Updated: Mar 24
There are trillions of good bacteria and fungi in your gut (the small and large intestine). Despite some traditional beliefs about germs, many of these microorganisms are vital to the the healthy functioning of your body. They make up what is known as the "gut microbiome." When you ingest things that harm your microbiome, it can also harm your mental health. This interaction is known as the gut-brain connection.
The good bacteria in your gut - your “biome buddies” as I like to call them - fight off bad bacteria, support immune function, create vitamins, absorb nutrients, control inflammation, create neurotransmitters, and more. Each of these factors affect your thoughts, feelings, and behaviors, impacting your mental health.
What kills good gut bacteria?
If you want to fight mental illnesses like anxiety and depression, improving the health of your gut microbiome can certainly help. This means consuming foods and/or supplements that build up your microbiome, as well as minimizing foods or toxins that damage it.
Below are things that can kill your good gut bacteria or alter the balance of your gut microbiome:
Conventional meat & dairy
Lack of sleep
Drugs, alcohol, and cigarettes
Antibacterial soaps and sanitizers (the skin microbiome)
Long list, huh? Right about now, you're probably thinking "gosh, this guy Jake Kastleman is a nut." And you'd be right. I am a nut. Which is why I am writing this blog - to help others who are nuts like me.
Don't let this list I've created fool you. I don't avoid all these all the time. And if I tried to, it would only serve to make my mental health worse (been there, done that). My purpose in writing this article is not to give you ulcers, but to give you a place of reference for what to avoid, and to educate you on the effects of many things that we consider “normal” in today’s society.
Don’t expect to avoid all of these things all of the time. Your body is resilient, and it can manage some exposure just fine. That’s what your immune system and microbiome are for!
So, take a deep breath. It’s time to learn.
Antibiotics kill good gut bacteria
Antibiotics are designed to kill bacteria. They save people’s lives in some circumstances, and they have performed miracles more than once. But unfortunately, antibiotics do not distinguish between good and bad bacteria.
Taking antibiotics can lead to what is known as “gut dysbiosis" - or a severe imbalance in the microbial species within your gut. With enough antibiotic treatments, your gut can become a hostile environment for good microbiota, killing them off until there are far too few of these biome-buddies left. What takes their place is an over-abundant number of "opportunistic" species of microorganisms, such as Candida, H. Pylori and others.
These opportunistic species are not "bad" necessarily, rather they can take the opportunity to grow too prolifically when there is a shortage of competing species. When they do this, they can begin releasing too many toxins into the body - as may be the case with Candida - and their over-abundance can prevent other species from keeping their foothold in what should be a balanced and diverse ecosystem. When this happens, it can potentially lead to some pretty rough stuff.
Disruption of gut microbiota can lead to “diabetes, obesity, inflammatory bowel disease, asthma, rheumatoid arthritis, depression, autism, and superinfection in critically ill patients.” (Zhang & Chen, 2019)
How long does it take your microbiome to recover from antibiotic use? Research shows that it takes an average of 6 months for your gut to recover from one round of antibiotic use. That being said, this timeframe is based on your individual diet and environment.
If you have a diet low in vegetables and other fibrous foods, absent of probiotic foods, high in processed and packaged foods, and are constantly subjected to toxins in your food and environment - such as pesticides, chlorine, and fluoride - it could take a long time for your gut to recover, if at all. That being said, you can heal your gut through a good diet and lifestyle changes.
Herbicides & pesticides kill good gut bacteria and can impact physical and mental health
Much of our food in the U.S. and throughout the world is sprayed with herbicides and pesticides. Glyphosate (RoundUp) is the most commonly used herbicide, with 280 million pounds sprayed annually worldwide.
Unfortunately, glyphosate is bad news for your microbiome. This is in part because it was originally patented as an antibiotic, and so it is responsible for killing helpful microbes that are crucial to our health, both in topsoil and in our bodies.
According to medical and environmental expert Dr. Zach Bush, findings that glyphosate kills the microorganisms in our body are especially concerning because the microorganisms in our body are the "velcro" that hold together biological barriers such as the gut lining and blood-brain barrier. Without proper biodiversity and the presence of enough helpful microbial populations, our gut lining and blood-brain barrier can begin to break down, allowing foreign invaders in and out, leading to inflammation and infection. The breakdown of the gut lining and blood-brain barrier are correlated with chronic physical and mental illness and disease.
