How to Improve Your Gut Microbiome

The gut microbiome is a complex community of bacteria that lives in the gastrointestinal tract. The gut microbiome is composed of trillions of microorganisms and is considered the “body’s virtual organ” given its importance in maintaining our health. Disruptions in the gut microbiome are also called “dysbiosis” and have been associated with many conditions, including gastrointestinal disorders such as irritable bowel syndrome, diarrhea, and constipation.

why gut health matters infographic.

This community of bacteria helps us digest food, synthesize vitamins, and fight off infection. Recent studies have shown that the gut microbiome can also play a role in weight loss, mood, and chronic diseases like diabetes and cancer. In fact, there is research which suggests that the health of our microbiome might affect our mental health, and many other aspects of our life.

This article will show you how to improve your gut microbiome by eating the right foods, taking probiotics, getting enough sleep, and staying active. But there is a bit more than that, and we will reveal many aspects that often get forgotten.

Be prepared for a long read. If you want a fast article, that is just a general introduction, this is not it. At time this article might be a bit hard to follow, but read it twice, and feel free to check the cited literature, if you are curious. You might find more info in the citations.

Let’s jump in and see why our gut microbiome is so important and how to improve our microflora.

Table of Contents

    Why is Our Microbiome Important for Our Health?

    Before skipping this section, let me tell you this: don’t. Most people who find this article, have a great idea why our microbiome is important for us, but if you find just one thing you didn’t know here, it’s a big win. It will help you and people close to you for ever.

    The human gut harbors a complex and diverse community of bacteria, the gut microbiome. This bacterial community helps us digest food, synthesize vitamins, and fight off infection.

    Recent studies have shown that the gut microbiota can also play a role in weight loss, mood, and chronic diseases like diabetes and cancer. In fact, there is research which suggests that the health of our microbiome might affect our mental health, and many other aspects of our life.

    The gut microbiota contains about 100 trillion bacteria from 1000 different species – more than any other organ in the body. Our microbiome contains more genetic material than our own genome. The collective genomes of gut microbes are estimated to encode 100 times more genes than the human genome, but it is important to note that these numbers are just estimates, because we have not sequenced all the bacteria in the gut yet.

    The number of genes a microbe has is important, because it determines how much that particular bacterium can do. For example, some bacteria have genes that allow them to break down complex carbohydrates and fiber, while others have genes that make them resistant to antibiotics.

    The gut microbiome has many different functions that are important to human health. One of the main functions is providing energy from food, especially carbohydrates that we cannot digest ourselves and fiber. The microbes in our digestive tract produce short chain fatty acids that can be used as fuel by cells in the gut, liver and brain.

    Other functions of the microbiome include

    Most of these functions are still being studied, so we don’t know everything about them. However, it is clear that the gut microbiome is important for human health, and we need to take care of it.

    Why Do We Need to Improve Microbiota?

    Before reading the whole article, it important to understand why do you need to improve your microbiota? I am not saying that this is your case, but I’ve seen many people that wanted to fix their microbiome, but they didn’t need to. Okay, I’ll admit, even if your are the healthiest person on a 50 mile radius, you can still benefit from reading this article. There are things that I only found after I abused my body for a while. And your body is resilient, it will last a while… So hopefully, this will stop you from doing the silly mistakes I did. Chances are though that you actually need a change in your lifestyle now.

    Before making any change, make sure you know what is your end goal. What is the health issue that you are trying to improve? Your microbiome is important, and you need to take care of it, but if you are healthy, make sure you are not disturbing it by making drastic changes. Your microbiome is self-regulating and it is very good at balancing itself. If you are healthy, make sure you adjust lifestyle habits first, they work wonders.

    Is Your Gut Healthy?

    man suffering from stomach pain

    When people think about gut health, they usually think of regular transit. Well, that’s an important part of your health, but regularity is one of the milder problems with your gut. There are various degrees of how much your gut health is affected. In some cases the diagnostic is pretty easy, in some cases you live with an unhealthy gut for a long time until the superficial balance is broken. But there are little signs that your gut is not well, and you should listen to these signs, before getting sick. It’s always easier to prevent than to treat.

    Here are some signs that your microbiome is not in a good shape, and you should start take steps to amend it.

