A Healthy Gut Is the Hidden Key to Weight Loss | Chris Kresser
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A Healthy Gut Is the Hidden Key to Weight Loss


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In a previous article in this series on diabesity and metabolic syndrome I briefly mentioned the role of gut health in obesity and diabetes. I’d like to go into more detail on that subject here, especially since it’s not a very well known relationship.

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.

Recent research has shown that the gut flora, and the health of the gut in general, also play a significant role in both obesity and diabetes. I’ve seen this anecdotally in my practice as well. Nearly every patient I treat with a blood sugar issue also has a leaky gut, a gut infection, or some other chronic inflammatory gut condition.

We now know that the composition of the organisms living in your gut determines – to some extent, at least – how your body stores the food you eat, how easy (or hard) it is for you to lose weight, and how well your metabolism functions. Let’s take a closer look at the mechanisms involved.

Intestinal Bacteria Drive Obesity and Metabolic Disease

A study published this year in Science magazine found that mice without a protein known as toll-like receptor 5 (TLR5) in their gut gain excessive weight and develop full-blown diabetes and fatty liver disease when fed a high-fat diet. If we think of the gut flora as a community, TLR5 is like a neighborhood police force that can keep the houligans in check. Without TLR5, bad bacteria can get out of control.

The study authors found that these bad bacteria caused a low-grade inflammation in the mice, which caused them to eat more and develop insulin resistance. They also found that treating these mice with strong antibiotics (enough to kill most of the bacteria in the gut) reduced their metabolic abnormalities.

But the most interesting part of this study is what happened when the researchers transferred the gut flora from the TLR5-deficient overweight mice into the guts of skinny mice: the skinny mice immediately started eating more and eventually developed the same metabolic abnormalities the overweight mice had. In other words, obesity and diabetes were “transferred” from one group of mice to the other simply by changing their gut flora (as shown in the image below).


Other studies have shown that the composition of the gut flora differs in people who are obese and diabetic, and people who are normal weight with no metabolic irregularities.

One possible mechanism for how changes in the gut flora cause diabesity is that different species of bacteria seem to have different effects on appetite and metabolism. In the study on TLR5 deficient mice I mentioned above, the mice with too much bad bacteria in their guts experienced an increase in appetite and ate about 10 percent more food than their regular relatives. But it wasn’t just that these mice were hungrier and eating more; their metabolisms were damaged. When their food was restricted, they lost weight – but still had insulin resistance.

Other studies have shown that changes in the gut flora can increase the rate at which we absorb fatty acids and carbohydrates, and increase the storage of calories as fat. This means that someone with bad gut flora could eat the same amount of food as someone with a healthy gut, but extract more calories from it and gain more weight.

Bad bugs in the gut can even directly contribute to the metabolic syndrome by increasing the production of insulin (leading to insulin resistance), and by causing inflammation of the hypothalamus (leading to leptin resistance).

How Modern Life Screws up Our Gut and Makes Us Fat and Diabetic

What all of this research suggests is that healthy gut bacteria is crucial to maintaining normal weight and metabolism. 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

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 and obesity in the future.

It’s interesting to note that the diabesity epidemic has neatly coincided with the increasing prevalence of factors that disrupt the gut flora. I’m not suggesting that poor gut health is the single cause of obesity and diabetes, but I am suggesting that it likely plays a much larger role than most people think.

How to Maintain and Restore Healthy Gut Flora

The most obvious first step in maintaining a healthy gut is to avoid all of the things I listed above. But of course that’s not always possible, especially in the case of chronic stress and infections, and whether we were breast-fed or our mothers had healthy guts.

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


Join the conversation

  1. Hello, i have recently started on the loette contraceptive pill but i also started drinking yakult well the cheap version pro-b. I was wondering if that affected the pill at all?

  2. Hi Chris,
    I wanted to know if you or anyone else on this thread has heard of the Plexus products ProBio5 (a probiotic) & Biocleanse. They are GREAT at helping get the gut healthy, as well as The Plexus slim. Numerous testimonies support these products. I’m sure this isn’t a place to “promote” personal websites or business but I mainly wanted to know if Chris has any insight to the research w/ Gut Health & Plexus??


    • I have started 3 weeks ago, already seeing a dramatic change in my sugar numbers… I am type two diabetic… taking triplex from plexus.

