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The Microbiota and Bone Health: Yet Another Reason to Protect Your Gut


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Could there be a gut–bone axis? Researchers are constantly finding new connections between the microbes that inhabit our bodies and our health, and emerging science suggests that bone disease might begin in the gut. Read on to learn how your gut microbes shape your immune system, influence nutrient status, and maintain skeletal health.

bone health
The connection between the gut microbes and the skeletal system is significant. istock.com/Wavebreakmedia

The trillions of bacteria that inhabit our gastrointestinal tract play an intricate and increasingly appreciated role in human health. Deemed by some as the “forgotten organ” (1), new connections between these microorganisms and our physiology are being discovered all the time.

In recent months, I’ve written extensively about these connections. Check out my other blog articles to learn more about the influence of the gut microbiome on your health:

Next up in the series, and yet another reason to protect your gut microbes: bone health! Before we dive in, let’s review a few fundamentals of bone physiology and how we determine bone health.

Bone Health: The Basics

Bone is not a static structure and is constantly being remodeled. Mature bone tissue is regularly removed from the skeleton by cells called osteoclasts (a process called resorption), and new bone tissue is formed by cells called osteoblasts (a process called ossification). Remodeling helps to reshape bone following fractures and also responds to mechanical loads like exercise (2). An imbalance in bone resorption and formation can result in bone diseases like osteoporosis and arthritis (3).

There are numerous measures of bone health. In humans, researchers often use a DEXA scan to determine bone mineral density. In rodent models, scientists can also measure bone mass, length, volume, and mineral composition to get a more complete assessment of bone structure. In general, higher bone mineral density is associated with reduced risk of fracture and bone disease. However, increased bone mineral density, bone mass, and bone length do not always suggest better bone health (4).

Three ways your gut microbes can support healthy bones.

The Association between Gut Microbes and Bone

One of the key ways that researchers study the effects of the microbiota on an organ system is using mice that don’t have one at all. Called “germ-free” (GF), these mice are born and raised in sterile incubators. Studies of skeletal health in GF mice have found mixed results. In one type of mice, GF mice had reduced bone mass compared with conventionally raised animals, which have a full consortium of microbes (5). In another type of mouse, the GF environment resulted in increased bone mass, while the conventional environment increased measures of bone turnover (6). Although it is difficult to reconcile these contradictory findings, the key feature of both studies was that the mere presence or absence of a microbiota significantly changed the structure of the bone.

Antibiotic models provide further evidence for an association between gut microbes and bone, and the results are much more translational to humans. One study found that exposing mice to subtherapeutic doses of antibiotics at weaning resulted in a significant increase in bone mineral density after three weeks (7). Another study found that animals treated with tylosin, amoxicillin, or a mixture of both had larger bones and a higher bone mineral content than control mice (8). Low-dose antibiotics have long been used in the agricultural industry in animal feed for this very reason; they influence skeletal growth and make for larger, more profitable livestock.

Bone Disease Is Partly Heritable and Associated with GI Disorders

All that nitty-gritty science in animal models is great, but what about humans? Is there evidence of a gut–bone connection in humans? Epidemiological evidence and observational studies suggest that there is.

In adult humans, bone mineral density is 50 to 80 percent heritable (9). For quite some time, heritable traits were thought to be only passed on from parent to offspring through DNA. We now know that vertical transmission of microbes occurs at birth—as a baby passes through the mother’s birth canal, he or she acquires crucial microbes that shape the composition of their gut microbiota (5). It’s possible that in addition to the heritable traits encoded by our own genetics, additional determinants of our bone health are acquired based on our microbial inheritance.

Bone complications are often seen in individuals with GI disorders. Patients with inflammatory bowel disease (IBD) have an increased risk of osteopenia, osteoporosis, and bone fracture. This has been attributed to malabsorption of calcium, reduced blood levels of vitamin D and K, or bone loss after glucocorticoid treatment (10). Gut and systemic inflammation are also associated with increased production of cytokines that are key contributors to bone loss (11). We’ll discuss this in detail in the next two sections.

