How to Restore Healthy Microbiome
and how to get rid of bad bacteria in the gut
Article by Stefan Burns - Updated October 2022. Join the Wild Free Organic email newsletter!
As our understanding of the gut microbiome and gut-brain axis increases, more and more people are asking the smart question of how they can improve their gut microbiome to upgrade and optimize their physical, mental, and emotional health.
At first it may seem bizarre that small microorganisms can influence foundational aspects of our being like our metabolism, memory, focus, and how we feel emotionally, but with a greater understanding of the microbiome and gut-brain axis it becomes clear quite quickly why cultivating a healthy gut microbiome is so important for not only gut health but for overall health and wellness.
There are two main strategies for improving the gut microbiome, and the first is to diversify the microbiome with more symbiotic microbes and to support their growth, and the second is to select against and reduce pathogenic microbe populations. When both strategies are paired together it’s possible to shift the microbiome towards greater symbiosis in a significant way quite quickly.
To educate you on how to restore healthy gut flora populations, in this article we’ll cover the following topics:
The microbiome and gut-brain axis
What is gut dysbiosis and why you should improve your gut microbiome
How to increase good bacteria in the gut naturally
How to starve out bad bacteria
Are you ready to heal you gut?
Read to the end to receive a special 10% discount on the Holistic Gut Health Guide, the all-in-one eBook to help you overcome your gut health and microbiome problems once and for all!
The Microbiome and the Gut-Brain Axis
The gut is collectively the largest overall organ, immune organ, and endocrine organ of the human body. Its functions are varied and complex enough that it has its own nervous system known as the enteric nervous system, often described as a “second brain” because the enteric nervous system functions relatively independently of the brain. An example of the independence of the gut, microbiome, and enteric nervous system is how it maintains itself and its functions even in those stuck in a vegetative state.
If we examine the gut from a numbers standpoint, it would best be considered a “microbial organ” because 90-95% of its total cell number are from microorganisms. Important for our understanding of the gut-brain axis is the concept that humans are a “superorganism” in which more than 90% of the total genes and cell numbers of the superorganism are microbial and not human in nature.
We’re more bacteria than human in some regards…
Humans have co-evolved with microorganisms for millions of years, and a healthy microbiome is vital to the optimal development and wellness of Homo sapiens, individually and as a species. Until just recently in our time spent on Earth, humans and the microbiome co-evolved under the conditions of a hunter-gatherer, or still very natural Neolithic villager lifestyle. As hunter-gathers humans were exposed to a wide range of natural environments. Every environment like the ocean or the jungle has a unique microbiome, and by spending time in these different environments, humans inoculated themselves with a wide range of microorganisms, thereby supporting diverse microbiome populations in their guts.
With the recent modernization of human society, dramatic changes to the individual and collective human microbiome have occurred, and exposure to the beneficial microorganisms of the world’s different natural environments has greatly reduced for most people. These alterations in the human gut microbiome are well correlated with the changes in disease patterns in modern society.
Whereas the human gut microbiome used to contain many more symbiotic microorganisms, now the average human gut microbiome contains less symbionts and more pathogens and commensal microbes.
Symbiotic: Symbiotic microorganisms like lactobacillus and bifidobacteria work with you to process food like fiber that you can’t digest into beneficial compounds like short-chain fatty acids and neurotransmitters that you use biologically throughout the body. Inside the gut symbiotic microorganisms interact with the digestive system to keep integrity of digestive barriers high, the immune system strong, the hormone (endocrine) system functioning properly, the activity of the nervous system stable and coherent, and brain functionality at optimal. As you can see, the microbiome touches nearly every aspect of human health.
Pathogenic: Pathogenic microorganisms like C. difficile, salmonella, E. coli, and E. faecalis can inhabit the gut in small or large percentages depending on one’s state of health, and their presence is problematic because pathogens don’t work with you the host, instead they seek to exploit you for their every advantage. If pathogens are able to expand in population unchecked they cause health problems that can range from mild like fever, diarrhea, and pain to severe like chronic disease, cancer, mental health problems, and organ failure.
Commensal: Commensal microbes are typically the most numerous in number, they’re helpful but not to the same degree as symbiotic microbes, and commensal microorganisms will shift to become more symbiotic or pathogenic in nature over time depending on the evolutionary conditions they experience.
What Purpose does the Microbiome Serve?
You can imagine how the human digestive system is a cozy place for microorganisms to live because it’s warm, protected from dangerous ultraviolet radiation from the sun and other hazards, and there is usually a constant influx of food. In exchange for these comfy conditions, a healthy microbiome beneficially influences the development and functioning of you, the host, by working with the cells of the digestive system to better digest food, by influencing and supporting immune and endocrine functions, and by producing valuable neurotransmitters that your nervous system and brain needs. Normal aspects of psychology, such as cognition, emotion, pain perception, social behavior, stress response, and a person’s character are all influenced by the microbiome of the gut.