    These are the most common ones. If you experience any of these and you can’t find a reason for it, think about your gut health. Do not be shy to talk with your doctor about this, they should understand how important is your feeling healthy.

    What Is a Healthy Microbiome?

    To be honest, I don’t know, and anybody that claims they know they would be lying. We have a fair idea of which are the beneficial microorganism colonies, but we don’t know the exact relationship between these colonies. How much of which we should host, what happens if we wipe out certain colonies.

    The answer is not a simple one, because certain bacteria and yeast that can be pathogen if overgrow, can be beneficial in a controlled number. For instance, Candida Albicans, which cause fungal infections in many people, when kept at bay can be beneficial for our immunity. This is being still studied, and we may not have a full answer soon, but here is what we know now.

    A healthy microbiome is dominated by Prevotella and Bacteroides species, while Firmicutes and Enterobacteriaceae dominate in people who have metabolic syndrome and obesity.

    The lack of microbial diversity in a bacterial community structure, diminishes its ability to withstand perturbation. Here is an article that discusses microbiota composition and its influence on our health in more detail.

    The species that are dominant in your microbiota also depends on many other factors, such as how old you are, where you live and what kind of food you eat.

    We might not know exactly what is the perfect microbiome composition, but empirically, we proved that some of the lifestyle choices change the microbiome, and this change comes with a host of health benefits. There might not even be a single one perfect microflora composition, but more adaptations, depending on where you live, and what kind of foods you eat predominantly. And adjusting your microbiome might be more of a removing foods from your diet, rather than introducing new one, to a certain extent.

    Now that we discussed this much on what is the perfect microbiome composition, and we graciously concluded that we have no idea, we can jump in and see how can we improve it? Note the self sarcasm… But I promise, the info in the following section is all worth.

    How to Improve Your Gut Microbiome

    Now that you know a bit more about the importance of our gut microbiome, let’s see how we can improve your microflora.

    Because the dysbiosis can be different, and the degree of severity also different, there is no single regimen that can help everybody. And it is beyond the purpose of this public article to give medical advice. We simply list various ways that can work or not, depending on your situation. Please, consult your doctor when making drastic life changes. Some of the foods we recommend might make you worse, depending on your condition. Keep a diary and see which foods worsen your condition.

    This might sound anti climactic. After so much hype in the first half of the article, now I discourage you by saying it might not work. The reality is that can get a general idea, but each person is different, and your microbiome might be more damaged than someone else’s.

    The alternative is to get a  microbiome test, which will give you insights into what are the next steps.

    Steps To Take in Order To Improve Your Microbiome

    Improving your gut microbiome is a complex process and it’s a two fold process that involves healing your intestinal lining, and improving the balance between the various microbe populations.

    Here are main ways to improve your microbiome:

    • Lower your stress levels
    • Get enough sleep
    • Stay hydrated
    • Eat the Right Foods the Promote a Good Microflora
    • Remove Foods from Your Diet in Order to Restrict Pathogen Microbes
    • Practice intermittent fasting
    • Eat fermented foods
    • Take probiotic supplements
    • Practice mindfulness or meditation
    • Stop using artificial sweeteners
    • Avoid taking antibiotics unless absolutely necessary
    • Avoid smoking
    • Choose your cleaning products wisely
    • Heal your gut – foods and supplements
    • Avoid NSAIDs
    • Drink quality water

    This was only an introduction in the microbiome world, I just wanted you to have a list of things that you need to be aware of. Maybe print a list with these and put it on your fridge, so you see it on a regular basis. Ideally, you’ll want to address all items in the list, but I know for many that not realistic. But if you fix half of the things you need to fix, it’s a great step forward. You will feel a difference.

    Let’s jump in and see practical ways to improve your microbiome. Whenever I found literature to support the claims, I included it in the text, for those who want to read more and evaluate the scientific evidence behind the claim.

    Eat the Right Foods the Promote a Good Microflora

    fermented cabbage sauerkraut sour glass jars
    Fermented preserved vegetarian food concept. Cabbage sauerkraut sour glass jars

    The easiest way to improve your gut microbiome is by eating the right foods. The typical low fibre Western diet works against our gut by lowering the diversity of our microbiome,  and by allowing the degradation of the mucus barrier.

