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. Just wondering if the admonition to avoid grains and legumes on these diets includes lentils and chickpeas, and thus that humus is also off the list.

  2. Great article. I have read many similar ones and I am interested in learning more about “good bacteria” and “gut cleansing” for purpose of detoxification. My little boy has just turned seven. He struggles with chronic constipation/diarrhea. For two years now his PCP has merely recommended Miralax to correct the constipation. My child is obese with stomach distention (pot belly). An X-ray once confirmed this boy gets very compacted. I have suggested that toxins and almost “tapeworm type of deal” (not that i think he has one but using the example to point out his increased hunger). He does not eat out of boredom, and he does not loaf, He is actually go go go! When he eats its on purpose, it’s his body seeking nutrition. I feel there is malabsorption going on here. I feel there is an overload of bad bacteria in his intestines which over whelm him and which have now lead to symptoms of ADHD, Why will no one listen to me? I don’t want to consider ADHD meds when i feel the primary problem is with his digestive tract. Can you lend some advice on gut cleaning options? I read that the leaky gut and toxin build up can become fatal. I am not willing to overlook this likely cause of his compaction, high hunger level, hyperactivity and recent ADHD diagnosis which i believe all to be due to trapped toxins.Thank you Chris!

  3. Hi – I’m always extremely heath-concious, although currently I have no health problems other than being overweight. I don’t eat sugars (including most fruits), any grains or processed foods. I’m basically following the paleo diet with lots of raw green juice (juiced myself), raw green vegetables, grass-fed meats and eggs. I do eat greek yogurt, drink kombucha and coconut water regularly. However, I take a birth control pill every day and I’m concerned about my gut flora. I don’t take any other medications, not even pain killers like Aleve. At this point, I don’t see a way around taking the birth control though, so what would be the best way to help defend my gut flora? Anything else besides yams and sweet potato? What is the best high quality pro-biotic? Thank you so much!

    • Hey Allison,

      I saw that you mentioned birth control I recently became engaged and started battling the inevitable birth control- which I really, really, really didn’t want to take due to synthetic hormones and their effects on the emotions, gut, body, and more. My future mother-in-law went with natural BC by measuring her basal temp every morning to determine when she was about to ovulate. With that said, I recently found the lady comp, which basically measure your basal temp and gives a green light if you aren’t soon to ovulate and a red light 5 days before ovulation to prevent pregnancy. It’s really amazing, and you don’t have to worry about hormones. I’m so excited that someone came along with this method and was innovative enough to come up with a ovulation predictor like lady comp. Here’s the link if you’re interested.

  4. How should one take prebiotic and probiotic supplements? With food? At different times of the day? Together?

  5. HI Chris, PLEASE RESPOND, I NEED INFO. One of the steps you list to restore intestinal flora is Treat any intestinal pathogens (such as parasites) that may be present. 1 year ago took a course of antibiotics to kill h. pylori. I continued to have symptoms. 4 months ago I was diagnosed with celiac. (I’m not sure the diagnosis is accurate, because I have only 4 of the 5 diagnostic positives- the most important one (tissue samples) was negative.) I now follow a gluten free/milk-free diet. I continue to have symptoms, but much milder. I have always maintained a stable weight with no effort. Now, however, my weight climbs steadily without serious calorie restriction. I must eat no more than 1300 calories and exercise 90 minutes 6x/wk intensely to maintain a weight 5-8 lbs higher than I’ve been since reaching adulthood. The math doesn’t add up. My questions are:
    1. Is h.pylori considered to you a “good” or “bad” microorganism. I’ve been told it helps regulate appetite.
    2. I’ve also learned that some bacteria can actually prevent your body from using fat stores. What are they? Can I test for them?

  6. I like your article. Here’s my two cents’ worth: A couple years ago I really started noticing and having to work around a problem with wheat. If I ate wheat (especially commercial wheat), I had to spend about 3 days near a bathroom. So I began avoiding wheat in December 2011 and had improvement. In the meantime, someone said they had cured their problem (wheat? gluten? I don’t remember) by using a probiotic called Yakult, which originated in Japan. Because they used the term “cured” I thought I would look into it. I found that it is available at one store in my state (in another town), and I have been going to that town once a week anyway, so I started buying it. I decided I would give myself 6 weeks to really try it. I took the probiotic every day and tried even harder to avoid wheat – even organic wheat. I did see an improvement fairly quickly, but I also noticed that whenever I drank tap water or ate/drank foods made with tap water, my improvements went away. So I started wondering if there was something in the tap water that was killing off my good bugs. Long story short, after talking with the people who run the water works near me, I suspect that chloramine in the tap water has been killing off my good bugs. So now I avoid it by using spring water or well water from a friend’s farm. I can eat any amount of any type of wheat now without repercussions – as long as I avoid the tap water. Of course, eating more wheat is a mixed blessing. I can eat a wider variety of food; but I do need to lose some pounds, and I have to minimize wheat to make that happen. And I learned today that Obamacare is going to make obese people pay something like fifty percent more for their health insurance, so guess what’s on my agenda now! I really don’t want to ruin my gallbladder, though. I know several people who did that when they lost a lot of weight.