Glyphosate inhibits the shikimate pathway in plants. The shikimate pathway is the metabolic process that plants use to create amino acids. While this does have implications for the nutritional content of our food (to learn more about that watch this), it is very important to note that many microorganisms also utilize the shikimate pathway. Thus this inhibition from glyphosate stunts their growth and destroys them.
The original theory in the 70's was that glyphosate would not harm humans, because we do not use the shikimate pathway as plants do. Back then, we knew next to nothing about the microbiome or our dependence on microorganisms for our survival. We also had no idea that we relied on the microorganisms in soil for the quality and nutritional content of our food. But now, we understand these things.
We have been well aware of the presence of the microbiome since we finished the microbial gene map of the human body in 2007. We have come to understand that consuming glyphosate and other herbicides and pesticides is harmful to humans because it is harmful to the trillions of organisms throughout our body that we rely on for a plethora of processes. It is also harmful because glyphosate destroys the microorganisms in topsoil, severely altering the nutritional makeup of our food.
What can this lead to?
“The pathologies associated with altered microbiomes after exposure to environmental chemicals include immune dysfunction, altered carbohydrate and lipid metabolism, and neurological and behavioral impairments.” (Dr. Chui, Implications for Human Health: Pesticides and Other Environmental Contaminants Alter Gut Microbiome)
Pesticides are used on many foods including wheat, rice, fruits, vegetables, and canola. Of particular note are wheat and rice, which have high averages of pesticide exposure.
For some practical advice on how to detox and protect your body against glyphosate, you read my article on it here.
Again, remember that you are not going to avoid exposure to pesticides/herbicides altogether. It is important to do some things to help, but know that your body is resilient and caring for your mental health means letting some things go so you can live with balance. Learn, make some changes here and there, and beyond that live with joy and gratitude! The world is a wonderful place!
Glyphosate and Glycine
Glycine is an amino acid that your body uses to create proteins. It is one amino acid that is responsible for the production of hormones and enzymes among other things. Hormones play an important role in mood, energy, and mental well-being. Your body also utilizes glycine for the detoxification of the body.
As a neurotransmitter in the brain, glycine contributes to cognition, mood, digestion and appetite, perception of pain, immune function, and sleep.
The commonly used pesticide glyphosate is an altered amino acid. From what I have come to understand in my studies on the subject, glyphosate takes over glycine receptors in our brain and body where the amino acid glycine would typically reside. This inhibits glycine’s function in the body.
It is interesting to me that anxiety and depression rates have grown so much in the last few decades, while at the same time we began glyphosate during the 70’s. It kills good bacteria that are responsible for producing hormones and neurotransmitters for our brain, and it also interferes with glycine, which plays a direct role in brain function.
Could glyphosate be a contributing factor to our rates of mental illness which have increased over the last 50 years?
What Can You Do?
Check out my article on how to detoxify and protect your body from pesticides/herbicides. You'll find it here.
Conventional meat & dairy can kill good gut bacteria
Ahh... ice cream and pizza. The fantasy foods of us all. Delicious, decadent, and...deadly? That’s right. The ice cream, pizza, and steak that we so adore are killing our biome-buddies.
Which is a real bummer, cause ice cream is absolutely delicious.
But why? Well, cows are meant to eat grass. Animals raised in big business, on the other hand, almost always eat run-of-the-mill corn, wheat, or oats. So, what do these foods contain most of the time?
You guessed it. Pesticides… which are antibiotics.
And guess what else? Many of these animals, such as cows and chickens, are pumped full of additional antibiotics too.
Well, for one, antibiotics kill good bacteria and lead to an imbalance in the gut microbiome, which invariably leads to weight-gain. So, this makes the cows and chickens fat faster. And that’s good for business.
In addition, many of these animals are put on diets that make them sick and are raised in cramped, filthy environments to save farmers money and increase profit. Which I totally understand, as farmers often don't make enough money to feed their families. Cows are eating corn, wheat, and soy which they are not meant to eat, because these crops are subsidized by the U.S. government - meaning they are cheap and abundant. Corporations use an enzyme solution which they feed to the cows to get their bodies to process the stuff. But this doesn’t change the fact that cows are meant to eat grass, not grain or soy.