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Leaky Gut and Bone Health

If you’re an avid reader of my blog, you might be thinking: leaky gut, again? Yep. When the intestinal barrier becomes compromised, microbes or parts of microbes can translocate from the gut lumen to the bloodstream. Your immune system recognizes these bacterial components in the bloodstream and launches a systemic immune response. Indeed, studies have found a strong association between microbial translocation and joint pathologies like rheumatoid arthritis (12, 13).

The most common of the bacterial components include peptidoglycan, lipopolysaccharide, and flagellin. These stimulate various “toll-like” receptors (TLRs) on innate immune cells: peptidoglycan is the primary component of bacterial cell walls and stimulates TLR2; lipopolysaccharide is located in the outer membrane of gram-negative bacteria and stimulates TLR4; and flagellin is the main protein that makes up the filamentous “tail” of bacteria and stimulates TLR5 (14, 15, 16).

Stimulation of innate immune receptors has effects throughout the body, which is why a leaky gut can manifest as a number of different chronic health conditions. In regard to bone health, stimulation of innate immune cells has a direct effect on bone remodeling.

Microbes Shape the Systemic and Mucosal Immune System to Influence Bone Remodeling

The microbiota plays a key role in the initial development of the immune system as a child and the maintenance of proper immune responses later in life. This represents yet another pathway by which microbes are connected to bone health, as the immune system is intricately involved in the regulation of bone metabolism and physiology.

Immune cells that are activated by microbes in the gut can migrate to bone and directly regulate bone remodeling via osteoclast-inducing factor, RANKL, and other bone-active molecules (17). Increased levels of activated innate immune cells have been shown to increase expression of the signaling molecule TNFα in bone marrow. TNFα stimulates stems cells in the bone marrow to differentiate into osteoclasts. This tips the normal balance of bone resorption and formation, resulting in higher levels of bone breakdown and lower bone density (18, 19)

Gut Microbes Regulate the Availability of Nutrients Important for Bone Health

Healthy bones require a multitude of nutrients, including calcium, phosphorus, vitamin D, vitamin K2, vitamin A, and magnesium. Recent research has also suggested a role of several B vitamins and even vitamins C and E in bone health (20). Animals raised on a nutrient-depleted diet have reduced bone length (21).

Disruption of the microbiota can significantly alter nutrient absorption. Gut dysbiosis has been shown to increase the number of calories absorbed from food (22, 23). Yet it can also result in inflammation of the gut epithelium, the location of nutrient transporters that allow for the absorption of vitamins and minerals. This paradoxically results in individuals that are both overweight and malnourished (24).

In addition to influencing absorption and metabolism, microbes themselves also synthesize some of our vitamins. These include thiamin (B1), niacin (B3), pantothenic acid (B5), biotin (B7), folate, tetrahydrofolate, pyridoxal phosphate, and vitamin K2 (25, 26).

Protect Your Microbes to Support Healthy Bones

While there are certainly many factors that influence bone health, including genetics, diet, mechanical loading, and other environmental factors, gut health seems to play a crucial role. Below I have compiled a list of ways to support a healthy gut flora and how each might improve bone health.

  • Probiotics. Eat your fermented foods! Adult male mice treated with Lactobacilli for four weeks showed increased femoral bone volume, increased bone formation, and a reduction in circulating pro-inflammatory cytokine expression (27). Lactobacilli were also shown to prevent bone loss in a model of type 1 diabetes (28). You can find Lactobacilli in sauerkraut, kimchi, and other fermented vegetables.
  • Prebiotics. Prebiotic fibers in dandelion greens, plantains, and other foods promote the growth of beneficial bacteria. Prebiotics have been shown to have a beneficial role in mineral metabolism, enhancing calcium absorption in both rodents and humans (29, 30). This enhanced absorption translates to increased bone density (31). While different fibers have different effects, a study testing eight different prebiotic fibers in young rats showed that most prebiotic fibers had significant effects on bone density measures (32).
  • Bone broth. Bone broth supports a healthy gut lining and a healthy microbial community.  Homemade broth also provides all of the necessary vitamins and minerals for building bone, as well as the proteins collagen and glucosamine for healthy joints and cartilage.
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Join the conversation

