How To Heal Your Gut After Antibiotics

Now that you’ve learned what probiotics to take while you’re antibiotics, you’re probably concerned with what you should do after you’ve finished your course.

Antibiotics take a toll on our microbiome, destroying lots of our good bacteria and causing overgrowth of others like yeasts. This imbalance of gut bacteria is called dysbiosis. So how do we fix it?

Probiotics After Antibiotics

There is some recent research suggesting that probiotic consumption after antibiotic treatment may delay your microbiome from returning to its normal state, so if you’re not experiencing any digestive complaints after finishing your course of antibiotics, I recommend focusing mostly on prebiotics (see below) as opposed to probiotics.

If, however, you’re struggling with some post-antibiotic digestive woes, you may want to try a probiotic in addition to the other suggestions in this article. If you already began taking probiotics during your course of antibiotics, you can continue that probiotic for a month or two after finishing up your course.

Take a Probiotic Supplement

If you weren’t taking a probiotic during your antibiotic course, you can choose one of the below (which I recommended in my previous article):

  • Saccharomyces boulardii biocodex (now called Saccharomyces boulardii CNCM I-745) is found in the Florastor brand probiotic and helps to prevent C.diff infections (5) and even helps those who tend to have recurrent C.diff infections. (6). This strain does not need to be refrigerated, so it’s very easy to buy saccharomyces boulardii online.
  • Visbiome (a multi-strain probiotic) has also been shown to reduce the incidence of antibiotic-associated diarrhea.(7) Note that if you buy Visbiome online, you should choose a retailer that ships it refrigerated. (Please note: I used to recommend VSL #3 as it was the brand that use the De Simone probiotic formula. However, they have since lost access to the well-researched formula, and now Visbiome has the only rights to it. Make sure you get Visbiome and NOT VSL #3 if you’re looking for the De Simone formula.)
  • Lactobacillus rhamnosus GG (found in the Culturelle supplement) has been shown to reduce the occurrence of antibiotic-associated diarrhea, as well.(8) Like Florastor, it’s easy to buy Culturelle online since it does not need to be refrigerated.

Eat Probiotic Foods

You’ll also want to focus on including plenty of probiotic-containing foods for the next few months (you should always include these in your diet, but it’s especially great to do so right after taking antibiotics). Here’s a list of fermented foods, including (but not limited to) the following:

  • Water or Dairy kefir – fermented water (often with juices or fruit included for flavoring in a “second ferment”) or dairy with kefir “grains”. Click here for a recipes, or purchase at your local natural foods store
  • Kombucha – a fermented tea drink. Click here for a recipes, or purchase at your local natural foods store
  • Kimchi – a spicy fermented cabbage, a Korean staple (and my personal favorite!). Click here for a recipe and try it at a Korean restaurant for a taste. You can often purchase this in tubs at Korean grocery stores as well.
  • Sauerkraut – another fermented cabbage, but a German version this time! Click here for a recipe or you can pick up some Bubbie’s sauerkraut at Whole Foods or other natural foods store
  • Pickles – the deli classic can be made by fermenting cucumbers! Click here for a recipe and keep in mind these are different from the pickles in vinegar you’d find on the shelf of your regular grocery store.
  • Salsa – another classic dish that can take a fermented turn! Click here for a recipe and give it a shot!
  • Beet kvass – a fermented beet juice drink. Click here for a recipe or you can usually find this in your Whole Foods or other natural foods store.
  • Yogurt – if you tolerate dairy, yogurt is a great source of probiotics. Click here for a recipe or of course you can pick some up from your grocery store (choose one that uses a good quality milk though and always buy full fat!)

Keep in mind that you can ferment pretty much anything! My favorite resource for fermentable foods is the book Wild Fermentation by Sandor Katz and you may also want to check out Fermented by Jill Ciciarelli. This is one of the most fun ways to experiment in the kitchen, so get fermenting!

Prebiotics After Antibiotics

Prebiotics are a wonderful thing to incorporate into your diet and supplement routine after antibiotics. A prebiotic is a “nondigestible food ingredient that beneficially affects the host by selectively stimulating the growth and/or activity of one or a limited number of bacteria in the colon, and thus improves host health.” (1) This definition was later revised to include that a prebiotic:

“a) resists gastric acidity, hydrolysis by mammalian enzymes and gastrointestinal absorption;

b)  is fermented by the intestinal microflora;

c) stimulates selectively the growth and/or activity of intestinal bacteria associated with health and wellbeing.” (2)

Supplementing with Prebiotics after Antibiotics

Prebiotics work by selectively feeding your beneficial gut bacteria, which in turn, helps to push out unwanted or “bad” bacteria that might be hanging out in the gut.

You can think of the microbiome as a parking lot — there’s only so many spaces available. Taking prebiotics helps your good bacteria to take more of those parking spots and leaves less spots available for any bad bacteria.

Best Prebiotics:

1) Fructo-oligosaccharides: FOS is found is a variety of foods including Jerusalem artichokes, chicory root, onions, bananas, honey, garlic and leeks. (3) The appropriate dose of FOS is about 10 grams per day (this leads to increases in bifidobacteria and has the least amount of side effects (which tend to be gas and bloating)). (4) Whether you get this dose from food or supplement is up to you, but it will help to correct the dysbiosis caused by antibiotic treatment. My favorite FOS supplement is NOW Foods UltraFlora FOS powder. (P.S. it tastes like cotton candy.)

2) Galacto-oligosaccharides: GOS isn’t found in many foods, so if you’d like to try this one you’ll need to supplement. A dose of 5 grams per day has been shown to be bifidogenic (increases bifidobacteria counts) in most healthy people while consuming it along with their usual diet. (5) Try Klaire Labs Galactomune supplement.

3) Sunfiber (galactomannan fiber or partially hydrolyzed guar gum): Sunfiber is a great choice as it is low-FODMAP and thus typically very well tolerated even by those who are experiencing digestive issues. I recommend 6 grams per day, which has been shown to be a bifidogenic dose. I love Sunfiber so much that it’s the prebiotic I use in my drink company, Gut Power Drinks! Give our Gut Power Matcha a try as an easy way to incorporate both prebiotics (Sunfiber) and probiotics into your routine in a delicious way.

gut power matcha

When starting on prebiotic supplements, it’s important to begin with a small dose and work your way up slowly. It’s normal to experience a bit of extra gas or bloating when increasing your dose, but it should dissipate within a couple days.

Incorporate High Polyphenol Foods Into Your Diet

Polyphenols, a type of antioxidant that gives our food color, actually act as prebiotics in the gut. This means that the more high polyphenol foods you incorporate into your diet (like berries, tea, spices, etc), the better balanced your microbiome will be.

This is another great reason to give Gut Power Matcha a try — matcha is one of the best things you can consume to get lots of gut-healthy polyphenols into your diet!

Because each different polyphenol feeds different classes of healthy bacteria, it’s best to incorporate a wide array of colorful fruits and veggies into your diet.

What if Probiotics and Prebiotics Aren’t Enough?

Because of the intense effect antibiotics can have on our gut flora, sometimes simply adding probiotics and prebiotics doesn’t quite cut it.

Maybe you’ve noticed that your digestion is just off after taking a course (or a few courses) of antibiotics. What do you do then?

Well, a good first step is to have your gut bacterial balance tested.

There are two common imbalances that can result from antibiotic treatment. The first, which we just discussed, is called dysbiosis.

The second is something called SIBO (small intestinal bacterial overgrowth).

Both of these conditions can cause many annoying digestive symptoms and can be difficult to deal with.

You can learn more about both of these conditions and the testing you need to identify them in this blog post.

If you’re experiencing lots of digestive symptoms like bloating, gas, diarrhea or constipation long after being on antibiotics, it’s definitely time to test for SIBO and dysbiosis. (Note: you’ll need to wait at least 2 weeks after being on antibiotics to do these kinds of tests.)

Once you identify these imbalances, you can get to work clearing out bad bacteria and healing your gut. This typically involves an antimicrobial protocol (or antibiotics — but don’t worry, these ones aren’t like the ones that got you here in the first place!), gut-healing supplements, stress management, and a proper diet.

I have an entire 8-week course dedicated to this process called Build Your Biome. If you’re totally overwhelmed by all the research you need to do to kick these symptoms to the curb, I invite you to join me in BYB where I make it all super easy!

Takeaway: By getting probiotics and prebiotics in the diet (or via supplementation), you’ll be helping your gut recover from the traumatic experience of dealing with antibiotics. However, some people may find that they are left with nagging symptoms even after incorporating probiotics and prebiotics. In this case, it’s very important to test for common conditions like dysbiosis and SIBO.


1) Pharmaceutiques, Universitad Catholique de Louuain. “Dietary modulation of the human colonie microbiota: introducing the concept of prebiotics.” Journal of Nutrition 125 (1995): 1401-1412.

2) Gibson, Glenn R., et al. “Dietary modulation of the human colonic microbiota: updating the concept of prebiotics.” Nutr Res Rev 17.2 (2004): 259-275.

3) Chow, JoMay. “Probiotics and prebiotics: a brief overview.” Journal of Renal Nutrition 12.2 (2002): 76-86.

4) Bouhnik, Yoram, et al. “Short-chain fructo-oligosaccharide administration dose-dependently increases fecal bifidobacteria in healthy humans.” The Journal of nutrition 129.1 (1999): 113-116.

5) Davis, L. M. G., et al. “A dose dependent impact of prebiotic galactooligosaccharides on the intestinal microbiota of healthy adults.” International journal of food microbiology 144.2 (2010): 285-292.

6) Bouhnik, Y., et al. “Lactulose ingestion increases faecal bifidobacterial counts: a randomised double-blind study in healthy humans.” European Journal of Clinical Nutrition 58.3 (2004): 462-466.

You might assume that, as a dietitian who works with those with digestive problems and gut microbiome imbalances like SIBO and dysbiosis, I spend the majority of my time counseling my clients on diets like the low-FODMAP diet, SCD diet, GAPS, or any other number of restrictive dieting approaches out there.

Want the truth?

I spend the majority of my time talking to my clients about things other than the types of foods they’re eating. We talk antimicrobial herbs, stress reduction, sleep, exercise, calorie intake…but specific food choices? We don’t spend much time on those beyond general healthy eating concepts.

In my 7 years of working with digestive health clients, I’ve found that taking a diet-first approach to fixing microbial imbalance in the gut is the wrong move.

Here’s why.

Restrictive Diets Don’t Address the Real Problem

If you have gut issues like SIBO or dysbiosis, heavily restricting your diet doesn’t solve the problem. I’ve written about this concept specifically in regards to a low-FODMAP diet before, but it applies to practically every other restrictive dietary approach out there. The only exception to the “rule” would be the elemental diet (which I don’t even consider to be a “diet” per se; rather, it is a supplement food alternative), which is quite effective in clearing SIBO.

You can’t “starve” bacteria while you’re eating real food. Sure, when they’re not getting enough fiber or prebiotics, they’ll become somewhat dormant and symptoms will dissipate. But bacteria aren’t going away or being killed off by a restrictive dietary approach.

This is something I’ve talked about before quite a bit, but it really does bear repeating given the massive amount of misinformation I see floating around the internet. There are health gurus out there promoting dietary changes as the way to get rid of bad bacteria in the gut.

Unfortunately, this is simply not true and ends up making people wait to get real treatment (i.e. antimicrobials or antibiotics) for the microbial issues.

It is necessary to actually kill off and get rid of bad bacteria, parasites, candida to feel better, and you can’t do that with diet alone.

Restrictive Diets Aren’t Necessary For Results

You might already know that diets don’t kill off bacteria, but still believe that a restrictive diet is a key element to a gut-healing protocol.

I used to think the same thing myself! I had clients following strict elimination diets, thinking that I was helping them to reduce inflammation and get them results faster than if they were just following a generally healthy diet.

But what I found was that my clients eating really restrictive diets and those who were following a much more liberal approach both got great results as long as they were balancing their microbiome, supporting their health in other ways, and keeping in mind their own personal dietary “triggers”.

That meant using targeted antimicrobial herbs or antibiotics to push out any unwanted bacteria, supporting digestion with digestive enzymes, demulcent herbs, probiotics, prebiotics, etc, focusing on sleep and stress, eating enough, exercising appropriately, and finding time to spend with family and friends and do the things they love.

It also involved identifying any major dietary triggers and keeping those out of the diet. Note that these are triggers that are extremely obvious to the person without having to do any sort of dietary restrictions to figure out.

It became rather clear to me at that point that if I could get my clients the same great results without having them go on a super restrictive diet, why on earth wouldn’t I do that?

These days, I’m recommending a pretty liberal diet (more on that below) to my digestive health clients and we’re still getting rid of bloating, excessive gas, diarrhea, constipation, and abdominal pain. No restrictive diet required.

If I can make the healing process just a little bit easier for my clients, I’ll do it all day every day. They are grateful to not have the added frustration, complication, and expense of eating an incredibly strict diet when they don’t have to and they still get the same end result: no more digestive issues.

Restrictive Diets Make You More Likely to Undereat

One of the biggest issues I have with really restrictive dietary approaches is that they make it so much more likely that my clients are going to accidentally eat less than they should. When you cut out a lot of foods and don’t have many choices to replace them with, chances are you’re going to undereat relative to your needs.

When you’re trying to heal and nourish your body, the last thing you should be doing is feeding it less than it needs. Undereating can lead to symptoms like irritability, moodiness, low blood sugar, hormonal problems, sleep issues, and more. My friend Laura Schoenfeld, RD goes into more detail on a lot of these symptoms and how they’re related to undereating here.

And this not something to think about just from a calorie and macronutrient perspective, either. When you’re on a restrictive diet, it’s also much easier to skimp on important vitamins and minerals that come from some of the foods you’re restricting.

Micronutrient deficiencies can lead to lots of health problems as well — so again, when you’re trying to heal your body, undereating becomes a massive problem.

Instead, I make sure my clients know how much food they should be eating to properly fuel their body and help them eat a diverse, nutrient-dense diet.

Restrictive Diets Mess with Your Relationship with Food

I can’t tell you how many people I’ve worked with who are just truly afraid of food. They get worried about every symptom they experience and spend a ridiculous amount of time trying to trace every symptom to a food they ate.

It makes for a really messed up relationship with food.

I have to spend a lot of time educating them that the root cause of these symptoms is more likely to be an imbalanced gut (and the resultant inflammation) than specific foods they’re eating. That inflammation can cause digestive issues regardless of the foods they’re eating.

When you’re dissecting your diet for potential problematic foods, all food becomes a potential “trigger” for the negative symptoms you experience instead of a source of nourishment and pleasure.

This mindset also tends to lead to further and further restriction. Someone might start off by just limiting FODMAPs, but then they read about other potential food triggers and take those out, read about other triggers and take those out, and the cycle continues until they’re barely eating any foods at all.

By only using more restrictive dietary approaches when they are truly necessary, you can avoid damaging your relationship with food and view food as a nourishing, pleasurable thing instead of something that is attacking your body.

Dietary Restrictions Distract from Other More Important Changes

When you’re so focused on diet, you’re less likely to pay attention to (what I would consider) the heavy-hitters like stress, sleep, exercise, and social relationships.

After all, we only have so much we can think about and dedicate ourselves to. When diet takes up a huge amount of our headspace, it’s easy to forget about these other, less “sexy” topics.

I’d argue that these other changes are more important things to focus on than diet (provided that you’re eating a relatively healthily). When my clients stop spending all their time focusing on what they’re eating and instead start paying more attention to their sleep quality, stress management, and exercise habits, they feel better than they ever have before.

Focusing less on diet also gives you more time to focus on yourself and your community. You can spend time enjoying your hobbies, or socializing with friends and family. Research has shown that social relationships play a huge role in our health, and that as society, we’re getting lonelier. Laura and I have talked about the importance of social relationships in the past and how prioritizing social relationships over diet can actually improve your health and well-being.

It might sound strange to hear a dietitian say this, but…there is so much more to life (and health) than food. Don’t let yourself get caught up in the idea that diet is a cure-all, and don’t let diet distract you from all the other healthy habits you could be incorporating into your healing regimen.

Long-Term Restrictive Diets May Negatively Impact Your Health

Most clinicians know that restrictive diets like the elimination diet should really only be used as a short-term therapy while we’re working on fixing the underlying root causes of your health issues.

But when patients start implementing these diets on their own and put off treating root causes of their problems, they often end up staying on restrictive diets for years. This can happen even if they are also treating the root cause of their issue, simply because they become too afraid to reintroduce foods once they start feeling better (see above).

Researchers are concerned about the health implications of staying on restrictive diets for the long-term, like changes in the microbiome, nutritional inadequacy, and fostering disordered eating habits.

While the jury is still out about the true consequences of long-term restrictive eating, those reasons alone are enough to give me pause.

If I can stop someone from getting on the restrictive diet train (and still get them results, of course), I’ll do it in a heartbeat.

Is a Restrictive Diet Ever the Right Choice?

There’s definitely a time and a place for a more restrictive diet, I just don’t believe it’s at the beginning of someone’s health journey (for most people).

The only time I might recommend an elimination diet or other restrictive approach right from the start is if someone has extreme health issues that are incredibly disruptive to their day-to-day life in a way that does not allow them to function. This might mean someone who is having diarrhea 8-10 times per day and can’t work because of it, or someone whose abdominal pain makes it so that they can’t even think about anything else because they’re constantly in pain. Of course, in situations like these, getting symptom relief is priority #1 and if we can do that in a way that isn’t necessarily fixing the root issue but is faster, that makes more sense.

But those with milder issues may never come to the point of needing a more restrictive diet. As I mentioned above, a restrictive diet isn’t necessary for most people to see great results. But if you’ve re-balanced your microbiome (and tested to make sure you’ve actually cleared out any bad bugs), addressed nutrient deficiencies, sleep, stress, exercise, socialization/community, and you’re still having some digestive problems or other health issues…that’s when you might want to consider taking out some additional foods to see if you have a true sensitivity that’s causing some of your problems.

