Are you actually absorbing the nutrients you eat?
In my last article, I talked about the nutrients your bones need to stay strong. But eating a nutrient-rich diet is only part of the story. Your digestive system also needs to break down your food and absorb those nutrients so your body can actually use them.
And there’s another fascinating part of the picture that we’re only beginning to understand: the trillions of microorganisms living in your gut may also influence your bones.
This relationship is increasingly referred to as the gut–bone axis — and emerging research suggests it may influence bone health through nutrient absorption, inflammation, microbial metabolites and interactions with the immune and endocrine systems (Lee et al., 2025).
Nutrient absorption
Your bones rely on a steady supply of nutrients including calcium, magnesium, protein and vitamins D and K. Gastrointestinal conditions such as coeliac disease and Crohn’s disease can interfere with nutrient absorption, while other digestive problems and medications may also affect nutrient status.
This means that simply eating a nutrient-rich diet doesn’t always tell us the whole story. We also need to consider whether those nutrients are being adequately digested and absorbed.
The gut microbiome’s impact on bone formation
One way your gut microbes may communicate with your bones is through the substances they produce. When certain gut bacteria ferment dietary fibre, they produce short-chain fatty acids (SCFAs), including butyrate, acetate and propionate. These compounds have effects well beyond the gut. They help support the intestinal barrier and regulate immune and inflammatory activity, and experimental research suggests they may also influence the balance between bone formation and bone breakdown (Wang et al., 2026; Lucas et al., 2018).
SCFAs strengthen gut barrier integrity, which reduces systemic inflammation — a known driver of bone resorption (Lucas et al., 2018).
You might ask what influences SCFA production. As these are metabolites of gut microbes, our diet is the biggest factor here. When we eat a nutrient-rich diet, for example a Mediterranean style diet with plenty of fibre, we produce plenty of microbes. However, when we eat a mostly low-quality diet, beneficial microbe production is reduced and our gut barrier integrity is also reduced (Wang et al., 2026). The latter is what is commonly referred to as ‘leaky gut’.
An inflamed gut can accelerate bone loss
When we experience intestinal permeability (or ‘leaky gut’), the gut intestinal wall is not as tight as it should be, and the result is that substances that shouldn’t ‘leak’ into our bloodstream now can get into the bloodstream (Gu et al., 2025). When barrier integrity is impaired, bacterial components such as lipopolysaccharide (LPS) may enter the circulation and contribute to low-grade systemic inflammation. (Wang et al., 2026).’
This matters because chronic inflammation can influence bone remodelling, favouring increased bone resorption. Researchers are therefore investigating intestinal permeability and immune activation as another potential link between the gut microbiome and osteoporosis. (Gu et al., 2025).
Gut Health, estrogen and bone health
Oestrogen and the gut microbiome appear to have a bidirectional relationship. Gut microbes are involved in oestrogen metabolism, while declining oestrogen across menopause may itself influence the gut environment. Researchers are still determining exactly what this means clinically, but this interaction may be particularly relevant to bone health during and after menopause (Lim et al., 2026).
Proton pump inhibitors (PPIs) and nutrient absorption
PPIs reduce stomach acid and, with long-term use, have been associated with changes in the status or absorption of some nutrients and a modest increase in fracture risk in observational research (Thong et al., 2019). However, the relationship is complex and doesn’t mean PPIs should be stopped without medical advice
Talk to your doctor about if you have any concerns and ask them to do a DEXA scan to see where your bone health is at
What can you do to support your gut health?
For someone experiencing significant digestive symptoms, or where there are reasons to suspect impaired digestion or absorption, further investigation may sometimes be appropriate. The type of testing I recommend depends on the person’s symptoms, medical history, diet and existing pathology results.
When it comes to food, I’d recommend the following:
Eat plenty of diverse plant foods.
Vegetables, fruit, legumes, whole grains, nuts and seeds provide fibres and polyphenols that support the gut microbiome.
Include enough fibre.
Certain fibres provide substrates that gut microbes can ferment into beneficial metabolites such as SCFAs.
Eat enough protein and bone-supporting nutrients.
A healthy microbiome can’t compensate for an inadequate diet.
Investigate persistent digestive symptoms.
Ongoing bloating, diarrhoea, constipation, reflux or other gastrointestinal symptoms shouldn’t simply be ignored — particularly where nutrient absorption or bone health is a concern.
The takeaway
Your bones don’t exist in isolation.
We can eat plenty of calcium, protein and other bone-supporting nutrients, but we also need a digestive system capable of breaking down our food and absorbing those nutrients.
Emerging research suggests the relationship goes even further. Our gut microbiome may communicate with our bones through microbial metabolites, immune signalling, inflammation and hormonal pathways — an area of research that is developing rapidly.
This is why digestive health forms an important part of my approach to bone health. Rather than looking at a DEXA result or calcium intake in isolation, I want to understand the whole person — including nutrition, digestion, medications, hormones, lifestyle, muscle and other factors that may influence long-term bone health.
Want to understand what’s influencing your bone health?
Bone health is about much more than calcium intake or a number on a DEXA scan. Your diet, digestive health, hormones, medications, lifestyle, muscle mass and individual risk factors can all form part of the picture.
In my Bone Health Program, I take a personalised, whole-person approach to identifying the factors that may be affecting your long-term bone health and developing a practical plan to support stronger bones and healthy ageing.
Learn more about my Bone Health Program or book a free discovery call.
References
Gu C, Du H, Li N, Zhou Y, Li S, Sun Y, Han Y, Xu X and Li X (2025). The gut–bone axis in osteoporosis: a multifaceted interaction with implications for bone health. Front. Endocrinol. 16:1569152. https://doi.org/10.3389/fendo.2025.1569152
Lee, K., Kim, H., & Wang, J. H. (2025). Clinical evidence linking osteoporosis and the gut microbiome in postmenopausal females: A systematic review. Bone, 201, 117644. https://doi.org/10.1016/j.bone.2025.117644
Lim, M. J. S., Parlindungan, E., See, E., Gan, C. H., Yap, R., & Yong, G. J. M. (2026). Diet, the Gut Microbiome, and Estrogen Physiology: A Review in Menopausal Health and Interventions. Nutrients, 18(7), 1052. https://doi.org/10.3390/nu18071052
Lucas, S., Omata, Y., Hofmann, J., Böttcher, M., Iljazovic, A., Sarter, K., Albrecht, O., Schulz, O., Krishnacoumar, B., Krönke, G., Herrmann, M., Mougiakakos, D., Strowig, T., Schett, G., & Zaiss, M. M. (2018). Short-chain fatty acids regulate systemic bone mass and protect from pathological bone loss. Nature communications, 9(1), 55. https://doi.org/10.1038/s41467-017-02490-4
Thong, B. K. S., Ima-Nirwana, S., & Chin, K. Y. (2019). Proton Pump Inhibitors and Fracture Risk: A Review of Current Evidence and Mechanisms Involved. International journal of environmental research and public health, 16(9), 1571. https://doi.org/10.3390/ijerph16091571
Wang, Y., Xu, M., Dong, Q. et al. The gut-bone axis: impact of diet on gut microbiome and osteoporosis. Bone Res 14, 61 (2026). https://doi.org/10.1038/s41413-026-00550-4