Gastrointestinal disturbances affect the gut microbiome, and gut microbiome disturbances affect the functioning of the gastrointestinal system, and disturbances to either can be caused by many different factors, including an unhealthy diet, lifestyle and stress, excessive use of medications and antibiotics, mental illness, environmental toxins, and more. Gut dysbiosis can lead to the eventual development of neurocognitive disorders like mood disorders, depression, anxiety, ADHD, autism spectrum disorders, Alzheimer's disease, and Parkinson's disease.
The reason why humans and microorganisms evolutionarily formed a symbiotic relationship is thought to be primarily for metabolic reasons. The metabolic actions of the microbiome provides additional energy from food that otherwise wouldn’t be extractable, which is highly advantageous from an evolutionary standpoint, and because the composition of microorganisms of the gut microbiome can rapidly adapt to dietary changes, it provided humans an ability to adapt to new environments and novel foods faster, increasing the evolutionary fitness of our ancestors. Additionally, it’s thought that microbiome-brain interactions were a critically important factor that guided the evolution of the human brain and the development of the social brain. It’s our evolutionary history that explains why the gut-brain axis is such an important and powerful system in the body.
To boil it down our gut microbiome makes us more efficiently metabolically, confers upon us brain-development and cognitive benefits, and gives us greater survivability in a diverse range of environments. With this known, who wouldn’t want the best gut microbiome possible?
Together the digestive system and microbiome are the foundation of health from which everything else is dependent on.
The Holistic Gut Health Guide contains all the information you need to identify and understand the gastrointestinal and microbiome problems you may have while also providing you the most effective natural methods you can use to heal your gut. No gut health problems are unsolvable, give yourself every possible advantage along your gut health journey by reading an implementing the advice shared in the Holistic Gut Health Guide.
Some of the information in the Holistic Gut Health Guide isn’t common knowledge but when implemented it is highly effective in healing the gut and shifting the microbiome towards symbiosis. Give yourself every possible advantage along your gut health journey by reading an implementing the advice shared in the Holistic Gut Health Guide.
Why you Should Improve your Gut Microbiome
The are three main reasons why everyone should strive to cultivate the healthiest microbiome possible:
Improved digestion
Better metabolism
Increased consciousness
It’s impossible to have a good metabolism if digestion is inefficient. Metabolism can be defined as the uncountable amount of life-sustaining reactions that occurs every second in our body. By providing a lot of the chemicals required for metabolism, and by facilitating some of those reactions themselves, a healthy gut microbiome is essential for having the best metabolism possible; a metabolism that keeps you lean, healthy, and mentally sharp.
The general flow is Digestion ➞ Metabolism ➞ Cognition
And this cycle repeats around because you (hopefully) consciously choose what to eat! Because the microbiome affects digestion and the gut-brain axis, factors perturbing the gut microbiome affect the brain and mind simultaneously. This is important to know because if gut dysbiosis is experienced, then by result mental health problems have a much greater likelihood of developing.
If you’re reading this you either have a preventative interest in improving your microbiome, or you have some level of gut dysbiosis and are looking for ways to treat your condition. In the next chapter we begin our discussion on how to increase symbiotic microbes in the gut, but first what exactly is dysbiosis?
Gut Dysbiosis
Dysbiosis Definition: Dysbiosis is an unhealthy microbiome imbalance that results from unfavorable changes in the diversity, metabolic activities, and distribution of the gut microbiota
As we mentioned earlier, the diversity of the human microbiome has decreased dramatically with the widespread lifestyle changes that have occurred as people have moved from rural communities to large cities and also from the advent and overuse of antibiotics, pesticides, and antimicrobial cleaning products.
While most people don’t consider themselves to have dysbiosis, the reality of the situation is that unless you take great care to cultivate a healthy and diverse microbiome, then you share in the larger gut dysbiosis that human society is experiencing currently. Then on top of that if you are particularly unhealthy for whatever reason, be it diet, lifestyle, disease, or drug related, then your gut dysbiosis will be even worse.
Gut Dysbiosis Symptoms
Because the microbiome interacts with so many different systems throughout the body, there are a wide range of symptoms that result from gut dysbiosis. The most common symptoms are:
Irritable bowel syndrome (IBS) - gas, bloating, diarrhea, constipation, abdominal pain
Candida (yeast infection)
Food allergies, intolerances, and sensitivities
Nutritional deficiencies
Fatigue
Headaches, brain fog, poor memory
Mental health problems like anxiety, depression, insomnia
Skin issues like rashes, acne, eczema, psoriasis
Auto-immune disorders, allergies
Asthma
Gut Dysbiosis Treatment
There are many ways to treat gut dysbiosis and a pathogenic microbiome, some being safer and more effective than others. Unfortunately many common treatment methods like antibiotics are prescribed by those with an dangerously limited understanding of how the microbiome works, and while symptoms of dysbiosis may improve temporarily as the microbiome dies off from the antibiotics, the dysbiosis gets worse once the course of antibiotics is finished and pathogens expand outwards.