    The advice “Eat your vegetables!” works perfectly. Eating whole foods such as fresh produce, whole grains, nuts and seeds feeds the good microbes and keeps the pathogens and opportunistic microbes in control.

    The best foods for the gut microbiota are those that are high in fiber and complex carbohydrates. These types of foods feed the good bacteria in our guts, which helps keep them healthy. Fiber and complex carbohydrates are compounds that humans cannot digest, so they pass through the stomach untouched. When they reach our gut, our microbiome feeds on them and populate the intestine. These compounds are called prebiotics. Note the PRE in the name, this signifies that they help probiotics thrive.

    The benefits of a high fiber diet are well researched, and there is no doubt that it could benefit anyone. The fiber diet should contain both soluble and insoluble fiber.

    Insoluble fiber helps mostly with the intestinal transit, but also feeds certain microbial populations.

    Soluble fiber is equally, if not more important, because it feeds a wider variety of microbial species in our gut.

    The take away is to make sure you get enough of both soluble and insoluble fiber. A common misconception is that eating foods with high cellulose content, fulfils the microbiome needs. This is not true, cellulose is insoluble fiber, so it solve only part of the problem. It is confusing, because nutrition labels do not make a distinction between soluble and insoluble fiber.

    Some high prebiotic foods are: carrots, cruciferous such as cabbage, broccoli, cauliflower, leafy greens such as spinach and kale, garlic, onion, leeks, barley, psyllium, and legumes. Check our dedicated page for a complete list of prebiotic foods.

    IMPORTANT NOTES: It is important that you eat a great variety of the prebiotic foods, as some of them contain some prebiotics, some contain others. Various prebiotics selectively stimulate the growth of certain probiotic strains. So in order to promote a diverse microbiome, you need to eat a variety of foods.

    There is also an important note about cooking vegetables, but that’s covered in the next section.

    Do Not Overcook Vegetables

    Cooking vegetables destroys some of the soluble fibers  and phytochemicals. These are what make your vegetables great for your microbiome. Eating some raw vegetables seems like the best choice then? Not really. When you cook your vegetables you can eat more of them. This ensures that you get plenty of micronutrients from your vegies. But you need to make sure you don’t over cook them, otherwise many of the beneficial nutrients are destroyed, as we said.

    As bad as overcooking is, there is one thing that is even worse for your friendly bacteria. We’ll touch on that in the next section.

    Remove Foods from Your Diet in Order to Restrict Pathogen Microbes

    You now have a list of potential foods to help you nurture your microflora, however, there are also some foods that can be harmful to the the balance of bacteria in your gut. It will prevent pathogens to grow, it will also keep opportunistic at bay, and it will help you manage your symptoms as you heal.

    The list is not universally applicable, because depending on your affection, you might need to remove different foods from your diet.

    For example, people who have Candida albicans overgrowth should avoid eating foods that feed the yeast. This includes high-sugar and starchy carbs (e.g., bread products).

    People with SIBO need to remove complex carbohydrates from their diet until the infection clears up, and those with IBS should avoid eating foods that are high in FODMAPs. Note that a low FODMAP diet is just the beginning of your healing journey. The objective is for you to be able to eat high FODMAP foods, because they are essential for a healthy microbiome.

    Though in general, removing sugar, and reducing starch consumption is great choice for anyone.

    This step is more of a DIY, since it depends on the foods that irritate YOUR gut. If you suffer from a serious condition, and all of the healthy foods irritate your stomach, consult a GI specialist and a dietician. Going alone on this journey is not advisable.

    What Diet Needs A Healthy Person for a Good Gut Health?

    If you are healthy and you just want to make sure you have a healthy diet before getting health issues, I commend you. This is the best approach. We spend so much in treating, but so little in preventing, when this should be the the approach in health. Ancient Chinese doctors were paid as long as the patient was healthy. When a patient got sick, the retainer fees ceased for the period the patient was sick.

    If you are healthy, the rules are relatively simple. Eat a lot of vegetables, whole grains, and include nuts and regularly in your meals. Fruits are great, but you can’t replace vegies for fruits, because the sugar in fruits can feed your harmful bacteria populations.

    Eat vegetables.