  3. I like to drink a super green powder mix,That is also great for your gut flora…It will give you a few extra servings of vegetables if you don’t get enough for the day.It is a good way to get a mixture of veggies in a powder drink mix.I have found one for only 13 bucks at Vitacost-It is Berrytastic.I am not one of these people that are going to spend 30 or 40 bucks on a protein or veggie drink mix.I think its a good way to get extra fiber and veggies and it does help out when you have to go to the restroom.

  4. Maybe somebody can give me advice:

    I can not tolerate fermented foods because of histamine intolerance. So I take a probiotic.

    I suffer from a chronic procitits. At the beginning I felt little pain and had bloody stool, higher calprotectin. Through a Paleo diet (no gluten, low histamine, diary and egg free) I got rid of many symptoms like the bloody stool and most of the pain (was not much pain). But I still suffer from irregular motility and mood and energy swings which correlate with my bowel movements. This means:
    I am often constipated for 2-3 days. Then I have either normal motility like I always had (2-3 per day) or I have one movement per day. When having my old motility back, I feel good energy. But the most time I feel like a little subdepressive and low energy…

    When I had acute proctitis the first and only time, I could not tolerate anything but rice and potatoes. Sugar and diary gave me massive mood swings (anxiety). Had to eat rice and potatoes for a week with a probiotic to get normal again…

    Since I suffer from proctitis I cannot tolerate any Gluten, or FOODMAPS. Foodmaps give me heavy brainfog and constipation (tried inulin)

    I tried Bimuno (GOS) which my gut tolerated well, but I react allergic to it (I react to many things :-/)

    So I ask myself if could use Lactulose as a prebiotic for a longer time. Is this an good alternative to inulin or FOS?

    In my probiotic is FOS, but the bacteria eat it all up during the preactivation- phase (has to be diluted in water 25 minutes before drinking)

    Or should I start with tiny amounts of FOS?! But even a tiny capsule of Inulin gaves me heavy brain fog for days last time I tried it. I have no idea where to go with there issues. There´s no Chris Kresser in Germany…:-/

    Can anybody help me with this?

    • I wouldn’t worry about taking a prebiotic, I don’t think they make a lot of sense — if you think about it prebiotics are designed to “feed” the probiotics in your intestinal track… but you’re also going to be “feeding” the BAD bacteria along with the good bacteria! It also doesn’t make sense to activate the probiotic bacteria BEFORE you ingest them — how will they get through your stomach acid alive? They are better left inactive until they get to the small and large intestine where they naturally thrive…. I would suggest that you just take a good probiotic. The strain Lactobacillus bulgaricus, strain LB-51 in the Natren line of probiotics is excellent for gut motility and improving constipation. I like their probiotics because they offer a powdered form which really allows you to start at a low dose (1/8 of a teaspoon or so..) and work up to a higher dose, it’s great for those of us with sensitivities!

      • Thank you for your reply.

        Bur I think you are wrong.

        Prebiotics feed mainly the good bacteria. And the probiotic which I take works even better than older ones because of the preactivation.

        L. Bulgaricus is histamine building and I am intolerant to histamine. So this would not be a good idea.

        As your info is exactly the opposite if what I learned: where do you have this information from?

        Thank you

        • I’ve read numerous studies about prebiotics because it just didn’t seem to make biological sense to me. At it’s very basic a prebiotic is something that our body doesn’t digest well (so it passes through the small intestine generally untouched) and our bacteria in our large intestine break it down instead. So, by their very nature, they are apt to disturb our digestion since they are non-digestible items…. and I think they do, they’ve shown that we don’t tolerate them well in large doses, so in small doses we just don’t notice what they are doing to our body, perhaps… ?

          I just don’t see how the good bacteria are more likely to utilize it? Bacteria are opportunistic organisms, I’m extrapolating here but I think that any of them would be able to use a prebiotic as an energy source. And I’ve seen studies where prebiotics have worsened pathogenic infections so obviously pathogenic bacteria are using these as well.

          Here’s a few studies on this topic that may interest you:



          I don’t know about histamine, so I’m sorry I can’t really comment further on that.

          • Hello again,

            thank you for your answer again.

            I don´t think that they can “eat” all prebiotics. I also read many studies and in most cases there was a specific class or sometimes even just a specific bacterium which proliferates most in the prebiotic group. At the same time in most cases, the overall count of bacteria was not influenced. So, there must have been a shift in population towards the specific bacteria which could eat the prebiotic.

            I only read one study where lactulose also enhanced a specific species of clostridia. But in most studies they found lactulose to enhance bifido bacteria.

            I found the same for Inulin, FOS and other GOS than Lactulose…

            Maybe the infection is the variable, which counts, because in the most studies I read about, there participants were healthy.