If you’re going to implement any kind of restrictive diet, I highly recommend working with someone to do so, as there needs to be a solid reintroduction strategy that is incorporated after a short-term restrictive diet to avoid the potential health consequences of a long-term restrictive approach.

If I Don’t Need to Restrict… What Should I Do?

If you have digestive issues, the first thing you need to do is test your gut bacteria to determine if your microbiome is imbalanced. This is the top cause of digestive problems!

From there, you need to actually address the issue. That means getting on an antimicrobial protocol or taking antibiotics, using probiotics and prebiotics and other supplements to help balance your microbiome. Remember — this is typically the root cause of digestive issues (among other health issues), not your food.

Beyond that, you’ll want to put a strong emphasis on stress management, getting good sleep, exercising appropriately, eating enough, and prioritizing social relationships.

This is what I cover in my Build Your Biome program.

But from a diet perspective, I simply recommend focusing on general healthy eating principles. If you’re familiar with a real food, Paleo, Primal, or Weston A. Price way of eating, these principles will be very familiar to you.

If you’ve been caught up in restrictive dieting, this diet is going to look like it’s full of “triggers”. Please remember that you’ve now been conditioned to think this way — to view food as the enemy rather than something that can nourish and heal you.

Here are the things I focus on when it comes to diet for my clients:

  • Eat Real Food
    • Less processed food, more real, whole food
    • Organic, non-GMO as much as possible (especially for dirty dozen foods)
  • Limited Restrictions — just the things that I really think make a difference.
    • Take out any major triggers for that individual (remember, these are super duper obvious and don’t require an elimination diet to figure out)
    • Swap industrial seed oils for better fats (as much as possible — most people won’t be able to take them out entirely)
    • Reduce sugar intake (though I don’t require my clients to take out sugar completely)
    • Reduce alcohol consumption
    • Take out gluten (not always, but I do recommend this somewhat often)
  • Be Grateful for Your Food
    • This is especially important if I have clients coming from a more restrictive diet — I actually tell them to create a “mantra” of sorts to remind them that food is nourishing and healthy. They might repeat something like this to themselves at meal time: “This food will help nourish and heal me.” We also focus on mindful eating habits like paying attention to the smells and taste of their food.
  • Eat Enough
    • As we discussed above, eating enough is vital to the healing process, so I make sure that my clients are eating enough to fuel their body. This means getting enough calories overall, as well as making sure their macronutrient breakdown makes sense for the type of activity they are doing.
  • Balance Blood Sugar
    • Blood sugar surges and crashes can lead to HPA axis dysregulation, along with a host of symptoms like moodiness, anxiety, and hormonal symptoms. Making sure my clients have well-balanced blood sugar is crucial.
    • This typically means combining carbohydrates with fats and proteins, as well as consuming enough fiber, to help regulate blood sugar.

That’s it! Simple, easy, and just focuses on the things that will really make a difference. We don’t worry about FODMAPs, dairy, grains, or legumes (all things taken out on elimination diets quite frequently) unless it’s clear foods within those categories cause problems for that particular client.

I’ll admit that this way of practicing is quite different from how most digestive health experts practice. Heck, I’m sure I’ll get some flack for this article.

But at the end of the day, what matters to me most is that I get my clients results in the easiest way possible while making sure they have the capacity to focus on things beyond diet that are important for overall health.

So let me ask you: how restrictive is your diet and how long have you been following that approach?


Probiotics have thundered onto the health and wellness stage — you hear about them everywhere now.  With claims running the gamut from “probiotics heal your gut” to “probiotics prevent cancer,” it seems as though they are just about a cure for everything.

But, do they actually do what they claim to? Or are these claims just another way to convince you to buy expensive supplements?

In this article I’m going to answer all of your pressing questions about probiotics. From the very basics of what probiotics are, through the details of probiotic strains, to the ways probiotics work at the molecular level; everything you need to know about this burgeoning field, you’ll find right here.

What are Probiotics?

Alright, first thing’s first. What are probiotics, exactly?

According to the Food and Agriculture Organization of the United Nations and the International Scientific Association for Prebiotics and Probiotics, probiotics are defined as: “live microorganisms that, when administered in adequate amounts, confer a health benefit on the host.” (1)

…And what, exactly, does that mean?

Well, basically, it means a probiotic is any species of bacteria, virus, fungus or tiny parasite that, if you get enough of them living on or in your body, makes you healthier. You can kind of think of these microorganisms as “reverse germs”. If they “infect” you, rather than getting miserable cold or flu symptoms, they make you feel extra healthy for a while.

Even though this is the official definition, when most people say “probiotic”, this isn’t exactly what they mean. They usually aren’t talking about the microorganisms directly; rather they are talking about products that contain these microorganisms — probiotic supplements. Probiotic supplements are capsules, pills, tablets, powders, lotions, liquids or even foods that have had probiotic microorganisms mixed in. (1)

That means when you hear people talking about how they’re “taking a probiotic”, they’re usually talking about taking a capsule or pill filled with probiotic microorganisms.

I realize that, in a lot of ways, this is a tiny distinction. After all, it’s the microorganisms that are the defining feature in both cases. But it’s helpful for being able to really visualize what the people in your life mean when they are talking about probiotics. And it helps you understand the way scientists, who stick to technical definitions, are using the term when you’re poking around in scientific literature.

I told you! We’re covering all our bases here!

What Do Probiotics Do?

So, now we know that probiotics are microorganisms that make you healthier. Cool!

But how does that actually work? What do probiotics actually do that leads to you becoming healthier?

That is an excellent question!

To really explain it, we’re going to have to make a small detour here and talk about something called the gut microbiome.

Introduction to the Gut Microbiome

The gut microbiome is the name scientists give to the collective host of trillions of microorganisms that naturally live in the human digestive tract. (2)

Yep. Whether you know it or not, your gut is loaded with microorganisms. Most of them are bacteria, but there are also viruses, fungi and other tiny single-celled organisms. (2) Your intestine is a veritable jungle of microscopic life!

And it’s supposed to be.

I know it feels pretty weird to think about because we’re so programmed to think of bacteria and viruses as gross and dangerous, but your gut is intended to function completely filled with microorganisms. Not just any microorganisms, though. These are microorganisms hand-selected over millions of years to be the perfect gut-buddies for humans. (3, 4)

I Feed You, You Protect Me: The Mutual Benefits of the Gut Microbiome

There are few relationships in nature as truly symbiotic (scientific slang for “win-win”) as that between you and your gut microbiome.

For your microbiome, this is the best gig ever. The bacteria living in your gut have a permanent, perfectly climate-controlled environment.  It’s balmy 98.6℉, all day, every day. They always have enough water. Food simply rains down on them three times a day. And when other germs show up and want to steal their cushy gig, their home literally helps kill them off.  (5, 6)

For you, your microbiome provides an ingenious solution to a serious problem: the overwhelming onslaught of potentially dangerous microorganisms coming in from the digestive tract.

The world is absolutely positively overrun with microorganisms. Everything you see, touch and eat is swarming with bacteria, viruses and all kinds of other little critters. You microbiome, thankfully, helps you kick out bad bacteria without it making it into your bloodstream to infect you.

Symbiosis to Dependance: Extensive Functions of a Healthy Gut Microbiome

As you might imagine, with such a good gig for both us and the bacteria, neither of us was planning to go anywhere. We got cozy, our gut bacteria settled in, and we started building a serious partnership that ran far deeper than just food and protection.

We started relying on one another, expecting one another to be there, and organizing our physiological functions around one another. This has gone on to the point that we are now really and truly dependent on one another for our health, wellbeing and survival. (6, 3, 4)

For our gut bacteria, this means that many of them can no longer thrive anywhere but in our guts.

And, for us, it means that we can no longer regulate our vast array of complex organ systems without gut bacterial help. Over the millennia, we’ve come to rely on our gut bacteria to properly (6, 3, 4, 7, 8, 9, 10, 11):

  • Digest food
  • Maintain our intestinal walls
  • Coordinate our intestinal wall movements
  • Regulate our immune system function
  • Coordinate nerve signaling and brain function

We need them in order for our body to work at all normally. And when we don’t have them, we become ill.

Probiotics and the Gut Microbiome

So what do probiotics have to do with the gut microbiome?

Well, probiotics are part of your microbiome.

When you take a probiotic supplement, the probiotic microorganisms are transported down to your digestive tract. Naturally, they take to it like a fish to water. They grow, divide and thrive.

They take up the mantle of microbiome responsibility – supporting digestion, gut health, immune health, nervous system health and, thereby, your whole body health. (6, 12, 13)

Probiotic Benefits

I guess, technically, I could leave the benefits of probiotics at “support[…] digestion, gut health, immune health and nervous system health,” couldn’t I?

But that’s a bit vague and impractical if you’re trying to decide if probiotic supplements are a good fit for you. It’s much more helpful if I break it down into individual symptoms. So, that’s exactly what I’m going to do!

Here are some of the main benefits of probiotics (that have been proven so far, anyway!).

1. More Regular Bowel Movements.

At first glance, this probably seems like more of a “convenience benefit” than a “health benefit”. But unhealthy bathroom habits can actually have serious consequences for your health. (14, 15, 16, 17)

For example, regular constipation (having hard to pass stools or less than three bowel movements per week) increases your risk of a painful and potentially life-threatening hernia, not to mention upping the odds of developing colon cancer. (14, 15)

Having extremely frequent bowel movements (more than three times per day), though, is also not healthy. Regular diarrhea puts you at risk of dehydration, electrolyte imbalances and nutrient deficiencies. (16)

What you want is to pass firm but soft stools, without straining, around once a day. (17) That offers you the best opportunity to absorb all the water and nutrients you need without increasing your risk of damaging your intestinal health.

Probiotics help you keep this healthy one-per-day rhythm by stimulating your enteric nervous system. (18, 19, 20)

Your enteric nervous system is responsible for generating the waves of muscle contractions that push your food from your stomach, down through the intestines, and out into the toilet. Strong, even, regular muscle contractions keep food moving smoothly and your bowel movements regular. (20, 18, 21)

2. Less Bloating and Flatulence

No need to explain how this one is a health benefit! Less belly cramps, bloating, belly aches and gas — I’m sold!

The bacteria in your gut microbiome break down bits of food you don’t absorb for their own food and make gases in the process. Healthy gut bacteria in the right place (in the large intestine, not small intestine) make fewer gases (though, not none!), reducing bloating, belly aches and flatulence.

By helping keep your gut stocked with healthy bacteria (and free of dangerous bacteria — see point 3!), probiotics can limit gas production and ease the associated digestive symptoms. (2, 22, 23)

3. Fewer Gut Infections

I bet you’re not surprised to see probiotic benefit number three — after all, keeping dangerous microorganisms at bay is kind of the whole point of the gut microbiome!

Adding probiotics to your gut helps your microbiome (24, 25):

  • Soak up nutrients and hog all the physical room in your gut, so dangerous microorganisms can’t set up a home
  • Produce organic acids that harm dangerous microorganisms
  • Produce antibiotic molecules to kill invaders

Together, these effects are potent enough to prevent and treat infections like E. coli (which can cause severe diarrhea and a fever) and H. pylori (which can cause stomach pains similar to gastric reflux, gastric ulcers and stomach cancer). (24, 25, 26, 27, 28)

More probiotic microorganisms, less gut infections!

4. Less Systemic Inflammation

Let’s move out of the gut and talk about the health benefits of taking probiotics on the rest of your body.

One of the most important, if not the most important, of these benefits is reducing systemic inflammation in your body.  

When your gut bacteria are out of balance, toxic molecules called lipopolysaccharides (LPS) makes it into your bloodstream, causing system-wide inflammation.

By helping to balance your microbiome, probiotics keep levels of LPS lower, thus reducing inflammation. (29)

Probiotics also help your gut microbiome calm your immune system, reducing inflammation. They do this by activating a group of cells called Treg cells in your gut, which move throughout your body and calm overactive immune cells. (30, 31, 32, 33, 34)

And reducing systemic inflammation is a huge deal for your health! Studies have clearly linked total body inflammation to multiple very serious conditions, including (35):

  • Obesity
  • Heart Disease
  • Diabetes
  • Dementia
  • Osteoporosis
  • Cancer

By easing systemic inflammation, probiotics can reduce your risk of all of these conditions.

5. A Healthier Body Weight

Yep, you read that right! Probiotics can help you lose weight. And help you keep it off, too. (36, 37)

This is probably partially due to the effect on systemic inflammation I just mentioned. Systemic inflammation messes with your metabolism and makes it more likely that you will put on weight and have trouble getting it back off. (38)

There may also be more direct effects as well. Healthy gut bacteria, like those in probiotics, don’t liberate as many calories from your food as unhealthy bacteria do. That means that boosting a healthy gut microbiome with probiotics may result in you getting fewer calories from the exact same meal. (39)

You can read more about the microbiome and the metabolic system in my article here.

6. Healthier Blood Sugar Levels

Researchers believe the improved blood sugar control from taking probiotics is due mostly to the reduction in systemic inflammation I mentioned above. (40)

Systemic inflammation makes it extremely difficult for insulin to do its job in your body, driving blood sugar up.  Elevated blood sugar levels, long-term, puts you squarely on the path to type 2 diabetes and other metabolic diseases. (40)

7. Less Plaque Build-Up in Your Arteries

Probiotics can modify two of the risk factors for developing plaque in your arteries: high cholesterol and high blood pressure. (41, 42, 43)

Probiotics can bind cholesterol from your food right in your gut, keeping it from getting into your bloodstream. This lowers the total amount of cholesterol in your blood, helping keep it from building up in your arteries and forming a plaque. (43, 44)

Probiotics also help release blood pressure-lowering phytoestrogens (“plant estrogens”) from the food they were in, so that they can be absorbed more efficiently and bring your blood pressure down. (45, 46, 43)

Combined, these two effects of probiotics can help protect your arteries and reduce your risk of having a heart attack or stroke.

8. Stronger Bones

Not itching to break a hip when you get older? Probiotics might help you out here, too!

As with nearly everything on this list, part of this benefit comes from the reduction in systemic inflammation that accompanies probiotics. Nipping the inflammation process in the bud can really help protect your bones.

Additionally, probiotics can help make sure your bones have all the nutrients they need to be rigid and strong. Probiotic microorganisms produce folate and vitamins D, C, and K, all four of which are super important for your bone health. Probiotics also help to break down foods in your gut, freeing up minerals like calcium so you can absorb more of them, too. (47)

Less bone breakdown and more bone-building nutrients — an excellent combination for life-long healthy, strong bones.

9. Decreased Autoimmunity

Autoimmune diseases are awful. Caused by your immune system attacking your own healthy tissues, they are painful, debilitating and, usually, really hard to treat.

Probiotics, though, may be able to offer some relief to those struggling with autoimmune symptoms. (48)

Probiotics help prevent your gut from becoming “leaky”, a serious risk factor for developing an autoimmune disease. The reasons for this are a little complicated, but, basically, a leaky gut lets too many foreign molecules into your body. This increases the risk your immune system will become overwhelmed, get confused, and start attacking the wrong things! (Check out my article on autoimmunity and gut health to learn more about how this works.)

If this weren’t enough, probiotics also help your gut microbiome produce specific molecules, called short-chain fatty acids (SCFAs) and histamine which can directly quell an overactive immune system. (49, 50)

10. Improved Reproductive Health

Trying to start a family? Or just want to make sure your sexy-time says healthy? Probiotics might come in handy, here, too.

For men, probiotics may be useful because they can reduce plaque buildup in their arteries… all their arteries. Blood flow to the penis is really important for male sexual health, which means so is having healthy arteries for the blood to flow through is, as well. By keeping men’s penile arteries plaque-free and able to let large amounts of blood flow as it should, probiotics can help prevent erectile dysfunction. (51, 52, 53, 54, 55)

For women, probiotics may be able to help prevent vaginal infections. Not only is this important for keeping sex from being cancelled altogether until the infection clears up, studies indicate that it is also important for having a healthy pregnancy. Women with active vaginal infections are at a higher risk of miscarriage. So, preventing infections, perhaps with a probiotic, before conception and during pregnancy is probably a good idea. (56, 57)

11. A Happier Mood

A more balanced mood, fewer feelings of stress and a generally sunnier outlook — all in the power of a probiotic, too!

Research now clearly shows that taking a probiotic can improve your mood, even effectively helping combat serious mood disorders, such as clinical depression. (58, 59)

This is thought to be because a healthy gut microbiome helps regulate the amounts dopamine and serotonin (“happiness hormones”) in your brain. They do this partly by helping the brain produce more of them on its own. But your microbes actually produce some for you, too! Really, they manufacture them for you in your gut, you absorb them, and then use them in your brain to help keep you happy. (60, 61)

Probiotic Side Effects

Probiotic side effects are fairly rare and usually mild. If you do experience side effects taking probiotics, it is usually a slight increase in digestive discomfort, such as mild worsening of your bloating or flatulence. In most cases, these symptoms resolve on their own after a few days, if you continue to take your probiotic normally. (62)

The only serious side effect associated with probiotics — an infection of the bloodstream with the probiotic microorganism — is extremely rare. There are a few conditions that you could have, however, that might make your risk of infection a touch higher.

If you have the following conditions, probiotics might be a bit riskier for you and you should speak to your doctor before taking them: (63)

  • A very weak immune system (if you have an HIV infection or are undergoing chemotherapy, for example)
  • Short bowel syndrome
  • A central venous catheters
  • Cardiac valve disease  

So, Are Probiotics Safe?

The short answer here is: yes! Scientists and doctors all generally agree that probiotics are very safe to take. (62)

The only exception could be if you have one of the conditions I mentioned above or if they are given to very, very young infants (whose immune system isn’t fully formed, yet). (63)

If you have any concerns about taking a probiotic, please speak to your doctor, pharmacist or nutritionist. They can talk to you about your concerns and your medical history and determine whether probiotics are a good fit for you, personally, or not.

