The Microbiome-Bone Connection: A New Frontier in Osteoporosis

Nurturing Your Bone-Building Bacteria

Jul 02, 2025

n this continuing series on osteoporosis, we turn our attention to an often overlooked yet powerful contributor to bone health, the gut microbiome.

For decades, the conversation around strong bones has focused on the familiar trio—calcium, vitamin D and weight bearing exercise. Emerging research, however, is now reshaping that view. Scientists have uncovered a surprising new influence in bone biology—the community of microbes living in our gut.

This connection, known as the “gut-bone axis,” is redefining how we think about osteoporosis prevention and treatment. It now gives us a broader understanding of what is means to support lifelong bone health.

Summary of this Newsletter

The gut microbiome plays a surprising role in bone health, shaping whether bone-building or bone-breaking cells dominate.
Short-chain fatty acids (SCFAs) produced by gut bacteria support bone growth by enhancing osteoblasts and inhibiting osteoclasts.
Not all microbes are equal—beneficial strains protect bones, while harmful ones fuel inflammation and bone loss.
The microbiome supports bone health by aiding nutrient absorption, reducing inflammation, and protecting the gut barrier.
Modern diets, stress, and certain medications (like antibiotics, PPIs, and SSRIs) can harm gut microbes and increase osteoporosis risk.
Fibre-rich and fermented foods increase SCFA levels and microbial diversity—key to both gut and bone strength.
Prebiotics like GOS and FOS, and targeted probiotics such as Lactobacillus reuteri, may protect against bone loss.
Caring for the gut is a powerful strategy for lifelong bone health—it’s not just what you eat for your bones, but what your microbes make of it.
The next newsletter will cover evidence-based prevention and treatment strategies for osteoporosis.
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In today’s newsletter we look deeply into the role of the microbiome and how it impacts osteoporosis. It is a fascinating look at the deep and intimate connection of the microbiome with our bone. We have discussed the basics of bone cells in a previous newsletter. You can read that newsletter here. There we talked about osteoblasts that build bone and osteoclasts that breakdown bone.

Your gut microbiome plays a key role in determining which bone cells take the lead—those that build bone or those that break it down.

We’ve previously explored the power of short-chain fatty acids (SCFAs)—beneficial compounds produced when certain gut bacteria ferment dietary fiber. These SCFAs support brain, gut, and immune health, and in this context, they also play a surprising role in bone health.

Specifically, SCFAs inhibit osteoclasts (the cells that break down bone) and enhance osteoblasts (the cells that build it). In other words, they help prevent bone loss while encouraging bone formation.

Take a moment to reflect on that: microbes in your gut—nowhere near your skeleton—can influence bone cell behavior. They are quietly shaping the balance between bone loss and regeneration, seemingly with no direct benefit to themselves. And yet, they do it—daily, silently, and profoundly.

But you have to have the right microbes

Not all microbes are created equal when it comes to bone health. Beneficial bacteria are linked to stronger bones and reduced osteoporosis risk. On the other hand, an overabundance of harmful bacteria can promote inflammation and bone loss.

How the Microbiome Shapes Bone

The gut microbiome influences bone health through several key mechanisms:

Metabolite production: Short Chain Fatty Acids (SCFAs) such as butyrate produced by microbial fermentation of fibre, inhibit osteoclasts (bone-resorbing cells) and stimulate osteoblasts (bone-forming cells).
Nutrient Absorption: Gut bacteria enhance the absorption of calcium, magnesium, vitamins D and K, all vital for bone strength.
Immune Regulation: The microbiome modulates immune responses, reducing inflammation that accelerates bone loss.
Gut Barrier Protection: A healthy microbiome maintains the gut lining, preventing damage to it that can result in systemic inflammation.

