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Gut Microbiome: How to Restore Healthy Gut Flora

Sarah Vordermeier

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What is the microbiome? From digestion to depression, healthy skin, and a strong immune system, our gut health – our gut microbiome – 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? 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.

Our gut is home to a hefty 100 trillion bacteria that influence our health and well-being – and even our mood. Our gut flora is important for digestion, protection against dangerous germs and toxins, and strengthening the immune system. Experts now link various diseases, allergies, skin conditions such as neurodermatitis, and even depression to the fact that our 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 – 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.

So, it goes without saying that the gut microbiome demands a lot more attention than we give it. Find out what exactly the microbiome is, typical unhealthy gut symptoms, how to restore healthy gut fora, and how to take the right probiotics!

What Is the Microbiome?

The microbiome, also known as gut flora or gut bacteria, is defined as a community of microorganisms – that is, bacteria, fungi, and viruses – that live in the human body. Our gut microbiome is, thus, the community of microorganisms that is located in our gut. 

Up to 100 trillion different organisms such as bacteria, viruses, and fungi make up our gut microbiome. Most of the bacteria are located where the digestion process is almost over, in the intestinal mucosa of the colon.[5] If digestion is impaired, and the bacteria migrate from the large to the small intestine, this can lead to 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: 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 that make up our 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 its influence on our immune system, it can inhibit immune cells that are responsible for triggering allergies. This link could be an approach for new treatment options for allergy sufferers in the future.[11]

person holding up hands in heart shape up to stomach

Why Is Our Gut So Important?

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.

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 “gut feeling” came into the picture, referring to intuitions triggered by a second brain.[1, 3]

How Does Gut Microbiome Affect Immune System?

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 our intestinal flora.

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, for example, due to an unhealthy diet with a lot of saturated fats and sugar or after taking antibiotics.[7]

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.

What Causes Imbalanced Gut Flora?

The composition of our 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 – but above all, diet. You can influence which bacteria colonize your intestine yourself through your food choices.[13]

Person with bloating holding their stomach

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

    Imbalanced Gut Flora: Taking Probiotics with Antibiotics

    Antibiotics have brought us progress in fighting bacterial infections and thus dangerous diseases. But they also have their downsides – 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 microbiome – 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 – 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 restore 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.[18–20]

      What Are Typical Unhealthy Gut Symptoms?

      What Are Signs of Bad Gut Health?

      Is your microbiome healthy? That’s not always an easy question to answer. But there are some unhealthy gut symptoms you will be able to recognize, 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

        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 signs of bad gut health include:[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 food allergies and intolerances. To investigate this, taking a food test that analyzes your blood for certain antibodies may be very useful.

        man lying down in pain on a sofa

        What Diseases Are Linked to Gut Bacteria?

        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 digestive health, but also, for example, the skin and our mental health.

        Can Intestinal Flora Cause IBS?

        Worldwide, it is estimated that between 10 and 15 percent of people suffer from irritable bowel syndrome – 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]

        How Is Imbalanced Gut Flora Linked with 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 gut microbiome 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]

        Does Gut Health Affect Mood?

        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 – however, this was the first review of this kind.[40] A 2011 study published in the journal Nature also showed impressive results – 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]

        Woman relaxing on her couch with her arms back

        Does Gut Health Affect Skin?

        Not only do numerous bacteria live in our gut – 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 and boost skin health.

        A study analysis published in 2019 concluded that probiotics and other gut health supplements 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]

        What about our complexion? Little is known about the effectiveness of probiotics and prebiotics or other skin health supplements in cosmetic products. It is possible that they stimulate the growth of healthy bacteria when applied directly to the skin. Researchers are still investigating this in further studies.[42]

        Is There a Test to Check 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.

        How to Restore Healthy 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.

        Why Should I Boost My 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 intolerance.

        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

        Should I Take Probiotics or Prebiotics?

        You can also heal the gut naturally by using probiotics, prebiotics, and resistant starch. They can restore healthy bacteria – especially in your colon. Probiotics and prebiotics not only promote healthy bacteria but also get rid of bad bacteria in our intestines.[4] Probiotics come in the form of capsules, powder, and drops, for example.

        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 supplements (often in capsule form), you can restore healthy 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 restore imbalanced gut flora. 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 – 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]

        How Can I Improve My Gut Health to Lose Weight?

        Our gut microbiome metabolizes the food we eat. They turn it into fats, vitamins, and minerals that our body can use for a variety of functions. If our 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, imbalanced gut 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 – 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.

          7 Tips on How to Promote a Healthy Gut

          1. 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.
          2. 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.
          3. 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.
          4. Avoid processed 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.
          5. 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.
          6. 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.
          7. 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 or other unhealthy gut symptoms. Your intestines must first get used to a larger amount of fiber. This way, you can avoid the unpleasant consequences of flatulence.

          What Is the Microbiome – at a Glance

          What Is the Microbiome?

          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.

          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 Does Gut Flora Do?

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

          What Causes Imbalanced Gut Flora?

          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 flora include frequent digestive problems, poor skin condition, respiratory problems, difficulty concentrating, and joint and muscle pain.

          How Do I Restore Healthy Gut Flora?

          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 – that is, foods and supplements containing living microorganisms, are considered particularly effective. 


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