Best Probiotic Supplements

It would be really nice if each and every one of these health benefits came from the exact same probiotic microorganism. Unfortunately, each member of your gut microbiome has a unique role in helping you stay healthy. So, different microorganisms are more effective at providing specific health benefits than others.

Why Probiotic “Strains” Are Important

Most probiotic supplements on the market today only give you their probiotic species information rather than their strain.

What’s important to know, though, is that probiotic strains dictate their effect, meaning that one strain of a probiotic can have a completely different effect on your body than another probiotic strain. (64) A supplement that only tells you its probiotic species vs its strains isn’t giving you a whole lot of information and it’s very, very possible that the supplement could be totally useless for what you’re trying to achieve.

I’ve written an entire article on this topic and highly suggest reading it if you’re currently taking a probiotic supplement. It will give you a completely different outlook on probiotics and show you exactly what to look for.

Below, I’ve listed the probiotic strain(s) with the strongest evidence for each health benefit, along with reputable probiotic supplements where applicable.

Best Probiotics for Digestive Health

Most probiotic and digestive health research has focused on irritable bowel syndrome. This is a functional digestive disorder with severe, but common, digestive symptoms, including constipation, diarrhea, abdominal cramps, gas and bloating.

To date, the best probiotic strains found for relieving IBS symptoms was the combination of:

  • Bifidobacterim breve (DSM 24732)
  • Bifidobacterium infantis (DSM 24737)
  • Bifidobacterium longum (DSM 24736)
  • Lactobacillus acidophilus (DSM 24735)
  • Lactobacillus delbrueckii subsp. bulgaricus (DSM 247634),
  • Lactobacillus paracasei (DSM 24733)
  • Lactobacillus plantarum (DSM 24730)
  • Streptococcus thermophilus (DSM 24731).

This exact combination has been tested in three double-blind, randomized, controlled trials and a single open-label trial, and all four found significant improvements in IBS symptoms. (65, 66, 67, 68)

Whether each of the strains would be helpful by themselves is not really known. But, that’s okay! You can actually buy this exact combination yourself under the brand name Sigma Tau VSL#3.

Lactobacillus plantarum 299v has also been shown to improve the symptoms of IBS and can be found in Jarrow’s Ideal Bowel Support supplement. (69)

Best Probiotics for Weight Management

The probiotic strain with the strongest evidence supporting its use to reduce weight is Bifidobacterium lactis B420. In a double-blind, placebo-controlled, randomized trial, B. lactis B420 helped overweight and obese patients lose 4% of their body weight in 6 months. (70) You can get this probiotic strain in Metagenics’ Ultraflora Control supplement.

To maintain weight and prevent new weight gain, studies suggest that the eight strains from Sigma Tau VSL#3 may be a better bet. (71)

Best Probiotics for Healthy Blood Sugar Levels

If you’d like your probiotic supplement help you to regulate your blood sugar levels, Lactobacillus acidophilus La5 and Bifodobacterium lactis Bb12 are the two best strains available. Multiple studies confirm these bacteria are able to lower blood sugar and A1c levels, even in those already struggling with diabetes. (72, 73)

A supplement containing both these strains is Standard Process Prosynbiotic.

Lactobacillus casei Shirota can also attenuate the development of insulin resistance when humans consume a high fat diet, which is known to be detrimental to the microbiome and human health. (74)

You can find this strain in the Yakult line of products.

Best Probiotics for Your Arteries

To reduce your cholesterol and protect your arteries, studies point to Lactobacillus reuteri NCIMB 30242. This probiotic microorganism was able to lower people’s total cholesterol by 9% and their LDL, specifically, by over 11%. (75)

You can buy this strain in Microbiome Plus Gastrointestinal Probiotics L Reuteri NCIMB 30242 GI Digestive Supplements.

If you’re more concerned about lowering your blood pressure to protect your arteries, Lactobacillus helveticus strains, particularly Lactobacillus helveticus LBK-16H and Lactobacillus helveticus CM4, are good choices. (76, 77) When these strains are combined with milk, they produce blood pressure lowering peptides. See the chart below for the impressive benefits seen with L. helveticus strains. (78)


Lye, Huey-Shi, et al. “The improvement of hypertension by probiotics: effects on cholesterol, diabetes, renin, and phytoestrogens.” International journal of molecular sciences 10.9 (2009): 3755-3775.

Unfortunately, there do not appear to be any products on the market (yet) that contain these exact strains of Lactobacilluls helveticus.

Best Probiotics for Your Bones

The Lactobacillus helveticus species seems to be very helpful for bone health. (79) Unfortunately, studies rarely report the actual strain used. And, when the do, the strains are not identical in every positive study, suggesting many Lactobacillus helveticus species may be effective.

This is our current problem within probiotics research — researchers haven’t been great about keeping track of the strains they’ve used thus far, and many studies focus on species versus strains. However, recent research indicates that it is the strain level that is most important in determining the effect of the probiotic and now researchers are starting to document their strain choices in their research to better help us, as consumers, know which strains might benefit us.

So let’s hope there will be some follow-up studies on probiotics for bone health (and other conditions!) that detail the strain used so that companies can start using these strains in their supplements for a healthier way to treat health conditions.

Until we have more data about individual strains, it’s tough to say whether supplementing with simply any Lactobacillus helveticus strains would be helpful. However, if you’re looking for bone health benefits and are okay with knowing that it’s somewhat unknown whether this particular strain would help or not, you can try Life Extension’s Florassist Mood, which contains Lactobacillus helveticus R0052.

In studies on mice, Lactobacillus rhamnosus GG (found in the Culturelle supplement, among others) and the strain combination found in VSL #3 have also proven to be useful for bone health. (80)

Best Probiotics for Autoimmune Conditions

The best probiotic for preventing and managing autoimmune conditions appears to depend on the exact autoimmune condition you’re looking to address.

For example, rheumatoid arthritis appears to respond to Bacillus coagulans GBI-30 6086 or a combination of Lactobacillus rhamnosus Gr-1 and Lactobacillus reuteri RC-14. (81, 82)

Ulcerative colitis, on the other hand, improves with Escheria coli Nissle 1917, Lactobacillus plantarum 299v, the combination of the nine strains of VSL#3, and Bifidobacterium longnum BB536 (83, 84, 85, 86, 87, 88, 89, 90), while psoriasis responds to Bifidobacterium infantis 35624. (91)

Unfortunately, we don’t have clinical trials for many autoimmune disorders at all. Since the effective probiotics are so different between disorders, it’s also really difficult to extrapolate and make educated, helpful suggestions without studies.

It is best to talk to your doctor about which probiotic strains she thinks might be helpful for you and your autoimmune disorder, personally. This is absolutely critical if you are taking immunosuppressants to control your symptoms, as this could put you at higher risk of infections with probiotic microorganisms. Do not start taking a probiotic if you are on active immunosuppressants without speaking to your doctor.

If you happen to be dealing with symptoms of rheumatoid arthritis, ulcerative colitis or psoriasis and have gotten the okay from your doctor, supplements you might want to check out are:

Best Probiotics for Your Mood

Human trials suggest Lactobacillus helveticus R0052 and Bifidobacterium longum R0175 are an effective strain combination for improving mood and reducing anxiety. (92)

You can get both of these probiotics in a single supplement with Pure Encapsulations Probio Mood or Life Extension Florassist Mood.

Best Probiotics for Women (Reproductive Health)

Lactobacillus rhamnosus Gr-1 and Lactobacillus reuteri RC-14 are, currently, the best strains researchers know of for preventing bacterial vaginosis and women’s reproductive health. (93, 94, 95, 96, 97)

You can get these strains in Jarrow Formulas Fem Dophilus Probiotic Supplements.

Best Probiotics for Men (Reproductive Health)

Since one of the key reproductive benefits you can reap from probiotics as a man is improved artery health (and penile blood flow) the best probiotics here are the same as those for artery health: Lactobacillus reuteri NCIMB 30242 and Lactobacillus helveticus spp. (98, 99, 100, 101, 102)

A supplement on the market that contains one of these strains is Microbiome Plus Gastrointestinal Probiotics L Reuteri NCIMB 30242.

Unfortunately, as you’re seeing throughout this article, the Lactobacilluls helveticus strains need to be detailed in the research being done so that consumers can be sure that the strains used in their supplements are actually helping their condition.

Probiotic-Rich Foods

Not sure you’re feeling the idea of taking a full-blown probiotic supplement? You can also get probiotics from your food. In general, the foods richest in probiotics are going to be fermented foods. (103)

Humans have been making and consuming fermented foods since the development of civilization. (104) By fermenting foods, we were able to preserve our food for later consumption without it going bad.

Probiotic-rich foods include:

  • Kombucha
  • Yogurt
  • Kimchi
  • Sauerkraut (refrigerated, if you’re buying it in the supermarket)
  • Kefir
  • Miso
  • Pickles or pickled vegetables (again, refrigerated)
  • Kvass

Much of the “hype” around fermented foods these days has been in regard to their probiotic content. However, fermented foods have a whole lot more going for them than “just” probiotics.

As part of the fermentation process, fermented foods produce other beneficial compounds such as short-chain fatty acids and antimicrobial and anti-inflammatory end-products. (105) This is in addition to any vitamins, minerals, and nutrients they contain as a whole food.

Probiotic Foods vs. Supplements

To begin this section, I’ll simply say that neither is “better” than the other; really, you should be consuming both!

Fermented foods that contain probiotic cultures provide a host of benefits, including (of course) probiotic bacteria and the other beneficial compounds I just mentioned above.

Fermented foods are typically studied as a whole food rather than their specific probiotic strains or beneficial compounds, so when researchers see humans benefit from fermented food consumption, it is unclear as to whether they are responding to the probiotics or the other healthy compounds contained in the food (or both, which is the most likely scenario).

With probiotic supplements, we can be more specific in the strains we are choosing, thus conferring specific benefits. As you’ve seen throughout this article, certain strains are useful for particular conditions, so if there is something specific you’d like help with it’s usually best to take a strain that has shown to be beneficial for that condition (in addition to regularly consuming fermented food).

That said, companies are adding well-researched strains to fermented food products, so it may be possible to get the best of both worlds. For example, the Lactobacillus casei Shirota strain (found in the Yakult probiotic drink) is a highly-researched strain that is useful for many different conditions, such as dysbiosis and weight gain prevention. (106, 107)

Ideally, I like to see my clients consuming both fermented foods and probiotics for maximum benefit, especially if they have specific health complaints or family history that they’d like to address.

If you’re completely healthy and you have no health conditions that you’re looking to prevent or improve, just consuming fermented foods may be all you need. But looking at the research on specific probiotic strains, it becomes very clear to me that you gain a lot of benefit from adding probiotic supplements to your routine in addition to regular fermented food intake, especially if you’ve got a health condition or a propensity to develop a health condition.

How Often Should I Take Probiotics?

Probiotics, whether they be in supplement or food form, should be consumed on a daily basis. When you take probiotics exogenously, they don’t stick around in the gut for a long time. Because of that, it’s important that you are regularly consuming them for maximum benefit.

So include fermented foods with your meals and set a reminder to pop your probiotic pill each day!

What if I Don’t Tolerate Probiotics?

Do you feel sick when you take probiotics? Perhaps you get digestive discomfort, or maybe you get high histamine reactions like flushing or hives.

If you don’t tolerate probiotics for any reason, it’s a sign that you may have dysbiosis (imbalanced gut bacteria) that needs to be addressed.

It’s imperative that you balance your microbiome for optimal health; just taking probiotics won’t get rid of all the bad bacteria in your gut in most cases if it’s already overrun (although they do really help!).

Want to know how to tell if you have imbalanced gut bacteria? Read my article on the topic here.

Wrapping It Up

Probiotics have a host of benefits, including promoting digestive health, regulating your immune system and protecting your metabolic health.

Probiotics are safe, with a minimal chance of side effects. They are also effective, as long as you choose the right probiotic strain for the health benefit you are looking for.

Fermented foods are also a great way to get probiotics in your diet (although you lose the benefit of knowing you’re taking a strain that is specific to your health condition). For best results, eat fermented foods and take a probiotic supplement regularly.

leaky gut syndrome

Is leaky gut syndrome real? Here’s what you need to know about this condition, how it affects your body, and how to heal for good.

Please note: there are affiliate links throughout this post. If you buy products through those links you help to support more great content like this!

What is Leaky Gut Syndrome?

Think about your digestive system for a second — from mouth to anus, it’s really just one long tube that dictates what can be absorbed into your bloodstream and what passes through the body. It knows that things like nutrients and water are important to absorb into the bloodstream, while toxic particles and undigested foods should make their way to the large intestine to be passed out of the body in the form of stool.

The gut barrier is one single cell layer thick and is connected by “tight junctions” that hold the cells together. This single layer of cells and the tight junctions between them are the only things preventing harmful particles from entering your bloodstream.

When the gut is functioning normally, these tight junctions hold the cells that make up your gut barrier together and only allow small particles (like nutrients) into the bloodstream.

Leaky gut syndrome, or increased “intestinal permeability,” is when the tight junctions holding the cells of your gut barrier together don’t function properly and the cells drift apart, allowing larger molecules like bacteria, undigested food particles, and waste products into the bloodstream.

Think of the gut barrier like a strainer. It only lets things of a certain size pass through, while anything too big will be kept out. Now imagine the holes in your strainer getting bigger, thus allowing larger particles through. That’s exactly what’s happening to your gut when you have leaky gut syndrome.

When you have leaky gut, your body is bombarded with unrecognized particles like lipopolysaccharides (LPS) that are present on the outer membrane of bad bacteria as they make their way through the bloodstream. Your immune system goes into high alert to try to protect you from these toxic particles, and as a result, you develop a high amount of inflammation.

This high level of LPS in the blood is associated with many conditions, as you can see below.

Rodriguez-Castaño GP, Caro-Quintero A, Reyes A, Lizcano F. Advances in Gut Microbiome Research, Opening New Strategies to Cope with a Western Lifestyle. Frontiers in Genetics. 2016;7:224. doi:10.3389/fgene.2016.00224.

I’ve written more about microbial imbalance and the resulting inflammation, and how that contributes to disease (specifically metabolic disease) in this article.

Is Leaky Gut Real?

There’s a lot of controversy over the term “leaky gut,” particularly the use of the term “leaky gut syndrome,” which seems to indicate that this condition is an official medical diagnosis.

Leaky gut syndrome is not a medical diagnosis, however, leaky gut is indeed a very real phenomenon that is seen throughout the scientific literature. Leaky gut is simply the more colloquial term for increased “intestinal permeability” or “intestinal hyperpermeability,” which are the terms you’ll see most often in the scientific research. (Though the term “leaky gut” is even catching on in research, and you’ll see that now too!)

In fact, at the time of this posting, there are over 90,000 Google Scholar results for the term “intestinal permeability”, and as you’ll see throughout the rest of this article, intestinal permeability is associated with a vast array of diseases and conditions.

What Causes Leaky Gut?

While there’s a lot we’re still learning about leaky gut, there are a few things we know of already that can cause this syndrome.

Gut Microbiome Imbalance (Dysbiosis)

Having an overload of bad gut bacteria (or dysbiosis) is one of the top causes of leaky gut syndrome. That’s because these bad bacteria have a toxic molecule on their outer membrane called lipopolysaccharide (LPS) that is highly inflammatory.

LPS causes gut inflammation, which causes the cells of the gut barrier to pull further apart, leading to leaky gut syndrome.

When you have both leaky gut and dysbiosis, the LPS that causes leaky gut then gets into the bloodstream, taking inflammation to the rest of your body and putting your immune system on high alert.

You can read more about dysbiosis and how it contributes to leaky gut and other diseases here.


Stress is also a huge factor when it comes to leaky gut syndrome. Researchers have known for a long time that severe physical stress such as trauma or surgery causes the intestinal lining to become “leaky”, but more recent research has started to look at the effect of chronic psychological stress on the gut barrier.

To approximate chronic psychological stress in humans, rats are repeatedly subjected to water aversion stress where they are placed on a platform surrounded by water. Researchers have found that this is a mild stressor to the rats, similar to the type of chronic mild stressors we face today. So what happens to these rats? They develop intestinal permeability that takes several days of no stress to heal.

This mild, chronic stress directly causes the cells of the gut barrier to drift apart, which, as discussed earlier, allows toxic particles to filter through into the bloodstream.

In addition to this, stress also imbalances gut bacteria, which also leads to the development of leaky gut syndrome in and of itself.

Certain Pharmaceutical Drugs/Alcohol

Certain drugs like NSAIDs (e.g. aspirin and ibuprofen, among others) are known to cause leaky gut. Alcohol also has the same effect.

However, it should be noted that it is chronic, excessive use of these items that leads to major intestinal permeability, so don’t worry if you like to enjoy a glass of wine or need to take an aspirin every once in a while!

That said, if you’re actively trying to heal from leaky gut (and not just trying to prevent it), it’s a good idea to limit your alcohol intake and avoid using NSAIDs as much as possible.


Diet plays a very important role in digestive health. An unhealthy diet, high in sugars and unhealthy fats while low in fiber, can lead to the development of leaky gut syndrome. This is because an unhealthy diet encourages the growth of bad gut bacteria. Unfortunately, this is common on a Standard American Diet (SAD).

In addition to eating unhealthily, consuming foods that you are allergic or sensitive to can also lead to irritation and inflammation in the gut and intestinal permeability.

Leaky Gut Symptoms

According to the scientific literature, there are a number of conditions that are associated with increased intestinal permeability, both within the digestive system as well as outside of it.

These conditions include:

    • Ulcers
    • Diarrhea
    • Irritable bowel syndrome (IBS)
    • Inflammatory bowel diseases (IBD — ulcerative colitis and Crohn’s disease)
    • Celiac disease
    • Cancer, esophageal and bowel
    • Allergies
    • Infections
    • Acute inflammation
    • Chronic inflammation
  • Obesity-associated metabolic disease

Now, this does not necessarily mean that leaky gut itself causes these conditions, just that intestinal permeability is commonly seen in these conditions.

