9 Steps to Perfect Health – #5: Heal Your Gut

February 24, 2011 in Perfect Health | 33 comments


All disease begins in the gut.

- Hippocrates

Hippocrates said this more than 2,000 years ago, but we’re only now coming to understand just how right he was. Research over the past two decades has revealed that gut health is critical to overall health, and that an unhealthy gut contributes to a wide range of diseases including diabetes, obesity, rheumatoid arthritis, autism spectrum disorder, depression and chronic fatigue syndrome.

In fact, many researchers (including myself) believe that supporting intestinal health and restoring the integrity of the gut barrier will be one of the most important goals of medicine in the 21st century.

There are two closely related variables that determine our gut health: the intestinal microbiota, or “gut flora”, and the gut barrier. Let’s discuss each of them in turn.

The gut flora: a healthy garden needs healthy soil

Our gut is home to approximately 100,000,000,000,000 (100 trillion) microorganisms. That’s such a big number our human brains can’t really comprehend it. One trillion dollar bills laid end-to-end would stretch from the earth to the sun – and back – with a lot of miles to spare. Do that 100 times and you start to get at least a vague idea of how much 100 trillion is.

The human gut contains 10 times more bacteria than all the human cells in the entire body, with over 400 known diverse bacterial species. In fact, you could say that we’re more bacterial than we are human. Think about that one for a minute.

We’ve only recently begun to understand the extent of the gut flora’s role in human health and disease. Among other things, the gut flora promotes normal gastrointestinal function, provides protection from infection, regulates metabolism and comprises more than 75% of our immune system. Dysregulated gut flora has been linked to diseases ranging from autism and depression to autoimmune conditions like Hashimoto’s, inflammatory bowel disease and type 1 diabetes.

Unfortunately, several features of the modern lifestyle directly contribute to unhealthy gut flora:

  • Antibiotics and other medications like birth control and NSAIDs
  • Diets high in refined carbohydrates, sugar and processed foods
  • Diets low in fermentable fibers
  • Dietary toxins like wheat and industrial seed oils that cause leaky gut
  • Chronic stress
  • Chronic infections

Antibiotics are particularly harmful to the gut flora. Recent studies have shown that antibiotic use causes a profound and rapid loss of diversity and a shift in the composition of the gut flora. This diversity is not recovered after antibiotic use without intervention.

We also know that infants that aren’t breast-fed and are born to mothers with bad gut flora are more likely to develop unhealthy gut bacteria, and that these early differences in gut flora may predict overweight, diabetes, eczema/psoriasis, depression and other health problems in the future.

The gut barrier: the gatekeeper that decide what gets in and what stays out

Have you ever considered the fact that the contents of the gut are technically outside the body? The gut is a hollow tube that passes from the mouth to the anus. Anything that goes in the mouth and isn’t digested will pass right out the other end. This is, in fact, one of the most important functions of the gut: to prevent foreign substances from entering the body.

When the intestinal barrier becomes permeable (i.e. “leaky gut syndrome”), large protein molecules escape into the bloodstream. Since these proteins don’t belong outside of the gut, the body mounts an immune response and attacks them. Studies show that these attacks play a role in the development of autoimmune diseases like Hashimoto’s and type 1 diabetes, among others.

In fact, experts in mucosal biology like Alessio Fasano now believe leaky gut is a precondition to developing autoimmunity:

There is growing evidence that increased intestinal permeability plays a pathogenic role in various autoimmune diseases including [celiac disease] and [type 1 diabetes]. Therefore, we hypothesize that besides genetic and environmental factors, loss of intestinal barrier function is necessary to develop autoimmunity.

The phrase “leaky gut” used to be confined to the outer fringes of medicine, employed by alternative practitioners with letters like D.C., L.Ac and N.D. after their names. Conventional researchers and doctors originally scoffed at the idea that a leaky gut contributes to autoimmune problems, but now they’re eating their words. It has been repeatedly shown in several well-designed studies that the integrity of the intestinal barrier is a major factor in autoimmune disease.