            But I don´t think that I have an infection (never found something like that in many diagnostic processes.

            And I also don´t think prebiotics are harmful for our digestion, as they lead to more bifidobacteria which is associated with many health benefits…


        • What you might try is a probiotic that also has an anti fungal, and chitonase to break the exoskeleton of bad bacteria. You want to fee the good while killing the bad. I take this with a magnesium supplement (Bio Cleanse) which flushes out the bad ensuring it is not reabsorbed into your system. Magnesium also oxygenates the body. It’s working for me. 🙂

    • HI there,

      does your probiotic contain the ingredient Chitosasane?? That ingredient is very beneficial in killing the bad bacteria in your gut that may cause so many symptoms. There are so many probiotics out there but you have to pay careful attention to see if they are just replenishing the good and doing nothing with the bad – if so you’re not getting the full benefits of a probiotic.

    • Hi,

      regarding your mood swings, you probably have a sensitivity to “free glutamic acid”, Chris has another post about this


      I have this myself, but it took years to find out that specific foods trigger neurological symptoms, cause it’s kind of all foods 🙁

      here’s a list of foods to avoid, if this is the case


      Did you consider getting a fecal transplant (Stuhltransplantation)?

      I also live in (the south of) Germany by the way 🙂

  5. Ugh. This really intrigued me, and then nothing. It felt like one of those scam emails that tells me everything I want to hear and promises a cure…once I click on a link and pay $49.95.

  6. Thank you.

    I’d like to know how to get more TLR5, where it comes from, or how it is made. I can’t learn a new word and not know what it’s all about. I’m guessing it has something to do with healthy habits and the avoidance of unhealthy habits.

  7. I’ve been reading about probiotics and insulin resistance and obesity, etc. I have been taking a good quality probiotic for a few months now and have just been diagnosed with insulin resistance for which I have been placed on medication. I also have high blood pressure, high cholesterol and thyroid antibodies causing hypothyroidism. The bacteria in my probiotic are Lactobacillus acidophilus, Lactobacillus rhamnosus, Bifidobacterium Ion gum, & Saccharomyces boulardii. Maybe they are just the wrong ones!

    • It’s an issue of quality over quantity too. If your gut is unhealthy you may not be able absorb all the nutrients you are eating. I too am insulin resistant. I take a chromium supplement (other ingredients too) which helps to maintain muscle, burn fat, make your body more sensitive to insulin, reduces carb cravings (a game changer for me!). I take a probiotic to feed good bacteria. It has an anti fungal and a protein to break down fibrous foods (3products in one)! And a magnesium supplement to ensure the bad stuff is flushed out and not reabsorbed. Within 4 days me GERD was gone (still is!) and I’d had it over 30 yrs bc I didn’t want to take a protein pump inhibitor. Energy up, carb cravings decreased, making healthier voices.

      Happy 4th! 🙂

  8. Hi chris, why are we told to eat healthy grains if they are so bad for gut health, and also, what defines healthy grains?

    • quinoa, buckwheat, amaranth, are all considered good grain quality. look up diet for parasite cleanse by hulda clark.

  9. Hello Chris, you write that Diets high in refined carbohydrates, sugar and processed foods can contribute to unhealthy gut flora.
    I am trying to find the scientific research that proofs this. I can not find this in your articles. Can you help me?

  10. Why are the specific species of bacteria that benefit us (or the mice)not mentioned? When you buy probiotics, the bacteria, by name, is noted on the label. This study had to have determined the specific bacteria that were helpful, and harmful, yet not one article or web site mentions the specifics. This information, absent specifics, is pointless! Aren’t we ridicules.

  11. Does having too big a variety of foods disrupts formation of healthy gut bacteria? Should we consistently eat the same healthy foods or mix them up as much as possible? Thanks for your time! Great article.

  12. The link attached to this statement is not working, I was interested in seeing the reference for this, do you have that available by any chance? –> “Other studies have shown that the composition of the gut flora differs in people who are obese and diabetic, and people who are normal weight with no metabolic irregularities.”

  13. Hi Chris,

    I am at wits’ end. I eat mostly plants, always real food (lean meat, vegetables, fruit), I stay away from all gluten and refined sugar. I exercise 6 – 7 times a week, I meditate and practice yoga. Most people in my office refer to me as a health freak, but really I live like all people should.

