Extensive research over the past several decades has revealed a dynamic connection between the gut and the bones. It turns out that bone health and strength is closely tied to the health of the digestive system. Gastrointestinal disorders contribute to the development of osteoporosis and, by extension, risk of fractures.

This line of research suggests that we can enhance bone health by implementing strategies to improve gut function. 

It’s a pressing concern. Approximately 43% of people over age 50 experience some degree of bone loss, and among those with gastrointestinal disorders the prevalence is even higher. Many different gastrointestinal disorders can contribute to bone loss. Clinically, it’s important that we consider bone loss in patients with digestive disease, and vice versa.

Regardless of the specific GI diagnoses, the common underlying causes of bone loss in all of these conditions are chronic inflammation, malabsorption, and dysbiosis.

Here’s a quick look at how common digestive disorders are linked to osteopenia and osteoporosis:

Inflammatory bowel disease (IBD): Up to 77% of people with IBD have bone loss (Pollak RD, et al.1998, Bjarnason I, et al.1997). Patients with Crohn’s disease (CD) have a 68% increased risk of a hip fracture, while those with ulcerative colitis (UC) have a 41% increased risk compared to people without these conditions (Card T, 2004) Surgery for UC can improve bone density to some degree, but it doesn’t eliminate the risk of fractures. In one study, 15% of patients who underwent proctocolectomy with ileoanal pouch anastomosis (IPAA) still had bone fractures despite the surgery (Abitbol V, et al. 1997).

Irritable bowel syndrome (IBS): People with irritable bowel syndrome (IBS) have up to a 95% increased risk of osteoporosis compared to those without IBS, and a 27% increased risk of fractures (Wongtrakul W, et al., 2020).

Liver disease: In patients with advanced liver disease, who are candidates for or who actually undergo liver transplant, bone loss and fractures occur in up to 60% prior to the transplant or within one year after (Abate EG, et al. 2025).

Peptic ulcers: Forty-two percent of people with peptic ulcer disease who undergo gastrectomy surgery develop osteoporosis, and up to 72% suffer bone fractures (Melton LJ, et al.1999).

Primary biliary cholangitis (PBC): Up to 45% of patients with PBC develop osteoporosis, and up to 22% have fractures (Trivedi HD, et al. 2020).

Short bowel syndrome: Ninety-two percent of patients with this rare condition had low BMD in one study(Moreno Braga CB, et al. 2015).

Regardless of the specific GI diagnoses, the common underlying causes of bone loss in all of these conditions are chronic inflammation, malabsorption, and dysbiosis. Also keep in mind that drugs used to treat serious GI disorders may also have detrimental effects on bone.

Chronic Inflammation: Highly prevalent in conditions such as IBS, Crohn’s disease, and ulcerative colitis, chronic inflammation stimulates bone-resorption by osteoclasts. Pro-inflammatory cytokines like TNF-alpha and several of the interleukins contribute heavily to this process (Ng QX, et al. 2018. Saez A, et al. 2023).

Drug Side-Effects: Medications that reduce inflammation, such as glucocorticoids (e.g., prednisone, dexamethasone) and other drugs used to treat GI disorders are often potent bone-destroyers (Card T, et al. 2004; Canalis E, et al. 2007; Van Staa TP, et al. 2003). Proton-pump inhibitors (PPI) and antidepressants (SSRI and SNRI classes) also promote osteoporosis and increase fracture risk (Diem SJ, et al. 2007, Khanassov V, et al. 2018 ,Moura C, et al. 2014).

Malabsorption: Chronic inflammation damages the intestinal mucosa and causes “leaky gut.” As a result, large unwanted particles are mistakenly absorbed into the bloodstream, prompting further inflammation. This has a detrimental impact on bone health (Paray BA, et al. 2020).

