Microbiome: How to Restore Healthy Gut Flora

Sarah Vordermeier


From digestion to depression, healthy skin, and a strong immune system, our gut health has a say of what¬†goes on elsewhere in our bodies. So, why is the gut still considered by many people to be nothing but an organ?¬†‚ÄúGut microbiome‚ÄĚ and¬†‚Äúmicrobiota‚ÄĚ are¬†indeed¬†becoming buzzwords, with which many¬†of us are now becoming familiar.¬†Although¬†the extent to which our gut influences our health all over our bodies is slowly coming to light,¬† some experts believe that this is just the tip of the iceberg. Find out why.

Our¬†gut¬†is home to¬†a hefty 100 trillion bacteria that influence our health and well-being ‚Äď and even our mood.¬†Our gut flora (also called the¬†microbiome or microbiota) is important for¬†digestion,¬†defense against dangerous germs and toxins, and¬†strengthening the immune system. Experts now link various diseases, allergies, and even depression to the fact that the intestinal flora is out of balance.[1]

In Japan, people regard the¬†gut as the¬†center of physical and mental strength¬†in our bodies. In this part of the world, however, our guts are often still considered a purely digestive organ ‚Äď and is thus grossly underestimated.¬†Flatulence, diarrhea, and constipation¬†are taboo subjects, and it seems as though¬†digestive health¬†does not appear high on the priority list for many people in the United States.

The bacteria in our guts that make up our intestinal flora not only contribute to healthy digestion. They also protect us from diseases and strengthen the immune system. Our intestinal bacteria influence whether we get neurodermatitis, develop an inflammatory bowel disease, or tolerate certain foods.

So, it goes without saying that the gut microbiome demands a lot more attention than we give it. Find out how to achieve a healthy gut, take the right probiotics, and boost your immune system in our latest article on gut health!


What Is Your Gut Health?

What does it mean to have a healthy gut? There may be more to it than meets the eye. Leading scientists have defined five criteria that constitute good gut health, including:[1]

  • no intestinal diseases
  • effective digestion and absorption of food
  • normal and stable intestinal flora
  • a strong immune system
  • general well-being

Among other things, your intestine also influences whether you have an intolerance or allergy to certain foods or substances, such as lactose.

Did you know that, at 5.4 to 8.2 yards in length, the intestine is our largest internal organ?

How Can I Improve My Gut Health?

Gut flora is complex, and scientists have by no means solved all the mysteries surrounding it. However, there are some ways you can support your microbiome, according to the latest research:[2]

  • exercise regularly
  • avoid chronic stress
  • eat a healthy diet that is¬†high in fiber and low in sugar,¬†saturated fats, and¬†processed foods
  • take¬†probiotics and prebiotics, if necessary¬†

How Do You Know If You Have a Healthy Gut?

Is your microbiome healthy? That’s not always an easy question to answer. But there are some symptoms that indicate gut problems, such as a bloated stomach or frequent diarrhea.

Conversely, there are also signs that indicate a healthy microbiome:

    • bowel movements once to three times a day
    • well-formed stool
    • flat, not bloated abdomen
    • little flatulence
    • no complaints after eating certain foods

    What Is the Function of Our Gut?

    Our intestines are constantly busy processing food and fighting off pathogens. The most important phase of digestion takes place in the small intestine. It digests our food until all the important nutrients, vitamins, and minerals have been absorbed. The rest of the food enters the large intestine, from which it is excreted.[3]

    Did you know that, from absorption in our mouths to our large intestine, food stays in our body for five to 70 hours?[4]

    But the gut has another function that has been underestimated for years: promoting a healthy immune system. The digestive tract constantly fends off pathogens such as bacteria, viruses, fungi, environmental toxins, and toxins.

    our microbiome is considered to be at the heart of immune system health

    How Do You Fix a Bad Gut?

    If there is an imbalance between the different types and strains of bacteria and the immune system, this weakens the defenses in our gut. The result can be:[4]

    • gastrointestinal problems such as¬†constipation, diarrhea, and even inflammation
    • intestinal diseases
    • tendency to be overweight
    • generally weakened defenses and thus¬†more frequent infections

    Problems in the gastrointestinal tract can also be an indication of allergies and intolerances. To investigate this, analyzing a blood sample for certain antibodies may be useful.

