Category: Science


Healthy Microbiome – Healthy Bones

Osteoporosis and osteopenia (meaning low bone mass) are extremely common problems here in America. The National Osteoporosis Foundation recently released data indicating that approximately 54 million American adults, age 50 or older, are affected by these issues. Shockingly, this figure is expected to increase to approximately 71 million by the year 2030. Bone fractures, including those involving the hip or spine, will increase in lockstep as the bone health of Americans continues to decline.

By and large, the emphasis in mainstream medicine seems to be focused upon the development of new treatments for bone thinning. Just watching the evening news often provides information about one or more osteoporosis products that may enhance bone density.

In truth, the medicines offered up for folks with thinning bones are often only minimally effective and can be accompanied by unwanted side effects. But this is an area where preventive medicine really shines. It’s quite clear that there is a significant increased risk of bone thinning in smokers as well as individuals consuming excess alcohol. Exercise, specifically weight bearing exercise, has long been a recommendation of healthcare providers, and with good reason. Exercise has been shown to prove very effective in reducing risk for osteoporosis and even helping to improve bone density. Even taking regular long walks has been associated with improvement in bone density. Dietary calcium plays an important role in maintaining healthy bones as does having adequate amounts of vitamin D and K2.

But what I find even more intriguing is new research that relates to the regulation of bone health. In a new report just published in the journal Current Osteoporosis Reports, researchers at Michigan State University revealed a profound relationship between the health of the gut microbiome and bone metabolism. Their report demonstrates how alterations in gut microbes leads to increased inflammation, as well as enhanced gut permeability or leakiness. They described how consuming both prebiotics and probiotics enhances gut microbe health and paves the way for stabilization of inflammation and improved barrier integrity through favorable changes in the microbiome, and how this affects various metabolites made by our gut bacteria. They then showed how these metabolites go on to affect how are bodies maintain bone density.

One of the ways that prebiotic fiber is thought to enhance bone density is through increased production of what are called short chain fatty acids (SCFAs). When our probiotic bacteria use prebiotic fiber as a fuel source, they increase their production of these SCFAs. The SCFAs then increase the ability of gut lining to absorb calcium. In addition, short chain fatty acids are thought to lower the pH of the intestine, which makes calcium more soluble, and therefore more easily absorbed.

The researchers then go on to describe how using specific species of probiotics in animal models that basically do not have a microbiome, increases calcification of bone.

The authors conclude their report by stating:

There are many studies supporting a role for the gut and its microbiome in the regulation of bone density and health…We envision that modulation of the intestine-microbiome interaction to improve bone health will play an important role in human health and allow physicians to reduce the dependence on current pharmacological interventions for osteoporosis (which can have unwanted side effects).

How interesting it is that again we are seeing a direct relationship between inflammation as a consequence of disturbed balance of the microbes living in the gut, and yet another disease entity, in this case bone thinning. The net that is thrown is certainly wide in terms of what happens when the microbiome is disturbed. Nonetheless, let’s look at this glass as being half full as it looks like researchers like these are providing incredible that new insights into some of our most challenging disease processes by exploring the new frontier that is the microbiome.

  • Beenthere

    I’m one that stumbled (no pun intended!) into this. I’ve been taking pre- and pro-biotics for many years. I’d also been taking calcium, glucosomine, K2 and D3 in addition to other supplements. Then, for various reasons (mainly because I gag on the tablets) I stopped taking calcium, K2 and glucosomine four years ago. I also stopped eating wheat because of general overall achiness in my muscles and joints, which cleared up by eliminating wheat. Last year I learned that my bone density is very strong, with no indication of osteopenia, let alone osteoporosis. (BTW, I’m 72, female, with a previous history of osteopenia.) I started looking into this and found that research in Japan and Germany has shown a correlation between diets high in dairy and wheat consumption (populations of Northern Europe, US, and Canada) and incidence of osteoporosis vs diets low in dairy and wheat consumption (populations of East Asia) where incidence of osteoporosis is much lower.

