A healthy gut is the hidden key to weight loss

October 29, 2010 in Diabesity | 32 comments

https://thehealthyskeptic.org/images/fatmouse.jpgIn a previous article in this series on diabesity 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:

  • Remove all food toxins from your diet
  • Eat plenty of fermentable fibers (starches like sweet potato, yam, yucca, etc.)
  • Take a high-quality probiotic, or consider more radical methods of restoring healthy gut flora
  • Treat any intestinal pathogens (such as parasites) that may be present
  • Take steps to manage your stress


DancinPete October 29, 2010 at 11:16 am

Hi Chris,

How do you deal with the issue that the cure for chronic infections is antibiotics – which is also not good for your gut bacteria. At which point does the cure become worse than the disease its trying to combat?

Chris Kresser October 29, 2010 at 12:05 pm

Excellent question.

The sequence goes like this: first remove, then replace, restore and repair.

It’s important to clear the infection first, because any attempts to repair the gut without doing that will otherwise be ineffective. Once the infection is cleared, the gut flora can be restored with probiotics and prebiotics, or fecal bacteriotherapy.

Mallory October 29, 2010 at 3:48 pm

ahhh i love this article…now, if you could focus the big link between the brain-gut regulation i think you’d have a masterpiece…. a lot of what happens in the gut is a by product of the brain and vise versa…nice to see someone isnt focusing on calories and carbs :)

Heather October 29, 2010 at 3:57 pm

I wonder if the same could be true for being underweight. My husband has a difficult time keeping weight on. I think he has some digestive issues. Recently his GP said that he might have a Candida problem. Could that be connected to his steady weight loss?

Chris Kresser October 29, 2010 at 3:59 pm

Heather: absolutely. I’m amazed to hear a GP diagnose candida. You must have a very progressive GP!

keith basham pa-c October 29, 2010 at 4:06 pm

hello. i was wondering if you could list some more fermentable starches. interesting topics dude. i would like to know some more of restoring gut health for my patients after antibiotic use for long term nsaid use.

Chris Kresser October 29, 2010 at 4:08 pm

The best choices are primarily starchy tubers like sweet potato, yam, yucca (a.k.a. manioc root), taro and lotus. White potatoes are also okay, but peeled since the skin has toxins and anti-nutrients.

Mark October 29, 2010 at 4:11 pm

Chris – Any suggestions for high quality probiotics? And what do you think about prebiotics (e.g. fructooligosaccharides) as a potential supporter of gut health? Thanks!

Chris Kresser October 29, 2010 at 4:14 pm

Unfortunately, most of the highest quality brands aren’t available directly to consumers.

For brands you can buy in the store or online, I think Biokult (http://www.bio-kult.com/) is probably one of the best.

Prebiotics may ultimately be even more important than probiotics in restoring healthy gut flora, but some people don’t tolerate them well. They can cause a lot of gas and bloating, especially if you don’t build up the dose slowly.

Jesse October 29, 2010 at 4:18 pm

Hey Chris,

Since some of the studies you cited found bad effects on gut flora with a high fat diet, would you recommend a low-fat diet as a way to have healthy bacteria?

Mia March 10, 2011 at 10:18 am

Hi Chris,
Love your article. One question, do I take probiotics forever or do we take it for a couple of years then give it a break and start again.

Ethan October 29, 2010 at 4:27 pm

Hi Chris,

Thanks for another excellent post. This is a subject that has fascinated me since it first came to my attention in your podcast interview with Dr. Guyenet. Since then I’ve been reading about the physiological role of fermentable fibers, and have found much scientific support for these ideas.

For example, check out this study, which found that an experimental group supplemented with resistant starch (a fermentable fiber) extracted from kidney beans lost more fat than a control group, even though both were fed a high-carb diet:


Recently I began taking psylium husk supplements (1-2 grams) with each meal, and in the past two weeks I’ve averaged over a half-pound of weight loss per day, even though I’ve continued eating carb-heavy foods such fruit, orange juice, and brown rice and haven’t changed my exercise routine. Your readers might try this for themselves.

Heather October 29, 2010 at 5:23 pm

We do have a progressive GP. Too bad the NHS isn’t as progressive. He’ll have to see a private doctor to see get something done about the problem.

Jesse October 30, 2010 at 11:02 am

Also, Chris, do you agree with everything on those perfecthealthdiet.com links? Because some claims in them were reaallly not science-based, and I know you want to structure your posts according to the best evidence.

mike October 30, 2010 at 11:32 am

Good posts!

What are your thoughts on drinking chemically treated municipal water? Does chlorine etc have an effect on gut flora? Should we be using appropriate filters? Or is this a non issue.


Chris Kresser October 30, 2010 at 11:35 am

I do recommend using a water filter. Chlorinated water can harm the gut flora.

Razwell October 31, 2010 at 12:56 pm

Solid science, Chris. Gut microbiota is strongly linked. Keep on getting the message out there. Let these fraud Internet gurus who push dieting hear you.

Obesity is extremely complex. There are vast unknowns and uncertainties. Real researchers already know this and admit it. My blog discusses a lot of the same thing . Obesity is only simple and certain to the $ 100 billion a year dieting industry which rests precariously on false assumptions and false promises .

Also ,please look into Urgelt from youtube. He says a lot of what you say too. That man is very intelligent and has a lot to say on obesity :) )

Take care,


Hans Keer November 1, 2010 at 2:30 am

Nice HOT new topic. I wonder if the gut flora question can be seen without considering other gut undermining forces like gluten, lectins, saponins and glycoalkaloids. Very best regards, Hans

Chris Kresser November 1, 2010 at 7:54 am


All of the toxins you mentioned play a significant role in dysregulating the gut flora, so yes, they have to be considered.

Tom November 2, 2010 at 3:05 pm

It is more complicated than just replacing the gut flora. I had a colonoscopy earlier this year. I’d already switched to a primal diet a couple of months before the procedure and had my pro- and prebiotics ready for recolonization after the procedure. No real change in my health, still have high blood sugars etc.

Ted Hutchinson November 4, 2010 at 1:15 pm

Where you say
“Take a high-quality probiotic, or consider more radical methods of restoring healthy gut flora” the link leads to Bowel Disease, Part II: Healing the Gut By Eliminating Food Toxins
I wonder if you intended to link to go to Bowel Disease, Part IV: Restoring Healthful Gut Flora

Kaitlyn November 5, 2010 at 9:06 am

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.

Chris Kresser November 5, 2010 at 1:04 pm


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.

Ryan November 9, 2010 at 5:47 pm

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.

Chris Kresser November 9, 2010 at 6:01 pm

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.

lynn November 13, 2010 at 8:47 am

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


Chris Kresser November 13, 2010 at 9:04 am


MAS November 25, 2010 at 2:17 pm

What are your thoughts on kimchi for improving gut flora? – thanks!

Chris Kresser November 26, 2010 at 9:05 am

Kimchi is great for that, but it must be raw. Same with sauerkraut and other fermented vegetables.

James Beattie January 20, 2011 at 8:35 am

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.

Phoebe February 1, 2011 at 1:26 pm

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.

Chris Smith April 26, 2011 at 12:24 pm


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?

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