    The Gut as the Second Brain

    The gut is also¬†home to a nervous system¬†that contains more neurons than the entire spinal cord. Scientists realised 100 years ago that bacteria in the gut constantly communicate with neurons in the brain. This is how our guts have gained recognition as our second brain.¬†This is arguably how the phrase¬†‚Äúgut feeling‚ÄĚ came into the picture, referring to intuitions triggered by a second brain.[1, 3]

    What Is Gut Flora?

    Up to 100 trillion different organisms such as bacteria, viruses, and fungi live in your gut. These microorganisms are collectively called the gut flora or microbiome.

    Most of the bacteria are located where the digestion process is almost over, in the intestinal mucosa of the colon.[5] If the process is impaired, and the bacteria migrate from the large to the small intestine, the result can be severe flatulence, abdominal pain, joint pain, nutrient deficiencies, and anemia. This still partly unexplored health issue is called bacterial overgrowth.[6]

    Bacterial colonization can occur, for example, if you take broad-spectrum antibiotics. Broad-spectrum antibiotics are drugs that are effective against many types of bacteria and are often used for dangerous diseases.[6]

    What Is Gut Microbiome and Why Is It Important?

    Bacteria are not always harmful. In fact, gut bacteria is essential for human survival. Among other things, the gut microbiome plays a very important role in the digestion of food.

    The good bacteria of the intestinal flora, which are vital for our body, have numerous other functions, for example:[9, 10]

    • They produce what is known as¬†butyrate¬†from our food, which has been shown to contribute to good gut health by promoting mechanisms to¬†combat stress
    • ¬†They produce a number of¬†essential amino acids
    • They produce certain vitamins, such as vitamin K and water-soluble B vitamins

    A study published in the journal Science revealed that the gut microbiome can block allergic reactions. Through their influence on our immune system, they can inhibit immune cells that are responsible for triggering allergies. This connection could be an approach for new treatment options for allergy sufferers in the future.[11]

    Gut Flora and Immune System Health

    There are many complex connections between the gut microbiome and the immune system. A total of 70 to 80 percent of the cells of our immune system is located in the intestine. The microbiome thus plays an important role in protecting the body from pathogens and inflammation.[2]

    To promote our body’s defense, information is constantly exchanged between the immune system and the good bacteria. These healthy bacteria include above all the genera of lactobacilli and bifidobacteria, which also make up a large part of the intestinal flora.

    Curious to find out more about our immune system? Head over to our article on boosting immune system health to gain more insights into immune system boosters, including supplements, vitamins, and more.

    Does Gut Health Affect Immune System Health?

    If there are fewer good bacteria and bad bacteria begin to dominate, inflammation can spread more easily, and pathogens can penetrate the body more easily.

    Such an imbalance (dysbiosis) of the gut microbiome can occur, among other things, due to an unhealthy diet with a lot of saturated fats and sugar or after a course of antibiotics.[7]

    What Causes an Imbalance in Gut Flora?

    The composition of the gut flora is different for every person and changes over the course of a lifetime. Over the last 20 years, researchers have been able to identify patterns by which a healthy gut can be recognized. Nevertheless, a large part of the functions performed by our gut microbiome is still unknown.[12].

    What is known so far is that there are factors that continuously influence the composition of gut bacteria. These are¬†age, gender, and genetic predisposition¬†‚Äď but above all,¬†diet. You can influence which bacteria colonize your intestine yourself through your food choices.[13]

    Unhealthy microbiome can lead to bloating

    What Causes an Unhealthy Gut?