  • ri

    Dr Perlmutter I received a notification yesterday from Empowering Neurologist on Youtube that there was a new video in which you discussed depression it was about 40 minutes and now I cant find it. Where did it go? did you remove it?

  • Lynn Dell

    I bet it’s the vitamin k2 in fermented foods that does so much good here.

    • It is more: Vitamin K2 together with sufficient Vitamin D, Magnesium and Boron (not mentioned in the article) are required for optimal absorption of Calcium in the bones. Each of these molecules help but the combination is powerful.

  • Dr. Duc Viet Nguyen, Ph.D.

    Per my own research on Health to be self-career, I have applied what you have shared to public users and followed up with Medical Doctors who I can trust.

  • Mary Lyles

    For years, our family have used a lot of bone in soups and vegetables, even in Italian spaghetti sauce to add flavor. Primarily they used pork bone, which actually has little meat but lots of flavor. It naturally sweetened our foods both because of the fat and now I believe the marrow itself. How good is bone marrow for overall health and in particular bone health?

  • maria

    A very welcome piece of information, Dr. Perlmutter. I have problems with bone-density due to having had undiagnosed celiac for many years. Could you please comment on these two issues in regard to bone density.
    1. Strontium. I added strontium to my supplements and was able to increase my bone density a couple of percent. (I also lift weights, and take Mg, D3 and K2) But now my bone doctor tells me to discontinue the strontium as taking strontium is related to strokes. Do you think this is true? On the internet I only see pharmaceuticals containing strontium to be linked to strokes. Would taking strontium on its own be dangerous?
    2. Do you think that a vibrating platform called “Power Plate” would positively impact bones? I have read that Power Plate is helpful for increasing bone density and wanted to get your opinion.
    Thank you.

    • Hi Maria, after years of Calcium depletion, my functional medicine doctor prescribed Calcium, Magnesium, Vitamin D3, Vitamin K2 and Boron. Boron also builds bones but does not have the toxicity issues that Strontium has.

  • Miranda Paymer

    Loss of bone density due to excess alcohol makes much sense since alcohol is essentially sugar and sugar feeds the wrong microbes.

  • Sue Stantejsky

    There is also evidence that ingestion of fluoridated water leads to brittle bones and we’ll as interfering with calcium absorption. Since we live in the most highly calcium-supplemented country, yet our bones are thinning and breaking, calcium and pharmaceuticals are NOT the answer. The toxic soup that is our drinking water, as well as the preponderance of processed food and glyphosate in our diets are what ails us. Filter your water and eat organic whole foods. And follow Dr Perlmutter’s awesome advice!

    • donny

      Hello Sue I have problems with my bones , and i am very interested in the effects of fluoride and chlorine in our water. Can you send me a link for more info. Thanks !

      • Sue Stantejsky

        I’m so sorry to hear that you’re having trouble with your bones. I have been researching the effects of fluoride in our drinking water, and have discovered a lot of creditable scientific information about its ability to cause bone and joint pain. Most doctors are unaware of the damaging affects of water fluoridation. Here are a few links:






        The fluoridealert.org website is a great resource for fluoride information. They collect creditable research papers from all over the world, and provide links to any paper that they quote. I am a biostatistician, so I can vouch for the quality of the studies that they refer to. On the website, you can search for any topic (such as arthritis), and you will find many, many articles that explains the latest research.

        Wishing the best for you, Sue

        • donny

          Thank You Sue for those articles. I am certainly more aware of the dangers of Fluoride in our drinking water. I was at an organic food conference yesterday and there were many speakers talking about the toxic effects of Fluoride. They are petitioning the county to stop adding Fluoride to our water. This will probably take years to succeed, but in the meantime what filters do you believe are the best to remove the Fluoride in my faucet ?