This new theory holds that the intestinal barrier in large part determines whether we tolerate or react to toxic substances we ingest from the environment. The breach of the intestinal barrier (which is only possible with a “leaky gut”) by food toxins like gluten and chemicals like arsenic or BPA causes an immune response which affects not only the gut itself, but also other organs and tissues. These include the skeletal system, the pancreas, the kidney, the liver and the brain.

This is a crucial point to understand: you don’t have to have gut symptoms to have a leaky gut. Leaky gut can manifest as skin problems like eczema or psoriasis, heart failure, autoimmune conditions affecting the thyroid (Hashimoto’s) or joints (rheumatoid arthritis), mental illness, autism spectrum disorder, depression and more.

Researchers have identified a protein called zonulin that increases intestinal permeability in humans and other animals. This led to a search of the medical literature for illnesses characterized by increased intestinal permeability (leaky gut). Imagine their surprise when the researchers found that many, if not most, autoimmune diseases – including celiac disease, type 1 diabetes, multiple sclerosis, rheumatoid arthritis and inflammatory bowel disease – are characterized by abnormally high levels of zonulin and a leaky gut. In fact, researchers have found that they can induce type 1 diabetes almost immediately in animals by exposing them to zonulin. They develop a leaky gut, and begin producing antibodies to islet cells – which are responsible for making insulin.

In Step #1: Don’t Eat Toxins, I explained that one of the main reasons we don’t want to eat wheat and other gluten-containing grains is that they contain a protein called gliadin, which has been shown to increase zonulin production and thus directly contribute to leaky gut.

But what else can cause leaky gut? In short, the same things I listed above that destroy our gut flora: poor diet, medications (antibiotics, NSAIDs, steroids, antacids, etc.), infections, stress, hormone imbalances, and neurological conditions (brain trauma, stroke and neurodegeneration).

Leaky gut = fatigued, inflamed and depressed

Here’s the takeaway. Leaky gut and bad gut flora are common because of the modern lifestyle. If you have a leaky gut, you probably have bad gut flora, and vice versa. And when your gut flora and gut barrier are impaired, you will be inflamed. Period.

This systemic inflammatory response then leads to the development of autoimmunity. And while leaky gut and bad gut flora may manifest as digestive trouble, in many people it does not. Instead it shows up as problems as diverse as heart failure, depression, brain fog, eczema/psoriasis and other skin conditions, metabolic problems like obesity and diabetes and allergies, asthma and other autoimmune diseases.

To adequately address these conditions, you must rebuild healthy gut flora and restore the integrity of your intestinal barrier. This is especially true if you have any kind of autoimmune disease, whether you experience digestive issues or not.

How to maintain and restore a healthy gut

The most obvious first step in maintaining a healthy gut is to avoid all of the things I listed above that destroy gut flora and damage the intestinal barrier. But of course that’s not always possible, especially in the case of chronic stress and infections. Nor did we have any control over whether we were breast-fed or whether our mothers had healthy guts when they gave birth to us.

If you’ve been exposed to some of these factors, there are still steps you can take to restore your gut flora:

  • Remove all food toxins from your diet
  • Eat plenty of fermentable fibers (starches like sweet potato, yam, yucca, etc.)
  • Eat fermented foods like kefir, yogurt, sauerkraut, kim chi, etc., and/or take a high-quality, multi-species probiotic
  • Treat any intestinal pathogens (such as parasites) that may be present
  • Take steps to manage your stress

{ 33 comments… read them below or add one }

Clarissa February 24, 2011 at 9:43 am

Hello Chris,

I have been following your series with great interest. I have followed a strict paleo diet excepting the inclusion of a small amount of high fat pastured dairy products for about 5 months. I have struggled with chronic facial hives and rash for several years and, if anything, these have gotten worse on the paleo diet. I started a dairy-free challenge a few days ago, and if I don’t see an improvement within the next couple of weeks, will try an egg-free challenge. Because of the dairy-free challenge I am reluctant to add kefir or yogurt to my diet. Any recommendations on specific brands of probiotics? There is a bewildering assortment out there.

Angela February 24, 2011 at 11:45 am

Hi Chris
I’m on a low carb/GAPS diet to deal with chronic yeast overgrowth and h.plyroi overgrowth and I can’t have sweet veggies or starches like yams, sweet potato, etc. Are there other sources of fermentable fiber? Also, I have not come across this term before, can you describe what you mean by it?