To treat gut dysbiosis that isn’t immediately life-threatening, one must look back to the factors that caused society’s larger gut dysbiosis to develop, and to then seek to integrate into one’s lifestyle the beneficial gut microbiome practices that our ancient hunter-gatherer and Neolithic ancestors followed, which were:
Interacting with a large variety of environments, getting “dirty” in the process
Eating a diet rich in fruits, vegetables, and fiber, all free of chemical contamination
Living a relatively stress-free and active lifestyle
Experiencing occasional periods of nutrient deprivation (aka fasting)
Utilization of the healing medicinal herbs that exist
What is the Fastest Way to Heal the Gut Microbiome?
To heal the gut microbiome we have our two strategies of promoting microbial diversity and the growth of symbiotic microbes while also selecting against pathogenic microbes. If you integrate into your life the lifestyle and dietary factors above, both goals can be accomplished simultaneously. Fasting and utilizing antimicrobial herbs are particularly useful in treating dysbiosis because not only do they support the growth of helpful symbionts but they in the same stroke make life much more difficult for pathogens. We’ll get into the specific reasons why that is in the next two sections.
The most effective strategy to heal the gut microbiome will be one that combines multiple strategies together holistically in a way that is safe and sustainable to maintain. The gut microbiome cannot be healed in one day, it will take at least a week to begin seeing progress and months to see significant progress, and in reality their is no final end destination as the microbiome is always changing and in flux. For these reasons, in order to make serious and lasting improvements in the microbiome, the recommendations given below must be incorporated into one’s lifestyle and diet naturally and without fuss (indeed they should be happily welcomed!) and become permanent life changes.
How to Increase Good Bacteria in the Gut Naturally
To increase the populations of good bacteria in the gut naturally it’s first required to expose yourself to these different symbiotic microbes in order to diversify the gut microbiome, and then it’s necessary to support their growth. Most people turn to probiotics in order to increase their microbial diversity, and this works because it’s easy to take probiotics, they’re widely available, and different multi-strain formations exist. A much more natural method for increasing microbial diversity is to place yourself in a variety of different environments. Eating fiber and fermented foods also increase good bacteria in the gut naturally. We’ll cover all the main strategies for increasing helpful microbial diversity and then discuss how to support the population growth of symbionts in the microbiome.
Expose Yourself to Different Natural Environments
Microbiomes exist everywhere, not just in the gut. Your skin has a microbiome, your bed has a microbiome, and every toilet has a microbiome. Some microbiomes are beneficial to exposure yourself to because they are full of useful microbes, whereas others like the toilet microbiome are best avoided (yuk!).
Microbes float through the air, live in the water we drink, and exist in the soil. These natural microbiomes, the ones that we interact with to varying degrees just by existing have proven themselves to be on the whole incredibly safe over millions and millions of years, and it’s exposure to the air, water, and soil microbiomes of nature that are the most beneficial for developing good gut health and a strong, diverse, and resilient microbiome. Perform the following activities to not only improve your health and fitness but also to exposure yourself to the diverse microbiomes of nature!
Hiking: Hiking through nature is an excellent wellness activity not only for the physical, mental, and emotional benefits, but also for the microbiome benefits. The fresh oxygen-rich air of a forest has special healing properties and this forest air will lightly expose you to different microorganisms. The density of microbes in the air is very low, but they do exist, and with a long hike with plenty of deep breathing the effect is not insignificant.
You can increase your exposure to the natural microbiome of the environment you’re walking/hiking through by interacting respectfully with the environment. Run your fingers through the moss, splash your face with water from the stream, forage on edible herbs that you may find like miners lettuce or mint. Some of these tips require common sense and some skills, for example don’t drink the stream water or splash it directly into your eyes, and don’t eat plants if you’re not a herbalist and haven’t 100% positively identified them as being safe, but if you have the sense and skills necessary to engage in these practices then it’s a powerful way to increase the diversity of your gut microbiome.