    I am constipated and I find it beyond difficult to lose weight. I am starting to find out (after much research) that it may be the bacteria in my gut and the health of my gut. As a child and into my early adulthood (I am 28 now) I had severe tonsillitis and having antibiotics as the only treatment, I had it quite severe one year needing a shot of penicillin in my back and very strong antibiotics. A year after this I developed gluten intolerance. Some days I want to cry because its all too hard.. why, when I do everything right does it seem like I am punished.

    I have recently started taking a good quality probiotic.. I am wondering what else I can do? I have been to so many doctors that palm me off and tell me to increase my dietary fibre.

    I would also like to thank you for all the useful information you provide!


    • Well, in this case, the doctors can be right. Many people make the mistake of not getting enough fibers when they switch to a low carb diet. Getting more fiber will definitely help with the constipation.

    • Hi,
      I noticed what you’re eating is rather “healthy” as per what has been taught for a number of years bar 2 things you didn’t mention.
      How much water do you drink?
      And most importantly, you haven’t mentioned and fat in your diet?
      Healthy diets consist of 30% fat. Adding fat to your diet will loosen your faeces and lube them up. My mother has suffered from severe constipation for years and has finally added fats back into her diet and, literally within a week, her constipation has disappeared.

    • Far too little fat. That will make anyone constipated, as your colon needs to be ‘oiled’. Eat more oily fish, add olive oil to salads, and cook in butter (not vegetable fats). Lack of fat will be impeding weight loss as well. Simple rule of thumb; eat fat to lose fat, eat carbs to gain fat.

      Also, try taking an L-Glutamine supplement, very good for repairing damaged intestines and contributing to normal gut flora.

      Good luck 🙂

    • hey mate read you story and we have a similar problem
      ive had lots of antibiotics for tonsillitis and have a gluten problem too..i also struggle with acne and a flaby stomach dispite being fit and slim everywhere else..its definetly a lack of good flora in the gut..as of yesterday I started eating fermented sauerkraut and swallowed 15 probiotics.. I read that 1 a day is useless you should swallow 15 at once 2 times a month to flood the body….hope this helps.

  14. Hi Chris,
    Just wanted to check if you can recommend any efficient weight loss plan or anything that could assist in weight loss?
    I’ve recently being taking Garcinia but did notice much of a change.
    Also what thoughts do you have on Yakult? Does this assist in weight loss at all?
    Thank you

  15. I’m trying to find info on treating parasites naturally bc from what I have gathered so far (with a lot of methods used) is that the parasites become resilient. How do you suggest parasites are treated best?

    • Have you heard of humaworm? It is a natural parasite treatment that uses herbs. I am planning to do it again soon; although I did not get drastic results like some of the reviews online, I found that my eyes began to itch and I began sneezing more. Someone suggested to me that I may have stirred something (parasites? yeast?) up…Diatamaceous earth is another parasite cleanser; you can research it. Hope this helps.

    • After taking a yeast assessment and scoring extremely high I started taking a pro biotic (which also contains an anti fungal and a protein to break up fibrous foods so your body can absorb the nutrients you are consuming). I combine it with a magnesium supplement which works to flush out the toxins and yeast the probiotic is killing. It’s less expensive than the expensive probiotic my doctor recommended and within 4 days my acid reflex was gone. After over 30 years! While the two my dr gave me did nothing that I could notice.

      I’m not an expert, just know what’s been working for me. 🙂

  16. Help , I must be stressed , I have been like this since they told us our jobs are leaving , tests from the Dr. Concludes , I have more bad flora then good , it makes it really hard to go to work , always going to bathroom , can’t keep it in , I’m finding fluids are the best , and I’m gaining weight , probably fluid..

  17. Healthy gut flora is important. However eating less food and eliminating sugar and other offending foods/poison which for me include grains will lead to weight loss without the need for supplementation. Eating a diet rich in veggies & quality fish, meats will work for most people.

  18. What would you recommend for a type 1 diabetic with gastroparesis? In and out of the hospital with severe stomach pains for a year. Started acupuncture, juicing and removed gluten from the diet 3 weeks ago and haven’t been in the hospital since. Still underweight though and nervous to eat anything. Besides sweet potatoes, etc., what would you recommend eating/ supplementing with? I’m considering starting on l-glutamine, fish oil, magnesium and extra virgin coconut oil. Is it safe to eat grass-fed butter, beef and fish? Your FODMAP has been an excellent guide as have the 9 nutritional steps. Thank you.

  19. Would you mind recommending a specific panel that you have found to be the most advantageous for the first step in determining gut issues. Is the Genova Comprehensive Digestive Stool Analysis 2.0™ (CDSA 2.0) with Parasitology a good one?

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