Category: Science


Bears and the Human Microbiome

As many of you know,  I have written extensively over the past several years about the important role of the microbiome. Those 100 trillion organisms that live within the gut, as well as their genetic material, are essential to the body’s regulation and metabolization of food. Notably, this has specific relevance as it relates to obesity.

Previously, I have described how researchers have taken the fecal microbiome from overweight humans, and transplanted it into laboratory mice that specifically lack any gut bacteria (germ-free mice). When germ-free mice are inoculated with the gut bacteria from overweight humans, they begin to gain weight quite dramatically, without any changes to their diet.

Last week, a very fascinating bit of research was published in the journal Cell Reports. The scientists who published the paper studied the gut bacteria of 16 wild brown bears during both the summertime and wintertime hibernation. Understand that when a bear is foraging for food in the summertime it is consuming a fairly high-calorie diet, rich in carbohydrates, which helps the bear store body fat for the long process of hibernation. During hibernation, bears are able to tap into their body stores of fat as an energy source.

What the researchers found, when looking at the microbiomes of these bears, is that there is a dramatic difference in the array of bacteria in the summertime versus the wintertime when the bears enter hibernation. During the summertime, when a bear will as much as double its body fat, there was a high representation of the group of bacteria called firmicutes, while the group bacteriodites was reduced. The opposite was true in the winter time when firmicutes were generally lower and bacteriodites were increased.

Interestingly, these are the same changes in ratios that are observed in humans. We see higher levels of firmicutes being associated with obesity and diabetes, and this is precisely the type of changes seen in these bears when they were experiencing rapid weight gain.

What was even more exciting about this study is that they took groups of germ-free mice and inoculated them with the fecal microbiomes from the summertime bears, as well as from bears during hibernation. Incredibly, the mice who received the fecal transplant from the summertime bears demonstrated dramatic increase in both weight and body fat in comparison to the mice that were inoculated with the microbiomes from hibernating bears.

What this tells us is really quite profound. It indicates that the balance of bacteria within the gut play a huge role in regulating how we deal with the foods we eat, notably in terms of producing fat, or not. It looks like higher levels of firmicutes act in such a way as to make it more likely to signal our body that winter is coming, and that we have to store fat for survival. Diets that are higher in sugar and carbohydrates in general, as well as diets with higher levels of various artificial sweeteners, are associated with a microbiome that is higher in the firmicutes group.

The main point I want to emphasize is that we’ve got to pay very close attention to the health and balance of our got bacteria if we want to maintain healthy body weight.

  • Lynn Dell

    I suppose fasting helps tilt the balance to raising bacteriodetes and lowering firmicutes?

    • SO, how often should we fast? I am 70 years old and take several medications that require being taken with food. I find myself wishing that we could just simplify this whole idea of healthy eating. I have pages of notes, and tons of emails from different sources promoting their recommendations and products. I lost over 64 pounds on the Grain Brain diet, and continue to follow it, for it makes more sense than anything else! What worries me is that we can’t possible know how healthy the food we buy is, even if it is fresh…. unless we grow it ourselves, and even then there is still pollution of air and soil, let alone water. I am so thankful of the hope I have of living in a New System of things after Jehovah cleans up this earth. Linda Penn

      • Lynn Dell

        Congratulations on success with the Grain Brain diet! As you know, the Grain Brain plan includes exercise, fasting, a proper food plan, and sleep. ALL these things must be customized for your specific needs. For example, I can fast for 3 to 4 days, and you cannot.

        There is an art to the personalization and application of Dr. Perlmutter’s general recommendations. If your doctor is agreeable, you could fast after taking your meds with a healthy meal, for 24 hours. Breakfast to breakfast. So just eat one meal a day. OR, if you have to take meds twice a day, try to keep your two meals 6 or so hours apart, and practice caloric restriction with those meals. That would restrict calories and give a 16 to 18 hour fast time. That counts as fasting, especially if the two meals are light on the days you fast.
        There are many ways to customize a fasting plan to your needs. Best wishes to you, and again, congratulations.

  • margobaldwin

    And doesn’t it correlate with burning glucose in the summer vs burning ketones in the winter?

  • Lynn Dell

    This man whacked his microbiome by going high fat/protein and near zero carbs including fiber which feeds the microbiome. As a result, his bacteriodetes greatly increased and his firmicutes dropped. He assumed this was due to a more alkaline gut, which favors bacteriodetes, due to starving out the lactic acid fermentation, the acid producing bacteria not having the fiber: http://humanfoodproject.com/going-feral-one-year-journey-acquire-healthiest-gut-microbiome-world-heard/

    • Lynn Dell

      This suggests several things to me. First, that Dr. Atkins was on to something with the induction phase of his eating plan, which was hi fat/protein and very low carb. Secondly, fasting, by definition reduces gut lactic acid fermentation because no fiber is being consumed. The acid producing bacteria die off, tilting the balance toward bacteriodetes in the gut, as it shifts slightly more alkaline. Thirdly, if the above is true, it kind of creates a conundrum. Perhaps going very high fiber and probiotic supplementation may be best to start a diet with if the microbiome is one that already favors obesity. Perhaps fasting is the best way to kick start a diet, followed by a brief induction phase. Lastly, I wonder if the ratio of F to B is barking up the wrong tree in this discussion, and if the real driver to this is something we are not seeing yet.