Swimming: Swimming in natural and clean bodies of water is another way to increase microbiome diversity as the full body gets immersed in the microbiome of the water. Swimming in the ocean is fantastic as the salt water naturally keeps a lot of harmful microorganisms low in concentration, and if you swallow some water every now and then accidentally after let’s say being hit by a large wave, that’s not necessarily a bad thing (but don’t go out of your way to do this). The key is natural exposure to the microbiome of the environment, what happens happens! Your gut microbiome is already a highly competitive place with limited space and access to resources, and whatever microbes that come in from the environment, your food, or probiotics will have to compete and carve out space and resources for themselves in order to survive and flourish in your gut whether they are symbionts, pathogens, or commensal microorganisms.
Gardening: Digging your hands into the soil, growing plants, and harvesting the food that results is one of the absolute best ways for the average person to increase the diversity of their gut microbiome. Gardening isn’t limited to just those who live in rural places, if you' live in the city you can likely find a community garden and establish a garden there, or you can garden at home outside on a small plot or inside using pots.
Gardening is the easiest and most fruitful way to expose yourself to the rich and highly diverse microbiome of the soil. Just as with us and our microbiomes, the soil microbiome is of key importance in the health and growth of plants and fungi. Soil microorganisms are the foundational biologic and chemical communication layer that life depends on, and digging around in good soil with your bare hands is a very effective way to improve the diversity of your microbiome over time. I can personally attest to this as gardening over the summer of 2021 noticeably improved my gut health, and anytime I have the opportunity to garden consistently my gut health seems to be more resilient.
Gardening also improves gut health and the microbiome through the cultivation of food. If growing fruits and vegetables without the use of any fertilizers or pesticides (highly recommended), then you can pick food directly off the plant and eat it. Every piece of produce has its own little microbiome, and eating food this way overtime is incredibly effective at diversifying and improving your own microbiome.
Probiotics for Gut Health
Certain species of bacteria have been studied scientifically for their effects on gut health, and as the biologic benefits of more of these strains have been quantified more varied probiotic supplements have hit the market. In some ways choosing the right probiotic can now be overwhelming as there are so many choices available! While probiotics are certainly useful in restoring populations of healthy microbes in the gut, I think it’s best to keep probiotic supplementation simple and consistent and instead spend more time in healthy natural spaces like our paleolithic and Neolithic ancestors did rather than fuss over which probiotics are best for you. It’s the fact that we’ve strayed away from lifestyle’s like theirs, not a lack of probiotics, that has led to the now “normal” gut dysbiosis that most people have.
Probiotics are definitely helpful though, and one reason why probiotics are useful for gut dysbiosis and gut health problems is that some of the microorganisms contained in the probiotic will form biofilms and colonize the mucosal layer of the digestive barrier, these biofilms persisting for a week or longer. If probiotics are taken daily then many probiotic biofilms colonize the gut and permanently change the diversity and composition of the microbiome. It’s like the colonization of North America by the British, French, and Spanish. One ship wasn’t enough to establish permanent colonies, but repeated ships of colonists and time turned out to be successful.
Biofilms are structures that certain microorganisms create that provide them shelter and help them adhere to surfaces, and they are arguably the most successful form of life on Earth, existing in nearly every environment. In the gut environment, both pathogenic and symbiotic microorganisms produce biofilm structures made of mostly polysaccharides, proteins, nucleic acids, and lipids and then adhere them to the intestinal mucosa where they can persist for a long period of time.
Used consistently probiotics have been shown to improve functional brain responses in healthy people, reducing psychological distress and anxiety conditions. Probiotics containing strains of lactobacillus and bifidobacteria appear to be the most effective, and these probiotic formations have also shown small but consistent benefits for those experiencing IBS. A multi-strain probiotic is usually more effective than a single-strain probiotic, and probiotics should be taken with a meal so more of the beneficial microbes survive the harsh acidic conditions of the stomach and can begin populating in the intestines, specifically the large intestine.
I have used the following multi-strain probiotic from Nature’s Bounty successfully many times when experiencing a gut health flareup and I recommend you use take it daily when experiencing a worsening of gut health symptoms.
Eat Fermented Foods for a Healthy Microbiome
Foods that contain sugar, starches, and/or fiber are able to be fermented by microorganisms, and most fermented foods benefit the gut microbiome by diversifying it with new species and strains of beneficial microbes from the fermented food. Fermented foods like kombucha, pickles, kimchi, sauerkraut, and others are typically easy to digest and contain many bioavailable nutrients; it’s no surprise that fermented foods have been cultured for thousands of years by different cultures around the world.
The best fermented foods are the ones that contain abundant fiber, as the fermentable fibers and starchy carbohydrates they possess further positively support the gut microbiome. Some of the symbiotic microbes of fermented foods will survive the transit through the harsh conditions of the stomach, and once this wave of food reaches the large intestine the survivors will establish themselves while the rest of the gut microbiome will begin metabolizing the leftover food as best as possible, producing beneficial biologic compounds like short-chain fatty acids.