    How does bacterial colonization become imbalanced? There are many possible causes. Some of the most common are:[14]

    • Contact with environmental toxins and poisons
    • Poor diet (few anti-inflammatory foods)
    • Smoking cigarettes
    • Taking certain medicines like antibiotics
    • Long-term stress
    • Infection with harmful pathogens

      Taking Probiotics with Antibiotics

      Antibiotics have brought us progress in fighting bacterial infections and thus dangerous diseases. But they also have their downsides ‚Äď diarrhea¬†or an inflamed colon (and occasionally¬†an inflamed small intestine) are the most common and noticeable¬†side effects of antibiotics.[15]. In addition,¬†antibiotics¬†affect our¬†gut flora¬†‚Äď a side effect that you will not necessarily notice. With long-term use, the¬†ratio of good bacteria to bad bacteria¬†shifts and becomes imbalanced.[16]

      Did you know that, according to a projection, global antibiotic consumption has risen by 65 percent in the last 15 years?[17]

      Antibiotics are made to kill bacteria¬†‚Äď in this way, they help against dangerous bacterial infections. However, they do not only fight harmful bacteria, but also good intestinal bacteria. They also leave behind a lot of dead bacteria in the intestines, which we have to¬†get rid of by having¬†more frequent bowel movements. Our¬†gut flora then has to be restored, which takes time. Through a targeted diet, we can nourish our bodies with bacteria-friendly food and accelerate the growth of¬†a healthy gut microbiome.[16]

      The World Health Organization considers antibiotic resistance to be one of the greatest threats to health worldwide. Bacteria become immune to antibiotics, so that deadly diseases can no longer be treated with them. One reason for resistance is that too many antibiotics are prescribed for colds.[18‚Äď20]

      Gut Health: How Do I Increase Good Gut Bacteria?

      Studies clearly show that our diet also influences our gut flora. What we eat plays an essential role in maintaining the biodiversity and function of our gut flora. This is because our bacteria feed on what we give them through our diet. In order to make your diet gut-friendly and balanced, getting professional nutritional advice may be worthwhile.

      How Do I Boost My Gut Health?

      Enjoy coffee, black tea, or alcohol only in moderation. Coffee and alcohol have a strong laxative effect in high quantities, while black tea causes constipation.

      Opt for eating several small meals per day. Too much food at once overloads our digestive system. Eat at regular times and only when you feel hungry. Stop eating when you feel full.

      Make sure you drink enough fluids. It is best to drink still mineral water or  herbal tea. This softens the stool so that no constipation occurs and the bowels are emptied without any issues.

      Avoid ready-made products! They contain additives that are not tolerated by everyone and can cause discomfort. Avoid sauces and batters as much as possible, especially if they contain a lot of fat. They are difficult to digest and can cause abdominal pain and diarrhea. Also avoid high-fat, high-sugar, and high-protein foods.

      Make sure you chew thoroughly! This makes it easier for the intestines to absorb the food, leading to fewer complaints such as constipation, flatulence, and heartburn.

      Eat fiber-rich foods such as whole grains, oatmeal, and flaxseed. Your stools will be looser, and more harmful substances can be eliminated. Fiber is also crucial for our all-important gut microbiome. Five portions of fruit and vegetables a day are also good for your intestines. Besides vitamins and minerals, they also contain water and fiber.

      Make sure you get enough exercise. External movement is good for the internal movement in your gut.[27]

      Tip: If you want to make your diet richer in fiber, you should start with small amounts first. Otherwise, you may experience a lot of flatulence, which will lead to stomach pain. The intestines must first get used to a larger amount of fiber. This way, you can avoid the unpleasant consequences of flatulence.

      Gut Health and Weight Loss

      Our gut bacteria metabolize the food we eat. They turn it into fats, vitamins, and minerals that our body can use for a variety of functions. If the gut flora changes, the way our body processes food also changes. Recent studies show that this is why, for example, the composition of the gut flora changes significantly in people who are overweight.[1] Conversely, an imbalance of the intestinal flora also increases the risk of gaining weight.[28]

      In some studies, the bacterial strain Firmicutes was highly prevalent in overweight people. Firmicutes extracts energy from food particularly efficiently.¬†The presence of Firmicutes means¬†more excess energy is utilized and stored in fat deposits ‚Äď thus¬†increasing the likelihood of you¬†putting on weight. In study participants with fewer Firmicutes, more food was not utilized for energy and was excreted again via the stool.[29]

      If you follow our tips for a healthy and gut-friendly diet, this can also have an effect on the colonization of Firmicutes bacteria. If the Firmicutes bacteria strain is less prevalent, this may help you lose weight.