  1. Lately I have had a flare up in pain from what I think is arthritis. The usual pain in hands and neck seems to be mild compared to the pain in my right elbow. Because my gut has been pain free for quite a while, I began testing my gut health with a variety of foods that I have avoided in the past. However I have put on weight around the middle and feel bloated – way too much.
    So now I think I need to get strict again with my diet. I take 150 mg Risedronate per month for osteoporosis.
    Magnesium, D3, Q10, and try to eat foods with your recommended nutrients. My blood work shows all normal and no deficiencies.

  2. Have been diagnosed with osteoporosis with minimal fractures was interesting to read about the gut connection mine has been playing up since I did the fracture have been researching the natural way to go as what the treatments doctors want to put you on is rather horrific have increased vitamin supplements androids rich in the vitamins needed and trying to go more the paleo way I have always eaten healthy just have to rethink a few things do physical work and want to be able to keep doing so was great to read about vitamin K2

  3. Please help? I was diagnosed with osteopenia in my hip about 4 years ago, and since then my doctor has said my bones are looking pretty thin. I’ve been dairy free for 3 years now, and have tried hard to increase my calcium intake in other ways. My problem is, I can’t eat sauerkraut or even drink the juice because it causes a histamine reaction after a day or so, so apart from coconut yoghurt which I have now and then, I don’t get any probiotics via food sources. Should I just buy a good daily supplement? I’m loathe to take anything that will upset my gut equilibrium tho.

    • From what I understand, leafy greens in their uncultured state are a better bet for calcium than dairy and the folk in our gut like them too.

      • Well that’s good news, thank you, AND much easier. I eat kale and silver beet very regularly.

  4. I am so glad you mentioned the gut and absorption of nutrients beyond calcium and vitamin D for bone health, such as vitamins E, C, K and A. Too much focus is on calcium and not enough on other nutrients and their proper absorption, or the importance of weight bearing exercise for healthy bones. Also, new studies are shedding light on importance of balance of nutrients best done with eating whole foods with a good functioning GI tract to absorb them.

    Personally, I like eating tons of cooked greens, and sometimes a little broccoli high in vitamin C, and sauerkraut at breakfast to get my bone nutrients; love my bok choy, lucinato kale and collards with a bit of balsamic vinegar.

    I recently read a surprising article, at least for me, about the toxic effects of excess vitamin A on bone health. It described how studies showing increased fracture risk of vitamin A, which could be related to known effects of vitamin A in bone breakdown and suppression of cells for bone formation.

    This may be part of mystery of the calcium paradox: Why countries, like America, on a Western diet, have the most calcium intake, but highest rate of osteoporosis. Maybe part of it is our high intake of vitamin A, from fortified foods like dairy, supplements, and having one of highest intake of animal foods high in vitamin A vs. carotenoids, which did not show increased fracture risk, even with increased consumption. The article did warn of high supplement doses, eating liver and dangers of cod liver oil.

    Link: http://www.webmd.com/osteoporosis/news/20030122/vitamin-bone-poison

    • From what I understand, the high osteoporosis rates related to dairy consumption in countries like the US is because the ratio of calcium to other minerals in the dairy is inappropriate for humans and creates a calcium loss instead of gain. Calclium needs other minerals to be properly metabolized. Absorption is thereby impaired and less calcium is available for the bones.

      • A report out today suggests all calcium should come from food and not supplements. Too much could lead to calcified arteries, heart etc. Yet another thought re the balance of minerals etc overall.

        • I agree but plant sources I feel are best especially greens, seeds, sea veggies and herbs with all the critical synergistic supporting properly balanced minerals.

