Dysbiosis refers to an imbalance in the microbiome – the trillions of organisms that live in and on your body, mostly in your GI tract. This imbalance can lead to overgrowth of some organisms, undergrowth of others, and a change in the metabolic activity of the microorganisms. That metabolic activity determines the byproducts that your microbes are making; things like hormones, and vitamins, and neurotransmitters that are involved in virtually all of your bodily functions. And that’s why dysbiosis doesn’t just affect your gut – it’s associated with a wide range of problems, including autoimmune disorders, skin conditions, mental health problems – and more. In this episode: how and why we get SIBO.
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On today’s show. One of the most misunderstood GI conditions – and one that millions of people suffer from. I’m talking about dysbiosis. SIBO – small intestinal bacterial overgrowth, is a form of dysbiosis and I’m going to discuss SIBO more specifically later in this episode, but I want to make sure you understand the principles behind dysbiosis before we delve into SIBO. In today’s show I’m going to focus on causes and symptoms of dysbiosis, and then in next week’s episode I’ll go over testing and treatment.
Dysbiosis refers to an imbalance in the microbiome – the trillions of organisms that live in and on your body, mostly in your GI tract. This imbalance can lead to overgrowth of some organisms, undergrowth of others, and a change in the metabolic activity of the microorganisms. And this last part is important because that metabolic activity determines the byproducts that your microbes are making; things like hormones, and vitamins, and neurotransmitters that are involved in virtually all of your bodily functions. And that’s why dysbiosis doesn’t just affect your gut – it’s associated with a wide range of problems, including autoimmune disorders, skin conditions, mental health problems – and more.
So what causes this imbalance? One of the biggest contributors to dysbiosis is the fact that we live in a super sanitized environment: we are over medicated; our food is processed and full of pesticides and chemicals; we don’t spend enough time in nature exposed to soil microbes that help to replenish our own microbiome; we’re constantly cleaning our homes – and our bodies with products that strip our microbiome, and we’re really stressed out, and I’ll explain later in this episode, why stress is a major microbial disruptor.
So while there are many different factors that can cause dysbiosis, I want to give you a framework of 4 major categories to help you think through what may be disrupting your microbiome.
1. Medications
2. Food
3. Emotional factors
4. Anatomy & Physiology
You may think of your medicine cabinet as the place to go for solutions, but when it comes to dysbiosis, it’s often the source of the problem. I’m going to go over the 4 biggest offenders, but keep in mind, this is not a complete list. Let’s start with the most problematic: Antibiotics prevent death from serious bacterial infection every day, but they’re also tremendously overprescribed. Conservative estimates from the CDC suggest that as much as half of all antibiotic use is inappropriate and unnecessary. The startling statistic is that just five days of a broad-spectrum antibiotic like the kind used to treat a sinus or urinary tract infection can remove up to one-third of your gut bacteria. And the problem is that antibiotics don’t just kill off pathogens, they also destroy many of the helpful species that play an important role in your overall health. When you remove these essential microbes, you allow more problematic ones that are normally present in low amounts to flourish, and the result is dysbiosis. Most of us with a healthy gut can tolerate a course of antibiotics every couple of years, but if you’re averaging more than two rounds of broad-spectrum antibiotics a year or taking longer courses, or if you’re under 18 and your microbiome is still forming, the drugs can do serious and sometimes lasting damage. In my practice, I see lots of people with autoimmune conditions who have a history of months (and sometimes years!) of antibiotics for things like Lyme disease or acne. And the science now clearly shows that frequent antibiotic use – especially in childhood – is a risk factor for developing autoimmune disease. So I want to remind you again, as I often do, about the most important question ask your doctor if you are being prescribed an antibiotic, and that is: “is this antibiotic absolutely necessary”. If you want to learn more about the other follow up questions that are also important to ask, check out my second book The Microbiome Solution.
