Article Archive
May/June 2017

Bugs and Bones: Connecting Gut Bacteria and Bone Health
By Diane L. Schneider, MD, MSc
Today's Geriatric Medicine
Vol. 10 No. 3 P. 14

Experiments in mice have found that gut microbiota regulate bone mass. Modification of these microbiota with probiotic supplementation showed a beneficial effect on general bone health under nondiseased conditions and reduced bone loss in estrogen-deficient mice.

If, like me, you've been out of training for a few years, you'll remember we referred to nonpathogenic bacteria in the intestine as normal flora. Now microbes in the gut and other parts of the body are called microbiota. Our bodies carry around trillions of microbes that include bacteria, viruses, and other living things. These microbes live in groups in many places on and inside our bodies, such as the skin, mouth, nose, gut, and vagina. However, the gut is populated by the largest number of microbes. The human body has an estimated 30 trillion human cells and 39 trillion microbial cells.1 Therefore, Rob Knight, PhD, director of the Center for Microbiome Innovation at the University of California, San Diego concludes, "We are an organism that is 43% human." That's a statement to ponder.

Many of these microbes help to keep us healthy, while others contribute to disease.2 Changes in our health can affect our microbes. Similarly, changes in our microbes may affect our health. Factors such as where we live or work, age, ancestry, health status, and diet and many other things we don't yet know about may play a role in our microbial makeup.

The Human Microbiome
The biology and medical significance of the microbiome and its collective genes (the metagenome) is a burgeoning field of scientific investigation. The National Institutes of Health launched the Human Microbiome Project in 2008 as a five-year initiative.3 Its goals were to learn about the human microbiome by studying the DNA of the microbes, determining what chemicals they produced, and how microbes interact with each other and with their human host to contribute to health and disease. One project was to characterize the "normal" microbial makeup of healthy humans using genome sequencing techniques.

Humans have 20,000 human genes. In contrast, human microbial genes may range from 2 million to 20 million. Taking the highest number, that translates to suggest only 1% of genes in the body are human.4 The Human Microbiome Project studied approximately 250 healthy volunteers. The DNA analysis of microbes generated terabytes of data. In order to make sense of all the data scientists developed a computational technique to take the DNA sequences of human microbiome and translate the data into graphic displays like maps.

The researchers found different regions of the body have different microbes in them that make up a "community" for that site. When the communities of microbes are visually displayed for one person, they look almost like continents on a map. Microbial communities in different parts of the body are significantly different from one another. The differences are enormous even within a few feet of one another, for example from the mouth to the gut.

In addition, one person may share only a small percentage of microbes with another person.5 For instance, only 10% of gut microbes may be similar. In adults microbial communities are relatively stable. Even when an individual lives with someone else, separate microbial identity appears to be maintained over a periods of weeks, months, and even years.

First microbial communities are dependent on how one is born. Babies born via vaginal delivery are populated first by vaginal microbes. In contrast, babies delivered by C-section have microbes that look like skin. These differences may explain why babies born by C-section have more allergies, asthma, eczema, and even obesity. Interestingly, all of these have been associated with microbes. Clinical trials are underway to see whether coating C-section babies with vaginal secretions immediately after birth will have a protective effect.

Over subsequent two years in life, researchers following weekly fecal samples found that a child rapidly develops differences in his or her microbial community. By the end of two years, the gut microbiome approaches that of a healthy adult. With the rapid changes in the gut microbiome, researchers are investigating what happens if an intervention occurs, such as treating an ear infection with antibiotics before a child reaches the age of 2.

Investigations into the microbiome and its connection to health and disease are rapidly increasing worldwide. Over the past few years, inflammatory bowel disease, heart disease, colon cancer, and even obesity have been linked to alterations in the gut microbiome.6 Experiments with mice are investigating the impact of transplanting microbes for health and disease.

Changing the microbiota as treatment in clinical practice is already occurring. Recent studies indicate that the main cause of Clostridium difficile infection is an imbalance in the normal gut microbiota. The restoration of a healthy gut microbiota composition via fecal microbiota transplantation is being done regularly in clinical practice for recurrent or severe C difficile infection after clinical trials showed superior results in comparison with treatment with antibiotics.

