and/or proteins.

Nanoparticles – Particles at dimensions between 1 and 100 nm (nanoemulsions). These nanoemulsions are applied in the food industry in order to protect, encapsulate, and enhance delivery of bioactive components such as lipids, flavors, vitamins, preservatives, and nutraceuticals. Nanoparticles increase the intestinal permeability by facilitating the transport of molecules and drugs through the gut lining. Chitosan is a common component of nanoparticles with the shown ability to enhance permeability and intestinal absorption of active agents.

There are other compounds shown to increase the intestinal permeability, such as L-alanine, tryptophan, and epigallocatechin galat (polyphenol in green tea).

3. Use of medication such as non-steroidal drugs like aspirin, birth control pills, steroid drugs, chemotherapy

4. Chronic Stress

Where does a leaky gut take us to: Diseases on the rise

Over the past decades there has been an increasing incidence of autoimmune and other diseases. Many of them have been associated with increased intestinal permeability and a leaky gut. The entry of foreign antigens (toxins, microorganisms, gluten, etc) to the inner host, due to the increased intestinal permeability and leakage, can, in susceptible individuals, initiate immunological-autoimmunological responses.

Leaky Gut Diseases

How do I heal a leaky gut?

  • Eliminate (if known) foods (gluten, sugar, dairy products, GMO products etc) and factors (stress, toxins, pesticides) causing a leaky gut
  • Drink Bone Broth = proline, glycine and collagen will soothe and help repair the gut lining
  • Eat healthy and raw foods (vegetables) = Feed yourself and your gut microorganisms nutritious foods
  • Reduce sugar consumption (consider a low FODMAP diet) and processed fat consumption = avoid energy-dense western diet
  • Avoid processed foods. They contain a lot of food additives that may compromise the gut lining and barrier and compromise your bodies’ acid-alkaline balance
  • Eat probiotic (kefir, sauerkraut, kimchi) and prebiotic (leak, chicory root, onions, banana) rich foods
  • Consider L-Glutamine supplementation
  • Consider probiotic supplements (with Lactobacillus plantarum, Lactobacillus rhamnosus GG, Lactobacillus casei, Lactobacillus salivarius, E. coli Nissle 1917)
  • Add anti-inflammatory foods (Omega-3 rich) to your menu
  • Consider Zinc supplementation (zinc carnosine)
  • Consider Quercetin supplementation
  • Consider Vitamin A supplementation

How do I know if I have a leaky gut? Are there any lab tests?

Suffering from any of above mentioned diseases may indicate you have an impaired intestinal permeability and an impaired intestinal barrier. Discomfort related to food sensitivities, cramps, gas, bloating, and/or aches and pains may also be a sign.

Leaky Gut Assays


“Intestinal permeability – a new target for disease prevention and therapy”. Bischoff at el., BMC Gastroenterology 2014, 14:189

“Changes in intestinal tight junction permeability associated with industrial food additives explain the rising incidence of autoimmune disease”. Lerner & Matthias, Autoimmunity Reviews 2015, 479-489.

“Intestinal permeability regulation by tight junction: implication on inflammatory bowel diseases”. Sung Hee Lee, Intest Res 2015; 13 (1): 11-18.

Microbiome and gut health
Early antibiotic use may impact health later in life

Antibiotics, once being the best intervention ever, now lead to antimicrobial resistance, posing one of the greatest threats to human health

Antibiotic dilemma

My first experience with an antibiotic dilemma was directly after my first daughter was born. Three hours after giving birth, we were heading home from the hospital, with my daughter in a newborn car seat. About 15 minutes later, I noticed she turned pale and I became suspicious. We returned immediately to the hospital, where the medical team discovered she had a respiratory insufficiency. No one knew the cause of it. She had no fever but doctors, following our approval, gave her antibiotics just in case it was an infection. We were told that if it turned out to be an infection, not giving her antibiotics would risk her life. That was a clear message which made us decide to go for antibiotics. Nobody, however, warned us about the potential consequences of (unnecessary) antibiotic exposure at such a young age.

shutterstock_135415859Eventually, it turned out that it wasn’t an infection. The microbiological tests came back negative. Doctors found no cause of a respiratory insufficiency. I have, however, a theory that placing her in a car seat (bended body, bended head) was a trigger leading to breathing difficulties. The antibiotic she was given at this very critical lifetime might have compromised her gut microbiome establishment and her immune system development, and hence could be the colic as the first sign of it and later on frequent sicknesses. Around her 2nd birthday she had 3 antibiotic courses, one for impetigo and two for ear infections. Each time she was prescribed an antibiotic, I was hesitant to give it to her, wondering what the price she will pay for it in the future. I can imagine many parents face similar situations. Often out of fear and to feel like we are in control, we allow our children to be given antibiotics. In the short term, there is usually an improvement, which makes us believe that the antibiotics were the right choice. Antibiotics are often the only way but we still need to be careful when subjecting our children to antibiotics.