    The chloramine apparently was put into use by many utilities starting in 2010 in response to changes in EPA standards. It doesn’t kill germs as fast as plain chlorine, but it stays in the water pretty much permanently. It won’t gas out. Salt won’t neutralize it. It will kill your fish. It is deadly to use in kidney dialysis. It won’t boil out. If you want to remove it, you have to use at least a two-step process that involves exposing the water a long time to high quality activated charcoal, and then putting it through reverse osmosis (RO). One of the water works people I talked to mentioned that RO water is “aggressive”, in other words, it will eat up your pipes faster.

  7. Hi Chris, I recently began hearing about fecal bacteriotherapy and am very interested. I have something called Polycystic Ovarian Syndrome (PCOS) and in 2009, went off most carbs, dairy and sugar to lose weight and get healthy/relief from the PCOS. I lost 60 lbs in a year, but also ruined my gallbladder and had it removed in 2010. For a while, I maintained my weight, but beginning in 2012, the weight started to creep back on, I’m sick more often (my old habit of recurring sinus infections are back), brain fog is back, poor sleep, etc. And I don’t know what to do to fix it (I still refrain from carbs, dairy and sugar with the exception of sweet potatoes). Am I a candidate for fecal bacteriotherapy? Is there a doctor near Delaware who will perform this for me? I don’t know if I have leaky gut either … so I’m interested in fixing it all!

  8. Chris-
    My husband and I have been on the Primal diet since September. Things have been going great, but about a month ago my husband developed a skin rash that started on his belly and has spread to his chest and back. He has psoriasis, but this is different. They are red, but they do not itch. I am not sure if it has anything to do with the diet, but I was wondering if you have any thoughts about this. Recently, I read in the Personal Paleo Code that taking a Probiotic might cause a skin rash in some people. I think he started taking “Ultimate Flora: Adult Formula” by Renew Life a couple of weeks before he got the skin rash. He also eats fermented foods. In addition, we have been taking Vitamin D, Cod Liver Oil, and Magnesium (as we both got leg cramps in the night).

  9. A couple of links appear to be broken/missing:

    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.

    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.

    Can you provide the references for these two (might be the same reference)?


  10. Hi,

    I have had gut problems for the past year (diarrhea, bloating, cramps etc.), and severe mood swings and depression. I remember that I took a course of antibiotics for acne at the start of last year, could this be the cause? I have seen a few doctors, and they say it’s IBS or stress. I have ordered some “Biokult”, but are there any prebiotics that you would recommend?

  11. Hey Chris, thank you so much for this article. It’s fascinating. I am in the process of presenting an overview of the benefits of my company’s new probiotic, prebiotic and enzyme support product that was just launched at our global training conference last week and your article has given me some great clarification. I would be interested to get your perspective on our new product. I see you recommend the UK brand Biokult. Have you heard of Arbonne? We are a botanically based, Swiss formulated product line that’s vegan, gluten free and absolutely cutting edge. I’d be interested to get your perspective on our new Digestive Plus product. I am learning it’s not what you eat, it’s what your absorb and I think our product would be of benefit to your readers. http://www.arbonne.com. Thanks for all you do and the insight.

  12. A fantastic British probiotic brand is http://www.optibacprobiotics.co.uk – i have tried a few, and these products are all specifically tailored to different health conditions, so the products make you feel fantastic. Whats more their customer service is outstanding! and i think that goes an awfully long way in this day and age.

  13. You mentioned a probitoic brand here before. Which one was it that you recommended? I recall it was an English company.


  14. If that’s the only thing that can help in the short-term, sure. But I’d advise you to consider addressing the underlying mechanism of IBS, which is almost always intestinal dysbiosis and/or a chronic G.I. infection.

  15. Hey Chris,

    I have IBS, and I manage the foods I eat accordingly because I know what bothers me and what does not. The only thing that really triggers an immediate urge for a bowel release is the onset of stress usually in the form of anxiety or panic (which developed because of the IBS). So I take Immodium AD regularly to control this urge. Any problem with taking this aid? It is the only thing that works.

    • Ryan, you said you manage the foods you eat for your IBS. Have you done a completely gluten and dairy free trial, and if so, for how long? My sister-in-law suffered many years with an IBS diagnosis which turned out to be gluten, dairy and a few other foods based on testing, even though she thought she was managing her foods. She also takes certain probiotics and supplements under the guidance of the practitioner who found the problem. I know what you mean about the stress trigger, but like Chris says there are underlying problems.

  16. Kaitlyn,

    First, most people (but not all) with an unhealthy gut will have digestive symptoms of some sort. Skin problems, brain fog, behavioral and mood issues and problems with mineral and vitamin absorption are also signs.

    The best way to find out is get a comprehensive stool test that screens for pathogenic organisms and measures major species of gut flora, intestinal pH, and a number of other factors.


    Yes, I did mean that second link. I’ll fix it – and thanks for the tip.

  17. Hi Chris. How can we definitively find out if we have an unhealthy gut? What’s the first step? Is there a specific doctor we can see or is our best option an elimination diet and our own judgment? I suspect that I do have an unhealthy gut, but knowing for sure would give me greater motivation to strictly abstain from problematic foods. For example, I read on the Perfect Diet that as little as 1 milligram of gluten per day can prevent recovery from bowel disease, so it is essential that grains be eliminated entirely from the diet. I try not to let my dietary changes affect other people too much so I don’t always follow my typical dietary style in some social or family situations. However, I would NOT be lenient anymore if I knew that I had a leaky gut or some other bowel disease.

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