However, there is research that indicates that leaky gut is present before the development of disease which makes researchers believe that it may be a “requirement” of sorts to develop various diseases.

However, it has given researchers a lot to think about as they explore leaky gut treatment possibilities to help prevent, treat, or reverse some of these conditions. I, for one, am very excited to see where the science leads us.

Testing for Leaky Gut

Leaky Gut Tests on the Market

There are two common tests for identifying leaky gut: differential sugar tests (like the lactulose mannitol test) and the zonulin test.

Differential sugar tests (DSTs) are considered the “gold standard” in leaky gut testing. For this test, you drink a solution containing specific sugars and then the levels of these sugars are measured a few hours later in your blood or urine. The idea here is that large oligosaccharides, like lactulose, do not pass through the gut barrier, while small monosaccharides, like mannitol, do. By testing for the sugars in the bloodstream or urine after consuming them, you’re able to see the degree of intestinal permeability that is present.

Testing for zonulin in the blood is, unfortunately, not a great way to determine if you have leaky gut. Zonulin levels do not seem to correlate with other markers of intestinal permeability (like the DSTs mention above), and zonulin levels are constantly changing, making one single measurement of this protein a fairly useless measurement of intestinal permeability.

Testing for zonulin antibodies, on the other hand, may prove a more useful measurement.

If you want to test for leaky gut, a differential sugar test or a zonulin antibody test is your best bet.

But that brings us to our next question… Is testing for leaky gut even worth it?

Is it Worth Testing for Leaky Gut?

I’m going to cut right to the chase here and say… No.

I’m not a big fan of testing for leaky gut because it never changes how we’re going to address it.

Truth is, there’s always something else causing leaky gut, like bad gut bacteria (dysbiosis), a poor diet, stress, food intolerances, etc.

So I’d much rather test for or evaluate those areas of my client’s lives than test for leaky gut.

Because, really, if I see someone who has digestive issues or an autoimmune disease or any of the conditions I mentioned above that are associated with leaky gut, I’m 99% sure that they have leaky gut anyway. I don’t necessarily need a test to tell me that because it’s not going to change how I approach the situation.

Instead of testing for the “symptom” (leaky gut), you want to test for the root cause (gut bacteria, stress, diet quality). Because when I know that a client has dysbiosis and their diet isn’t great and they have a stressful job, addressing all of those things is what is going to heal their leaky gut.

Save your money for gut bacteria testing instead of spending it on leaky gut tests!

Healing Leaky Gut

Now, just because testing for leaky gut is somewhat pointless doesn’t mean you shouldn’t treat leaky gut. As I hope you realize by now, leaky gut is indeed a real phenomenon that is important to address.

You may have heard that you can take supplements alone to heal leaky gut, but the crux of a leaky gut syndrome treatment plan tackles gut microbial imbalance, diet, and stress (with supplements to help along the way).

Leaky Gut Treatment Plan

The Leaky Gut Cure: Balancing Your Microbiome

The #1 cause of leaky gut is an imbalanced microbiome (dysbiosis). It is absolutely vital that you determine if you have bad gut bacteria and balance your microbiome if you want to cure leaky gut.

If you find you have imbalanced gut bacteria through SIBO testing or stool testing, you must get rid of that bad bacteria in order to heal leaky gut.

This is done by using herbal or pharmaceutical antimicrobials, dietary changes, stress reduction, and more. You can read more about how to get rid of bad bacteria here.

If you want to learn more about bacterial imbalance and how to fix it, I encourage you to take my free training by clicking the image below!

leaky gut syndrome

Leaky Gut Diet

As mentioned previously, a Standard American Diet full of unhealthy fats and sugars and low in fiber is a recipe for disaster when it comes to leaky gut.

Researchers are also worried about the impact of processed food additives, like emulsifiers and solvents, on our gut barrier, so avoiding processed foods is a good idea.

The best thing you can do from a dietary perspective to heal leaky gut is to eat an organic, nutrient-dense, whole foods diet that is high in fiber and prebiotics and low in unhealthy fats and sugars. You can read more about my dietary philosophy when it comes to supporting a healthy gut here.

The best foods to heal leaky gut include:

    • Non-starchy vegetables (broccoli, cabbage, leafy greens, etc)
    • Starchy vegetables (potatoes, sweet potatoes, yucca, taro, squash, etc)
    • Fruits (bananas, oranges, berries, apples, etc)
    • Meats (beef, pork, chicken, duck, etc)
    • Seafood (oysters, scallops, shrimp, sardines, etc)
    • Healthy fats (Olive oil, avocado oil, animal fats, etc)
    • Nuts (walnuts, macadamias, almonds, etc)
    • Legumes (if tolerated — lentils, beans, chickpeas, etc)
  • Dairy (if tolerated — yogurt, cheese, etc)

As much as possible, choose organic foods to avoid pesticides and additives. When trying to heal from leaky gut, it’s also wise to limit the amount of alcohol you consume.

Repair a Leaky Gut with Stress Management

Chronic stress induces intestinal permeability, so it’s imperative on any leaky gut treatment plan to incorporate stress management techniques.

Deep breathing, meditation, chi gong, yoga and more are options, but really, any stress management technique that you enjoy and are likely to do on a regular basis is best!

I find that my clients benefit more from practicing these techniques for shorter periods of time more often (for example, 5-7x/week) than doing a long session, say, once a week.

Best Supplements for Leaky Gut

There is a lot of really promising research looking at the best supplements for leaky gut, but it’s important to remember that supplements do not negate the need to address things like dysbiosis, diet, and stress.

You can take a million supplements for leaky gut, but if you’re not addressing those main causes of intestinal permeability, supplements really won’t get you very far. As much as I would love to tell you otherwise, there is no magic pill.

Supplements are used to “supplement” an existing treatment plan; they can help speed up the process of healing or make it easier, but they themselves won’t cause any lasting change on their own.

Antimicrobials Kill off Bad Gut Bacteria

It is clear that imbalanced gut bacteria, or dysbiosis, plays an enormous role in the development of leaky gut.

Because of that, it’s absolutely necessary to kill off bad bacteria and encourage healthy growth of beneficial microbes.

Most often, getting rid of bad bacteria is going to require being on antimicrobials of some kind (whether they are herbal or pharmaceutical).

As a dietitian, I’m a big fan of herbal antimicrobials. Here are some of my favorites to use:

    • Oregano oil (found in Biotics Research ADP — I like this one in particular because it’s a time-released oregano supplement)

Probiotics for Leaky Gut

Probiotics, in general, have proven to be very helpful in restoring and maintaining proper gut barrier integrity.

However, we need to remember that probiotic effects are strain-specific, so it’s important to pay attention to the exact strains that have been shown to be helpful (so that if you buy a probiotic to take, you know you’re getting a strain that actually has been proven to improve leaky gut!).

Here are the best probiotics for leaky gut:

Prebiotics for SCFA Production

Prebiotics are a powerhouse when it comes to healing leaky gut. It has been shown that supplementing with prebiotics reduces LPS concentrations in the blood. Remember that LPS is the toxic molecule on the outer membranes of bad gut bacteria. When you have a permeable gut, more of this toxic particle gets into your bloodstream and wreaks havoc from there. So when researchers are trying to determine whether a substance reduces leaky gut or not, they can look at the amount of LPS that ends up in your blood.

Now, prebiotics are different from probiotics. You can think of prebiotics as the food or fuel for probiotics; in essence, they feed your good bacteria so that you have plenty of the good guys around.

In addition to this, prebiotics also increase your production of short-chain fatty acids (SCFAs) which help to heal and seal the gut barrier as well as reduce inflammation (since less inflammatory LPS particles are getting through to the bloodstream).

My favorite prebiotics include:

A quick note about the Sunfiber supplement is that, unlike other prebiotics like GOS or FOS, Sunfiber is low-FODMAP and thus does not tend to increase digestive symptoms like bloating or gas like higher-FODMAP choices do. It also mixes really easily with water or other liquids, so it’s super easy to take.

Quercetin Seals a Leaky Gut

Quercetin is a really useful tool for helping to heal leaky gut. In fact, I’ve written a whole article on the topic!

We’ve already discussed the fact that stress increases intestinal permeability. Part of how this happens is that stress “destabilizes” or “degranulates” mast cells.

You may have heard of mast cells before as the cells responsible for allergy symptoms, like congestion, runny nose, etc. This is because when mast cells “degranulate” or become “unstabilized,” they release histamine, the chemical that causes allergy symptoms.

But you have mast cells all throughout your gut too, and when they “degranulate” or become “unstabilized” there, they cause leaky gut.

So how does quercetin fit into the picture?

Quercetin is one of the most abundant flavonoids present in our food supply, found in high amounts in onions, kale, and apples. It is well-known for many things, including its anti-allergy properties, anti-cancer effects, and as an antioxidant. But did you know that it can heal leaky gut too?

Since intestinal permeability is caused (at least in part) by unstabilized mast cells in the gut, it makes sense that quercetin would have this effect. This is because quercetin stabilizes mast cells and prevents the release of histamine and other chemicals from these cells. When researchers breed rats to have no mast cells in the gut (thus they are unable to have unstabilized mast cells that release histamine), they no longer develop intestinal permeability.

Quercetin has also been shown to enhance gut barrier function by having a “sealing” effect due to its role in the assembly and expression of tight junction proteins. Tight junctions regulate our intestinal permeability by connecting intestinal cells, thus only allowing the nutrients that we need in and keeping everything else out.

As you can see, adding quercetin to your leaky gut supplement protocol can really do a lot to help keep that gut barrier sealed up!

There are plenty of quercetin supplements on the market, but one of my favorites is the Source Naturals Activated Quercetin supplement.

Collagen Repairs a Leaky Gut

Collagen is the most abundant protein in our body, and is found in high amounts in the gut. It is also a potent source of the amino acid glycine.

As humans, we are meant to eat a mix of both glycine and methionine (among other amino acids), but in the modern world where we don’t tend to eat nose-to-tail, that can be difficult. You see, glycine is abundant in animal products that we don’t usually consume, like tendons, ligaments, and bone while methionine is present in high amounts in muscle meat (think steak, chicken breast, etc). This altered ratio of methionine:glycine intake is thought to be related to our increase in chronic disease rates. I highly recommend watching Denise Minger’s Ancestral Health Symposium talk on this topic.

Because of its role in the gut, collagen peptides have been found to heal leaky gut by improving tight junction function.

There are many collagen peptide supplements on the market right now, but I’m a big fan of the Vital Proteins line.

L-Glutamine Fuels Gut Cells

Glutamine is an amino acid and is a major fuel source for intestinal cells.

It has been studied and used for years in relation to its ability to reduce intestinal permeability in critically ill patients.

In addition to this, glutamine supplementation can also improve gut bacteria balance.

This gives you a great combination of benefits: glutamine balances your microbiome and heals leaky gut.

While capsules may seem like the easiest to take, you’re actually better off getting a powder for supplementation. This is because you’re generally going to want fairly high doses of glutamine to get the benefits for leaky gut.

In healthy adults, the observed safe level of l-glutamine is 14g/day. Considering that most capsules contain a maximum of about 1000mg, you’d have to take 14 of them every day!

Therefore, an L-glutamine powder is a much better choice for leaky gut.

Vitamin D Keeps Your Gut Healthy

Vitamin D is one of those vitamins that you sit and wonder… “What can’t Vitamin D help with?!”

From bone health to the immune system, Vitamin D plays a role in almost every facet of our being — and that includes preventing and healing leaky gut.

You see, Vitamin D deficiency makes you more likely to have leaky gut. The good news, however, is that supplementing with Vitamin D can keep your gut barrier in good condition.

You can get Vitamin D from sun exposure, food, and supplementation. Getting proper sun exposure is the best way to get your Vitamin D, of course! There are very few foods that contain a lot of Vitamin D, so it’s somewhat difficult to get your D from your diet.

If you’re not getting enough sun exposure to get adequate Vitamin D, your next best bet is to supplement.

I recommend taking a Vitamin D3 supplement. Depending on your current blood levels, taking anywhere from 2000 – 5000 IU per day is a good idea.

And because fat-soluble vitamins work synergistically, I recommend taking a combination supplement that also includes Vitamin K2, like Thorne’s Vitamin D/K2 Liquid.

Zinc Improves Gut Barrier Integrity

Zinc is an important mineral that is used in a variety of processes within the body to keep us healthy.

When you’re deficient in zinc, your body’s ability to heal wounds may become impaired, your immune system may not function as well, and you might develop anemia, hypogonadism, or mental illness.

In addition to this, your gut barrier may become impaired. Zinc supplementation has been shown to improve gut barrier integrity in those with Crohn’s disease. It does this by strengthening the tight junctions that hold the cells of the gut barrier together.

I like to incorporate zinc into any leaky gut supplement protocol for these reasons. Zinc carnosine is my favorite form of zinc for leaky gut as it’s been shown to heal leaky gut and help repair gut cells.

I like Integrative Therapeutics’ Zinc Carnosine supplement.

How Long Does It Take to Heal Leaky Gut?

As I mentioned before, treating leaky gut requires a multi-pronged approach. You need to get rid of bad gut bacteria, manage your stress, and eat well. Supplements can help you do these things, but they’re not the end-all-be-all of leaky gut treatment.

When people ask this question, what they really mean is “How long will it take before I feel better?” That can really depend.

If you have an autoimmune disease and believe leaky gut is playing a role in that, the truth is you may never fully recover from autoimmunity. That said, healing your gut can improve your symptoms immensely. I’ve seen symptom improvement in as little as a month, while others can take 6 or more months to really see significant benefits.

If you have digestive issues that you think are caused by leaky gut, I’ve found that healing your gut goes a long way toward recovery. Just as with autoimmune diseases, I’ve seen significant improvement in as little as a month when really addressing all aspects of a leaky gut treatment plan.

When it comes down to it, how long it will take you to heal leaky gut totally depends. It depends on how long you’ve been dealing with gut issues, how much you’re able to commit to the changes that need to be made to heal your gut, and then it’s just about how your body (we’re all different, right?) responds.

The short answer: on average it can take anywhere from 1-6 months to actually feel better when you’re trying to heal from leaky gut (though it may take longer for your gut barrier to completely repair).

Heal Leaky Gut For Good

While I hope this article has given you a lot to start thinking about, if you want to learn exactly how to address digestive issues, I’d like to invite you to join my free training.

You’ll learn:

    • How to fix digestive issues even if you feel like you’ve tried everything before
    • How to determine the cause of digestive issues and heal them for good
  • How to overcome food sensitivities

I’ll go into more detail on the gut bacteria imbalances that cause leaky gut (remember you have to get rid of those bad guys if you ever want to heal leaky gut!).

Want to join me? Click the image below to sign up!

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bad gut bacteria

You’ve probably heard the words “gut microbiome”, “gut bacteria”, or “gut flora” quite a bit these days.

Maybe you’ve even read a few articles on why you should pay attention to your gut bacteria and how important they are for your overall health.

You know that “bad bacteria” aren’t great for your health…But now you’re wondering – how do I know if I have bad bacteria? Hint: you might have bad bacteria even if you don’t have digestive issues.

Let me walk you through it!

What is the Microbiome

First, it probably makes sense to go over exactly what the gut microbiome is because this is what becomes unbalanced, leading to chronic health conditions.

The gut microbiome is often referred to as the “forgotten organ” by scientists because it plays such a vital role in your health. Just like your heart and your lungs are required for you to thrive, so is your gut microbiome.

Your gut microbiome is comprised of trillions of bacteria, yeasts, and viruses. We generally classify all of these microorganisms into three different categories:

Normal Flora

Normal flora are exactly what they sound like — the normal bacteria that you expect and want to find in your microbiome. These are our good guys; the flora that do all the good things we associate with a healthy microbiome like make vitamins, support the immune system, and more.

That said, you can have perfectly normal flora growing in the wrong place, which can also cause symptoms. This is the case for SIBO (small intestinal bacterial overgrowth), which can cause diarrhea, constipation, and excessive bloat

Potential Pathogens

Potential pathogens are gut flora that have the potential to be pathogenic (harmful, causing symptoms). While some of these can be found in small amounts and not be problematic, if they start to grow out of control, they can become pathogenic and cause you symptoms. So it’s important to make sure that these flora are found in small amounts (or the right amount) and are not overgrowing with the potential to cause symptoms.


Pathogens or pathogenic bacteria are the bad gut bugs — these are ones that, if found, are very like to make you symptomatic. Depending on the pathogen, that could mean symptoms from anything like bloating, excessive gas, flatulence, abdominal pain, diarrhea, constipation, reflux, and more. Basically, we don’t want to see these on your testing!

When your gut microbiome is well-balanced, it helps you digest food, make nutrients, influences the immune system and the metabolic system, and more. Clearly, we want these bacteria balanced!

When gut bacteria become imbalanced, they can cause a host of symptoms including diarrhea excessive gas, bloating, constipation, diarrhea, abdominal pain, reflux, and more. Imbalanced gut bacteria can also cause symptoms outside of the digestive system, too, which I’ll talk more about in a few moments.

What is Unbalanced Gut Bacteria?

When you hear the terms “bad gut bacteria” or “imbalanced gut flora” or “unhealthy microbiome”, this can refer to a number of different conditions. The most common include small intestine bacterial overgrowth (SIBO), microbial dysbiosis (an imbalance of gut flora in the large intestine), pathogens, or parasites.

Let’s do a quick rundown of each of these conditions:


The small intestine should be relatively sterile when compared to the large intestine, which houses the majority of our bacteria in the microbiome. When bacteria translocate to the small intestine for any reason and overgrow, you now have an overgrowth of bacteria in the small intestine; hence, “small intestine bacterial overgrowth” or SIBO. This is a very common condition and one I see a lot in my practice.