Nutrition Link to Bone Health via the Microbiome
These recent advances in understanding how the gut microbiome contributes to health and disease have generated interest in the bone field. Bone has long been associated with the gut, which regulates the absorption of the key bone mineral calcium. In 2012 experiments with mice found that gut microbiota regulated bone mass.7 Since that time, studies have looked for nutritional factors that would decrease bone loss. A number of research groups have focused on treatment with prebiotics to select for growth of certain bacteria in the gastrointestinal tract and treatment with probiotics to deliver beneficial bacteria directly to the gastrointestinal tract.8,9

Prebiotics are nondigestible (by humans) fermentable food ingredients that promote the growth of beneficial microorganisms in the intestine as well as promote health-benefiting changes in microbiome activity. Prebiotics encompass compounds found in a variety of foods such as chicory, garlic, leeks, Jerusalem artichokes, dandelion greens, bananas, onions, and bran. A significant amount of the food may be necessary to obtain enough prebiotic for activity. Therefore, prebiotics such as inulin, which is extracted from chicory root, are manufactured in a variety of forms. Prebiotics appear to be safe when given to healthy children and adults. They have no major side effects but may cause bloating, gas, and increased bowel movements because of the large sugar subunits contained, as with inulin.

In clinical trails with adolescents and postmenopausal women, prebiotics increased the absorption of calcium and magnesium. But does the increase observed in calcium absorption translate into better bone health with increased bone density and improved architecture? Most human studies were not long enough to show changes in bone density. However, one year of treatment reduced bone loss in a small study of postmenopausal women.

As to the effects of prebiotics on bone turnover, several studies indicate that prebiotics can increase osteoblast bone formation or decrease osteoclast activity, depending on the prebiotics used in short-term studies.9 While many animal studies demonstrate prebiotics can benefit bone health, the exact mechanisms are not fully clear.

The word "probiotics" was initially coined as an antonym for "antibiotics." Bacterial species now recognized as probiotics have been utilized since ancient times for use in cheese and for fermentation of products. Over the years, the definition of probiotics has been refined and is now defined as "live microorganisms that when administered in appropriate amounts can provide certain health benefits to the host."8 Generally probiotics are provided as concentrated cultures in dairy products (eg, yogurt), as inoculants in milk-based foods, or as dietary supplements in the form of powder, capsules, or tablets.

Modification of microbiota in mice with probiotic supplementation showed a beneficial effect on general bone health under nondiseased conditions and reduced bone loss in estrogen-deficient mice, which were used as the animal model for postmenopausal women.9 Estrogen depletion was associated with decreased numbers and diversity of microbiota. The probiotic supplementation contained different bacteria that modified the gut microbiome of the mice. The probiotics restored a greater number and diversity of bacteria. The research suggests that decreased diversity contributes to bone loss induced by loss of estrogen.

One Yogurt a Day Boosts Bone Density
A real world example of the benefit of probiotics can be found in of the impact of yogurt consumption on the gut microbiome. Yogurt is a calcium-rich food. Depending on the type of yogurt, one serving may provide 200 to 450 mg of calcium. Recent research suggests the beneficial effects of yogurt may go beyond just the calcium content. Yogurt also contains fermented dairy products and probiotics, which were found to be beneficial for bone health in animal laboratory experiments. Bacteria contained in yogurt ferment the milk.

The possible protective effect of fermented dairy products on postmenopausal bone loss led Swiss researchers to examine yogurt consumption in healthy men and women who were recruited at the age of 65. This study included 733 healthy postmenopausal women who underwent bone mineral density scan at baseline and again three years later. At the beginning of the study, women who consumed yogurt had higher bone density and were thinner than women who did not consume yogurt.

At the follow-up assessment three years later, women who ate at least one serving of yogurt per day experienced less bone loss than those who did not eat yogurt. These findings were independent of any other factors that could account for differences in bone density, such as physical activity, protein, and total calcium intake. Also, the number of fractures trended toward a lower rate: 19% among yogurt consumers vs 29% for nonconsumers.10

The researchers hypothesize that bacteria contained in yogurt populate the large intestine, where they improve calcium absorption and decrease inflammation. They have suggested that the protective effect of yogurt on bone has to do not only with calcium and protein but also with the fermentation that occurs in yogurt, all three of which are believed to be good for bone health.