So how can we solve this? Well, we can buy organic or grass-fed meat or dairy. This should essentially solve the problem.
But, if you’re like me and you need to save a couple bucks, you can go for options that say “no antibiotics used.” This doesn’t solve the problem of the animal’s consumption of pesticides, or their poor diets or environments, but it is at least a halfway point for those who lack the budget for grass-fed or organic.
A better solution though, would be to find a local meat and dairy farmer that uses humane and earth-friendly means of raising their animals. You can buy raw milk and dairy in some states. This is also often a better choice because raw dairy contains the naturally occurring probiotic bacteria that helps your body break down and digest the dairy. This is not the case with pasteurized dairy, because it's had all the good bacteria cooked out of it.
This guy's dying for some sleep...
Lacking sleep alters your microbiome
A study published in October of 2019 found convincing evidence that lack of sleep has a negative impact on the diversity of gut microbiota. Less diverse microbiota in the gut essentially leads to worse physical and mental health.
The study found that specific populations of gut bacteria increased while others decreased depending on the amount of sleep both human and non-human subjects had.
Other studies have shown that, just like humans, gut bacteria function on a circadian rhythm. It is important that we have a regular sleeping schedule when we can, in part because our microbiota sleep when we do. But of course, there are times when things like family, friends, children, or simply staying up to have a good time once in a while takes precedence. And that's okay!
Stress can break down your gut wall
High stress has been shown to influence the microbiome and the gut lining via the intimately connected gut and brain, a.k.a. the “gut-brain connection” or “gut-brain axis”.
Here’s how it works.
Within your intestines are trillions of microbiota (bacteria). Your intestines have a gut wall and two layers of mucus. One of the layers of mucus does not contain biome-buddies (bacteria). The second layer of mucus - just inside the wall - does contain biome-buddies.
Turns out, when we are under high stress, these mucus layers begin to break down. If they break down far enough, then antigens from bacteria may begin to break through your intestinal wall, entering your circulation - a place you don't want them to be.
If your intestinal wall breaks down far enough, due to stress or other nutrition factors, you can develop what is called “leaky gut syndrome.” This is when proteins that are being digested enter your bloodstream through holes in the gut wall. These partially digested proteins - seen as intruders by your immune system - are then targeted by your body’s defenses.
This sets your immune system on overdrive, which can put you in a state of fight-or-flight; hence, chronic anxiety. This is certainly only a piece of the equation, but a piece nonetheless. For more information on how your gut and brain connect, you can read my article on the 4 Ways the Gut and Brain Connect.
Sugar inhibits the production of good gut bacteria
It probably doesn't come as a surprise to you that refined and processed sugars are bad for your gut and harmful to the gut microbiome. Let's be real, none of us is under the illusion that sugar is a winning health food, am I right?
Large doses of glucose and fructose - the building blocks of refined white sugar, sucrose, and corn syrup - impede the production of proteins that feed certain good bacteria. One of these bacteria, Bacteroides thetaiotaomicron, ferments dietary fiber from fruits, vegetables, whole grains, and beans, turning that fiber into nourishing molecules for the brain and body.
Refined sugar, especially high fructose corn syrup, can lead to inflammation in your gut and other parts of your body. Inflammation causes “arthritis, asthma, atherosclerosis, blindness, cancer, diabetes and, quite possibly, autism and mental illness.” (Vanderbilt School of Medicine, 2015)
Inflammation in the gut can lead to neuroinflammation, which is linked with depression.
Sugar is also responsible for feeding a fungus that lives inside your gut called Candida. This fungus is necessary for the absorption of certain nutrients and the decomposition of the body after death. Just as is the case with most microorganisms - if not all of them - Candida plays its essential role in the diverse ecosystem of microbes. However, if you consume too much sugar regularly, Candida can grow and multiply too prolifically, leading to an overabundance of this species, which inhibits the functionality of other beneficial gut microbes and breaks down the gut lining. It can be a serious problem for digestion, skin health, energy levels, and mental health.
To learn more about Candida and how to treat it, check out this article.
Is all sugar bad for me?
Now here’s an important question that I found myself asking when I learned these things. If fructose and glucose inhibit proteins that feed good bacteria from being assimilated and they feed Candida as well, does that not mean that fruit or other natural sugars like raw honey and maple syrup are bad for me?