The term “dysbiosis” simply means an imbalance of bacteria (which could be anywhere in or on the body), but it’s commonly used to describe an imbalance of gut bacteria in the large intestine, specifically. I like to break down dysbiosis into two categories (well, 3 really, but we’ll talk about the 3rd option – parasites and pathogens – next).

Insufficiency Dysbiosis

This is when you don’t have enough beneficial bacteria like Lactobacillus or Bifidobacteria hanging out in the large intestine. These should be present in high amounts, but it’s very common to see folks with very little or no growth of these beneficial microbes.

General Imbalance 

This is when you have too few beneficial bacteria and overgrowths of one or more commensal bacterial strains. Commensal bacteria are bacteria that are normal to find in small amounts and typically don’t cause any harm to you. However, when they start growing in high amounts, you might start developing symptoms.

Parasites or Pathogens

Parasites or pathogens are specific strains of bacteria that, when present, can cause harm or disease. With potential pathogens, you can usually have a small amount that won’t necessarily be problematic, but they may start to cause symptoms as their numbers grow higher.

Symptoms of Imbalanced Gut Flora

Okay, so now that you know what different types of imbalanced bacteria you might have, what are some symptoms you might experience if you were to have any of these types of bacterial issues?

The symptoms that can accompany the different types of imbalance are quite diverse. However, there are a few general symptoms you can look for with the different imbalances that might clue you in to whether you’re more likely to have one or the other.

Remember, though, that you can have these imbalances and have absolutely zero digestive problems; some people just don’t exhibit digestive symptoms even if they have a severe imbalance in their microbiome. But just because you don’t feel digestive symptoms doesn’t mean that an imbalanced microbiome isn’t harming you; it’s still having a negative impact on all your other body systems. Very important to take care of it even if you don’t notice any digestive symptoms.

heal your gut

Symptoms of Bad Gut Bacteria

SIBO Symptoms

Wondering what causes bloating? The most common symptom of SIBO is excessive bloating or stomach distension. You get bloated when you have SIBO because when the overgrowing bacteria in the small intestine are exposed to carbohydrates or fiber from your diet, they ferment them and produce gas as a result. As you can imagine, this can not only cause bloating but it can also lead to symptoms like flatulence or excessive gas. The increased pressure in the GI tract can also lead to reflux. (1) SIBO is also associated with diverticulitis. (2)

When you test for SIBO, there are two different types that will show up: methane-positive or hydrogen-positive.

Methane-positive SIBO commonly causes you to become constipated, while diarrhea is associated with hydrogen-positive SIBO. (3)

You can also exhibit no digestive symptoms at all when it comes to SIBO. This is because having an infection in the gut can cause disease outside the digestive system. We’ll talk more about these different conditions in the next section, but I just want you to know that you can have absolutely zero digestive symptoms and still have bacterial imbalance in the gut.

To recap, SIBO symptoms include:

  • Bloating/Bloated Stomach/Distended Stomach
  • Excessive Gas
  • Constipation
  • Diarrhea
  • Abdominal pain
  • Flatulence
  • Belching

Large Intestine Dysbiosis Symptoms

The symptoms for gut dysbiosis in the large intestine vary a lot, and I find that a lot of the time dysbiosis is associated with disease states that occur outside of the digestive system. However, there are certainly people who develop gastrointestinal symptoms when they have dysbiosis.

With insufficiency dysbiosis, the most common symptom I see is constipation. Symptoms of just a general imbalance of bacteria in the large intestine vary widely. They can include constipation, diarrhea, bloating, or general pain or sensitivity in the abdomen.

Pathogens and Parasites

These have more specific effects depending on which parasite or pathogen you have. For example, if you have H.Pylori you might have reflux or ulcers, while klebsiella pneumoniae is associated with ankylosing spondylitis. Other pathogens and parasites can simply cause ongoing digestive symptoms like diarrhea or bloating.

Conditions Associated With Imbalanced Gut Bacteria

As I mentioned previously, you do not need to have digestive symptoms to have imbalanced gut flora. Imbalanced gut flora is probably more common than most people think because of this – after all, it’s strange to think that the bacteria in your gut have anything to do with the rest of your body.

Conditions/Diseases Associated with SIBO

Conditions/Diseases Associated with Dysbiosis

Specific Pathogens/Parasites and Their Associated Symptoms/Diseases

Gut Microbiome Testing

Testing your gut for imbalanced bacteria is hugely important. You may not even know that you might have an imbalanced microbiome!

I wish it was cheaper to test (and hopefully we’ll see prices go down on these tests in the coming years) because I think everyone should do it. Since a healthy, balanced microbiome is vital to your overall health, you owe it to yourself to make sure your microbiome looks good.

Because there are so many different symptoms of bacterial imbalance, I find it’s very useful to test so you know what bacteria you actually have and what might be missing.

Because not all bacterial imbalances show themselves in the way of digestive symptoms, you may not think you need to worry about your gut bacteria, but hopefully, you’ve learned a thing or two in this article that makes you think twice about that assumption!

To test your gut bacteria, I recommend doing two types of tests: a SIBO test and a stool test.

SIBO Testing

I’m currently using the SIBO test from Biohealth in my practice, which I like a lot. If your doctor is familiar with SIBO or is open to learning more about it, you may be able to get them to order a SIBO test for you that might be covered by your insurance plan.

However, many doctors won’t test for it, unfortunately (though this is becoming less and less common as the topics of the microbiome and SIBO become more popular). If your doctor will order a test for you, I recommend asking to make sure it’s at least a 2-hour test that looks at both hydrogen and methane gas. Remember I said that which gas you produce dictates how you deal with it, so it’s important to get that information!

You can also order SIBO testing online.

Stool Testing

As for stool tests, my favorite is the GI-MAP test from Diagnostic Solutions Laboratory. It’s a very accurate test, needing only one stool sample for parasitology. Other stool tests companies recommend getting the higher sample rates (for example, Doctor’s Data offers a 1 sample, 2 sample, or 3 sample kit) but GI-MAP can get it all in just 1 sample.

I still think other options for stool testing are good, like Doctor’s Data, Biohealth, and Genova, but personally, I’m liking the GI-MAP these days. These types of stool tests tend to be a bit harder to get from your doctor unless you’re going to a functional medicine doctor. I’ve seen some tests be covered by insurance (at least partly) before, but a lot of times it’s difficult to get these tests from someone who can help get it covered by insurance, sadly!

If you want to test your gut bacteria, I recommend asking your doctor about your options first. If you can’t get it covered or they can’t or won’t order them, you’ll need to find another healthcare practitioner to order through, or you can order it online.

In my online program, Build Your Biome, you get these tests (at a discount) and I’ll tell you what everything means and how to deal with it appropriately.

How to Get Rid of Bad Bacteria in The Gut

If you’ve done some of this testing and find out that you have SIBO, dysbiosis, parasites, pathogens, candida, H. Pylori or something else, you’ll want to make sure to clear out any bad or overgrowing bacteria for optimal digestive and overall health.

Depending on what your microbiome is dealing with, you have a few options.

Herbal Antimicrobials

Many herbs have antimicrobial properties, meaning that they kill off microbes. When you have overgrowing microbes in your gut, this is exactly what we want! Some common antimicrobial herbs and nutrients include: oregano, berberine, garlic (allicin), artemisinin, black walnut, caprylic acid, and more.

I highly recommend working with a professional if you’re going to go this route as you want to make sure that the antimicrobials you are choosing are appropriate for the bacteria found in your testing.

Pharmaceutical Antibiotics

While antibiotics can have a lot of unfortunate side-effects, they have a time and place. If you have a microbial imbalance that warrants antibiotics, it’s smart to take them as prescribed.

It is always wise to bring any gut testing that you’ve had done to your doctor so that they can advise you on the proper next steps.

Prebiotics and Probiotics

One of the best things you can do to rebalance your microbiome is to consume both prebiotics and probiotics. Prebiotics and probiotics help to shift the microbiome back to a more favorable state by pushing out bad bacteria and helping good gut bacteria thrive.

I created a prebiotic and probiotic product specifically for those with digestive issues called Gut Power Matcha. It’s a prebiotic & probiotic matcha blend, so you just need to drink one cup a day to help shift your microbiome! Easy, tasty, and effective.

gut power matcha

Gut Power Matcha

Elemental Diet

An elemental diet is a meal replacement diet that consists of highly broken down nutrients. They’re so broken down, in fact, that they don’t even make it to your small or large intestine where they can feed bacteria.

Because this type of diet (really, it’s a supplement more than anything else — diet doesn’t fix microbial imbalance) doesn’t feed bacteria, it can be used to starve bacteria and kill them off. You need to use it long enough for it to have this effect, though (generally at least 14 days).

While it’s not the most pleasant thing to be consistent with, it works very well.

If you’re interested to read more about an elemental diet, you can read my article (originally published on here.

Lifestyle Changes

To be clear, lifestyle changes alone do not get rid of microbial imbalance. However, they make your antimicrobial/antibiotic/elemental diet so much more effective at killing off bad gut bacteria and keeping bad bacteria away once you finish up your course.

The lifestyle changes I incorporate into my Build Your Biome program include stress reduction, stress management techniques, gut-directed hypnosis, dietary changes (making sure you’re eating enough and choosing healthy options), journaling, sleep enhancement, proper exercise (both the amount of exercise and recovery that you do), and more.

Even though these things alone can’t get rid of bacteria, they are the foundation upon which your digestive health stands. If these factors aren’t taken care of, you make your body’s job so much harder and it’s going to take you longer to get rid of bad gut bacteria and keep it away for good.

If you want to know more about how to get rid of the microbial imbalance that causes digestive problems (and more), check out my free training on the topic by clicking the image below.

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Wrapping it All Up

Gut health is so crucial to overall health, as I hope you’ve learned by reading this article! Imbalanced gut bacteria is associated with many health conditions and diseases, and clearing bad bacteria can make a world of difference if you’re suffering.

Testing your gut microbiome for bad bacteria is the best way to determine if you have any nasty gut bugs that need dealing with. I recommend two tests: the SIBO test and the Stool Test (GI-MAP being my favorite).

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ibd ulcerative colitis crohns

Inflammatory Bowel Disease (IBD) refers to a group of diseases characterized by changes in the intestinal immune system and chronic inflammation of the intestinal walls.

The most common of these conditions are Crohn’s disease and ulcerative colitis. (1, 2, 3, 4)

Crohn’s Disease

Crohn’s disease (CD) is an inflammatory bowel disease that can affect any part of the digestive tract, from mouth to anus. (2, 5)  It causes patches of inflammation that extend deep into the intestinal wall, sometimes going all the way through. These inflamed patches are typically separated by areas of healthy tissue.  (2, 5)

The inflamed patches of intestine are very painful and the defining symptom of Crohn’s disease is abdominal pain. Poor digestion and absorption of food by the inflamed gut walls also leads to diarrhea (which can be bloody or mucus-filled), weight loss, and nutritional deficiencies (particularly anemia and vitamin B12 deficiencies). (3, 5)

Though the diagnosis of Crohn’s disease mostly relies on changes in the digestive tract, the overactivation of the immune system in CD is not restricted to the gut. Abnormal immune function in the disease leads to a variety of non-digestive symptoms, as well, including:  (3, 5)

  • fever
  • arthritis (in the joints or spine)
  • canker sores
  • inflammation of the eyes and
  • inflammation of fat cells below the skin (erythema nodosum)

Ulcerative Colitis

Though similar to Crohn’s in many ways, ulcerative colitis (UC) has some distinct features.

In UC, the immune system only attacks the surface of the colon and/or rectum, not deep into the intestinal wall.  The inflammation in UC is also continuous, rather than patchy. It never skips over patches healthy tissue. (2, 5)

These differences in nature of the intestinal inflammation in UC lead to slightly different symptoms.

Rather than abdominal pain, the defining symptom of UC is frequent, urgent and severe diarrhea that is nearly always bloody.

UC can cause abdominal pain and unwanted weight loss, but, since the inflammation in UC is more limited and doesn’t involve small intestine (where nutrients are absorbed), these symptoms are less common in CD. (2, 5)

Though the intestinal inflammation in UC is less widespread than in CD, it would be a mistake to think the immune dysfunction itself is somehow “limited”. It is still significant and has full-body effects. Similar to the body-wide symptoms of Crohn’s, UC can cause: (2, 5)

  • fever
  • osteoporosis
  • mouth ulcers
  • leg ulcers
  • arthritis
  • inflammation of the bile ducts
  • inflammation of the eyes
  • formation of blood clots in the legs or lungs

What causes IBD?

The exact cause of IBD has baffled researchers for decades. (2, 6)

Studies clearly indicate that there are genetic factors at play. Population studies show different rates of IBD amongst different ethnicities and a strong clustering of IBD within families. (3, 4, 7) Detailed genetic studies have even been able to find over 160 unique gene mutations directly linked to an increased risk of IBD. (7)

But data also clearly shows that IBD isn’t an actual genetic disorder, either.

None of the 160 risk genes identified are common to everyone who gets IBD. (7)

There is no decisive inheritance pattern for IBD, like one sees with true genetic disorders such as hemophilia or cystic fibrosis. (8)

IBD can’t even be the result of a combination of high-risk genes since identical twins (who have identical DNA) don’t always both get IBD if one does. (9)

To summarize, genes play a role in IBD development, but don’t seem to cause IBD.

How does that work?

The leading theory at the moment is best explained by the “loaded gun analogy”. (10)

The Loaded Gun Analogy

As the name suggests, the “loaded gun analogy” imagines the development of IBD to be similar to firing a bullet from a gun.

In order to fire a bullet from a gun you need to do two things: First, you have to load a bullet into the chamber. Then, you have to pull the trigger.

If you leave out either of these steps, you can’t actually fire a bullet!

If you load the bullet but don’t pull the trigger, the bullet just sits harmlessly in the gun. And if you pull the trigger, but forgot to load the bullet, nothing happens.

Similarly, researchers now think that developing IBD requires two steps.

The first step (“loading the bullet) comes from your genetic risk. Inheriting IBD-promoting genes acts like loading a bullet into the chamber of the gun.

The second step ( “pulling the trigger”) comes from something completely non-genetic: your environment. The right environment acts like a finger on the trigger of the gun, actually firing the bullet.

If you leave out either of these steps, you don’t actually get IBD. If you have the genes for IBD, but are never exposed to the right environment, your genes sit harmlessly in your cells. If you live in the perfect environment to develop IBD, but have no IBD genes, nothing happens.

Pulling the Trigger of IBD

Clearly, not every environment can “pull the trigger” for IBD, or everyone with a genetic risk would get the disease.

Only specific things in the environment, then, can be capable of “pulling the trigger”.

Have researchers been able to find any solid candidates for these environmental “trigger-pullers”?

Quite a few, actually.

Scientists compared the environments of people who developed IBD and people who didn’t (even though they had a genetic risk) and found lots of differences.

They found that those who got IBD tended to:

  • live in specific parts of the world (North America or Europe) (4)
  • live in cities (11)
  • include less fruits and vegetables in their diet (12, 13)
  • work white-collar jobs (13)
  • be stressed out for long periods of time (13)
  • have been bottle-fed as an infant (14)
  • have been exposed to cigarette smoke (for Crohn’s disease only) (13, 14)
  • have been exposed to excessive air pollution (14)
  • have low vitamin D levels (15)
  • have taken non-steroidal anti-inflammatory drugs (NSAIDs), like ibuprofen (13)
  • not had their appendix removed (ulcerative colitis only) (13)
  • have had an intestinal infection (6, 13)
  • and have an unhealthy balance of gut bacteria (6, 14, 15, 16, 17, 18, 19, 20, 21, 22)

While scientists think all of these environmental factors are important, one has started to stand out over the last few years as one of the most important IBD-trigger: having unhealthy gut bacteria.

Unhealthy Gut Bacteria & IBD

There are 5 known ways that the microbes living in your gut can influence the development of IBD.  

Unhealthy Gut Bacteria Interact with the NOD2 Gene

The NOD2 gene is one of the most commonly mutated genes in IBD. It encodes a protein responsible for recognizing when bacteria are trying to sneak into the body. It sounds the alarm when this happens, telling the immune system to attack.

When it is mutated, NOD2 becomes very sensitive to unhealthy changes in the numbers and types of bacteria in the gut. Even small changes can cause NOD2 to tell the immune system to mount an enormous response.

Unfortunately, an enormous immune response damages the wall of the intestine. This damage is really small — smaller than the tiniest paper-cut you can imagine — but enough that bacteria from inside the gut can end up getting into the wall of the intestine itself.

Once in the intestinal wall, guess what these bacteria do? They are recognized by NOD2 because they are not supposed to be there. Of course, NOD2 tells the immune system to attack more. The wall of the intestine becomes more damaged. More bacteria can get in.

It becomes a vicious cycle that can lead to the symptoms of IBD. (6, 23, 24)

Unhealthy Gut Bacteria Interact with ATG16L1

It sounds kind of crazy, but some white blood cells have to be able to “swallow” bad bacteria before they can kill them. (If you’ve never seen a white blood cell gobble up a bacteria to kill it, you should check it out on YouTube. It looks really cool!)

One of the proteins these immune cells need to be able to “gobble up” bacteria is ATG16L1. If the gene that encodes for this protein is mutated (which it often is in IBD), ATG16L1 can’t do its job. This means that immune cells can’t “eat up” bacteria very well.

If unhealthy gut bacteria trigger immune cells to try to “eat” them, but the immune cell can’t because of a mutated ATG16L1, it has to resort to plan B. Plan B, unfortunately, is really bad for developing IBD.

Immune cells that can’t “eat” bacteria start spewing as many inflammatory chemicals as they can to try to kill the bacteria anyway. These inflammatory chemicals damage the wall of the intestine.

Just as we saw with NOD2, this damage can create a vicious cycle.