    Eat a variety of vegetables, as much as a variety as you can, and cook these vegetables as little as you can. As we showed earlier in the page, you need to balance how much you cook your vegetables

    The variety is needed because vegetables have their own nutritional make up, and they have different types of fiber and different phytochemicals that can stimulate your helpful bacteria species.

    Eat whole grains.

    Whole grains provide your microbiome with amazing nutrients including: resistant starch, non-starch polysaccharides, unsaturated triglycerides, and phenolics. This in turn will alter your gut microbiome for the better. Although all whole grains are good for your microbiome, oats contain more soluble fiber the all other grains, so they are the most effective. My favorite grain besides oats is non-sweet corn, the one that is used for tortillas and polenta.

    Eat nuts and seeds.

    The nuts and seeds are a source of fibre, unsaturated fatty acids and polyphenols, which all impact the composition of the gut microbiota. Here are some examples of nuts and seeds you can add to your diet for a healthy gut: almonds, cashews, chia seeds, flaxseeds, hazelnuts, peanuts, Brazil nuts, hemp seeds, pecans, pistachios, pine nuts, pumpkin seeds, sesame seeds, sunflower seeds, and my personal favorites the walnuts.

    Take Probiotics to Restore the Balance of Good Bacteria

    Taking probiotics is another way to improve your gut microbiome. Probiotics are microorganisms that can benefit our health. Probiotics colonize our gut, and are in perfect symbiosis with the human host. We offer food and shelter, they offer help with digestion and metabolism. Probiotics are the beneficial microbes in our microbiome. We have a longer article about what are probiotics, and how they help us.

    Fermented Foods, or Probiotic Foods

    We can also take probiotics from foods and supplements in order to promote healthy bacteria in the gut.

    Fermented foods are the best way to control bad bacteria proliferate. Fermented foods are sometimes called probiotic foods, to make a distinction between fermented foods that have been pasteurized, and they don’t contain probiotics anymore.

    Besides eating a healthy diet, probiotic foods are the best way for a healthy person to boost the welfare of their microbiome. In essence, we are introducing billions of colony-forming units in our gut. Even if the microbes don’t colonize, which might be the case with many fermented foods, the added probiotics help your microbiome by killing overgrown opportunist microbes, and pathogens. This is a a great win.

    Some great probiotic foods include sauerkraut, kimchi, miso, any sour pickles, (not vinegar pickles), yogurt, kefir, kombucha, water kefir.

    Probiotic Supplements

    For those who can’t have fermented foods, probiotic supplements are a great way to help your gut. The only problem with the probiotics is that the market is unregulated, and you could pend your money on stuff that doesn’t work. However, the concept of probiotic supplements is amazing, since it allows us to target specific benefits, by using specialized microorganisms.

    The work in the probiotic medicine is in its infancy, but even so, there are amazing results. Conditions such as IBS, Ulcerative Colitis, Pouchitis, can be drastically improved with probiotic supplements. Probiotic supplements can also help us rebalance our microbiome, prevent infections with opportunistic pathogens after antibiotics, control weight, etc…

    A common problem with taking probiotic supplements is that people sometimes think of them as vitamins. While the risk associated with probiotics is very low, there is no reason you should take them if you don’t need it.

    However, if you can’t eat fermented foods, or you can’t find them around you, some general maintenance probiotic supplements are good for you, even if you are healthy, as a preventive measure. The strains that are excellent tolerated and benefit you, are from the Lactobacillus and Bifidobacterium genus.

    Here are a few strains to get you started with your research:

    • Lactobacillus acidophilus
    • Lactobacillus fermentum
    • Lactobacillus paracasei
    • Lactobacillus rhamnosus
    • Lactobacillus reuteri
    • Lactobacillus Bulgaricus
    • Bifidobacterium longum
    • Bifidobacterium bifidum
    • Bifidobacterium Infantis

    We aren’t going to get into the details of what benefits they provide, because that is the subject of an entire article, but do your own research into these strains, or find a supplement that contains a combination of these.

    Another amazing microbe is Saccharomyces boulardii, which you can find in Florastor. It kills bad microbes, restoring a healthy microbiome.

    There are also Soil Based Organisms that could benefit us, but those are for healthy people. Since SBOs are not part of the human microbiome, they could potentially create more problems than solve, in people with immunity problems.