Here are a few things to keep in mind about the differences between refined sugars and natural sugars:
GMO sugar beets and pesticides/herbicides
Most of the refined white sugar in the U.S. comes from sugar beets. Essentially all of those beets are genetically modified and sprayed with a high amount of herbicides/pesticides. So, when you consume refined sugar within a processed or homemade food, you are typically also consuming glyphosate (RoundUp).
As we've already discussed, glyphosate is a patented antibiotic. So by consuming it, you are potentially killing your gut bacteria, giving room for opportunistic species to grow and beneficial species to wane. As beneficial microbes are what keep your gut lining together, glyphosate is thereby responsible for breaking down your gut lining and potentially leading to "leaky gut" which is associated with many chronic physical and mental health conditions.
GMO corn and pesticides/herbicides
Corn syrup and high-fructose corn syrup are made from GMO corn that is sprayed with herbicides/pesticides and/or corn that is genetically modified to produce its own pesticide.
Refining and processing lead to poor low nutrition & high inflammation
Refined white sugar and corn syrup are processed, refined, and hydrolyzed. While I'm sure the reasons this is problematic are more than a few, here is what I have come to understand on the subject.
Refined sugars like corn syrup and refined white sugar are a far higher concentration of sugar than you would find in raw maple syrup or raw honey - or even raw cane sugar for that matter. Refined sugars process via digestion much faster than natural sugars do. They can leave you craving more and never being satisfied because of how quickly they process in the body and the absence of any substantial nutrition. They spike your blood sugar quickly and intensely, soon followed by a come down (much like a drug), potentially causing you to desire that same rush so you can be "up" again.
You'll typically consume more refined sugar than natural sugar because it is not combined with healthy fiber like fruit is. Fiber helps the body process carbs and also brings a feeling of satiety, not to mention it feeds beneficial bacteria (in a way undoing damage sugar might cause to beneficial gut microbes). Raw sugars contain only a percentage of glucose or fructose and the rest is other plant compounds including phytonutrients, enzymes, vitamins, and minerals. Refined sugars do not contain fiber or any other beneficial compounds - only an extraction; a portion of the diverse, beneficial whole. Fruit juice concentrate is the same way unfortunately.
White sugar, corn syrup, fruit juice concentrate, and especially high-fructose corn syrup can be extremely addicting, as they trick your body into thinking it will obtain sustenance by consuming it, and then receives only empty calories. These sugars spike your blood sugar and dopamine neurotransmitters to unnatural highs, leaving your receptors damaged or at least habituated to higher stimulation than is normal. Refined sugars also alter your taste buds and flavor preferences to desire food that is far sweeter than the foods we have evolved alongside as a human species for thousands of years.
So, would it be potentially problematic for my body and brain if I were to eat a ton of fruit all at once? Yes. Would it also be a problem to consume a bunch of raw honey or raw maple syrup all at once? Yes. That is why I need balance in all things. That being said, it is far easier to overdo it when something is a hyper-concentrated form of its original self. It will also leave me craving more when my body does not obtain the beneficial compounds like fiber, vitamins, and phytonutrients that its genetic composition expects when it encounters sugar. It is not able to adequately handle such a rush of one compound without the diverse substances that are meant to accompany it.
Medications can alter your gut microbiota
I realize that medications are a God-send for some individuals, and so I am not referring to it here with the intent to upset anyone. I know people who depend on their medication to live a functional life, and I accept the degree of good that medication has done for the world.
If you take a medication, this section is not meant to dissuade you from taking it. That is your journey and decision and I fully respect it. My only purpose is to educate you.
Below are medications that are known to impact the composition of your gut microbiome.
These over-the-counter medications can radically alter your gut bacteria, leading to gut dysbiosis. They are also toxic to the liver and kidneys. They include medications like Aspirin, Advil, Ibuprofen, Naproxen, and Celecoxib.
I understand how commonplace these medications are in western society, but they are truly damaging to the gut microbiome and should be avoided if possible. That being said, I understand that you may be someone who uses them regularly for pain management and I can imagine how difficult the thought of coming off of them could be.
If you suffer from chronic pain, you may consider getting a food sensitivity test done, such as an IgG or IgA blood test, to see if you have any food sensitivities. These could be contributing to the inflammation in your body. Inflammation is always involved in chronic pain, and foods such as refined sugar, processed dairy, or gluten can be contributors.