          • Sue Stantejsky

            There are only a few filters that can get fluoride out of the water. The common filters like Brita do NOT remove it. My understanding is distilled water removes the most at 99.9%. However, if you buy distilled water, it comes in cheap plastic bottles that contain BPA, a known carcinogen. Reverse Osmosis filters also work, and can be put under your kitchen sink or even a “whole house filter” where the water enters your house. Affordability is an issue. I buy reverse osmosis-filtered water from Natural Grocers for 25 cents/gallon. I purchased a few 3-gallon BPA-free water bottles, and refill them every week. Our local Kroger store also has a machine, but charges 75 cents/gallon. On the internet, you can also buy a water distiller machine. Drinking filtered or distilled water will reduce the amount of fluoride that you ingest, but be aware that we all still bathe in it, and the skin absorbs things. I put a cheap ($15?) filter on my shower from Home Depot so at least most of the chlorine is filtered out. I also switched to a mostly organic whole food diet, no processed food, very low sugar and salt. Between the water “purification” chemicals and fluoride that is added to our “clean” drinking water AND the Roundup (glyphosate) and other chemical herbicides and pesticides that is sprayed on our food, it is no wonder that chronic conditions are occurring with such regularity in everyone we know. Personally, when I quit eating grains (grown in soil which has been sprayed with Roundup, and then the mature grains are sprayed with it as a desiccant), the inflammation in my hands and joints totally disappeared. I sure hope that you can find out what’s causing your problems and eliminate the cause. Here’s a link about water filters:

          • Sue Stantejsky

            Donny, I just saw this posting. It contains excerpts from a National Research Council publication in 2006 about brittle bones and water fluoridation:

            2006 US National Research Council report Fluoride in Drinking Water: A Scientific Review of EPA’s Standards

            p 5/6 “Fracture risk and bone strength have been studied in animal models. The weight of evidence indicates that, although fluoride might increase bone volume, there is less strength per unit volume… Biochemical and physiological data indicate a biologically plausible mechanism by which fluoride could weaken bone. In this case, the physiological effect of fluoride on bone quality and risk of fracture observed in animal studies is consistent with the human evidence.”

            p 108/9 “the general conclusion is that, although there may be an increase in skeletal density, there is no consistent increase in bone strength [in humans]. A carefully performed comparison study between the effects of fluoride (2mg/kg/day) and alendronate in minipigs likely points to the true effect: ‘in bone with higher volume, there was less strength per unit volume, that is, …there was a deterioration in bone quality'”

            p 113 “fluoride did not prove to be an effective treatment [for osteoporosis]”

            It’s kind of hard for me to believe, but the medical community thinks that because fluoride gets taken up by your bones, that it was tested as a medicine to help with osteoporosis. But this was published back in 2012:

            “Due to its ability to increase bone mass, fluoride has been used as an experimental treatment for osteoporosis. The results, however, have generally been disastrous. Rather than prevent bone fractures in osteoporosis patients, fluoride therapy (at doses of 20-34 mg/day) was repeatedly found to increase fracture rates. One of the most common sites for fluoride-induced fracture has been the hip, specifically the femoral neck. Several clinical trials found that fluoride treatment caused the hip to “spontaneously” fracture — meaning the hip fractured in the absence of any physical trauma. Fluoride’s ability to cause spontaneous hip fracture is likely the result of fluoride-induced stress fractures, which have also been well documented in the clinical trials.

            Besides bone fracture, other reported side effects of fluoride treatment included gastrointestinal disorders, ‘lower-extremity pain syndrome’ (which, in some cases, may be the result of stress fractures), and osteomalacia. Based on this track record, the Food & Drug Administration has rejected fluoride therapy as an approved way of treating osteoporosis.”

            Fluoride is proven to be bad for your bones and joints.

  • Elene

    I am astonished that you didn’t recommend or even mention magnesium!

  • Luc Chene

    Thank you for this. I have a question. Is there a relation between bone density and fracture risk for one same person, that is are there studies showing a positive correlation between bone density and fracture risk? Some studies suggest that bone density is not a reliable predictor fracture risk as such in the population at large.

  • Jacqueline Collins

    my doctor wants to put me on prolia biphosphate medication for osteoporosis but I have read that it can cause gut problems ? what is the best plan for osteoporosis ? I am excercising weights & walking ,what natural supliments work the best?

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