Acid-blocking drugs like PPIs transform the normally inhospitable acidic environment of the stomach into a friendly place for bacteria to grow and multiply, throwing off your microbial balance and causing dysbiosis. A study of patients treated with omeprazole (PPI) or cimetidine (H2 blocker) found that bacterial overgrowth was present in 53% of patients who received omeprazole, and 17% who received cimetidine. And I also want to point out that acid blocking drugs, like antibiotics, are also very over prescribed. So this is another situation where you should ask your doctor: is this acid blocker absolutely necessary.
Birth control pills are the most common form of contraception in the United States today and are used by millions of women for additional reasons besides preventing pregnancy, like to decrease menstrual cramps, for acne, endometriosis. Unfortunately, both birth control pills and hormone replacement therapy increase estrogen levels, which can affect your microbial ecosystem and lead to chronic yeast infections and other signs of dysbiosis. Giving up birth control pills or hormonal therapy can be tricky since there are plenty of good reasons to take these medications, but if you’re suffering from dysbiosis, it may be time to ask your doctor about a nonhormonal alternative.
Immunosuppressive drugs like prednisone, which is a steroid, are used for almost every form of inflammation, but because of their extensive side-effects and ability to dampen the immune system, they’re also a major source of dysbiosis. They suppress friendly bacteria and allow the proliferation of fungal species, which can create chronic dysbiosis. A weakened immune system also makes steroid users more prone to infection.
In addition to needing specific raw materials and nutrients in order to survive, gut bacteria also need to be protected from toxins and chemicals in food, and from the wrong types of food that lead to the overgrowth of undesirable species. Like the medication category, this is a long list, but I want to focus on 5 of the most important food offenders when it comes to dysbiosis.
Artificial sweeteners are fermented by gut bacteria in your colon, which produces lots of gas, but a 2014 study published in the journal Nature suggests that they also damage gut bacteria in the process. More recent evidence suggests that artificial sweeteners interfere with signaling pathways between gut bacteria that are responsible for important bodily functions. And you know, their name says it all: these are artificial foods, not real foods and they are definitely not good for you or your gut microbes.
Next on the list: a high-fat/high-sugar diet. Italian researchers compared children in Florence, Italy, eating a typical Western diet with a rural group in Burkina Faso eating fiber-rich beans and vegetables. Gut bacteria were similar in the children when they were breast-fed babies, but as soon as they started to eat their local diet, significant differences emerged. The European group eating the high-fat/high-sugar Western diet had less microbial diversity and more species associated with diarrhea, allergies, and obesity. The African children had lots of species associated with leanness and also much higher levels of beneficial short-chain fatty acids that protect against inflammation. Now, it’s important to point out that neither group of children were actually sick, but the researchers were already seeing changes in the microbiome of the Italian kids on the high-fat/high-sugar diet that were associated with developing disease in later life. So just like antibiotics in childhood can have a detrimental effect on your health later on, the same is true about the childhood diet.
Not enough fiber can be even worse for your microbiome than too much sugar and fat. Most Americans only eat about half the recommended 25 to 35 grams of fiber daily, and much of it in processed, less beneficial forms like cereal and bread that don’t do much for our microbiome. Certain types of dietary fiber are what we call prebiotics: non-digestible ingredients that encourage the growth of beneficial species and are a crucial part of maintaining microbial balance. Foods like lentils, beans, oats, apples, nuts, and flaxseeds increase the population of helpful Lactobacillus species in the gut. Not eating enough dietary fiber is one of the biggest risk factors for dysbiosis – and not something that you can fix by just taking a probiotic, because to get meaningful repopulation of the gut, you must provide the basic substrate for these beneficial species – which is dietary fiber.
Before we had antibiotics to kill bacteria, we had alcohol. This is what we used to sterilize things in the operating room, and it’s still what we use when you go to get blood drawn, for example. They use an alcohol swab to clean your skin and kill off any surface bacteria. So alcohol is clearly bactericidal – meaning it kills bacteria. Studies show that just one alcoholic drink per day can induce dysbiosis and bacterial overgrowth, and the incidence of small intestinal bacterial overgrowth (SIBO) in alcoholics is three times that of the general population.