Recalling the gut-brain axis, it’s been shown that the consumption of fermented foods is inversely associated with neurocognitive issues like neurosis and social anxiety. Even those at a higher genetic risk for social anxiety disorders showed improvements in their condition when consuming more fermented foods.
Eat a diversity of fermented foods at least a few times per week to receive the greatest benefit and to give yourself the best advantage in establishing a healthy gut microbiome.
Fiber Feeds the Gut Microbiome
Fiber is a type of carbohydrate the body is unable to digest. Some types of fiber are soluble in water, whereas others are insoluble, and some fibers are fermentable by the microbiome whereas others aren’t. The solubility and fermentability characteristics of fiber influence the entire digestive process, notably gut motility, and the more fiber is consumed, the bigger the effect on digestion.
Fermentable fibers are converted into short-chain fatty acids and other biologically useful metabolites by the microbiome of the large intestine, which are then absorbed into the bloodstream for various metabolic and cognitive functions. For example, the short-chain fatty acids that cross the highly selective blood-brain barrier regulate brain development and brain tissue homeostasis through their interactions with microglia immune cells of the nervous system. Disruptions to microbiome short-chain fatty acid metabolism have been linked to the development of neurocognitive disorders.
In general, most people consume too little fiber and would be well served to increase their fiber intake to forty-plus grams a day to improve their gut health, energy metabolism, and microbiome. Fruits and vegetables are the best sources of fiber because they also come paired with abundant vitamins and minerals in addition to useful plant phytochemicals. Plant polyphenols for example like flavonoids are also metabolized by symbiotic microorganisms in the gut microbiome, supporting their growth and your health.
How to Restore Healthy Gut Flora with Herbs
Spending time in natural environments, probiotics, and fermented foods increase microbial diversity, and eating adequate fiber is one of the best ways to then support the growth of a healthy microbiome, and the useful strategies for improving the gut microbiome don’t stop there. Herbs are one of the most powerful ways of reshaping the gut microbiome because not only do certain herbs support the growth of symbiotic microorganisms, they also select against pathogenic microorganisms at the same time.
How is it that herbs can do this, and what is the best way to use herbs for this effect?
One of the main reasons herbs are so good for the microbiome is because of the plant phytochemicals they contain like flavonoids. Flavonoids are secondary metabolites plants produce via the shikimate pathway for functions like protection against ultraviolet light; defense against insects, fungi, and harmful microorganisms; as antioxidants; and as plant hormone controllers. Flavonoids are biologically useful chemicals for plants, microorganisms, and humans.
With gut dysbiosis it’s also common to have gut health problems like leaky gut and IBS, and flavonoids like apigenin and quercetin are valuable in treating these conditions alongside their microbiome improving effects because they possess antioxidant, anti-inflammatory, and antimicrobial properties. Drinking herbal teas, or consuming herbs like parsley, rosemary, thyme, and others as part of your regular diet increases the amount of flavonoids that your body has access too.
As these flavonoids move through the digestive system some are directly taken up and used by the tissues of the gut like intestinal epithelial barriers, some flavonoids are transported and metabolized by the liver before being circulating throughout the body, and whatever flavonoids remain make their way to the large intestine where they interact with the microbiome. Throughout this whole process flavonoids are reducing inflammation throughout the body by neutralizing unstable and highly reactive free radical compounds, stimulate the natural healing and regenerative pathways of the body (autophagy), and improve the functioning of the cardiovascular and cognitive systems.
Flavonoids, and herbs by extension, are so useful for restoring healthy gut flora because they possess selective antimicrobial properties that inhibit the growth of various pathogens while supporting the growth of useful symbiotic genera like bifidobacterium and lactobacillus. These symbiotic microbes also produce their own antimicrobial compounds that make life difficult for pathogens, and in this way using herbs acts like a one-two punch in remedying gut dysbiosis.
Flavonoid-microbiome interactions further improve gut health and heal dysbiosis because they help regenerate mucosal and epithelial digestive linings. When digestive linings are thin and degraded, biofilms begin to affix directly onto epithelial cells, causing systemic inflammation by triggering a strong immune response, and the consistent use of herbs, say through drinking herbal teas daily, helps to dissolve these biofilms while restoring digestive barriers to healthy integrity. Once this happens symbiotic microbes can begin to reclaim “lost territory” and fulfill their normal role of keeping pathogenic bacteria populations in check by outcompeting them.
My favorite way of using herbs to promote the growth of a healthy microbiome is to drink herbal teas often and to utilize herbs in my cooking daily. A great herbal tea for gut health and the microbiome is a 1:1:1 blend of chamomile, dandelion, and peppermint. These three herbs are very well-known for their digestive enhancing effects, they contain abundant plant phytochemicals like flavonoids, and they have a track record of safe use thousands of years long. Plus this tea blend is remarkably tasty unlike some other effective anti-microbial herbs like wormwood.