      Probiotics and Prebiotics

      You can also heal the gut naturally by using probiotics, prebiotics, and resistant starch. They¬†can restore healthy bacteria¬†‚Äď especially in the colon. Probiotics and prebiotics not only support the formation of healthy bacteria, but also displace bad bacteria in our intestines.[4] Probiotics come in the form of capsules, powder, and drops, for example ‚Äď you can find many probiotic products in our online shop.

      When the ratio of gut bacteria is out of balance, doctors call this dysbiosis. This means that there is an excessive amount of certain types of fungi, yeasts, or bacteria that negatively affect the body. By consuming probiotic foods and food supplements (often in capsule form), you can restore balance.

      What Are Probiotics?

      Probiotics are living organisms (bacteria) that are added to many foods. Once in the gut, they contribute to a well-functioning gut¬†microbiome. They absorb nutrients and fight infections.[6, 21] Probiotics are normally produced during the natural fermentation of foods. This is why they are found in yogurt, kefir, and sauerkraut, for example. However, the process of fermentation is time-consuming ‚Äď and is therefore often omitted in modern food production. As a result, many foods that are actually probiotic¬†aren‚Äôt beneficial for¬†gut health.[22]

      To promote healthy gut bacteria, it can be beneficial to include more probiotic foods in your diet.

      Studies suggest that probiotics can improve lactose intolerance, reduce diarrhea, constipation, and flatulence, lower cancer-promoting enzymes, help with vaginitis, mitigate food allergies, and have a beneficial effect on atopic dermatitis.[4]

      Improving gut health with probiotic foods

      How Can I Get Probiotics Naturally?

      Generally, fermented foods ‚Äď that is, those produced by fermentation ‚Äď contain probiotics. The following foods are commonly probiotic and can support your gut microbiome:

       Probiotic Foods
      Kefir¬†‚Ästcontains ten to 34 probiotic strains, even more than yogurt
      Yogurt¬†‚Ästproduced with¬†milk from organic farming
      Apple vinegar¬†‚Ästcontains healthy acids that support the function of probiotics
      Miso¬†‚Äď Japanese¬†paste made from fermented soybeans
      Kombucha¬†‚Ästfermented tea with antibacterial effect
      Kimchi¬†‚Ästfermented Chinese cabbage with garlic, ginger, and chili
      Sauerkraut¬†‚Äď freshly prepared so that it still contains the lactic acid bacteria
      Cheese¬†‚Ästmozzarella, cheddar, and Gruy√®re, in particular, contain probiotics
      Gherkins¬†‚Ästonly the variety fermented in brine

      Are Probiotic Drinks Actually Good for You?

      In recent years, many probiotic drinks have been advertised as particularly healthy. Probiotic drinks and yogurts with added probiotics can definitely be useful. However, you should consider a few things when buying them:

        • The probiotic content decreases continuously after the drink/yogurt¬†is bottled. The fresher the probiotic, the better.
        • The¬†sell-by date does not indicate when the food is off. After expiry, however, the product no longer¬†contains the minimum number of bacteria that makes it probiotic.
        • Only 10 to 40 percent of the lactic acid bacteria actually survive¬†their passage through the¬†stomach because of the stomach acid.
        • Beware of high sugar levels. Sugar serves as an energy source especially for bad bacteria.

        How Do I Heal My Gut after Antibiotics?

        A few years ago, it was not recommended to take probiotics at the same time as antibiotics. Yogurt, kefir, and sauerkraut were to be avoided during antibiotic treatment. It was thought that the antibiotic would kill the probiotics. Today, we know that probiotics can be very useful during antibiotic treatment to promote the formation of good gut bacteria. The best time to take probiotics is at least one hour before or two hours after taking the antibiotic.

        A clinical study investigated the effect of probiotics during antibiotic treatment. Of the study participants who took probiotics at the same time, 25 percent fewer participants got sick with diarrhea.[15]

        How Many Probiotics Should I Take?