More bacteria get into the intestinal wall where it is damaged. These bacteria, who aren’t supposed to be there, activate new immune cells, which try to “eat” them. They can’t, of course, so these immune cells release more inflammatory chemicals. And on it goes. (6, 24, 25)

Unhealthy Gut Bacteria Make Toxins

Some of bacteria that are found in high numbers in the digestive tract of those with IBD can make gut-damaging toxins.

For example, two kinds of bacteria, called D. piger and B. wadsworthia, found at abnormally high levels in IBD, make a chemical called hydrogen sulfide. Hydrogen sulfide is a strong acid that can damage the walls of the intestine. (26, 27)

And, as we saw above, damaging the walls of the intestine can lead to inflammation of the gut wall and IBD.

Unfortunately, it is difficult to tell if you have hydrogen sulfide producing bacteria in your gut, especially your small intestine. Tests for unhealthy bacteria in your large intestine may pick up these toxin-producing bacteria, but a SIBO breath test can’t (yet, at least).  (28)

This makes hydrogen sulfide a potentially potent driver of IBD. Left undetected, this acid can damage gut walls for long periods of time, making it even more likely that the gut inflammation will progress to IBD.

Unhealthy Gut Bacteria Lead to Leaky Gut

Healthy bacteria produce molecules that help the intestinal wall stay strong and healthy. They do this by helping the cells that make up the wall of the intestines produce something called “tight junction proteins.” These proteins seal up the gaps between individual cells to create a seamless wall of cells, with no holes or gaps.

Unhealthy gut bacteria, on the other hand, don’t make enough of the chemicals that help the gut wall make tight-junction proteins. And without enough tight-junction proteins, holes and gaps can start forming in the intestinal wall, leading to a condition called “leaky gut”.

Once your gut is “leaky”, bacteria get through into your body and wreak havoc. They cause the immune system to go nuts, releasing inflammatory chemicals into the intestinal wall and bringing us into the vicious circle of IBD. (29)

Unhealthy Gut Bacteria Cause an Inflammatory Storm

Healthy gut bacteria make a group of chemicals called short-chain fatty acids (SCFAs). SCFAs have an important job in regulating the immune system. They help a group of immune cells, called T-regulatory cells, mature and function.

Mature T-regulatory cells do exactly what their name sounds like they do — they regulate the immune system. Specifically, they help turn off cells that release inflammatory chemicals, such as those damaging the gut wall in IBD.

Unhealthy gut bacteria do not make as many SCFAs, leaving the immune system with fewer T-regulatory cells. This makes it much harder to stop inflammatory chemicals from damaging the intestinal walls and stop IBD from progressing once it starts. (6, 30, 31)

Taking the Bacterial Finger Off the Trigger

Clearly, having unhealthy gut bacteria can be bad news when it comes to developing IBD.

If you have a genetic risk (a close family member who’s already been diagnosed, for example), is there anything you can do to prevent unhealthy gut bacteria from pulling the IBD trigger on you?

Research shows that there are a few things you can to do support healthy gut bacteria and potentially prevent IBD. These include:

  • Quit smoking — cigarette smoke harms your healthy gut bacteria. (13, 14, 32)
  • Limit alcohol intake — excessive amounts of alcohol can harm your healthy gut bacteria. (33)
  • Reduce the use of NSAIDs — NSAIDs can damage the walls of your intestines, making it more difficult for healthy gut bacteria to survive. (13, 34)
  • Eat lots of fruits and vegetables —  fruits and veggies are rich in fiber and prebiotics, both of which help support healthy gut bacteria. (12, 13)
  • Increase your intake of fermented foods or probiotics — These contain healthy gut bacteria which help support the immune system.  (35, 36, 37)
  • Get regular exercise — exercise helps healthy gut bacteria thrive. (38)
  • Drink enough water — proper hydration helps to prevent constipation, which can have negative effects on your gut bacteria can keep your healthy gut bacteria from growing properly. (39, 40)

If you know you are at risk for IBD or have already been diagnosed with IBD, you should absolutely test your gut microbiota.

Testing can identify unhealthy levels of gut bacteria that need to be treated more aggressively with antibiotics or antibiotic herbs.

Un-Firing the Bullet

What if you already have IBD? Can addressing poor gut bacterial health also address your IBD symptoms?

Research shows that fixing imbalanced gut bacteria can help IBD symptoms, but not always. We need more studies to be done in this area, but the current research shows that the beneficial effects of fixing imbalanced bacteria depend on both the type of IBD and the type of treatment used to balance unhealthy bacteria. (6, 41)

But a few treatments seem to be helpful for IBD patients, which I’ll go over below.

Researchers wondered the exact same thing and put it to the test. (6, 41)

Ulcerative Colitis Treatments

Studies show that treatment with the probiotics VSL#3 and E. coli Nissle 1917 are the most helpful bacterial-treatment option.

These probiotics contain purified strains of healthy gut bacteria and have been shown to improve the symptoms of ulcerative colitis better than placebos in multiple studies. (6, 42, 43, 44, 45, 46)

Ulcerative colitis symptoms may also respond to treatment with germinated barley foodstuff, a prebiotic.

Healthy gut bacteria can use germinated barley foodstuff for food and fuel, helping them get the upper hand on unhealthy gut bacteria and regain normal ratios. (6, 47, 48, 49)

Given the response to this particular prebiotic, it would make sense to suspect that other prebiotics, like FOS or GOS, may be useful, as well.

Crohn’s Disease Treatments

Studies show that fecal transplants can be very beneficial for Crohn’s disease patients. (6, 50)

Fecal transplants are medical procedures that do exactly what they sound like. Doctors use stool from a healthy donor without IBD, blend it, filter it and introduce the filtered liquid into the gut. This can be done via an enema, a colonoscopy or a tube threaded through the nose and throat into the gut. (6)

Studies show that fecal transplants are very effective at treating Crohn’s disease symptoms for months at a time. This is mostly true for those who have Crohn’s disease and an intestinal infection with a pesky bacteria called C. difficile. (6, 51)

Treatment Safety

While doctors and scientists believe that prebiotics, probiotics and fecal transplants are generally safe to use, they are not entirely without side effects. (6)

Most side effects are mild and include things like gas, bloating, or diarrhea. Not great when you’re trying to treat digestive issues, but not life-threatening. (6)

In those with IBD, however, there is a slight risk that probiotics and fecal transplants can lead to a very serious side-effect: blood poisoning. (6, 52, 53)

Both probiotics and fecal transplants contain live bacteria that can, in rare cases, get through the damaged gut wall in IBD and into the bloodstream. This is extremely dangerous. It can cause septic shock and death if not treated quickly and properly. (6, 52, 53)

For this reason, it is important that those with IBD discuss all treatments for unhealthy gut bacteria with their doctor and only take over-the-counter supplements under their doctor’s supervision.

Healthy Gut Bacteria: A Magic Bullet?

Even a couple of decades ago, no one imagined that gut bacteria could play such an important role in the development of IBD. Nor would anyone have imagined that the painful, debilitating, sometimes life-threatening symptoms of IBD might be cured with simple, easy treatments to address gut bacterial health.

While that is not yet a reality for everyone — there is no single magic bullet cure for IBD in treating unhealthy gut bacteria — researchers, doctors, and patients are starting to imagine it!

Maybe, with continued research, those dreams just might come true.

Have you been diagnosed with IBD? Have you tried balancing your gut bacteria to help your IBD symptoms? Let me know in the comment section below!

psoriasis microbiome gut bacteria

Psoriasis is a common immune-mediated condition affecting between 1% and 4% of the population. (1)

The defining characteristic of psoriasis is a unique patchy skin rash. The rash is made up of one or more individual “psoriatic plaques”, which are areas of thickened, inflamed skin covered by a layer of silvery-white flakes. (1)

These plaques burn, sting and itch. In some cases, the itching is severe enough to cause people to scratch the plaques open. The resulting wounds may bleed, ooze, scar or even become infected. (1)

In addition to these serious skin symptoms, psoriasis has many less visible effects. These include (1, 2, 3, 4, 5, 6):

  • social ostracization by those who believe psoriasis is contagious
  • changes in personal and intimate relationships
  • loss of a healthy social life
  • development of chronic joint inflammation (“psoriatic arthritis”)
  • development of clinical depression, anxiety, & suicidal thoughts
  • increased risk for metabolic syndrome (obesity, diabetes, high blood pressure)
  • increased risk for inflammatory bowel disease (Crohn’s disease, ulcerative colitis)
  • severely decreased quality of life

Current Psoriasis Treatments

Thankfully, there are many treatment options available to help people manage the many symptoms of psoriasis. Light treatments, medicated ointments, steroid creams, prescription pills and injections can all be effective in helping minimize psoriasis’ effects on a person’s life. (1)

However, none of these treatment options is without its downsides.

Topical skin treatments aren’t always strong enough to really heal psoriatic plaques and can’t address non-skin symptoms. (1, 7)

Immune-modulating pills and injections are more effective when the skin rash is severe and they can provide relief for whole body symptoms. But they can also cause serious side effects and can cost a small fortune. (1, 8, 9, 10)

These downsides have left patients and researchers looking for more effective, safer and cheaper options. (4)

Recently, there has been growing hope that efforts to support healthy gut bacteria might provide just that. (11, 12, 13, 14)

Where has this hope come from?

To understand the answer to this question, it is useful to take a quick step back and review exactly how psoriatic plaques develop in the first place.

Immune Dysfunction in Psoriasis

When the immune system is healthy, immune cells patrol the skin for wounds, infections and cancer. These immune cells communicate with each other, sending signals to one another to ensure that they all attack when there is danger and no one attacks when there isn’t. (15, 16, 17)  

Researchers believe that in people with psoriasis this communication between immune cells breaks down. Specifically, one group of immune system regulating cells, called T regulatory cells (Treg for short), loses its ability to control another group of inflammation-promoting immune cells, called Th17 cells. (15, 16, 17)

Treg cells regulate the immune system and keep other inflammatory immune cells like Th17 from wreaking havoc.

Th17 cells release inflammatory chemicals and oxidants into the skin around them, harming or even killing the skin cells they come into contact with. This leads to pain, swelling, redness, and itching and a build-up of silver-white dead skin cells. (15, 16, 17, 18)  

Unfortunately, once Treg cells lose control of Th17 cells, it’s difficult to ever get them under control again.

This is because the same chemicals damaging the skin also draw new Th17 to the skin and tell them to start making even more inflammatory chemicals. This creates a vicious cycle, with ever more Th17 cells arriving and overwhelming any effort by Treg cells to bring them back under control. (15, 16, 17)

Immune Regulation and Gut Microbiota

So why might changes in gut bacteria be helpful in breaking this cycle?

Well, there is growing evidence that healthy gut bacteria do something remarkable: They increase the function of Treg cells and decrease the function of Th17 cells. (19)

This is exactly what we’re looking for when trying to control an autoimmune response.

Helping Treg cells control Th17 cells while simultaneously making the Th17 cells less powerful gives Treg cells a fighting chance to get the upper hand again and stop Th17 cell attacks on the skin altogether.

Boosting Treg Function

Healthy gut bacteria provide a double boost to Tregs’ ability to stop Th17 cells. They can enhance Treg cell function directly and increase the number of Treg cells you have.

Improving Function Directly

Healthy gut bacteria make a group of chemicals called short-chain fatty acids (SCFAs) (19, 20, 21), which are powerful modulators of Treg cells. SCFAs enter the cells and make their “stop attacking” signals stay turned on, halting the attack on your skin. (19, 20, 22)

This ensures that Treg cells can produce and send tons of these regulating signals out to Th17 cells. The more signals make it to attacking Th17 cells, the more likely they can all be brought back under control.

Increasing Treg Numbers

In addition to making each Treg more efficient at producing regulatory chemicals, healthy gut bacteria also help increase the number of active Treg cells in the body.

This they do indirectly by boosting the functions of a different group of immune cells, called dendritic cells. (19, 23, 24)

Dendritic cells are responsible for sending signals to immature Treg cells that it’s time to “grow-up” and start controlling Th17 cells. (19, 24)

Remember the SCFAs that keep the “stop attacking” signal turned on in Treg cells? Well, those same SCFAs also help to send this “grow up” signal to immature Treg cells from dendritic cells.   

Interestingly, SCFAs aren’t the only molecules made by these healthy bacteria that have this boosting effect on dendritic cells — they also make a molecule called histamine, which stimulates dendritic cells to make more of the chemicals that allow Treg cells to mature. (19, 25)

Studies also show that dendritic cells are healthier, in general, when beneficial gut bacteria are around. This appears to be the result of an increased ability of dendritic cells to make their own vitamin A when healthy levels of these bacteria are in the gut. (19, 26)

Vitamin A is a powerful hormone that dendritic cells need to function properly. By increasing vitamin A levels, gut bacteria help ensure that Treg-cell stimulating dendritic cells are healthy, happy, and functioning optimally. (19, 27)

Hampering Th17 Function

The SCFAs and histamine produced by your healthy gut bacteria have another beneficial effect when it comes to controlling the autoimmune process: they slow down the production of inflammatory chemicals by Th17 cells. (19, 28, 29, 30)

These inflammatory chemicals are responsible for the swelling, pain, redness, itching, and other symptoms you get when you have psoriasis. (15, 16, 17, 18)

Healthy bacteria keep these inflammatory chemicals in check, thus keeping your skin healthy.

Getting Healthy Levels of Good Gut Bacteria

Clearly, improving the health of your microbiome can be useful in helping the immune system regain its balance and keeping psoriasis away for good.

If you’ve been diagnosed with psoriasis, I highly recommend testing your gut bacteria to see if you may have a microbiome imbalance, such as dysbiosis or small intestinal bacterial overgrowth (SIBO).

Both dysbiosis and SIBO have been linked to the development of psoriasis. In addition to this, more severely imbalanced bacteria correlates to worse psoriasis symptoms, and treating SIBO or dysbiosis is associated with improved psoriasis symptoms. (12, 31, 32)

If you have psoriasis and one of these gut bacterial imbalances, you want to find out and get it treated!

You can use a breath test to determine if you have SIBO, or a stool test to identify any bacterial colonies that are out of place in the large intestine. You can learn more about testing here.

If you discover that you have SIBO or dysbiosis, it’s very important to balance your microbiome using antimicrobial herbs, antibiotics, probiotics, prebiotics and more. This, in turn, will help to regulate your immune system!

Beyond identifying and dealing with any imbalances in your microbiome, you can also make some dietary and lifestyle changes that will help to balance your gut bacteria as well. Some of these changes include:

Increasing Probiotic Intake

Probiotics are really amazing in their ability to help regulate the immune system and have been shown to have positive effects on psoriasis symptoms and biomarkers. (33, 34)

Regularly consuming fermented foods like kimchi, sauerkraut, yogurt and kefir is a great way to get these helpful bacteria into your system. (35, 36)

You can also take a probiotic supplement to get these beneficial bacteria if you’re not a fan of fermented foods. (37)

Boosting Prebiotic and Fiber Intake

Healthy gut bacteria use prebiotics and fiber to survive, grow, thrive and make SCFAs. (38) Increasing fiber intakes can boost their levels and function in the gut within just a few days! (39)

Easy ways to increase fiber intake include loading up on fiber-rich foods, such as fruits and vegetables, or taking a fiber supplement. (37)

Getting Enough Exercise

Studies show moderate aerobic exercise can increase the health of your gut bacteria. (40) The introduction of a regular exercise routine has also been shown to be useful in easing psoriasis symptoms.  (41, 42, 43)

Drinking Enough Water

Dehydration can mess with your gut bacteria by promoting constipation. (44) Constipation slows down the movements of your intestinal wall. This can affect how well gut bacteria grow and lead to poor gut bacterial health. (45, 46)

Shifting to a Whole Foods Diet

Study after study shows that a western style diet rich in calories, fat, simple sugars, and salt and low in fruits and vegetables is harmful to healthy gut bacteria, while traditional diets rich in whole foods help these bacteria grow. (47, 48, 49, 50)

Multiple studies also show that putting individuals with psoriasis on a whole-food diet can improve their symptoms. (41, 42, 43)

The Impact of Diet on the Immune System

Diet plays a crucial role in regulating a healthy immune system and controlling psoriasis.

Evidence suggests that a shift away from processed foods towards whole foods may not only boost fiber intake, healthy gut bacteria numbers, SCFA levels and histamine levels, but it might very well provide its own direct inhibition of Th17 cells.

Th17 Function and Processed Foods

There are at least two components in processed food that may boost Th17 function: salt and advanced glycation end products.


While I’m not against a moderate amount of salt in the diet (and in fact higher levels of salt intake can be helpful in conditions like “adrenal fatigue”), research indicates that the high level of salt found in many processed foods is problematic when it comes to autoimmune disease.

Consuming large amounts of salt directly activates Th17 cells, which produce inflammatory chemicals and in turn lead to psoriasis symptoms.

Researchers have recently identified a special sensor in Th17 cells that is sensitive to the amount of salt around. If this sensor is activated by lots of salt, it causes the Th17 cells to produce more inflammatory chemicals. (51)

And this isn’t just at the cellular level. Studies show that eating diets containing lots of salt leads to worsening of symptoms of Th17-related diseases, such as asthma and multiple sclerosis. (52, 53, 54, 55)

Advanced Glycation End Products (AGEs)

Advanced glycation end products (AGEs) form when foods are heated to extreme temperatures, making them a common molecule found in broiled or fried foods like chips, french fries, chicken nuggets, fish sticks, etc. (56, 57)

Similar to how SCFAs and histamine help Treg cells mature, AGEs have been found to help inflammation-promoting Th17 cells mature. (58) This suggests that eating lots of fried junk food can increase the number of damaging Th17 cells.

Th17 Function and Whole Foods

On the other hand, replacing junk food with whole foods can help to reduce the damage from Th17 cells.


One nutrient rich in many whole foods that may play an important role in regulating immune function is potassium.