Serotonin is a neurotransmitter that stabilizes mood, gives you feelings of peace and well-being, and contributes heavily to your overall happiness. Recent studies are showing that 90% of your serotonin is actually produced in your gut, not in your brain. It turns out that your little gut bacteria-buddies in your microbiome - the Bifidobacteria and Lactobacillus species - are in part responsible for the processes that produce serotonin. They also help produce neurotransmitters dopamine and GABA.
There are two specific strains of gut bacteria by the names of Turicibacter sanguinis and Clostridia that are in charge of finding and transporting serotonin into other bacterial cells. According to studies in rats, these two strains of bacteria were reduced in the gut when rats were administered SSRIs. Further studies demonstrated that when SSRIs were present, Turicibacter and Clostridia were blocked from transporting serotonin into cells.
Other medications linked with negative effects to the microbiome
Anti-androgen oral contraceptives: birth controls, progesterone, acne medications
Beta-sympathomimetic inhalers: inhibit premature labor
Metformin: type 2 diabetes medications
Oral anti-diabetics: other diabetes medications
Proton Pump Inhibitors (PPIs): Heart-burn & acid reflux medications
Triptans: Migraine and headache medications
Artificial preservatives are found in many packaged foods. They are a cheap, convenient way of keeping food good long-term. It is understandable why businesses have turned to them. Unfortunately though, these ingredients cause damage to our bodies.
Research conducted at the University of Hawaii Maui College found that sulfites in food preservatives kill or inhibit the growth of good bacteria. These tests were conducted with preservatives that were present in levels regarded as safe by the FDA.
With such complex food labels these days, how do you know which ingredients are artificial preservatives? Here is a list of some different names for preservatives in food:
Ingredients that end in “sulphite” or “phite”
Ingredients that begin in “sulph” or “sulphur”
Ingredients that have the words “nitrate” or “nitrite”
Butylated Hydroxyanisole (BHA)
Butylated Hydroxytoluene (BHT)
Here is a list of preservatives that are specifically antimicrobial (kill bacteria):
Benzoic acids and benzoates
Acetic acid and acetate salts
Sorbic acids and sorbates
Now, this list doesn't mean that all of these things are "bad". Hydrogen peroxide, for instance, is used to clean wounds. This is just to help you be mindful of these ingredients and minimizing them in your diet. The best way to avoid these is to cook whole, plant-based foods that you buy from a local grower, or at least from the grocery store. If you can afford it, I also highly recommend Thrive Life foods. They are super easy to use, save tons of time, and because they are freeze dried the nutrient content is absolutely incredible - much like buying from a local grower.
Emulsifiers may alter your gut microbiome
Many emulsifiers are correlated with disruption and damage of the intestinal wall and other health issues. They cause inflammation (which can affect mental health) and are correlated with autoimmune disease, specifically Crohn's disease.
Polysorbate 80 in particular is correlated with the alteration of the gut microbiota. There is more research to be done on this topic. Currently, the Medical Research Council (MRC) is carrying out the Mechanistic Nutrition in Health (MECNUT) Emulsifier Project to see how emulsifiers affect health and the gut microbiome.
Drugs, alcohol & cigarettes harm your gut
Psychoactive drugs such as meth and others are shown to have a devastating effect on gut microbiota. Two beneficial bacterial species, Firmicutes and Bacteroidetes, were shown to be impacted the most. Firmicutes are in part responsible for breaking down carbohydrates in the gut that can't be broken down by your body's enzymes. Bacteroidetes also help digest carbs and possess genes that encode for specific enzymes in the body.
Cigarettes may cause an imbalance and alteration in gut bacteria. In certain studies, smokers showed an increased level of Bacteroidetes with decreased levels of Firmicutes and Proteobacteria compared with non-smokers. Proteobacteria are thought to prepare the gut for colonization of microorganisms by maintaining the anaerobic environment necessary for bacteria to survive.
Red wine in moderation (a glass per day) can be good for your gut bacteria due to its polyphenolic content. The health benefits of wine increase if it is from a vineyard that has healthy soil filled with soil-based probiotics (SBO's), as is the case with any plant food. SBO's are naturally occurring in soil that has not been treated with chemicals such as pesticides, herbicides, and synthetic fertilizers.