        To ensure that enough viable bacteria reach the intestine, a dose should contain at least one billion colony-forming units (cfu). Due to stomach acid and bile, some bacteria do not survive the journey to the intestine. Therefore, higher doses also exist. Lactic acid-producing bacteria such as lactobacilli are particularly sensitive. For this reason,¬†formulae with these bacterial strains often contain an enteric coating ‚Äď for example, made of cellulose. If there is a specific health-related reason for taking probiotics, your doctor may recommend a certain dose of probiotics.[30]

        What Are Prebiotics?

        Prebiotics are dietary fibers that are not or only partially digestible. They are found in certain foods, including chicory, asparagus, leeks, onions, and bananas. Prebiotics serve as direct nutrition for healthy bacteria in the colon and stimulate their growth. This creates healthy fatty acids and reduces intestinal pH. The best-known prebiotics are inulin and oligofructose.[21, 24]

        Did you know that there are also synbiotics? When probiotics and prebiotics are combined in one product (as a food supplement), they are usually called synbiotics. Synbiotics aim to increase the survival and activity of probiotics, as well as stimulate the bifidobacteria and lactobacilli gut bacteria.[25]

        What Are Resistant Starches?

        ‚ÄúResistant starch‚ÄĚ is the term used for starch and starch¬†by-products. Resistant starch reaches the large intestine undigested, where it serves as¬†a source of energy for the bacteria found there. It thus has physiological properties similar to dietary fiber:[26]

        • It improves¬†gut health
        • It increases the amount of stool

          The following foods contain resistant starches

          Amount Food Resistant Starches
          1 Banana (unripe) 4.7 grams
          1/4 cup Oats (uncooked) 4.4 grams
          1/4 cup Frozen peas (cooked) 4.0 grams
          1/4 cup White beans (cooked) 3.7 grams
          1/4 cup Lentils (cooked) 2.5 grams
          3  Boiled potatoes (cooled) 2.4 grams

          Test Your Gut Health

          In stool tests, laboratories can determine which types of bacteria are present in the sample. They can analyze the composition of the different bacterial strains and the balance between good and bad bacteria.

          There are furthermore self-tests that examine the concentration of good bacteria in your gut. Such tests analyze the number of lactobacilli and bifidobacteria and thus give you an indication of which probiotics and foods you could best use to strengthen your gut flora.

          Some tests even give you a more profound insight into your gut health by additionally analyzing the presence of individual species of the bacterial genera of lactobacilli and bifidobacteria, such as Lactobacillus reuteri and Bifidobacterium bifido. Modern DNA test methods are used for such tests.

          Food Allergies and Intolerances

          If symptoms occur mainly after meals or are particularly pronounced with certain foods, this can be an indication of an allergy or intolerance. In the case of an allergy, the symptoms are triggered by a malfunctioning immune system; an enzyme deficiency in the intestine often plays a role in intolerances.

          To discover more about the differences between a food allergy and intolerance, visit our dedicated Health Portal article. If you would like to test whether you are allergic to the most common food allergens in Europe, order a Food Allergy Test today!

          How Can I Diagnose a Food Intolerance or Allergy?

          Food allergies and intolerances can be tested in different ways. Allergies, for example, can be determined with the help of a blood test. The blood is analyzed for IgE antibodies ‚Äď too many of these antibodies indicate an allergy. This is possible with the cerascreen¬ģ¬†Food Sensitivity + Allergy Test, for example, which measures reactions to the most common food allergy triggers. You can also test for histamine intolerance by testing your blood for antibodies.

          Gut Health and Illness

          The gut and the rest of your body are connected on many levels. It is therefore hardly surprising that imbalanced gut flora can also be linked with many diseases. This can affect gut health, but also, for example, the skin and our mental health.

          Gut Flora and Irritable Bowel Syndrome

          In the United States, it is estimated that between 25 and 45 million people suffer from irritable bowel syndrome ‚Äď one of the most common chronic gastrointestinal diseases.[44]

          Recently, medical experts have recommended the administration of probiotics as a treatment option. Intestinal discomfort such as abdominal pain, flatulence, diarrhea, and constipation can be alleviated by taking probiotics.