In addition to herbal teas, utilizing herbs like parsley, sage, oregano, thyme, rosemary in cooking makes your meals tastier and healthier. Dried parsley is especially useful as it contains absurd amounts of nature’s most powerful flavonoid - apigenin, and dried parsley is really easy to incorporate into a variety of foods. Mix some along with some digestive-boosting black pepper into your favorite dips, spreads, or plain cream cheese. Sprinkle dried parsley onto favorite dishes like a grain bowl, pasta dish, or with potatoes, incorporate into a breading or season your protein of choice (meat, fish, tofu) with it. Herbs are highly versatile in the kitchen, and including more herbs into your diet improves your nutrition in addition to helping improve the health of your microbiome.
Herbs are one of nature’s best prebiotics, and if you have gut dysbiosis and/or are looking to improve your gut microbiome, I would recommend making a habit out of drinking herbal teas and in using herbs in your cooking daily. Personally it’s made a huge difference in my gut health and in the efficiency of my microbiome, and it can do the same for you.
Mountain Rose Herbs is my go-to supplier of organic herbs and spices, they sell all the herbs I mentioned which are dandelion root, chamomile flowers, peppermint leaves, and black peppercorns.
How to Starve Bad Gut Bacteria
Just as important as increasing microbiome diversity and supporting the growth of symbiotic microbe populations is to select against and reduce pathogenic microbial populations in the gut. This is very important for a few reasons, and it’s something that is underappreciated and often treated dangerously and inefficiently by the standard medical system.
The reason why reducing pathogenic populations in the gut must be a top priority alongside supporting the diversification and growth of symbiotic populations is because pathogens and symbionts compete against each other. When pathogen biofilms are numerous and deeply entrenched in the gut environment, they have established territory and nutrient streams, and from these “strongholds” they produce endotoxins that cause inflammatory and immune health problems and make life difficult for symbiotic microorganisms.
With gut dysbiosis, bringing in new symbiotic bacteria via probiotics (the standard recommendation) helps to beneficially shift the microbiome slightly, but for probiotics and other methods that increase good bacteria in the gut naturally, it’s much more effective to clear out pathogenic bacteria first and then overlap that effort with a symbiotic microbiome supportive protocol.
Salmonella among epithelial cells
The standard medical treatment that is done to accomplish the goal of reducing pathogens in the microbiome is one or more course of antibiotics, but as discussed antibiotics typically make gut dysbiosis worse in the long run unless the condition being treated is immediately life threatening. A better method of reducing pathogens is to cut them off from their food supply by changing the diet and via fasting. Switching the diet from highly-processed low-nutrition foods to whole and unprocessed foods rich in nutrients and fiber like vegetables is the first thing that will help a lot in reducing bad bacteria in the gut. The second thing that can be done which is highly effective in starving bad gut bacteria is to undergo a period of nutrient deprivation by fasting.
Fasting Kills Gut Bacteria
Fasting is incredibly useful in healing the gut and for reducing pathogens in the microbiome, but there is some nuance to the process. The length of a fast determines how strong the gut-healing and pathogen-reducing effect is, as does how often fasts are done, and the food eaten before and after a fast is incredibly important in the effectiveness of any fast. The composition of the microbiome is determined in large part by one’s diet, and eating poor quality food before and after a fast won’t make a noticeable difference in improving the gut microbiome over the long run.
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Intermittent fasting is the most popular type of fasting, typically scheduled as sixteen hours of fasting followed by an open eight hour feeding window. This ratio of fasting to eating can be shortened to 12:12 or lengthened to 20:4, with the longer intermittent fasts taking the body deeper into autophagy. The benefit of intermittent fasting is that by eating every day and with a long eating window, it’s much easier to maintain caloric balance or even a caloric surplus if trying to gain weight if underweight and/or build lean body mass if an athlete.
Intermittent fasting is most effective done consistently day after day, and overtime the slight daily increase in autophagy it stimulates during the fasting window heals and regenerates the body.
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Fasting for twenty-four hours is also known as one meal a day OMAD fasting. The most common type of OMAD fasting is eating dinner every night, though it’s not uncommon to do breakfast or lunch OMAD. OMAD is similar to intermittent fasting in that food is still eaten every day, and OMAD is typically done consecutively or for a certain number of days per week.