      • For me it’s not only about eating nutrients, but also absorbing them, and a chronically inflamed gut is not going to do his job properly.
        Western guts are very inflamed.
        Proibflammatory + lack of nutrients= perfect storm

  5. Another thought provoking post. I think that the idea that so many systems of the body work in isolation has had it’s time, although it seems that many in the medical world continue to treat people as if that was exactly the case.

    It seems so obvious that the health of the gut would influence so many other aspects of our bodies, if not all of them. The oft talked about example is bacterias and proteins crossing the blood gut barrier and stirring up autoimmune responses that lead to joint pain and tissue damage around the joints.

    I’m a massive fan of fermented dairy, sauerkraut, kimchi and bone broth too. Fingers crossed, it’s had a really positive effect on my joints as I push into my late 40’s.

    Great article Chris, always exploring the cutting edge stuff and explaining it in a really understandable way.

  6. I very much doubt that paleolithic man had time to contemplate bone health – or boron. Simply being the softest easiest being to eat they were just hunted until they found somewhere good to hide. But here we are – we survived and our ancestors gave us traits and identities.

    Knowing now that we are simply a tube of bacteria from front to back – with inherited bacteria forming 90% of us makes it important to listen to a possible remedy for modern degenerative diseases. They will carry you away early if you do not pay attention to the advice – so hard won and so critically essential to our health and longetivity. Beware the consequences of slow realisation of what this is all about.

  7. Great article, My bone health got better tremendously after i implemented a natural living healthy lifestyle. furthermore, sea moss and wild mushrooms help. My doctor was astonished after he last warn me about my bone health.

  8. I totally agree that the gut is the foundation of good or bad health depending on how well you take care of it.Great information! Thank you for the timely reminders. It is essential during flu and cold season to build a strong immune system through a healthy gut.

  9. Thanks for the great information again. Yet another great source that can link inflammation, and the HPA axis, with catabolic processes. Your articles are really helping me get a better and more well rounded grasp on physiology that we do not learn in school. Great information.

  10. Great article. Reminded me of Weston Price’s classic on Nutrition & Physical Degeneration (bones, teeth, skulls etc malformed due to modern diet deficits, which maybe stretches also to gut issues).

    I had Osgood Schlatters (knee) problem at 12, deranged teeth at 13, back scoliosis at 16. Wasn’t aware of gut problems until age 18. Some 40 years later, if I stupidly strip my gut lining & kill the microbiome by bingeing on alcohol, about 2 days later it shows up in painful joints and bones.
    So I’m a believer. Gut-bone axis seems to be part of the leaky gut & auto-immune collection. But you’ve added more to the story, thank you

  11. I have two family members with extreme bone loss and severe constipation. In both cases they would rather take excessive amounts of drugs (including pain medication), have multiple surgeries, take drastic measures just to go to the bathroom than to make changes to their diet. I realize that diet won’t magically make everything better but it could certainly help improve their situations. It’s extremely frustrating to watch but i won’t even bring it up to them again. This article is very helpful!

  12. I was diagnosed with osteoporosis when I was 28. It took some time for me to convince my endocrinologist that it was due to my gut issues.., this was a no brainer for me. I have struggled for years with parasitic infection, sibo, severe gerd and hence chronic inflammation And malabsorption. Not an easy thing to deal and not. Something that people with chronic intestinal issues usually think about.

  13. I have osteoporosis which I think was influenced by taking ppi medication for 4 years. I have managed to get off that with difficulty and I have refused medication for the osteoporosis. I make kefir & sauerkraut, take various vitamins & minerals including K2 & vit D. Also specific exercise is needed to maintain & increase bone mass. My mother had osteoporosis so according to your article I am highly predisposed to having it myself anyway.