High levels of potassium trigger the kidneys to produce a group of molecules called glucocorticosteroids. (59)

These molecules are natural steroids that work just like the drugs doctors prescribe. They are powerful inhibitors of inflammatory chemicals. (60)

Bioactive Phytonutrients

Many whole plant foods contain phytonutrients that have helpful health benefits. Some of these benefits include preventing the effects of inflammatory chemicals on the body. (61, 62, 63)

Some of these anti-inflammatory phytonutrients have powerful effects against inflammatory chemicals known to be important in damaging psoriatic skin.

For example, there is a phytonutrient in turmeric root called curcumin that blocks the effects of the inflammatory chemical TNF-alpha, which plays a major role in promoting psoriasis. (64, 65) In fact, curcumin blocks TNF-alpha nearly as well as drugs we designed to block it. (66)

In addition to the anti-inflammatory nature of phytonutrients, polyphenols (a type of phytonutrient) also boost the health of your microbiome. If you’d like to learn more about that process, check out my article on the topic here.


As their name suggests, antioxidants block the effects of oxidants.

Since one of the key chemicals Th17 cells use to damage skin cells are oxidants (called reactive oxygen species (ROSs)), antioxidants from fruits, vegetables, nuts, seeds, teas and spices may be helpful in reducing psoriasis symptoms. (18, 67, 68, 69, 70)

The Bottom Line:

The evidence suggests that a whole food diet rich in foods that help promote a healthy microbiome may help prevent and reduce the symptoms of psoriasis and other autoimmune diseases.


Have you been diagnosed with psoriasis? Do you notice a difference in your symptoms when you eat well and support your microbiome? Let me know in the comment section below!

You probably know by now that the health of your microbiome strongly influences the health of the rest of your body.  

Healthy gut bacteria promote digestive health, metabolic health, immune health, mental health and cardiovascular health. (1, 2, 3, 4) Unhealthy gut bacteria do the opposite, promoting a whole host of serious diseases, including anxiety, depression, obesity, infertility, polycystic ovary syndrome, autoimmune diseases, diabetes, heart disease, dementia, and cancer. (1, 2, 3, 4, 5, 6, 7) But what determines the health of your gut bacteria?

Factors That Lead to a Healthy Microbiome

There are many factors that play a role in a developing (and maintaining) a healthy microbiome. These include:  

  • Genetics (8)
  • Exposure to tobacco smoke (9)
  • Use of prescription, over-the-counter or recreational drugs (10, 11, 12)
  • Exposure to pesticides, detergents and industrial chemicals (13, 14)
  • Amount of daily physical activity (15)

One of the most important factors, however, is your daily diet.

Different types of diets promote different balances of gut bacteria — some are healthier, while others aren’t. (16, 17, 18, 19, 20, 21).   

And these changes in microbial balance can happen quickly — switching from diet to diet over a short period of time (from a day to a couple of weeks) is sufficient to significantly change the health of your gut bacteria. (22, 23, 24, 25)

It might seem odd that something as simple as food could have such a profound impact on the bacteria that play such a critical role in keeping you healthy. You’d hope that your bacteria would be pretty stable and keep working away to maintain your health, day-in, day-out, regardless of the food you eat.

But when you really think about it, it makes sense. After all, your gut bacteria come into direct contact with the food you eat, 3 times a day (or more!), every day. The food you eat (and its nutrients, contaminants, or toxins) can easily influence your bacteria’s normal biological and metabolic processes and, in turn, their overall health.

I’m often asked what the best macronutrient ratio is for gut health. Research has shown time and again that complex carbohydrates and fiber help to boost the health of your microbiome, while large amounts of sugar and fat have negative consequences on the health of your bacteria.

It’s easy to understand why carbohydrates and fiber are healthy for your gut bacteria since they are what your microbes feed on, but what causes a lot of confusion (and controversy) is the amount of fat that promotes a healthy microbiome.

So today, I’m going to focus on fat: how much is too much when it comes to gut health?

High-Fat Diets & Gut Bacteria

I’ll be the first to admit that I was a bit skeptical when I came across research that implicated high-fat diets as one of the causes of unhealthy gut bacteria. After all, I’m very much a “real foodie” and don’t shy away from recommending fats as a major component of a healthy diet.

But I kept seeing more and more research about fat and its negative impact on the health of the microbiome, and it became clear that I needed to investigate this further.

Truth is, there is a lot of research behind this idea and it’s pretty strong. Every type of study that’s been used — animal models, epidemiological studies, and human intervention studies — all show that your gut bacteria change in response to consumption of a high-fat diet. (16, 17, 22, 23, 26, 27, 28, 29) What’s more, the changes found by these diverse methodologies are, generally, very similar. (16, 17, 22, 23, 26, 27, 28, 29)

So what are those changes, exactly?

A high-fat diet appears to induce very specific changes in the ratios of the bacteria in the gut — high-fat diets are able to decrease the numbers of healthy gut bacteria while simultaneously increasing the numbers of less healthy gut bacteria. (16, 17, 22, 23, 26, 27, 28, 29)

This imbalance (a state referred to as dysbiosis), is an unhealthy situation for your gut bacteria, your gut, and you. It has been associated with gastrointestinal diseases, low-grade systemic inflammation and all of those serious conditions mentioned above. (1, 2, 3, 4, 5, 6, 7, 30)

Of course, this begs the question: Why? Why does a high-fat diet cause your gut bacteria to go so out of whack?

While we don’t know for sure yet (and there are many factors at play), there seem to be three main processes involved.

Let’s explore them one-by-one.

Increased Production of Bile Acids

Bile acids are molecules made by your liver to help your body digest and absorb fat. They work as a type of natural emulsifier, allowing fat from your food to mix into your water-based digestive fluids. This allows the fat you eat to come into contact with the necessary digestive enzymes to actually be broken down and absorbed.

Since bile acids are so important for being able to absorb fat efficiently, your body has an elegant system for making sure there are enough bile acids for all the fat from your food. When fat molecules, particularly big, bulky monounsaturated and polyunsaturated fat molecules, are detected by the cells lining the walls of your intestines, they begin producing a hormone called CCK. (31, 32, 33)

CCK is released in your bloodstream and is transported to your gallbladder, the small sack-like organ which stores bile acids from your liver until you need them. CCK tells your gallbladder to contract, causing the bile acids to be released out into your intestines. There, they can be used to help you absorb the fat you’ve eaten.

The greater the amount of dietary fat, the more CCK made, and the more bile acids released.

Okay, but what does any of this have to do with your gut bacteria?

Well, it turns out that some species of gut bacteria use bile acids to make antibiotics that kill off their neighbors. (22, 34, 35, 36) It’s a useful little trick for them, helping them make sure no one invades their patch of intestinal wall.

When produced in normal amounts in response to a moderate fat diet, these antibiotics help to ensure that the ratios between different species of bacteria in your stay balanced by preventing certain species from growing out of control.

However, high-fat diets produce high concentrations of these antibiotics, which can cause imbalances in bacteria to develop. When too many of these crafty bacteria’s neighbors are killed off, their populations may drop to unhealthy levels.

Researchers suspect that this might be exactly what happens in those eating a high-fat diet, and it may be one of the main reasons for the high-fat-diet-associated unhealthy changes in gut bacteria. (22)

Increased Absorption of LPS

Another mechanism strongly suspected of underpinning the relationship between high-fat diets and poor gut bacterial health is an increased absorption of a toxic molecule called lipopolysaccharide (LPS).

While “leaky gut” or intestinal permeability is the main way large amounts of toxic LPS get into your body, it turns out that small amounts of LPS are regularly transported through an entirely healthy gut wall by little transport vehicles called chylomicrons. (37, 38, 39)

Chylomicrons are small, round packages made by your body to hold digested long-chained dietary fats. They are responsible for transporting these fats through your intestinal wall and taking them to your liver for proper processing and re-packaging for transport to the rest of your body.

If you consume greater amounts of dietary fat, your body has to produce more chylomicrons to transport them all. The more chylomicrons, the more LPS can be accidentally packaged up with the dietary fat and absorbed into your body.

When LPS gets into your body, your immune system immediately (and accurately) recognizes it as dangerous and mounts an attack. (40, 41, 42) Your immune cells begin producing all kinds of inflammatory chemicals intended to help fight off any intruder and begin pumping them into your bloodstream.

These inflammatory chemicals signal to your gut that there danger is present, which in turn leads to changes in the walls of your intestine that affect how well your gut bacteria survive. (43, 44) Eventually, this leads to the development of dysbiosis, or the imbalance of good and bad bacteria in the gut.

Decreased Intake of Complex Carbohydrates

The final mechanism currently believed to play an important role in linking high-fat diets to changes in gut bacterial health is very indirect, but may ultimately prove to be one of the most important.

By definition, a high-fat diet must contain a lower percentage of calories from carbohydrates and protein. Researchers think that the drop off in the intake of these macronutrients, particularly complex carbohydrates, may be responsible for the development of dysbiosis. (45)

See, many gut bacteria use dietary fiber — sugar complexes made by plants that your body cannot digest — as their primary (or only) food source. (46) Without enough fiber, these species may fail to thrive. And in fact, we see significant improvements in gut health when bacteria have plenty of fiber to consume. (26, 45, 46, 47)

Problem is, nearly all high-fiber foods are also carbohydrate-rich (with the exception of foods like coconuts, avocados, and nuts). So those who follow a high-fat diet are mostly missing out on these high-fiber choices, especially if they are eating a Standard American Diet that consists of lots of processed junk food. Without the healthy fiber found in carbohydrate-rich foods, your gut bacteria suffer. (45, 48)

Are All Fats Bad for Gut Health?

When we dive into the research, there are clear hints that the type of fat, not just the amount, plays a key role.

For example, omega-3 fatty acids (found in fish) have been found to induce positive changes in the microbiome, while omega-6 fatty acids (found in industrial seed oils like canola oil) have a damaging effect. (49, 50)

As discussed earlier, the production of CCK stimulates the release of bacteria-harming bile acids. But CCK is produced much more efficiently in the presence of unsaturated fatty acids. This suggests that replacing some of these unsaturated fats with saturated fats may protect your gut bacteria. Since omega-6 fatty acids (a type of unsaturated fat) have proven harmful to microbial health, it makes sense to take some of these out and swap them for saturated fats.

Compared to omega-6 fatty acids, saturated fats do not cause nearly as much damage to the gut. (51)

But you also don’t want to overdo it. Switching to a diet containing primarily saturated fatty acids may end up harming your gut bacteria too.

There are a couple of reasons for this.

First, CCK produced from unsaturated fatty acids is also responsible for transmitting a key “I’m full” signal to your brain. (33) Without it, it becomes a lot easier to overeat. And overeating –regardless of macronutrient content– can harm your gut bacteria. (52)

Additionally, saturated fat may be less easily absorbed in your small intestine (perhaps as a result of less CCK and bile acid release). Studies indicate that if a diet contains too much saturated fat, the small intestine may not be able to absorb it all and some of the fat can make it into your colon and disrupt the delicate balance between the species of healthy gut bacteria. (53)

Finally, at higher concentrations, saturated fatty acids have been shown to be able to trigger an immune response by binding to a receptor on some of your white blood cells called TLR-4.

Similar to the effect seen when LPS triggers an immune response, immune cells activated by saturated fats release inflammatory chemicals that change how the walls of your intestines function, altering how well your gut bacteria survive. (54)

A happy medium may be to reduce your intake of omega-6 fatty acids from industrial seed oils and include some monounsaturated fats in your diet so that you have a healthy amount of CCK production, while still reducing the overall amount of omega-6 fatty acids that you consume.

Monounsaturated fat (like that found in olive oil), has been shown to mitigate the damage done by high-fat diets. (55) Scientists believe that some of the beneficial effects of olive oil may actually come from its polyphenols, as research indicates that virgin olive oil has a much more protective effect than refined olive oil. (56)

Given everything we know about how different types of fats affect the microbiome, it makes sense to avoid industrial seed oils (omega-6 fatty acids) and eat a mix of monounsaturated and saturated fats, with small amounts of omega-3 fatty acids coming from foods like fish and nuts. In this sense, the real food movement strikes a great balance when it comes to consuming the proper balance of fatty acids for gut health.

Do I Need to Eat a Low-Fat Diet to Have Healthy Gut Bacteria?

Interestingly, the negative consequences of a “high-fat” diet only happen when you start eating approximately 42% to a whopping 70% of your calories as fat

Moderately high-fat diets (35% or less calories from fat) do not show these same effects. (39)

That means that if you’re eating a 2000-calorie diet, you can have up to 78 grams of fat per day with no negative consequences to your microbiome.

Eating a calorically-appropriate diet is vital since overeating harms gut bacterial health as well.

On top of that, it’s important to eat the right types of fats. As I discussed previously, I believe consuming mostly monounsaturated and saturated fats with small amounts of polyunsaturated fats from fish and nuts is the right approach here. The key is to avoid high amounts of omega-6 fatty acids.

To review, here is what we currently know about the best diet to support your microbiome:

  • Eat a moderate fat diet (<35% of calories from fat)
  • Eat an appropriate amount of calories overall
  • Avoid industrial seed oils (like vegetable oil) and aim for a mix of monounsaturated and saturated fats, with small amounts of polyunsaturated fats from fish and nuts
  • Choose high-fiber carbohydrate foods

What If I Want to Eat a High-Fat Diet?

There are probably some of you reading this article who know you do best with a high-fat diet. You might have diabetes and a low-carb diet keeps your glucose levels normal, or perhaps you’re using a ketogenic diet to help manage a condition like epilepsy.

If this is you, don’t worry! There are ways to mitigate the negative microbial effects of a high-fat diet.

Here’s what the research says:

  • Eat enough fiber from the foods you can eat. If you’re following a high-fat diet, this means making sure you’re eating tons of fibrous veggies, berries, avocados, nuts and seeds that fit within you plan. Eating lots of plant matter also helps you consume plenty of polyphenols which have a protective effect on your gut bacteria as well. (57, 58)
  • Take prebiotics. Prebiotics have been shown to protect gut bacteria from the negative effects of a high fat diet. (59, 60)
  • Take probiotics. Much like prebiotics, probiotic supplementation can attenuate the negative impact of a high fat diet. (61, 62, 63)

Just as you should when following a moderate-fat diet, you should also consume an appropriate amount of calories and eat the right types of fats to promote microbial balance in the gut.

And even if you aren’t eating a high-fat diet, eating high fiber foods and taking probiotics and prebiotics is a great idea to ensure a healthy gut.

The Bottom Line:

Clearly, the relationship between the fat you eat and your gut bacteria is complex.

However, research indicates that a moderate fat diet (<35% of calories) is best, especially when you’re eating fats that are protective of your microbiome (like olive oil and omega-3 fatty acids).

If you want to consume a higher fat diet, choosing these types of fats may keep your gut healthier than if you ate a high omega-6 fatty acid diet. You can also consume prebiotics and probiotics to protect your gut bacteria while on a high-fat diet.

Now I’d like to hear from you: will you be changing your macronutrient intake as a result of the evidence presented in this article?

Although fibromyalgia is among the most common causes of chronic, widespread pain (believed to affect an estimated 5 million people in the US alone) it remains one of the least understood. (1, 2)

Researchers generally agree that the key problem in fibromyalgia is a change in how pain signals from the skin, joints and muscles are processed in the brain, leading to the characteristic and diagnostic long-term, body-wide pain. (1, 3) But, to date, no one has been able to definitively prove what causes these changes, and how. (3, 4)

However, growing evidence suggests that fibromyalgia may be caused by poor gut health — specifically, by a condition called “small intestinal bacterial overgrowth (SIBO)”, in which colon bacteria begin colonizing the normally relatively sterile environment of the small intestine. (5)

Let’s explore this growing body of evidence, what it means, and it’s possible implications for ways to address fibromyalgia symptoms.

Fibromyalgia, SIBO and the Breath Test

The most direct, and perhaps the most important, evidence supporting the idea that fibromyalgia may be caused by SIBO came from a 2001 study by researchers at Cedar-Sinai Medical Center which first linked the two conditions. (6) Inspired by epidemiological studies that showed extremely high rates of gut dysfunction in people with fibromyalgia, (7, 8, 9) the researchers decided to look at the state of their intestinal health more closely. Close examination of the epidemiological studies showed that gastrointestinal symptoms reported by fibromyalgia patients were similar to the symptoms seen in Irritable Bowel Syndrome (IBS). (7, 8, 9)

Since previous work in the Cedar-Sinai lab had established strong links between SIBO and IBS, they thought looking for SIBO in fibromyalgia patients may be a smart place to start. (10)

So, they put it to the test!

They organized a group of 123 volunteers with fibromyalgia to undergo SIBO breath testing. Results showed that nearly 80% of the group tested positive for SIBO, a much higher rate than seen in healthy groups of volunteers, or even in groups of individuals with IBS. (6)

Though not conclusive proof of a direct link, this data was a huge tip-off that it might be a relationship worth looking into further.

Does SIBO Cause Fibromyalgia?

To determine if there was a causal relationship between SIBO and fibromyalgia, researchers set up an experiment that compared markers of SIBO severity to markers of fibromyalgia severity. If one condition causes another, generally you would expect that increasing the severity of that condition would directly cause a worsening of the other.

As a marker for SIBO severity, researchers used the amount of hydrogen detected in a SIBO breath test. Since the hydrogen detected in the test is made by the bacteria in SIBO, greater levels of hydrogen generally indicate greater numbers of bacteria. And as a marker of fibromyalgia severity, they used self-reported pain levels. (5)

When the data was analyzed, they found that, consistent with a causal relationship, greater levels of hydrogen production were associated with greater reported pain levels. (5)

Now the question remained: did SIBO cause fibromyalgia or did fibromyalgia cause SIBO?

In order to figure this out, researchers took a step back and took a look at all the evidence linking gut health, gut bacteria, brain function and pain regulation and asked themselves: which direction makes more sense? Which one does the scientific literature support more?