Thanks for another great blog post!

Dana February 24, 2011 at 11:45 am

If you read the attachment parenting/pro-breastfeeding literature you will find discussions of the development of the infant gut. Apparently, babies come with leaky guts–the cells of the mucosa have spaces in between them, naturally. Those gaps close at about six months of age. Breastmilk coats the mucosa and plugs up the gaps, as it were, without causing harm. It is believed this also helps train the infant’s immune system.

Now think about all the parents out there giving solids to their babies at four months of age. What’s the most commonly introduced first food?

Not that formula before six months of age is a tremendous idea either. It typically contains corn syrup solids and vegetable oils.

Chris Kresser February 24, 2011 at 11:55 am

Angela: fermentable fiber = soluble fiber. They are long-chain glucose polymers (polysaccharides) so they’re not allowed on the GAPS diet. By definition, anything with a prebiotic quality is not allowed on GAPS because they’re all polysaccharides.

Rob February 24, 2011 at 11:59 am


Is the salt content of sauerkraut a concern?


sarah moore February 24, 2011 at 12:06 pm

Great thorough info… as a colon hydrotherpist I see how poor nutrition lack of good bacteria and overuse of antibiotics r aiding in a very sick world. I enjoy ur site.

Arvind Ashok February 24, 2011 at 12:26 pm

Great post, and great blog Chris! Thanks a lot for a ton of useful information! I love this series especially. I have a question – is the idea behind taking fermentable fibers to promote the growth of good bacteria?

Adam February 24, 2011 at 12:52 pm

Great article Chris. Sums up my experience with autoimmune issues. Once I started avoiding toxins (specifically gluten) and taking a quality pro-biotic, my psoriasis and eczema went away for the most part (occasional flare-ups when I stray from diet). Both also improved my hypothyroid symptoms to the point I experience less brain fog and can go through most days from 5:30am to 10pm without a nap.

I added high quality colostrum from grass-fed cows about two months ago, and it’s really helped too. Not sure what your thoughts are regarding that supplement, but I recommend it.

Harald February 24, 2011 at 1:16 pm

Hi Chris.
Thank you for your article, which points the way to improve one’s habits. -
I have an issue with the numbers; in North America, of course, it is customery to call a number with 6 zeros a million, with nine zeros a billion and with 12 zeros a trillion and so forth. This is incorrect, strictly speaking. When a million acquires another set of six zeros it would become a billion i.e. twice the group of zeros. A trillion would have 3 sets of 6 zeros. This is the custom in Europe including Britain. Enough said about this. -
Diabetes type 1 is often caused by the ACT of vaccinating, or any other violent act by a ‘grown-up(?)’ upon a small and helpless child. The child suffers a DHS, a biological conflict forming a Hamerscher Herd (HH) and effecting the Langerhans cells of the pancreas. It LOOKS like an autoimmune response, but it actually is a part of a SPECIAL Biological program of Nature we are all born with. The reasoning is, that there is not enough insulin production to have an effective defense response, therefore more of these cells need to be made. This would take place upon resolution of the conflict and this part of the pancreas would have more cells to enable the body to mount a more effective defense of itself. -
Generally speaking, while a lot of research is being done, the initial perspective is more often than not, backward. The responses of the biological body, are being looked at as the causes and a hypothesis is made to explain something, which for all intents and purposes, has been mis-identified.
Germanic New Medicine has been propagated using only 5 Biological Laws of Nature, whereas the conventional ‘wisdom’ works with over 5000 (and counting) hypotheses. Learn more about this here:
http://learninggnm.com .

Angela February 24, 2011 at 1:21 pm

HI Chris
Thanks for your response about fermentable fibers. What would you recommend in lieu of fermentable fibers since they are not allowed on a low carb/GAPs diet?


Harald February 24, 2011 at 1:30 pm

Sauerkraut would be a very good food, if ‘they’ did not insist on pasteurization. The salt in making it becomes part of one’s intake requirements and basically, if one ingests too much salt, the body responds by making one thirsty in order to bring the salt content of the intercellular space back to the .09 percent level.