Gut Microbiome — A New Frontier
Stay tuned to this concept as an exciting new area of research. These investigations are preliminary yet promising. These findings suggest that by optimizing the microbiome we may be able to build and maintain stronger bone. The connection between the gut and the skeleton offers the potential for novel strategies through nutrition modification. Research methods to shift the gut microbiome by interventions open the door for the discovery of treatments to improve health and ameliorate disease, including osteoporosis. In the meantime, it may be wise to encourage your patients to add a serving of yogurt each day for good measure.

Areas currently under investigation include the following:

• Understanding microbiome characteristics in relation to families: Which features are inherited, and which are not?

• Understanding secular trends in microbiome composition: Which taxonomic groups have been lost or gained?

• For diseases that have changed markedly in incidence in recent decades, do changes in the microbiome have a role?

• Do particular signatures of the metagenome predict risks for specific human cancers and other diseases that are associated with aging?

• How do antibiotics perturb the microbiome, both in the short term and long term? Does the route of administration matter?

• How does the microbiome affect the pharmacology of medications? Can we 'microtype' people to improve pharmacokinetics and/or reduce toxicity? Can we manipulate the microbiome to improve pharmacokinetic stability?

• Can we harness knowledge of microbiomes to improve diagnostics for disease status and susceptibility?

• Can we harness the close mechanistic interactions between the microbiome and the host to provide directions for the development of new drugs?

• Specifically, can we harness the microbiome to develop new narrow-spectrum antibiotics?

• Can we use knowledge of the microbiota to develop true probiotics (and prebiotics)?

Know Your Gut Microbiome
You can find out your own gut microbiome through a crowd-funded research study at the University of California, San Diego. Anyone can contribute to and participate in the American Gut Project. For more information or to enroll, visit Enrollees receive a kit with instructions on using it to swab a stool and return via mail. The American Gut Project team extracts the microbial DNA from the sample and uses a genetic sequencing technique to map which types of bacteria are there and how many there are of each type.

Not only do American Gut participants receive information about what's living in their own bodies, but they also can see how they compare with other participants with similar (or different) ages, diets, and exercise habits. What's more, participants are contributing valuable information (stripped of their personal identifying data) to an open access database. Since the microbiome data are paired with lifestyle information such as diet and exercise, researchers can use these data to study how nutrition and activity influence the microbiome and how that microbial makeup is associated with health problems.

— Diane L. Schneider, MD, MSc, is a geriatrician, epidemiologist, author, and cofounder of She is a former associate professor of medicine at the University of California, San Diego. An experienced writer and public speaker, she is frequently featured as an osteoporosis expert in numerous television and radio shows, internet articles, magazines, newspapers, and medical publications. Schneider is the author of The Complete Book of Bone Health.

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2. Sender R, Fuchs S, Milo R. Are we really vastly outnumbered? Revisiting the ratio of bacterial to host cells in humans. Cell. 2016;164(3):337-340.

3. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. The Human Microbiome Project. Nature. 2007;449(7164):804-810.

4. The Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486(7402):207-214.

5. Debelius J, Song SJ, Vazquez-Baeza Y, Xu ZZ, Gonzalez A, Knight R. Tiny microbes, enormous impacts: what matters in gut microbiome studies? Genome Biol. 2016;17(1):217.

6. Bakken JS, Borody T, Brandt LJ, et al. Treating Clostridium difficile infection with fecal microbiota transplantation. Clin Gastroenterol Hepatol. 2011;9(12):1044-1049.

7. Sjögren K, Engdahl C, Henning P, et al. The gut microbiota regulates bone mass in mice. J Bone Miner Res. 2012;27(6):1357-1367.

8. Food and Agriculture Organization of the United Nations. Probiotics in food: health and nutritional properties and guidelines for evaluation. Published 2006.

9. Li JY, Chassaing B, Tyagi AM, et al. Sex steroid deficiency–associated bone loss is microbiota dependent and prevented by probiotics. J Clin Invest. 2016;126(6):2049-2063.

10. Biver E, Durosier-Izart C, Merminod F, Chevalley T, Ferrari S, Rizzoli R. Yogurt consumption is associated with attenuated cortical bone loss independently of total calcium and protein intake and physical activity in postmenopausal women. Paper presented at: The American Society for Bone and Mineral Research 2016 Annual Meeting; September 16-19, 2016; Atlanta, GA.