Since OMAD takes the body deeper into a fasted state of autophagy across twenty-four hours than intermittent fasting, it’s a good way to begin experimenting with longer fasts and to examine one’s relationship with eating behaviors. Physiological hunger is quite different than a psychological food craving, and if struggling with making healthy dietary choices, consistent OMAD fasting is a great way to reset psychological behaviors and patterns in regard to dietary eating patterns. The gut-brain axis can be beneficially altered with OMAD and with time you’ll become better at identifying when you’re truly physically hungry or when you simply have a psychological food craving.
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Fasting for longer than 24 hours reduces the body’s glucose sugars stored in muscle cells and the liver, and around the 48 hour mark when all the glucose has been depleted is when the body will enter ketosis. Ketosis is a process that converts fatty acids to energy molecules known as ketones. The brain runs exclusively on simple sugars, or if those are not available, ketones. When carbohydrates are in short supply, either from fasting or from eating a high-fat ketogenic diet, the body begins producing ketones to keep all the metabolic systems running smoothly.
Just as fasting is an alternate operating system for the body, switching from sugar metabolism to ketone metabolism is another metabolic state change that can be used to improve health and diagnose health issues. A 48-hour fast is useful because it takes the body deep into autophagy, deeper than most people have ever gone in their lives except maybe during a bad flu (hmmm why is that?). 48 hours of fasting really gives the digestive system time to rest and regenerate and takes the body to the edge of or into ketosis. A longer 72-hour fast will take the body fully into ketosis and the autophagy healing effects are even stronger.
A 48-hour fast is short enough to be easily completed by most people without serious health issues as long as they have the willpower, it doesn’t require too much planning, and it’s also long enough to bring about noticeable differences in digestion and energy. The gut health observations made possible during a 48+-hour fast are invaluable in accurately diagnosing gut problems and, subsequently, in healing the gut.
Daily 16:8 intermittent fasting has been shown to be useful in changing the composition of the microbiome over time, and more effective are 24 and 48+ hour fasts. The longer a fast, the more food clears the digestive system, and typically at the 48 hour mark the digestive system is cleared of food and strong evolutionary pressures are increasingly placed on the microbiome. Fiber transits through the gut slowly, and being a nutrient that pathogens can’t utilize but symbionts can, if a fiber-rich meal is eaten at the start of a long fast, symbiotic microbes will be supported while pathogens die off from the lack of available “easy nutrients” like sugar that they feed on.
As pathogens die off and the linings of the digestive system repair, space once occupied by pathogens is freed up and symbiotic microbes are able to reclaim this territory in the gut. Then when the first healthy and fiber-rich break-fast meal is eaten, symbionts further expand in their populations and pathogens are further selected against.
In my experience just a single 48 hour fast can be transformative in healing the gut and changing the composition of the gut microbiome as long as the diet eaten around the fast is healthy, nutritious, and fiber-rich. Additionally as discussed earlier zero-calorie herbal teas can be enjoyed during the fast which through their plant phytochemicals and flavonoid content provide nutrition to symbionts while actively suppressing pathogens. Just because you’re not eating any calories doesn’t mean it’s not possible to feed the symbiotic gut microbiome, and combining fasting with herbalism is therefore one of the most effective ways to cure gut dysbiosis naturally.
Foods the Kill Bad Gut Bacteria
Diet has a huge influence over the composition of the microbiome, and regularly eating foods that are nutritious and supportive of the symbiotic microbiome while being selective against pathogens is an excellent way to heal from gut dysbiosis and restore healthy gut flora. Here are three foods that kill pathogens while supporting overall gut health.
Pumpkin seeds are an example of a food that specifically kills bad gut bacteria. Pumpkin seeds have anti-parasitic and anti-microbial properties, and eating a bolus dose of pumpkin seeds (2+ handfuls, can also be alongside something like a slightly-green banana) is not only incredibly nutritious, but it creates a wave of microbiome-supporting food that transits through the digestive system killing pathogens while supporting the growth of symbionts. Eat raw pumpkin seeds as a snack a few times a week and over time it’ll have a positive influence on your microbiome.
Another food that kills bad gut bacteria would be coffee. Coffee contains fiber and flavonoids and other useful compounds that have been shown to shift the microbiome towards greater symbiosis while improving the gut-brain axis.
Pickles are another food that are good at killing bad gut bacteria because not only are they fermented and contain abundant fiber, cucumber seeds like pumpkin seeds have anti-parasitic and antimicrobial properties. In fact all squashes are very nutritious, contains abundant fiber, and are super useful for the microbiome.
Strong Antimicrobial Herbs
Another way to reduce pathogens in the gut is to utilize some of the stronger antimicrobial herbs that exist like oregano, black walnut hull, wormwood, and clove.
Oregano: Oregano is a well-known herb that has powerful antimicrobial and anthelmintic properties. Specifically, oregano oil has been shown to be highly useful in killing and eliminating parasites from the body, and it appears most of this effect comes from its main active chemical, carvacrol.