Further, nutrient deficiencies are common among people with celiac disease, Crohn’s disease, and ulcerative colitis due to poor nutrient absorption. Vital bone-supporting nutrients—including vitamins K and D, iron, zinc, copper, selenium, folic acid, and B vitamins—are particularly affected. More than half of individuals with Crohn’s or ulcerative colitis show deficiencies in these key vitamins and minerals. Additionally, acid-blocking drugs hinder the uptake of calcium, magnesium, iron, and vitamin B12 (Lai Y, et al. 2022; Fletcher J, et al. 2019; Ghislan FK, Kiela PR, 2017; Nowak JK, et al. 2014; Rondanelli M, et al, 2019).

A 2023 metanalysis showed a significant shift in the microbiota composition among subjects with osteoporosis compared with non-osteoporotic controls. Those with osteoporosis showed increased abundance of opportunistic pathogens… and a concomitant decrease in beneficial short-chain fatty acid producing organisms.

Dysbiosis: The links between the gut microbiome, bone status, and systemic health are irrefutable. Intestinal dysbiosis increases inflammation and damages the intestinal lining. Dysbiosis is common among people with bone loss.

In a 2023 metanalysis, researchers at the University of Florida, Gainesville, describe “a significant shift in the microbiota composition” among subjects with osteoporosis compared with non-osteoporotic controls. Those with osteoporosis showed increased abundance of opportunistic pathogens such as Clostridium sensu stricto, Bacteroides, and Intestinibacter, and a concomitant decrease in beneficial short-chain fatty acid producing organisms (Akinsuyi OS, Roesch LFW, 2023).

As people get older, dysbiosis becomes more common because medications, poor diet, stress, lack of sleep, and environmental toxins—all of which tend to accumulate and compound as we age–can harm healthy gut bacteria (Karl JP, et al. 2018).

While human research is still evolving, animal studies show that restoring beneficial bacteria with probiotics can support bone mass. Mouse studies show that the gut microbiome plays a role in regulating bone mass (Sjögren K, et al. 2012). Vitamins produced by gut bacteria—especially microbe-derived forms of vitamin K (Menaquinones)–may influence bone matrix quality (Guss JD, et al. 2019).

In a dramatic demonstration of the gut-bone connection, researchers transplanted stool from women with osteoporosis into young, healthy mice. The donated fecal material quickly induced loss of bone mass in the recipient animals, an observation the investigators attributed to “aberrant gut microbiota” from the fecal transplants, which triggered inflammation and damage to the intestinal barrier (Chen T, et al. 2024).

In another study, researchers ovariectomized mice, putting them in a “postmenopausal” state, and then gave doses of healthy bacteria via fecal transplant to some but not all of the animals. The mice that did not receive the healthy gut bacteria quickly developed osteoporosis, while the treated mice showed no bone loss.

The investigators also found that the healthy microbiome transplants reduced inflammation, maintained the integrity of the intestinal lining, and suppressed osteoclast activity (Zhang YW, et al. 2022). In a separate paper, this research team posits that Fecal Microbiome Transplant (FMT) has potential as a potential future treatment for osteoporosis (Zhang YW, Cao MM, et al. 2022).

It remains to be seen whether this is borne out by future human studies, but FMT is already being used to treat other diseases. Human FMT studies show it is effective at inducing remission in people with ulcerative colitis (UC), Crohn’s disease, and intestinal Clostridium difficile infections (Fehily SR, et al. 2021; Moayyedi P, et al. 2015; Liubakka A, Vaughn BP, 2016).

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John Neustadt, ND, is Founder and President of the dietary supplement company, Nutritional Biochemistry, Inc. (NBI, nbihealth.com) and NBI Pharmaceuticals. Dr. Neustadt started NBI in 2006 when he couldn’t find products containing the doses of nutrients shown to work in clinical trials. He received numerous US FDA Orphan Drug Designations for potentially treating rare diseases using natural products. Dr. Neustadt is a Bone Health and Osteoporosis Foundation Corporate Advisory Roundtable member, and was Vice President and Treasurer of the California Naturopathic Doctors Association (CNDA). Dr. Neustadt has written four books, over 100 research reviews, and was recognized by Elsevier as a Top Ten Cited Author. His latest book is Fracture-Proof Your Bones: A Comprehensive Guide to Osteoporosis. Dr. Neustadt hosts the Delivering Health podcast.