Jordan Reasoner February 24, 2011 at 1:34 pm

Hi Chris,

Great article! I’ve been following a custom version of the Specific Carbohydrate Diet where I eat about 3,000 calories a day of 60% fats, 30% proteins, and 10% carbs consisting of fats, meat, veggies, and very small portions of raw fruit (like 10 raspberries). I’ve been following this very strict regimen for almost 2 years now.

Before the diet I was a mess from Celiac Disease with severe leaky gut and bacterial overgrowth. Going gluten free didn’t work at all. But now that I’ve been on my version of the SCD Diet I feel incredible with more energy, mental clarity, and better health that I’ve ever had in my life. Perfect poops everyday.

My friend and I even wrote a book about how we tweaked the SCD Diet to heal our guts and have helped many people with Celiac, Crohn’s, UC, and IBS do the same. This stuff works for so many people with autoimmune and digestive diseases… especially if you avoid dairy and egg.

I also wanted to add that I made huge strides with digestion once I started taking Vitamin D3, digestive enzymes, Betaine HCL, and 200 CFU’s/day of an 11 strain probiotic. And you’ve written some great content about that in the past.

So thanks for doing what you do! I always look forward to your knowledge.

Jordan Reasoner

Richard MacKenzie February 24, 2011 at 2:15 pm

Hello everyone. I have had psoriasis for the past 22 years.

I have just come off a drug called cyclosporine which gave me around 90% clearance, however I didn’t get on with the side effects.

On Saturday I am starting a gluten free diet to see if that will help. I am writing about my successes/failures with this approach at http://www.healthyhappieryou.co.uk/2011/02/can-a-gluten-free-diet-clear-my-psoriasis-part-1

I would be interested in getting any tips or advice from any of you that have tried this approach before Smiley



Felicia February 24, 2011 at 5:16 pm

You said that birth control can contribute to unhealthy gut flora. I have been trying to look up exactly how that happens, but I haven’t found an answer. So how does taking the pill harm your gut? I have long questioned whether or not birth control is really a good idea, so I would really like to understand this aspect as well.

Susan February 24, 2011 at 8:37 pm

I think you mean yuca (YOU-kah) rather than yucca (YUCK-ah). It’s almost impossible to eat a yucca root…very fibrous and not really edible. Yuca, on the other hand, is delicious.

Matt February 25, 2011 at 6:06 am

Excellent post Chris,

Can you hazard a guess why sauerkraut might be problematic for some? I seemingly get instant brain fog, stimulation, salivating and oddly cravings. The best I can come up with is a possible histamine, suplhur reaction.

Due to also avoiding dairy, are there any other whole food probiotics you would recommened?


Mario February 25, 2011 at 7:11 am

Regarding colostrum and leaky gut:


WP @ The Conscious Life February 25, 2011 at 8:01 am

I was on antibiotics for a good number of years so I can definitely attest to the ‘powers’ these drugs have on me — a weak digestive system, loose stools and lots of gas. Unfortunately, I only knew about the link much later. The doctors that put me on this path were most probably as clueless as me about the consequences and the alternative safer treatments available (there are as I found out years later). So if you’re on long-term antibiotics, you should really question why and find out other less destructive alternatives. If you look hard enough, there usually are. Don’t rely 100% on your doctor; do research on your own. Thankfully, the damages I’ve sustained were not so severe to the extent that they were completely irreversible. Now I regularly take probiotic foods like tempeh, kimchi and natto to restore my gut flora and avoid foods that give me bloating and gas (like beans). Thanks for writing about this topic, Chris. More people should be aware of the consequences of taking antibiotics for prolonged period of time.

Mary Branscombe February 25, 2011 at 9:20 am

Interesting to see more detail on this. In the 90s I had severe IBS symptoms, from stress and eating chicken-mushroom-mayonaise sandwiches for lunch for nearly a year (well, almost ;-) In desperation I ended up doing strict Hays diet food combining and avoiding dairy, yeast, alcohol (and as a consequence very little wheat) and after a few months I was able to get back to eating just about anything; I’ve often wondered what the mechanism was for defusing the food senstivities and ‘leakiness’ could fit.