Black Walnut Hull: The outer hull of black walnut seeds is rich in tannins and black walnut hull is a well-known antimicrobial and anti-parasitic herb. Typically, an extract will be made by soaking black walnut hulls in alcohol, and the resulting tincture is dosed, but powdered black walnut hull can also be used.
Wormwood: Wormwood is a super herb for killing pathogens and expelling parasites from the body, especially roundworms and enterobiasis. Wormwood has been used medicinally in Europe for thousands of years, and it used to be common during medieval times to perform an microbiome and parasite cleanse using it a few times a year. Wormwood is extremely bitter and difficult to drink as a tea, and for this reason, in my experience it’s best used as a powder supplemented in pill form. Ingesting too much wormwood can be dangerous but the amounts used for a microbiome cleanse are nowhere near harmful levels.
Clove: Cloves are effective in killing parasites and pathogens like malaria, cholera, scabies, tuberculosis, and others. The high levels of tannins and eugenol that cloves possess are the chief agents responsible for their antimicrobial and anthelmintic properties. Clove can be taken tinctured or powdered
To utilize these stronger antimicrobial herbs you can take an oregano oil supplement alongside HealthForce SuperFood’s SCRAM supplement which contains black walnut hull, clove, and wormwood. Follow the 17 day dosing instructions for SCRAM and take ~500 mg of oregano oil daily at the same time.
These natural antimicrobial herbs are relatively gentle on the good microbes in the gut but are tough on pathogenic microbes.
I recommend you follow a natural herbal antimicrobial protocol like this at the very onset of your gut dysbiosis healing endeavor, and use those first two weeks to make the dietary changes you need to make in order for the microbiome to stay healthy long after the herbal supplementation is over. During the SCRAM protocol practicing intermittent fasting is useful, and then at the end of the SCRAM protocol you’ll have enough experience with 16+ hour fasts to begin implementing longer 24 and 48 hour fasts 1-2x per week. All the while during this you can drink herbal teas and begin spending more of your free time in natural environments. Make a game of it, make it fun! Write out a plan and stick to it, and if you do all these things together, then with time and consistency your gut dysbiosis can be cured and the gut microbiome can be radically transformed.
The gut-brain axis improvements that result will be striking, you’ll be surprised by the abundant energy and mental clarity you now have, gut health problems will greatly reduce in severity and possibly go away entirely. Expect improvements in any of the gut dysbiosis symptoms you’re experiencing! No promises as everyone is highly individual in their health and wellness, but it’s highly likely and definitely worth a dedicated honest effort.
If we each heal our own microbiome imbalances we can together begin to heal society’s dysbiosis and make the world a happier and healthier place.
If you read all the way here then it’s clear to me that you’re ready to do what it takes to finally restore your digestive system and gut microbiome back to healthy and optimal function.
I wrote the Holistic Gut Health Guide to help you accomplish exactly this! It contains all the information that you need to understand the gastrointestinal system, gut-brain axis, and microbiome in-depth, and the Holistic Gut Health Guide also educates you on the natural methods you can holistically use together like fasting and herbalism to transform your health from the inside out.
I’m so excited to be able to help you along your gut health and overall wellness journey with the Holistic Gut Health Guide! Please contact me with any questions you have and wishing you the best.
This article features excerpts from the Holistic Gut Health Guide. The Holistic Gut Health Guide provides you the information and framework you need to finally make the changes needed to remedy your gut health problems.
References:
Modern City Dwellers Have Lost about Half Their Gut Microbes.; 2022
Cleveland Clinic | Disease and Conditions. my.clevelandclinic.org/health/diseases
Liang S, Wu X, Jin F. Gut-brain psychology: rethinking psychology from the microbiota– gut–brain axis. Front Integr Neurosci. 2018;12:33.
Mayer EA, Tillisch K, Gupta A. Gut/brain axis and the microbiota. J Clin Invest. 2015;125(3):926-938.
Sánchez B, Delgado S, Blanco-Míguez A, Lourenço A, Gueimonde M, Margolles A. Probiotics, gut microbiota, and their influence on host health and disease. Mol Nutr Food Res. 2017;61(1):1600240.
Appleton J. The gut-brain axis: influence of microbiota on mood and mental health. Integr Med (Encinitas). 2018;17(4):28-32.
Cassidy A, Minihane AM. The role of metabolism (And the microbiome) in defining the clinical efficacy of dietary flavonoids. Am J Clin Nutr. 2017;105(1):10-22.
Su J, Wang Y, Zhang X, et al. Remodeling of the gut microbiome during Ramadan-associated intermittent fasting. The American Journal of Clinical Nutrition. 2021;113(5):1332-1342.
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