          New studies have found that the gut flora of irritable bowel sufferers differs from that of healthy people. People with irritable bowel syndrome have imbalanced gut flora with a large number of bad bacteria. Doctors can select appropriate probiotics depending on symptoms.[31]

          Gut Health and Inflammatory Bowel Disease

          The chronic inflammatory bowel diseases Crohn’s disease and ulcerative colitis have become a worldwide problem since the beginning of the 21st century.[32] To date, scientists cannot say exactly what triggers these intestinal inflammations.

          Science agrees on one thing: Our gut flora is a piece of the puzzle when it comes to the development of intestinal inflammation.[33, 34] Studies show that the intestinal flora of both people with Crohn’s disease and ulcerative colitis contains significantly more bad bacteria than good ones, and bacterial diversity is lower. This imbalance can impair the immune system, presumably leading to greater inflammation.[35, 36]

          Scientific studies have just delivered promising results for the treatment of ulcerative colitis: the protective bacteria bifidobacterium and lactobacillus could improve gut flora as probiotics and alleviate disease symptoms. [25, 37, 38]

          Gut Health and Depression

          Our brain contains billions of neurons that are closely linked with the trillions of good and bad gut bacteria. The gut flora transmits signals to the neurons in our brain. In stressful situations, the gut flora can actually change, which may have something to do with this collaboration between neurons and our gut microbiome.[39]

          This has led scientists to suspect that probiotics could reduce the symptoms of depression. The assumption was confirmed in a study in 2016 ‚Äď however, this was the first review of this kind.[40] A 2011 study published in the journal Nature also showed impressive results ‚Äď feeding healthy mice probiotics helped reduce anxiety-like and depressive behavior compared to control mice. Future studies must show whether these results can be¬†seen in humans.[41]

          Gut Health and Neurodermatitis

          Not only do numerous bacteria live in our¬†gut ‚Äď the skin also has its own bacterial ecosystem. As in the intestine, there are microorganisms here that are classified as particularly useful, neutral, and/or pathogenic.[42] Scientists are currently investigating whether they can help people with neurodermatitis by influencing the bacteria of the skin via the¬†gut flora. In this way,¬†good¬†gut health could also protect the skin.

          A study analysis published in 2019 concluded that probiotics can help reduce the risk of atopic dermatitis in children. It did not matter whether the mother took the probiotics during pregnancy or the child received them from an early age.[30]

          Gut health and complexion: little is known about the effectiveness of probiotics and prebiotics in cosmetic products. It is possible that they stimulate the growth of beneficial bacteria when applied directly to the skin. Researchers are still investigating this in further studies.[42]

          Healthy Gut Microbiome ‚Äď at a Glance

          What Is Your Gut Health?

          Our gut is healthy when there are no diseases in the intestine, no food intolerances or allergies, no unstable intestinal flora, and no high susceptibility to infections.

          What Is Gut Flora?

          The human gut is home to 100 trillion different microbial organisms, including bacteria, viruses, and fungi. Together, these microorganisms form the gut flora, also called the microbiome. Most of the gut flora consists of bacteria.

          What Is the Function of Gut Flora?

          The bacteria in the gut strengthen our immune system, protect us from pathogens, produce important amino acids, vitamins, and butyric acid. 

          What Causes an Unhealthy Gut?

          There are various reasons why your gut may not be healthy. Possible causes are large amounts of antibiotics, environmental toxins, poor diet, and stress.

          What Are the Signs of Bad Gut Health?

          Symptoms of imbalanced gut health include frequent digestive problems, poor skin condition, respiratory problems, difficulty concentrating, and joint and muscle pain.

          How Do I Boost my Gut Health?

          Probiotics, prebiotics, and resistant starches can help¬†with imbalanced¬†gut¬†flora and promote¬†good gut¬†health. They are found in certain foods such as kefir, sauerkraut, cooled potatoes, and in food supplements. Probiotics¬†‚Äď that is, foods and supplements¬†containing living microorganisms, are considered particularly effective.¬†


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