    • I’m very glad to read this because I’ve been beating this drum for a while. Almost everything is connected to gut health.
      I’ve been suspecting for a long that bone health is related to inflammation.
      The calcium issue is a silly oversimplification, as usual, of a complex reality made of many variables working in concert.
      Aside from nutrient density from food, inflamed gut plays a crucial role in their absorbion. What I’ve seen during the years is the silly take on this issue. Clinicians tend to push hard with drugs and supplements.
      Instead of giving tons of supplements, we should focus on the absorbion.
      It’s like refilling a tank with a big hole on its side.
      It’s far better to close the hole.
      This is in my opinion another key factor that plays together with nutrient density.
      It makes perfectly sense from an evolutionary and scientific standpoint given the evidence we collected so far.
      I’m not a great fan of the acid/base hypotesis either, it’s too simplistic, it has many shortcomings shown in some studies, and doesn’t take into account antropological evidence of acid forming healthy diet from hunter gatherers (Inuit, Ache, etc)

        • Sorry, can you provide the font?
          Anyway, Inuit are not the only population with a net acid forming diet, Ache from Paraguay derive more than 70% from animal food and reading Kaplan studies, who is the most knowledgeable about them, I haven’t read about ostheoporosis.
          Btw Inuit are still an extreme case since they also lack of sun exposure.

  14. I believe that excessive Oxalate levels can be a significant contributor to bone loss (oxalates bind to minerals that are need to build and maintain bone). Oxalates can come from the diet &/or be produces endogenously.

    It seems that leaky gut and lack of oxalate-consuming bacteria like Oxalobacter Formigenes (and other) contributes to elevated oxalates (likely more related to dietary sources of oxalate). Dietary fat may be somewhat problamitic re: the absorption of dietary oxalates (unfortunately).

    It seems like Oxidative Stress is involved in the endogenous production of Oxalate.

    • I would like more explanation of oxidative stress and oxylates relating to bone loss please, it sounds very interesting.

      • Jan. Do you mean oxyliates and bone loss? I think oxyliates may not be so good.

        Too many in diet can cause other problems in some people. One British gp thought they could cause her fibromyalgia. She did a low oxyliates diet and felt massively better. She felt fogged before.

        I’m worse than 3.5 on decades scan in spine. Arthritis in feet as well. No bisphosphonates and no massive calcium doses either.

        Just a few thoughts to a very complex thing

        • Fibromyalgia is caused by the herpes virus staying active in the nerves. Daily over the counter l-lysine stops it, and the pain. Once it stops the immune system can calm down. I know because I have been healed from fibromyalgia.

  15. Thank you for the information about good things to eat for bone health. I appreciate articles about what is necessary for bone health – I mean all that is required – such as a comment or two about what causes depletion of bone. I always appreciate hearing about diet in populations of women who have no bone loss after menopause. There are a lot of us baby boomers out here looking for answers – who may not be eating many fat soluble vitamins due to our early learning about fat being the enemy. In addition to dexa scan, some of your readers may need to know there is a blood test – a bone panel to check for physiological problems in osteoporosis.

  16. I want to tell you that even though I had been eating plenty of fermented foods, prebiotic fiber, and bone broth (and I made the sauerkraut and bone broth), I continued to have bone loss year after year. And then I had to discontinue the ferments and bone broth due to histamine reactions and food allergies. At the same time, I also got plenty of exercise, vitamin D was good, and took magnesium.
    More recently I have added taking strontium in an attempt to rectify what is now osteoporosis.
    My point is that ferments and long-simmered bone broth can have some unwanted side-effects and don’t work for everyone.

    • I’ve been reading about the benefits of the mineral boron and it’s role in Arthritis specifically.

      I’d be very interested to hear what Chris thought about this mineral as he’s a FAR more thorough researcher than me!

      I’ve not dug too deeply but pharma seem to have been complicit in smearing borax/boron precisely because, in our depleted soils a boron deficiency is common and could be at the heart of many health conditions (people online are encouraging us to believe). There’s lots to read out there (some more worth reading than others) but it’s fascinating stuff.

      I have ms so am quite happy with the notion that pharma don’t have their customers’ best interests at heart.

  17. My gut and my bones thank you. I’m trying to build bone after recent osteoporosis diagnosis. T score – 2.6 Already taking the probiotic you recommend once a day. Given the importance of the gut in bone health do you think I should increase the amount?