    Other ways To Improve Your Microbiome

    For people who don’t digest properly, a digestive enzyme might be a boost. However, it is not very clear what is the effect on your microbiome in the long term, so try to not rely on it. Sauerkraut, on the other hand, is full of enzymes, and we know is good for your gut.

    A great way to boost your microbime health is to lower your stress levels. There is a feedback reaction between your microbiome and stress. In the article “Stress & the gut-brain axis: Regulation by the microbiome“, the authors show that certain microbes can increase your stress levels, but also a stressful environment could increase the populations of stress related microorganisms. In conclusion, try your best to reduce the stress in your life.

    Get enough sleep. Sleep has many benefits for your body, including helping with digestion and weight loss. You microbes play a big part in this. Apparently, a disorganized and insufficient sleep, will impact your microbiome composition, leading to dysbiosis. Scientist don’t know why microbes are affected by our lack of sleep, but they do know that sleeping too little is bad for you.

    Stay hydrated. Drink half plenty of water each day. A healthy microbiome needs water. Your gut health is also affected by the lack of water. Water helps your gut move things through your digestive system so you don’t get constipated. Anecdotical, it looks like a healthy microbiome causes you to be thirsty more often. I did not find any research to support this, though, so take it with a grain of salt. However, we do know that thirst is controlled by both our throat and our gut.

    Practice mindfulness or meditation. Interesting research shows that a Mindful Awareness Program altered the participants’ microbiota. The study involved people aged 60 t0 85 years old. While the mechanism is not known, the results show that we can influence the composition of our microbiome by practicing meditation and mindfulness.

    Avoid or completely remove artificial sweeteners. Non-caloric artificial sweeteners are widely used because they are considered safe. One of the problems with artificial sweeteners is that used on a regular basis they alter intestinal microbiota, leading to dysbiosis. Long term, this eventually leads to higher risk of metabolic disfunctions. Research suggests that artificial sweeteners induce glucose intolerance.

    Avoid antibiotics. Antibiotics are amazing, they saved countless lives in the course of the history. However, they come with side effects. They literally wipe out all bacteria in our body, indiscriminately. Good or bad, antibiotics wipe them out. If you have a serious infection that just doesn’t go away on its own, you don’t have a choice. But consult with your doctor twice before taking the antibiotic prescription. Ask if there is no alternatives, or if it’s absolutely necessary  to take antibiotics.

    Avoid Smoking. Smoking alters the intestinal flora, found a 2018 review on Smoking and the Intestinal Microbiome. We know this is a tough one, and it’s hard to quit. Smoking affects us in many more ways than we thought.

    Choose your cleaning products wisely. Cleanliness is next to godliness. We all agree with that, but trying too hard might be in your disadvantage. A 2018 research on exposure to household disinfectants analyzed the gut flora of over 700 infants aged 3 to 4 months.

    According to the study, the prevalence of Lachnospiraceae, gut microbes associated with type 2 diabetes and obesity, was twice as frequent in homes where cleaning products were regularly used. At age 3, these infants had a higher body mass index than children without exposure to such high levels of disinfectants.

    Heal your gut. If your gut lining is not healthy, your microbiota doesn’t have a great environment. Ensure you get enough collagen in your diet, this will help you heal your gut lining. You can also take collagen peptides. Bone broth and salmon are great ways to get some collagen from your diet. Other supplements that can help with your gut lining are L-glutamine, Zinc, butyrate and Deglycyrrhizinated licorice.

    Avoid NSAIDs. NSAIDs (Nonsteroidal Anti-Inflammatory Drugs) are in our life all the time. We take them for joint pain, head aches, or other minor pains. They are a miracle in our daily life, but when abused they can affect your gut lining and your microbiome health. Use them wisely.


    A healthy gut contributes to overall health and immunity.

    Making appropriate lifestyle and dietary changes, we can alter the diversity and number of microbes in the gut.

    We can make positive changes by taking probiotics, following a fiber-rich vegetarian diet, and avoiding unnecessary antibiotics and disinfectants.

    You can also make simple lifestyle changes such as getting enough sleep and exercising regularly.

    Before making any drastic changes to your diet, though, you should consult your doctor. Some people, like those with irritable bowel syndrome or other medical conditions, may not benefit from probiotics and fiber-rich diets or vegetarian diets.