Ultra processed foods: UPFs contain emulsifiers, stabilizers and other chemicals that are damaging to the gut microbiome – and the gut lining. You can probably get away with eating a bag of Doritos or Cheetos a couple times a year. But the reality is that ultra processed foods make up more than 50% of the American diet. And while most people recognize that Doritos or Cheetos are junk food, the problem is that we’re consuming plant based milks, yogurt products, granola bars, and all sorts of other foods that are marketed as health foods but in reality, are actually ultra processed foods. To learn more about what an ultra-processed food is, check out the NOVA classification.
Ok, we’ve covered medication and food, now I want to talk about emotional factors that can disrupt your microbiome. A study from Ohio State University showed that stress affects the composition, diversity, and amount of gut bacteria growing in your gut. Your adrenal glands churn out large amounts of substances called catecholamines like adrenaline, and dopamine as a reaction to stress, and those catecholamines can increase levels of harmful gut bacteria ten thousand–fold in less than twenty-four hours. These more pathogenic bacteria can crowd out beneficial species and lead to dysbiosis. In an experiment looking at the impact of academic stress on college students, beneficial lactic acid bacteria were measured and found to be much lower during high stress periods like exams, and higher when the students were under less stress, validating the link between stress and what’s going on in our microbiome.
Normal gut motility involves a series of events designed to move material through the GI tract, and we know that abnormalities in motility can result in stasis of intestinal contents and dysbiosis. And I want to point out here that a lot of these motility disturbances are a result of medications like opioid pain relievers, antidepressants, medicines for high blood pressure, weight loss medications, and allergy medications. So once again we see the medicine cabinet playing a role here. Inactivity is also a risk factor for delayed motility because being more sedentary means that your gut is also going to be more sedentary, which is why we see such tremendous GI problems in nursing home residents who are often just lying in bed all day. Gastroparesis is a chronic slowdown in stomach emptying that can develop from diabetes, infection, and medications like narcotics, and it’s also associated with dysbiosis.
The symptoms of dysbiosis, vary tremendously from person to person. Some people get frequent vaginal yeast infections; others have bloating or GI distress; some develop hair loss, acne, or unexplained hives. Extreme fatigue and just feeling “off” may be the only manifestation. It’s possible that the symptoms you develop may be linked to which species of bacteria are depleted and which ones are dominant in your microbiome, but the science of the microbiome is not yet at the point where it can tell us what sort of microbial profile is associated with specific symptoms, although researchers are getting closer to being able to characterize a microbial signature of certain diseases. Dysbiosis is a contributing factor to autoimmune diseases like Crohn’s disease, thyroiditis, lupus, multiple sclerosis (MS), celiac disease, and many others. But while alterations in the microbiome may play a role, and rebalancing gut microbes frequently improves symptoms, it’s important to keep in mind that dysbiosis isn’t the only cause of autoimmune diseases.
The list of manifestations of dysbiosis is vast, and it includes not just gut disorders and autoimmune diseases but also things like food allergies, skin conditions like acne, rosacea and eczema, and even some forms of cancer. But I want to focus on three symptoms that are really common, and that in my experience, dysbiosis often plays a role.
The first is food cravings. An article published in the October 2014 issue of the journal BioEssays “Is Eating Behavior Manipulated by the Gastrointestinal Microbiota?” raised the provocative idea that our bacteria may be controlling our food choices in order to ensure their own survival. We often blame food cravings on lack of willpower, but it turns out that our microbes might also be involved. Let me explain how that works: studies have shown that people who have a lot of sugar-loving species in their gut often crave – and eat – more sweets. What we think of as just a bad sweet tooth may actually represent specific communities of bacteria directing us to behave in a way that ensures their survival. Gut bacteria are able to influence our food choices by releasing molecules that affect our brain, including hormones like serotonin that affect mood and make us feel good after eating certain foods, like sugar. They can even change our taste receptors so that particular flavors are more or less satisfying to our palate. In my patients with an altered microbiome strong sugar or carbohydrate cravings are almost always part of their symptom complex—and also one of the first symptom to improve as their microbiome recovers. It also explains why people on a low-carb regimen have reduced cravings for sugary, starchy foods within a week or so of eliminating them from their diet: it’s because by reducing those foods, they’re also reducing the species that thrive on those foods. Although of course you have to be careful on a low carb diet that you’re not also reducing fiber – which is essential for creating a healthy microbiome.