  • Ri

    forget all these lifestyle changes just inoculate me with the microbiome of a hibernating bear LOL jk! but wouldn’t that be interesting if that could be the new approach to weight loss down the road

    • David Perlmutter

      The best shortcut to better health is smart choices!

      • ri

        we also need your thoughts about whey protein/whey isolates as an additional protein source in the diet..

      • Dawn

        I can’t help but wonder if there is a way to trigger the growth of gut bacteria that results in weight loss. Could it be fasting? Or is that what triggers the bacteria that results in weight gain, as the bear is basically fasting until he emerges from hibernation. Very interesting study.

      • SaschaBlue

        Speaking of smart choices…after reading Brain Maker (and also Dr. Jason Fung’s The Obesity Epidemic), I finally bit the bullet and went cold turkey, giving up artificial sweeteners (I’d been low carb, no sugar for ages, but would fall off the wagon so wasn’t 100%).

        I’ve been art. sweetener free for almost a month now (and drinking only distilled water, and abstaining even from fruit), and was hoping this would modify my palate in such a way as to allow me to enjoy things such as tea and coffee without added sweetener.

        So far, not happening…at all. I still can’t help but make a face when drinking either…so while I’m not yet giving up, I’m trying to figure out the least damaging sweetener, in case even with continued abstinence, nothing changes in my taste buds.

        Although you recommmended stevia if one insisted on using a.s., my understanding is that recent research suggests that stevia does affect insulin (I think it also suggests stevial also has a negative effect on gut microflora, but I can’t remember for sure– I’ve been researching so much I think I’m getting dizzy).

        I don’t have the cite(s) handy, but the online research I’ve done seems to indicate that erythritol has zero effect on insulin.

        With regard to its effect on the microbiome, I’m not done researching, but I did find some research at


        suggesting that erythritol passes through the body without change and without providing a meal for any gut flora– good guys or bad.

        So, first, if you read this and are able to respond, Dr. Perlmutter, in view of the recent research, would you recommend erythritol over stevia, if one must resort to a.s. ?

        And second, to anyone else in the community:

        I’m no way a science type, so I’m wondering if any of you more knowledgeable and/or science-literate folks could tell me if you know anything about erythritol and its effect on insulin and/or the microbiome, and/or if you could read the abstract I found and comment on whether it means what I think it does (i.e., no measurable effect on microbiota) and the level of signficance/reliability of this research ( Lynn? And Jake, are you still out there? :o) ),

        Thanks in advance for any help y’all can offer.

  • Honora

    One of my favorite cartoons …. First guy says you are what you eat… And the second guy says I should eat a skinny person. May end up being more true than we realize.

  • Cindy Fowler

    Very interesting research. I wonder if there is a relationship between less light and the changing gut flora or cravings for sugar/carbs that tell animals (us included) to eat more? It’s a fascinating field of research. Thanks for sharing this.

  • Are bacteriodites available in probiotics?

    • Jayne Morrison

      My understanding is that it currently cannot be cultured in a lab

  • John Brailsford

    I had a back operation and the drugs I was given killed all the Bacteriodites and as a result I put on over 60 lbs over 2 years. With diet, fasting and low carb high fat diet I finally got rid of the 60 lbs and the Beta blockers etc. So I have the Bacteriodites back and have gone from BMI 32 to 24 but my wife is stuck at BMI 27 although eating a low carb diet. Does anyone have suggestion how to get off the plateau?

    • Jayne Morrison

      I’m assuming that since you understand about Bacteroidetes that she’s eating the high-fiber, prebiotic foods necessary to nourish them. Have you considered that she might have some inflammation going on? There are some excellent books that discuss the relationship between inflammation and weight.

  • Janet

    In addition to grains being hybridized, grains were also ALWAYS soaked prior to consumption. Mother’s Oats used to inform purchasers to SOAK the grains overnight prior to cooking. This – in modern times – has been eliminated from their instructions. Yet, whether or not grains are soaked (and in what medium) can greatly affect our ability to digest and benefit from them. Corn was always soaked in lye prior to being ground into cornmeal. Dr. Weston Price studied civilizations throughout the world and many of them thrived on grains (albeit un-hybridized, but also soaked in whey, etc.). Could it be that if we use ancient grains — and soak them — we could utilize them to our benefit? Any thoughts in this regard ??

  • c gant

    firmicules metabolize cellulose into sugar, that’s why bears and humans gain weight, not because it signals something to the body. Perlmutter is wrong here. So having these bugs means that consumption of lettuce is turned into pure sugar, just like an herbivore.

  • Jack Kennedy

    Blue vein Cheese is not recommended in your book “Grain Brain”. Given the high probiotic load in Blue vein cheese and your increased emphasis on probiotics, has your opinion changed Dr Pearlmutter?

  • Caroline Marden

    Interested to know if you have done any studies involving fungi and the effect of any interaction between bacteria and fungi affecting disease. When you talk about the microbiome, why is bacteria the openly organism concentrated on?

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