Any thoughts on whether this issue would have an impact on asthma, especially adult onset? my husband has coughing (rather than wheezing) asthma irritated by nasal drip (no more adenoids), and while the leukinase-inhibitor immunosupressants are a huge help it would be interesting to see if diet can help reduce the minor attacks he still has…

E February 25, 2011 at 6:09 pm

I second Felicia’s comment on the negative aspects of birth control. I am currently on the pill and curious of any negative factors.

Goni February 25, 2011 at 8:56 pm

Hi nice post

I’m from Portugal and I would like to tell that there is a blog written in spanish called “Nutrición Primitiva y Salud Integral”, http://nutriprimal.blogspot.com/ ,
in which the author is just translating this series of articles, namely 9 steps to perfect health, to spanish without telling the readers that they are yours.
Very strange, maybe you want to do something about it.
Best wishes I amire your work

Dianne February 26, 2011 at 5:53 am

I take a organic probiotic that has worked better than anything else. Its helped my gut issues, my child’s issues and my mothers IBS. Its available worldwide but is bought from here http://www.organic4u.com.au Its called inliven. It has the foods in it that processes the probiotics better, and being certified organic, its very pure. I just add it to juice or a smoothie.

Mallory February 26, 2011 at 10:16 am

i am beyond convinced the gut is the path to health for everybody. if one can figure out whats wrong with their digestion, they will have health. seems once obesity or thyriod problems etc all of it set in, the problem is long established already with an unhealthy gut

Mallory February 26, 2011 at 10:17 am

wanted to add, what do you think of culturing lots of foods, like sweet potatoes, ketchup etc?? beneficial??

Healthy Hideout March 2, 2011 at 5:00 am

Hi Chris – Great article yet again. You don’t seem to touch too much upon colonic treatments or colon cleansing to help get rid of the “toxins” that are essentially stuck inside our digestive system. Is it worth taking a further look into this kind of treatment to help cleanse the gut? Do you have first hand experience?

Chris Kresser March 2, 2011 at 11:14 am

I’m not a fan of colon cleansing. There’s no evidence of “toxins” stuck in our digestive system, nor that colonics help remove them. Colonics do, however, remove a lot of healthy gut flora, and they can be quite harsh. People have different opinions on this subject. This is mine.

Steven Wright March 2, 2011 at 12:30 pm

Hey Chris – Love your work please keep it up!

Could you clarify your response to colon cleansing above, does that include the many different “therapeutic” enemas talked about around the web? For example coffee enemas for liver detox? Thanks!

Chris Kresser March 2, 2011 at 12:33 pm

I’m referring specifically to colonic hydrotherapy. Enemas are fine in most cases.

Mindy March 2, 2011 at 10:03 pm

Do you know much about the effects of metformin on gut health? I know it gets in the way of absorbing vit B12 and makes my lactose intolerance even worse. I used to be on it to treat PCOS, but went off while breastfeeding. Now that my son is weaned, I’m trying to re-educate myself on the benefits/risks. There have been a number of studies showing improvement even for non-obese, but I just wonder if it will wreck my gut.

sean March 3, 2011 at 4:10 pm

Chris, i love your blog, this is all fantastic and really thorough.
I wanted to ask, how does one treat internal pathogens like those you mentioned without knowing about them? what is required in order to find out?

Chris Kresser March 3, 2011 at 4:26 pm

Sean: a stool test is usually a good start. Must be a reputable lab, preferably one that uses DNA/PCR technology. A lot of false negatives with the typical labs.

Noreen Murphy March 4, 2011 at 9:38 am

Chris, is there a soy-free, lactose-free formula for babies, one that doesn’t contain fructose syrup. My grandson is 4 months old. He’s currently on lactose-free formula (since he was six weeks old for suspected lactose intolerance or sensitivity) which is soya based. All lactose-free formulae here in Ireland appear to be soya based. He now seems to be reacting to the formula. Any advice would be appreciated. Thanks

Chris Kresser March 4, 2011 at 10:24 am

Noreen: see this link for info on good formula options.

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