Bloating is another common symptom with dysbiosis. Now keep in mind, there are lots of things that can bloat you (I wrote a whole book with a list of 101 things that bloat you called The Bloat Cure!), but dysbiosis is definitely high on the list. Microbial imbalance leads to overproduction of bloat-causing hydrogen and methane gases, along with abdominal discomfort, a change in bowel habits, smelly gas, and sometimes explosive bowel movements. Although again here we see a correlation between the type of microbes and the symptoms: people who have more methane predominant bacterial overgrowth tend to have more constipation.
Weight gain is also a symptom that many people with dysbiosis struggle with. We can predict obesity with 90 percent accuracy just by examining your gut bacteria, and we can induce obesity in skinny mice by inoculating them with microbes from obese mice. And here’s the thing: studies show that overweight mice can actually extract more calories than their normal-sized peers from the exact same food. We see the same phenomenon in humans: if your gut bacteria are out of whack, you may be packing on the pounds despite eating a diet identical to that of someone who’s not gaining weight. When we view weight gain through the lens of an altered microbiome, it helps to explains the skyrocketing rates of obesity that parallel our widespread use of antibiotics and ultra-processed diet.
I started today’s show talking about SIBO in the context of dysbiosis, so I want to circle back to that. SIBO is really just another term for dysbiosis that occurs when large amounts of not-so-good bacteria take up residence in the small intestine – which typically has a lot less bacteria than the colon. Remember, as you move from north to south in the GI tract from the stomach down to the colon, the amount of bacteria increases, so the small intestine – which is higher up in the GI tract – should normally have a lot less bacteria than the colon. SIBO is defined as a bacterial population in the small intestine greater than about 100,000 organisms/ml. It’s normally supposed to have less than 1000 organisms/ml. Like dysbiosis in general, antibiotic use is a major cause of SIBO, but impaired bowel motility and partial bowel obstruction that result in stasis (i.e., slowing down or stopping the movement) of intestinal contents, as well as acid suppression that creates a hospitable environment for bacteria to overgrow in the small intestine, are also major risk factors.
In next week’s episode, I’m going to be talking about breath tests and stool tests for SIBO and dysbiosis and whether those tests are reliable – or necessary. Also in next week’s episode: treatment. I’m going to explain why using antibiotics to treat SIBO is a short sighted and problematic approach, and I’m going to provide you with an alternative way of treating microbial imbalance that can provide meaningful and lasting relief.
Before we go, I want to leave you with three takeaways about dysbiosis:
1. Be careful with the medicine cabinet. So many commonly used drugs like antibiotics, acid blockers, and pain medications may alleviate symptoms, but may also cause major problems in your microbiome that can have long lasting repercussions, so you need to carefully weigh the risks and benefits before talking any medication.
2. What you eat is the most potent tool for changing your microbiome. And let’s keep this one simple: less ultra processed food, more plant fiber.
3. Your microbiome is one of the most important determinants of your health. Studies show that within about 30 hours of food hitting your gut, you can start to see changes in the microbiome. So within less than two days of changing your diet, you can start to improve your health. This is a message of hope and optimism and self-determination. All of us, even those who struggle with chronic medical conditions and genetic diseases, can improve our health by paying attention to the incredibly important ecosystem in our gut.
So that’s it for this week’s edition of the Gutbliss Podcast on Dysbiosis and SIBO Part 1 coming up next week: diagnosing and treating dysbiosis.
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