Antibiotics have served their purpose in fighting bacterial infections, there is no doubt about that. Most bacterial infections, causing deaths decades ago, are under control thanks to antibiotics. Antibiotics became a miracle drug and are often generously prescribed. But do we know the long-term effects of antibiotic use? Decades ago, people were dying because of infections. Nowadays they are dying because of non-communicable diseases. Could there be a link between the use of antibiotics and the diseases we currently face? According to a review that just appeared in Cell Host & Microbe scientific journal, the use of antibiotics, especially at early age, may lead to microbial imbalances. These imbalances may contribute to dysbiosis associated diseases, such as obesity, autoimmune diseases and infectious diseases, apart from the already known drug-related adverse events and growing antibiotic resistance.

I want to increase an awareness about their potential long-term effects when administered early in life, based on the review mentioned above.

Children are prescribed antibiotics more than any other prescription drugs

It has been suggested that up to one third of antibiotics are unnecessarily prescribed. I find it alarming and worrisome.

The World Health Organization emphasizes that antibiotic resistance is one of the three greatest threats to human health.

The 3 most alarming effects of an inappropriate use of antibiotics include:

  • Antibiotic resistance (the prevalence of antibiotic resistance genes increases worldwide and infections caused by resistant bacterial strains lead to increased morbidity, mortality and increased healthcare costs)
  • Dysbiosis referring to microbial imbalance (recent findings indicate there is an association between exposure to antibiotics at early age and dysbiosis related diseases such as obesity, diabetes, or asthma)

The presence of microorganisms early in life is essential in the neurological, immunological and metabolic development of a child

The early exposure to certain factors - such as to microorganisms, to dietary antigens, hormones, or growth factors - is prerequisite for the development of the immune system, the establishment of healthy digestive function, gut motility, immune tolerance to foods and various antigens, and defense against pathogens. For more information please go to my blog on "Gut microbes in infancy".

This is the time when organs and systems are being developed and trained so they can serve throughout life. If perturbation occurs at early age (especially the first 6 months of life), such as exposure to antibiotics, it may have distinct and long-term consequences.

Image for Antibiotic blog

 The possible effects-scenarios of early (0-6 months of age) exposure to antibiotics:

  • Antibiotics temporarily decrease the bacterial diversity, without affecting the species critical for immune development so the immune system develops normally. On the other hand, the microbial community does not recover completely post-antibiotics and it gains a new state with altered microbial composition and altered metabolic capabilities. As a result, it could lead to obesity. From the animal studies we know that the exposure to sub-therapeutic levels of antibiotics increases adiposity, or fat accumulation. This is one of the reasons why livestock have been fed low doses of antibiotics to increase their body mass.  shutterstock_190122638
  • Antibiotics eliminate the key bacterial species during a critical window of the immune system development, leading to its maturation impairment. During the post-antibiotic recovery the key members of the gut microbiome return to occupy their niches and the microbiome reaches a state of “stasis.” The returned key species let the immune system develop further. However, the immune system remains impaired. As a consequence, the immunity is compromised and may lead to allergy, atopic disorders, and autoimmune diseases. A number of studies associate early antibiotic use, especially multiple courses of broad-spectrum antibiotics, with an increased risk of allergy and atopic disorders. According to a current hypothesis, gut dysbiosis caused by the loss of key bacterial players and overgrowth of pathogens may contribute to the development of allergy, atopic diseases, and autoimmune diseases. The genetic factor is known to be involved in the etiology of autoimmune diseases. However, scientists indicate that the gut microbiome may be as well an important player. There are results to suggest that early exposure to multiple antibiotic courses may increase the risk of juvenile rheumatoid arthritis and inflammatory bowel syndrome. In addition, animal studies showed that exposure to antibiotics led to alterations in the gut microbiome and the loss of keystone species, eventually affecting the immune system.
  • Antibiotics decrease the microbial diversity within the gut and at the same time create a niche for pathogens. The gut is “on fire”: the gut epithelium is inflamed, the pathogens begin to thrive, predisposing to chronic infections. Thus, exposure to antibiotics may cause an increased vulnerability to infections during the post-antibiotic recovery period. Studies with pre-term infants suffering from necrotizing enterocolitis associated this condition with prior-antibiotic use. Clostridium difficile infection in adults is a classic example of the post-antibiotic loss of microbial gut diversity and subsequent pathogenic colonization. It is also known that antibiotic-induced dysbiosis increases the risk of fungus infection, such as Candida albicans. In addition, the post-antibiotic effect has been linked with impaired immunity against the influenza virus.

Summing-up, there are four post-antibiotic types of dysbiosis proposed currently: loss of keystone species, loss of microbial diversity, alterations in metabolic capacity, and blooms of pathogens.

Hopefully, these findings will fuel further research on the post-antibiotic health consequences and will improve antibiotic prescription protocols. For example, doctors should select narrow-spectrum antibiotics to target only designated bacteria based on proper diagnostics.

29SCIB-videoSixteenByNine1050Lastly, I would like to encourage everyone to read an inspiring book of Dr. Martin Blaser: Missing microbes – how the overuse of antibiotics is fueling our modern plagues. The author will make you rethink the current concept of fighting infections, will make you cherish and appreciate your microbiome and will make you think twice before giving your child antibiotics.