What Harms the Microbiome and Your Bones

Modern lifestyles can disrupt the delicate balance of gut microbes, resulting in significant consequences for bone health:

Diet: High-sugar, low fibre and highly processed foods foster dysbiosis, resulting in lowered levels of SCFAs, increasing gut permeability and inflammation.
Medications: Oral medications can have significant effects on the gut microbiome, potentially altering microbial diversity and functioning. These changes can in turn affect bone health and contribute to the development or exacerbation of osteoporosis. However, they can be essential under the right circumstances and must not be discontinued without discussion with your doctor.
- Antibiotics are well known to have disruptive effects on the microbiome, leading to reduced diversity and other changes. This disruption can affect bone health negatively and also alter calcium and vitamin D absorption. They can also reduce the production of SCFAs.
- Proton pump inhibitors (PPIs) are widely prescribed for the treatment of acid-related gut disorders like reflux disease and peptic ulcers. PPIs can alter the gut microbiome by reducing stomach acid levels that can lead to an overgrowth of bacteria in the upper gastrointestinal tract. This is also called Small Intestinal Bacterial Overgrowth (SIBO). These changes can impact bone health by affecting absorption of calcium, iron, magnesium, folate, biotin, vitamin B12 and other nutrients as well as SCFAs.
- Nonsteroidal anti-inflammatory drugs (NSAIDs). These are commonly used to treat pain and inflammation, but their long-term use has been associated with an increased risk of osteoporosis. One of the most common NASIDs is ibuprofen.
- Selective serotonin reuptake inhibitors (SSRIs) are widely prescribed for the treatment of depression and anxiety disorders. Evidence suggests that SSRIs can impact the gut microbiome by altering the gut microbiome with consequences on bone health as discussed above. You may be interested to know that the more serotonin in produced in the gut that in the brain. Serotonin is also produced by osteoblasts and osteoclasts, and it has an inhibitory effect on bone formation. Their function is not fully understood but there must be a feedback loop to control the production of bone. This inhibition of bone formation maybe the reason why SSRIs may aggravate osteoporosis.
Environmental Pollutants: Food additives, chemical preservatives, and artificial sweeteners can cause dysbiosis and inflammation.
Lifestyle Factors: Chronic stress, poor sleep, excessive alcohol, and inactivity all reduce beneficial bacteria and increase harmful strains.

How to Support Your Gut and Your Bones

There are many actions that nurture the gut microbiome and protect bone health:

Eat More Fibre: Beans, whole grains, fruits and vegetables feed beneficial bacteria increasing SCFA production and mineral production.
Increase Fermented Foods: Yoghurt, kefir, kimchi and similar foods introduce probiotics that support gut and bone health
Exercise Regularly: Physical activity especially weight bearing exercises increase bone density.
Manage Stress and Sleep: Bothe are important for maintaining a healthy microbial balance.
Choose Polyphenol-Rich Foods: Blueberries, green tea and dark chocolate promote beneficial bacteria.

Supplements, Herbs and Natural Compounds

Probiotics: Studies have shown that specific strains of Lactobacillus reuteri can significantly reduce bone loss in older women.
Prebiotics: Galactooligosaccharides (GOS) and fructooligosaccharides (FOS) increase beneficial bacteria, improve calcium absorption and enhance bone density.
- GOS foods: Chickpeas, lentils, kidney, black and navy beans, soybeans
- FOS foods: Garlic, onions, leeks, asparagus, green (unripe) bananas, dandelion greens

The Role of Dysbiosis

An unbalanced gut microbiome (dysbiosis) can impair calcium absorption, increase inflammation and accelerate bone loss, contributing to osteoporosis and poor fracture healing. Addressing dysbiosis through diet, lifestyle and targeted supplementation are promising strategies for osteoporosis prevention.

Conclusion

The gut-bone axis represents a major shift in our understanding of osteoporosis. By nurturing the gut microbiome through diet, lifestyle and targeted supplementation, we can unlock new pathways to stronger bones and healthier ageing. The future of osteoporosis prevention and treatment is not just in our bones, but in our guts.

The next newsletter will cover evidence-based prevention and treatment strategies for osteoporosis.

Healthy Ageing