Overconsumption of alcohol, on the other hand, can lead to increased intestinal permeability (leaky gut), inflammation, and cell oxidation.
Chlorine alters your microbiome
Chlorination significantly alters the microbiome. This does make sense, as chlorine is used as an antimicrobial, and so it does kill bacteria in the but.
Chlorinated water lowers the biodiversity of species in your gut. The level of biodiversity of microorganisms in your gut is the most significant contributor to the health of your gut microbiome. The higher the biodiversity you have, the more checks and balances there are to ensure no one species overgrows, and the more variety of functions microorganisms can carry out.
Easy ways to avoid chlorine
If you didn't know this, it may seem overwhelming to hear it. Don't worry though, there are some fairly easy ways to avoid some chlorine.
Purify your drinking water
One is to get a high quality water filter. I studied this a fair amount to choose something that would work for my family. My recommendation would be to purchase a water distiller. Be sure to purchase one that does not come with a plastic container, as distilled water can leech plastic and then you end up drinking it. We use this one.
I will say that filling up the distiller and waiting for it to run for 6 hours does get a little old however. If that sounds like a pain, another great way to filter your water is to purchase a reverse osmosis unit for under the sink. Here is the best one I've found. I've had a few people recommend it personally. It does require installation, and you need to have an under-the-sink space big enough for it. So just bear that in mind.
Purify your shower and bath water
As your skin is the largest organ in your body and readily absorbs into your bloodstream whatever you apply to it, it is also a good call to get a filter for your shower and bathtub. I spent forever trying to find easy-to-install, high quality shower and bath filters. After hours of research, I'm happy to say I found the "golden units" if you will.
I recommend this shower filter by Aquasana. It is by far the best filter and easiest install (a child could do it) I found. It's pricey, but worth it.
I recommend this bathtub filter by CuZn. Why? Because it I searched for hours and it is literally the only viable one I could find. Not a great reason, but it's a reason. That being said, I purchased an under-the-sink filter for my kitchen by CuZn that is really great, so my opinion of their product was already a positive one. I trust that the filter works, plus it was as easy as set-and-forget to get it rolling.
Another route you could go is to get a whole home water filter. This is certainly something to look in to if it is an option for you.
Antibacterial soaps & sanitizers (the skin microbiome)
Antiseptics and antibacterial soaps and sanitizers kill bacteria. Just like antibiotics, they do not differentiate between bad and good bacteria. But of course, it's not like you're drinking these antibacterial products, so why be concerned about it? Because, your gut isn’t the only place that you have a microbiome.
You have good microbiota throughout most of your body and on the surface of your skin. Just like in the gut, these biota-buddies help balance your body and carry out many important functions. We scrub our bodies all day with antimicrobials, all the while we are mistreating our skin's ecosystem. This can lead to poor skin health.
So, how do you solve this? Simply stop showering. That's what I do. Okay, so I'm kidding. Using natural soaps like Dr. Bronner's can help a lot. That's what I use, and now my skin smells like a newborn baby.
Seriously, you oughta' smell it sometime.
Despite what some may say, I believe we should not be covering ourselves and our environment in antiseptics and antibacterial soaps and sanitizers. We need to seek to understand the full implications of doing this before we start killing all of the good and bad bacteria around us. In reality, there is not "good" and "bad" bacteria, but simply balance and imbalance.
Our planet, and the ecosystem that survives inside and outside our body, require biodiversity, balance, and harmony. When we attempt to kill all the "good" and "bad" bacteria, we create superbugs, allowing for the overabundance of some microorganisms and the depletion of others. This prevents our environment from healing itself, thereby eventually depleting our bodies and brains from having the ability to heal themselves as well.
Don't fall into microbiome madness, you hear?
My purpose in writing this article is to give a comprehensive overview of what kills and alters good gut bacteria. I am sure there are items that I missed, as there always is in life, right? It's part of being human.
I believe you deserve to know these things because I want you to feel empowered with knowledge to improve your health. Don't let all of it stress you out though, mkay? Nutrition is important for mental health, but taking it easy and making small, experimental changes over time is so much better for your happiness and peace than being afraid that you need to change everything all at once. Let one tiny change be good enough. You are good enough as you are, and you're simply learning as we all are. Let improvement come little by little.