In recent years, researchers have been studying the microorganisms living in your intestinal tract to determine their role in health and longevity. There are at least 1000 different species of microorganisms and trillions of bacteria, fungi, viruses and other microorganisms that make up what we call the gut microbiota. Not only does the gut microbiota play an important role in digestion, the production of some vitamins, and the immune system, it may also affect bone metabolism. A new field of scientific study called “osteomicrobiology” investigates how the gut microbiota can regulate skeletal development as well as bone loss that occurs with aging.

In a healthy gut, trillions of microbes protects us from invading pathogens, regulate intestinal immune responses, produce vitamins and aid in mineral absorption.

Microbiota influence bone health in several ways:

  • Gut bacterial population plays an important role in the synthesis of some key bone building nutrients, such as the B vitamins and vitamin K, in particular vitamin K2. The synthesis of these vitamins by the gut microbes contribute to our nutritional requirements of these vitamins.
  • It is also thought that the gut microbiota influence bone mass through its effect on the immune system. Immune cells that are activated by microbes in the gut can migrate to bone and directly regulate bone remodeling by stimulating the production of osteoclasts, the cells that break down bone, and inhibiting the activity of osteoblasts, bone building cells. (1)
  • Changes in the microbiota can also affect gut permeability. A rich microbiota diversity creates a strong intestinal barrier that prevents unwanted substances from passing through the intestines into the rest of the body where it can elicit a systemic inflammatory reaction. Systemic inflammation can also cause the increased production of osteoclasts and therefore can negatively influence bone density.
  • A healthy gut microbiota can also improve bone health by increasing calcium absorption and retention and through modulating the production of gut serotonin, a hormone that interacts with bone cells and has been suggested to act as a bone mass regulator. (2) The gastrointestinal (GI) tract contains much of the body’s serotonin and the microbiota plays a critical role in regulating its production.

What influences the composition of the gut microbiota?

Many factors such as genetics, environment, toxin exposure, age, medications and diet play a role when it comes to shaping the gut microbiota.

Diet is a major factor in the composition of the gut microbiota
A recent study showed that a diet devoid of one single micronutrient can disrupted the gut microbiota composition.(3) Additionally, a lack of micronutrients also results in the disruption of numerous functions required for the gut environment and the intestinal immune system, indicating that these nutrients are essential for the development of healthy gut microbiota. We also know that diets low in fiber and high in fat and refined carbohydrates have shown to affect gut bacteria and limit microbial diversity.(4)  It is thought that the more diversity in your gut bacteria, the better off your health will be!

How can we get the bugs in our gut to flourish?

Prebiotics: these are specialized plant fibers that can nourish the good bacteria already in your gut. Fermentation of fibers leads to increased production of short-chain fatty acids. These changes have been positively correlated with increased calcium absorption and increased bone density and strength in animal models. Dietary fibers may offer an additional means to enhance calcium absorption with the possibility of stimulating the gut microbiome to ultimately influence bone health. Prebiotics are found in many vegetables such as onions, garlic, leeks, asparagus, artichokes, chicory root, dandelion greens and fruit like tomatoes, apples, bananas and plums. Beans, high fiber wheat bran and nuts like almonds also contain prebiotics. The fibers in prebiotic foods support the gut microbiome which may influence bone health (5)

Probiotics: living micro-organisms that may restore the composition of the gut microbiome. Foods such as organic yogurt or Kefir are a great source of probiotics or fermented foods such as Kimchi (a Korean dish), sauerkraut, or products made from fermented soybeans such as miso, tempeh or Natto. Kombucha, fermented black tea, is also a potent source of probiotics. Taking supplemental probiotics can also help balance the gut microbiota when it has been affected by poor diet, infections, antibiotics or stress. A recent study showed that a 6 month course of probiotics slowed down the rate of bone loss in postmenopausal women. (6)

Learn how you can test your gut microbiota!


Your diet determines the composition of your microflora


The microbes hanging out in our intestines influence many aspects of our health, including weight, immunity and perhaps even our bone health! When our bacteria are in balance, there is a symbiotic relationship between ourselves and the microbes that helps in food digestion, nutrient production and absorption, and protects us from invading pathogens. However, when our microbiota get disrupted and there becomes an imbalance in our microflora, also called dysbiosis, we can experience numerous effects and illnesses, including altered bone metabolism. Dietary changes, medication, stress or pathogens can shift the composition of the gut microbiota and cause an immune response or systemic inflammation that can negatively impact the health of your bones.

Want to find out about your gut microbiota? I can help with that! Contact me to learn about gastrointestinal testing to determine the health of your gut and how to optimize your gut health to build strong and healthy bones!


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1. Charles, J. F., Ermann, J., & Aliprantis, A. O. (2015). The intestinal microbiome and skeletal fitness: Connecting bugs and bones. Clinical Immunology,159(2), 163-169. doi:10.1016/j.clim.2015.03.019
2. D’Amelio, P., & Sassi, F. (2017, September 30). Gut Microbiota, Immune System, and Bone. Retrieved November 20, 2017, from
3, Hibberd MC,  Wu M,  Rodionov DA et al. (2017)The effects of micronutrient deficiencies on bacterial species from the human gutmicrobiota. Science Translational Medicine,  390(2)
4. Daniel, H., Gholami, A. M., Berry, D., Desmarchelier, C., & Hahne, H. (2013). High-fat diet alters gut microbiota physiology in mice. The ISME Journal,8(2), 295-308. doi:10.1038/ismej.2013.155
5. Weaver, C. M. (2015). Diet, Gut Microbiome, and Bone Health. Current Osteoporosis Reports,13(2), 125-130. doi:10.1007/s11914-015-0257-0
6. Effects of a Multispecies Probiotic Supplement on Bone Health in Osteopenic Postmenopausal Women: A Randomized, Double-blind, Controlled Trial. (n.d.). Retrieved November 20, 2017, from

Other references used but not cited:

  • Jones, R. M., Mulle, J. G., & Pacifici, R. (2017). Osteomicrobiology: The influence of gut microbiota on bone in health and disease. Bone. doi:10.1016/j.bone.2017.04.009
  • Alou, M. T., Lagier, J., & Raoult, D. (2016). Diet influence on the gut microbiota and dysbiosis related to nutritional disorders. Human Microbiome Journal,1, 3-11. doi:10.1016/j.humic.2016.09.001

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