The clear answer here was — SIBO is more likely to cause fibromyalgia than the other way around. Close examination of all the evidence allowed researchers to find two step-by-step mechanisms by which SIBO could cause the symptoms of fibromyalgia.

Let’s look at them both!

SIBO May Cause a Tryptophan Deficiency

Tryptophan is one of the 20 standard amino acids and your body uses it to help build proteins. It is also absolutely critical for making an important chemical messenger used to carry nerve signals through the brain called serotonin. It is so important, in fact, that changes in tryptophan levels in your body is sufficient to directly change levels of serotonin in your brain. (11)

One of serotonin’s jobs in the brain is to modulate signals that control the sense of pain. (12)  Based on the symptoms of fibromyalgia, it was suspected that serotonin signaling might play a role in the disorder. And, indeed, when researchers compared those with fibromyalgia to those without the pain disorder they found that people diagnosed with fibromyalgia consistently had lower levels of serotonin in their bodies.  (13, 14, 15, 16)

So, how might SIBO be able to lower tryptophan and serotonin levels?

Well, tryptophan belongs to a group of amino acids called “essential amino acids.” This means that your body can’t make tryptophan by itself; you have to get all of it by absorbing it from the food you eat. SIBO can decrease your ability to absorb tryptophan in three ways:

1. By using up tryptophan from your food

Like us, bacteria use tryptophan to build proteins and keep their cell machinery functioning properly. They can even take it out of the food we eat, just like we can. (17) It doesn’t matter when bacteria do this to food in your colon because you’ve already absorbed what you needed while the food was still in your small intestine.

When colon bacteria move into your small intestine, though, like they do in SIBO, they may use up some of the tryptophan before you get a chance to absorb what you need, driving the levels of tryptophan in your body down. (17)

2. By damaging the lining of your small intestine

SIBO can damage the lining of your small intestine, where tryptophan should be absorbed. This damage may make it difficult for your intestines to absorb the tryptophan not snatched up by the bacteria normally. (17)

3. By decreasing sugar absorption

Changes in the function of your small intestine may also be able to decrease the ability of your body to absorb free sugars. Too many free sugars in your small intestine may directly impair tryptophan absorption. (16)

This is because free sugars, particularly free fructose, can react with tryptophan to create sugar-tryptophan complexes. These complexes are too big to be transported through the intestinal wall the way tryptophan normally is, so they can’t be absorbed. (16)

This, of course, may lower the amount of tryptophan absorbed by the body, and, in turn, lower serotonin levels. (16)

This theory of the development of fibromyalgia is supported by epidemiological studies which consistently show that the disorder is overwhelmingly seen in women; around 96% of those with fibromyalgia are women. (13)

Women’s bodies are less efficient at making serotonin out of tryptophan than men’s. This means that women need higher levels of tryptophan from their diets to make the same amount of serotonin. It also means that decreases in tryptophan absorption lead to a drop off in serotonin levels more quickly in women than men. If tryptophan deficiency were a driving cause behind fibromyalgia, one would indeed expect women to be at much greater risk for developing it, which is exactly what we see in the real world. (16)

SIBO Causes Systemic Inflammation

SIBO causes systemic inflammation, boosting levels of inflammatory chemicals throughout your entire body. (18, 19, 20)  

We now know that when these inflammatory chemicals get into the brain, they can directly induce changes in levels of two other chemical messengers believed to be involved in fibromyalgia called glutamate and γ-aminobutyric acid (GABA). (21) People with fibromyalgia have been consistently found to have an imbalance in signals carried by these two chemicals in a specific area of the brain, the insular cortex. (22, 23, 24)

This area is responsible for integrating sensory signals from the skin, muscles and joints of the body, including pain signals (25) and researchers strongly suspect that this imbalance in the insular cortex play a direct role in the pain dysregulation seen in fibromyalgia. (22, 23, 24)

This theory of the development of fibromyalgia is also strongly supported by epidemiological data. Studies consistently find that those with fibromyalgia have marked increases in levels of inflammation and oxidative stress in their bodies, (2, 19, 26) potentially stemming from SIBO.

What to Do if You Have Fibromyalgia

Given all we know about fibromyalgia, here are a few things to do if you want to reduce the symptoms you experience from this disorder:

1. Get Tested for and Treat SIBO

The evidence clearly supports at least getting tested for SIBO if you have been diagnosed with fibromyalgia.

SIBO is usually tested for by measuring the amount of hydrogen and/or methane in your breath over the course of several hours. It’s simple, non-invasive and may be covered by your insurance.

If your SIBO test comes back positive, your doctor may choose to prescribe a course of antibiotics for you which can kill off the bacteria in your small intestine. You can also use antimicrobial herbs to this effect.

SIBO is linked to a variety of medical conditions, so even if it turns out clearing SIBO does not affect your fibromyalgia, it is still something that absolutely should be dealt with.

If you’re interested in learning more about testing for SIBO and using antimicrobial herbs, check out my 8-week Build Your Biome program.

2. Support Healthy Serotonin Production

As discussed above, serotonin is very important when it comes to fibromyalgia. Here are some steps to take that may help support healthy serotonin levels in your brain:

  • Eat a diet full of tryptophan-rich foods, such as walnuts, rice, potatoes and dark chocolate (16)
  • Avoid foods rich in free sugars which might bind and inhibit tryptophan absorption, such as processed foods made with table sugar or high fructose corn syrup (16, 27)
  • Avoid foods containing aspartame, which can make it difficult for tryptophan to get out of your bloodstream and into your brain (16, 27)
  • Exercise regularly; physical activity has been shown to boost serotonin production in the brain and ease the symptoms of fibromyalgia (28, 29, 30)
  • Get outside; exposure to natural sunlight may boost serotonin production (29)

3. Decrease Inflammation and Oxidative Stress

The clear markers of systemic inflammation and oxidative stress in fibromyalgia also strongly suggest that steps to combat them may be useful in addressing fibromyalgia symptoms, even if determined not to be caused by SIBO.

Steps that may be useful in decreasing inflammation and oxidative stress include:

  • Eating a plant-rich diet; plants are rich in antioxidants and anti-inflammatory phytonutrients (27)
  • Avoid smoking and cigarette smoke which has been proven to cause oxidative stress throughout the body (31, 32)
  • Consider taking a CoQ10 supplement, which is a natural compound known to be depleted by oxidative stress and which has been specifically shown to be helpful in fibromyalgia (27)

If you have fibromyalgia, have you been tested for SIBO? Let me know in the comment section below!

Autoimmune disorders are conditions that occur when the body’s immune system attacks its own healthy tissues. There are many different autoimmune conditions, depending on which healthy tissues are attacked. Some examples include multiple sclerosis, rheumatoid arthritis and lupus.

Autoimmune conditions are often thought of as “rare” (1) because most of the individual disorders affect a relatively small number of people (2). As a disease class, though, autoimmune disorders are actually among the most common conditions in the United States.

In 2012, the U.S. National Institutes of Health reported that a staggering 23.5 million Americans have at least one autoimmune disease. According to the American Autoimmune Related Diseases Association (AARDA), however, even this remarkable number may be significantly too low, since it was calculated using data concerning diseases that are entirely autoimmune mediated. The AARDA estimates that, if all diseases believed to have any autoimmune component were included in the calculation, the real number of Americans affected by autoimmunity may actually be closer to 50 million.

That means that up to 20% of the population — or 1 in every 5 people — may suffer from autoimmune symptoms.

And autoimmune symptoms can be extremely severe. Depending on the tissues being attacked, autoimmune diseases can cause intense pain, disability, loss of quality of life, loss of income, and even promote premature death. (1, 3)  

Genetics are believed to play an important role (4), but so are a wide variety of environmental factors, such as birth-weight, infections, (5) dietary intake of certain compounds (like gluten, mercury or tryptophan), and exposure to toxins from things like cigarette smoke, air pollution and paint thinners.

While all of these factors have interesting implications for the development, prevention, and treatment of autoimmunity, this article will focus on the newly discovered connections between autoimmunity and the health of your gut microbiota.

Not only are these connections now among the most solidly established, (6, 7) they may also ultimately provide some of the most practical opportunities to develop new treatment options, since, unlike many other factors, gut bacteria are relatively easy to manipulate. (8, 9)

To fully understand the links between autoimmunity and gut bacteria, though, let’s first take a quick step back and look at how your immune system normally works, and what researchers now know goes wrong in autoimmune diseases.


If you think about it, your immune system has a really tricky job. It has to scan your whole body all day, everyday and find dangerous bacteria, infectious viruses, and sick or malfunctioning cells and kill them. If it misses any, you may end up with a serious infection or cancer, either of which could kill you — so it really can’t let any slip by!

On the other hand, your immune system also can’t overshoot and kill cells if it’s not positive they are dangerous because if it kills off your healthy cells, your organs can’t work. Of course, that can be fatal as well!

The immune system has to find the perfect balance: find each and every danger while leaving each and every healthy cell alone.

In order to be able to do this, the human body has evolved a very sophisticated network of immune cells that regulate each other directly (via proteins bound to their surfaces) and indirectly (via special hormones called cytokines).

There are hundreds of types of cells involved in keeping the whole immune system working properly, but for the functions that prevent/cause autoimmunity, the relationships between individual members of a family of cells called T-cells are considered among the most important. (6, 7)

There are three key members of the T-cell family: cytotoxic T-cells, helper T-cells, and regulatory T-cells.

  1. Cytotoxic T-cells (Tcyt-cells) are the cells responsible for actually killing a sick or malfunctioning cell once the rest of the immune system has found it.
  2. Helper T-cells (Th-cells), like their name suggests, help the cytotoxic T-cells. They double check that the cell really needs to be killed and gives the Tcyt-cells the “green light” to actually go through with it. They do this both via protein signals on their surfaces and the release of a special mixture of cytokines. Without these signals from Th-cells, Tcyt-cells are pretty powerless.
  3. Regulatory T-cells (Treg-cells) act as a counter-balance to cytotoxic and helper T-cells. Treg-cells use the proteins on their surfaces and a different mixture of cytokines to call off Tcyt-cells and Th-cells from carrying out attacks.

For a long time, researchers thought that under normal circumstances, all Tcyt-cells that recognized healthy cells in your body as dangerous were forced to undergo “apoptosis” (cellular suicide). In healthy people, this system worked perfectly and no self-reactive cells survived. In people who developed autoimmune diseases, however, one (or more) self-reactive Tcyt-cell did not die for some reason, allowing them free-reign to attack their bodies. (2, 10, 11)

Newer research indicates, however, that even in perfectly healthy people, there are always small numbers self-reactive Tcyt-cells that do not undergo apoptosis. They are always present in your body, trying to attack random, healthy organs, but are simply stopped from doing so by constant suppressive signals from healthy Treg-cells. (2, 10, 11) With a normal, healthy balance between Treg-cells and Tcyt-cell/Th-cells, no Tcyt-cells attack any of your healthy cells. This is referred to as the state of self-tolerance.

As you can imagine, though, this set-up to maintain self-tolerance means that even relatively small manipulations in the number of Tcyt-cells/Th-cells or Treg-cells can easily lead to a problem.

If your levels of self-attacking Tcyt-cells/Th-cells increase, or your levels of Treg-cells decrease, you may end up with too many Tcyt-cells/Th-cells and not enough Treg-cells to stop all of them. (6)

If this happens and Tcyt-cells/Th-cells begin killing your healthy tissue, you have, by definition, developed an autoimmune disorder.


So what do your gut bacteria have to do with any of this?

It turns out, a lot.

In fact, if we wanted to go down to the individual protein and cytokine signals, we would probably have thousands of effects and interactions to talk about!

Luckily, all of the effects gut bacteria have on regulating self-tolerance and autoimmunity can more or less be grouped together into two basic effects which we can talk about more generally:

  1. Regulating the ratios of Th-cells-to-Treg-cells in your body
  2. Influencing your risk of developing more self-attacking Tcyt-cells than normal

Let’s look at these one at a time.


Mounting evidence now clearly shows that the types, numbers, and ratios of bacteria in your gut directly influence how many Th– and Treg-cells you have in your body. (6, 7)

Healthy gut bacteria boost Treg-cell levels in your body by helping your immune system decide to turn immature T-cells into Treg-cells. (6, 7, 12)  Studies in mice have shown that healthy gut bacteria increase Treg-cell numbers through their production of a group of molecules called short-chained fatty acids (SCFAs). (13, 14) Healthy gut bacteria make SCFAs when they break down fiber for energy. (6, 15)

SCFAs can be absorbed into the bloodstream and enter immature T-cells which haven’t decided if they are going to be Tcyt-cells, Th-cells or Treg-cells. There, SCFA turn on the genes that turn them into Treg-cells. (13, 16) This leads to a greater number of Treg-cells in the body, decreasing the chances of a cytotoxic T-cell being able to slip past and start attacking your healthy cells.

Unhealthy gut bacteria, on the other hand, can boost the levels of Th-cells in the body, making it easier for Tcyt-cells to attack your body.

For example, studies show that the growth of even one species of unhealthy bacteria (B. adolescentis) in the gut is able to increase the numbers of Th-cells in the blood. (17)

This effect can even occur just from the wrong ratios of normally healthy gut bacteria in the gut! Overgrowth of the normally healthy E. coli species E. coli 2A, for example, has been shown to to boost Th-cell levels. (18)  

Combined, the effects of decreased healthy bacteria, abnormal ratios of healthy bacteria or the growth of unhealthy bacteria in the gut may shift the ratio of Th-cells-to-Treg cells decidedly in the favor of Th-cells. This can make it much more likely that the “attack” signals outweigh the “don’t attack” signals given to your Tcyt-cells, which can ultimately result in the development of an autoimmune disease. (6, 18)


In addition to helping to determine which balance of signals your Tcyt-cells receive, your gut bacteria also influence your risk of producing Tcyt-cells that recognize your body as dangerous in the first place.They do this through their role in helping your intestinal wall maintain normal “barrier function.”

Normally, healthy gut bacteria help create a solid barrier between you and the outside world, letting only small nutrients through, while keeping larger molecules and bacteria out. If your gut bacteria become unhealthy, however, you can develop a condition called a “leaky gut” that allows larger molecules to get into your body. (19)

Though rare, some of the molecules that can leak into your gut may be what researchers call “molecular mimics”. (20)

A “molecular mimic” is a molecule that happens to have a structure very similar to one that naturally exists in your body.

If one of these mimics gets into your body, your immune system correctly recognizes it as foreign and mounts a defense. As part of this defense, new Tcyt-cells are made that specifically recognize the molecular mimic. Unfortunately, these Tcyt-cells may also accidentally also recognize the mimicked molecule in your body, too. (20) For example, certain human retroviruses contain a protein, VP7, that happens to look very similar to a protein found on human pancreatic β-cells called IA-2. If you become infected with VP7, your body may make Tcyt-cells that correctly identify VP7 as dangerous. Unfortunately, they may also recognize IA-2, since it is so similar. If this happens, these Tcyt-cells may begin attacking the β-cells in your pancreas, leading to type 1 diabetes. (21)

By regulating how many foreign molecules get into your body through your intestinal wall (19), your gut bacteria help determine the risk of your immune system coming into contact with a molecular mimic and producing a Tcyt-cell that will attack both the mimic and your own molecule.

The fewer foreign molecules leak into your body, the smaller the chance one that makes it in will happen to look like one of your own proteins. The more molecules that leak in, the higher the risk!

When combined with the fact that the same unhealthy gut bacteria that cause a leaky gut also promote a high Th-cell-to-Treg cell ratio that encourages Tcyt-cells to kill their targets, you can see how poor gut health can put you at serious risk for autoimmunity.


Since poor gut health puts you at greater risk for developing an autoimmune disease, it stands to reason that protecting your gut health is likely a good way to help prevent an autoimmune disease from developing.

Here are some diet and lifestyle changes that have been shown to improve gut bacteria balance:

  • Avoid refined sugars and fats – Both processed sugar and fat can induce dysbiosis and a leaky gut, letting more potentially mimicking molecules into your body. Note that the type of fat seems to be of importance; I discuss this in more detail in this podcast episode.  (22, 23)
  • Eat lots of fiber and prebiotics – Fiber feeds your healthy gut bacteria. It can help prevent or reverse dysbiosis. (24)
  • Eat an abundance of phytonutrient and polyphenol-rich fruits and vegetables – Polyphenols can boost levels of healthy gut bacteria.
  • Drink plenty of water – Staying properly hydrated prevents constipation and constipation can promote the growth of unhealthy bacteria. (25)
  • Exercising regularly – Exercise has been shown to boost levels of healthy gut bacteria in your intestines. (26)

Can improving your gut bacteria balance actually treat autoimmune disorders? Is there any evidence that improving gut health may also be helpful for individuals after they have already developed an autoimmune disorder?

Relatively few studies have specifically looked at treating gut health to improve the symptoms of autoimmune diseases.

However, a few possibly useful dietary and lifestyle changes have already been identified. These include:

  • Eat plenty of fiber-rich foods – Fiber feeds the good gut bacteria that make SCFAs and promote Treg-cell development. (12, 28)
  • Add specific probiotics – Some studies suggest that probiotics containing specific bacteria (B. infantilis, for example), may be able to boost Treg-cell levels (29); ultimately, which supplements might be effective for you would be best determined by examining your gut bacteria and identifying which bacteria are out of balance. (6)
  • Consume vitamin A rich foods or take a vitamin A supplement – There is growing evidence that retinoic acid, a metabolite made from vitamin A in the body, works in conjunction with gut bacteria to help them increase the number of  Treg-cells in your body. (30) I would recommend 5,000 IU per day, and potentially more under the supervision of your doctor or dietitian.

As always, it’s important to consult with your medical provider for any treatments for your autoimmune disease.

If you’d like to learn more about how your diet and lifestyle influence your gut health, I recommend checking out my 8-week online course Build Your Biome.

Are you hopeful that scientists will eventually find a way to cure autoimmune diseases by manipulating gut bacteria? Let me know your thoughts in the comments below!