The Microbiome and Celiac Disease

The body depends on a balanced community of gut bacteria to support health and nutrition. Imbalance can cause illness. Some medical researchers are investigating whether such a disturbance could trigger celiac disease. Even though the human intestine on its own does not have the ability to digest gluten, gut bacteria normally help. This community, known as the microbiome, might also prevent the body from launching a needless war on gluten.

A new long-term study through Massachusetts General Hospital for Children in Boston will investigate these effects in infants at risk for celiac disease. The findings might explain why some people with the same genetic predisposition get sick while others do not. Future therapies to cure or prevent celiac disease might target the microbiome.

a sum of its parts

In 2008, the National Institutes of Health (NIH) launched the human microbiome project to describe some 100 trillion microbes that live on and in the human body. Medical science has viewed these microbes as a community for only about 10 years, according to Robert Karp, Ph.D., program director for genomic and microbiome studies at the National Institute of Diabetes and Digestive and Kidney Diseases based in Bethesda, Maryland. He specializes in genetics, the study of how all life—whether humans or microbes—inherits traits from one generation to the next.

More than 10 years ago, “Scientists tended to think in terms of what individual strains or species were doing, that they were acting on their own,” Karp explains. “People distinguished [disease-causing] pathogens from commensal bacteria that live in us but cause no harm and possibly cause benefit, but were not thinking in terms of how the whole community acts in a way that’s more than a sum of its parts.”

Dental microbiologists were first to note cooperation between bacteria, he says. Meanwhile, for decades ecologists had been studying microbial communities in nature. After these concepts spread to general medical research, the NIH’s human microbiome project began.


About 1,000 species have been associated with the human microbiome, but the average person has only about 500 or so, Karp says. Some are obscure and poorly understood even by scientists, such as archaea, which have a completely different metabolism than bacteria and are also found in deep ocean hydrothermal vents.

a revolution in research

According to Karp, “In classical microbiology, the only way to study a particular strain of microbe is to culture it in pure form in a test tube. Since we do not know how to culture the vast majority of members of the human microbiome, it is impossible to study them in this way.”

Innovative technology is providing new clues by decoding deoxyribonucleic acid (DNA), which stores the functional instructions in all life forms.

Karp says, “Fast, cheap DNA sequencing and advanced computational methods” allow scientists to sample the microbiome and disentangle the individual DNA sequences of all the microbes contained. “It is possible to deduce a great deal of information about the metabolism, physiology and general lifestyle of a previously unknown microbe from its genome sequence. Even if we can’t culture this microbe, we can clone its unfamiliar genes into a well-studied lab microbe in order to learn something about their function,” he says.


The human genome contains a mere 20,000 protein-coding genes, on par with the fruit fly. However, a 2005 review in the journal Science estimated the human microbiome collectively has at least 100 times as many genes. Its diversity empowers the human gut to extract more essential nutrients than we could manage on our own.


Karp says what fascinates him most about the microbiome is “how its members are adapted to life with us, how we have adapted to life with them. We survive better as a species than we would without them. [There are] hundreds of different ways in which they influence most aspects of our physiology. We don’t even know what most of those ways are.”

Alessio Fasano, M.D., director of the Center for Celiac Research and Treatment at Massachusetts General Hospital in Boston, leads research on the role of the microbiome in celiac disease. He says, “It’s a true symbiotic relationship. We give them hospitality, and in exchange they give us stuff that’s useful for us. For example, we can’t digest fiber, but when fiber reaches the colon, microorganisms can make products that are very good for us.”

For example, bacterial fermentation produces butyrate, which is essential for colon health.


“There’s a great deal of variability in the microbiome between different individuals,” says Karp. “Identical twins have a more similar microbiome than fraternal twins or other pairs of first-degree relatives. People who are cohabiting also tend to have microbiomes that are more similar to each other than people who are living someplace else.”

Lifestyle also affects the composition, he adds, “so someone living as a hunter-gatherer in Africa has a rather different microbiome from a Western European.”

focus on function

This variability makes it hard to draw conclusions about how the microbiome operates. Studies of individual bacterial species associated with disease often make contradictory observations. To sort them out, Karp points to the importance of meta-analysis.


This technique scans the scientific literature for all titles on a particular topic, weighs their research according to size and statistical integrity, and then combines them to see whether any significant effect can be measured overall. This combats the common error of cherry picking studies to make broad statements on health.

Research is also shifting focus from individual species to their functions. Early studies often conducted censuses of microbes, which “mask a greater functional uniformity,” according to Karp. A species that serves an important role in one person may be absent from someone else, in whom a different group serves the same purpose.

To study function, researchers can grow a microbe to identify the products of its metabolism or measure these metabolites in human blood or urine. Functional analysis is still in its infancy but may reveal more robust patterns, Karp says.

the infant microbiome

A key question is how an infant’s microbiome develops from birth. Although the fetus is exposed to a few microbes prenatally, many experts believe that passage through the birth canal provides an essential transplant of microbes. A child’s early microbiome resembles the mother’s vaginal microbiome.


“Over the first two to three years of life, the microbiome matures, so that by the time you’re 3 years old [it] looks like an adult microbiome,” says Karp. “We know something about when different strains appear. But we know very little about the mechanisms of how those changes happen.”

Fasano says, “One of the key functions for the microbiome, particularly early in life, is to teach the immune system to mature and make the right decision if and when to unleash inflammation.”

Beneficial microbes help the immune system recognize and defend itself against microbes that cause infection. A well-balanced microbiome will set the bar high for inflammation, Fasano explains. Otherwise the immune system becomes hypersensitive, reacting too easily and leading to continued injuries.

association with celiac

A nationwide Swedish study published in Gastroenterology in 2012 found children born by elective caesarean section were more likely to develop celiac disease. The authors say these findings support “the hypothesis that the bacterial flora of the newborn plays a role in the development of celiac disease.”

How this might occur remains unclear and yet to be investigated in detail, according to Yolanda Sanz, M.Sc., professor of research at the Spanish National Research Council based in Madrid, who studies the microbiome in children with celiac disease.

Sanz coauthored a 2009 paper in the Journal of Clinical Pathology that found an unbalanced microbiome in children with celiac disease. The sick microbiome included greater or lesser prevalance of certain bacterial species and, perhaps more importantly, a general reduction in species diversity. The microbiome only partially recovered after long-term treatment on a gluten-free diet.


More recently, Sanz and colleagues studied healthy infants who were genetically predisposed to celiac disease but had not developed it. Again, they found a distinctly atypical microbiome. The study, published in 2014 in Gut, suggests host genetics influence which specific microbes colonize the gut, which could in turn influence the onset of disease risk.

Further research published in 2015 in The American Journal of Pathology found certain bacteria trigger celiac disease in mice by promoting an inflammatory response to gluten in the diet. A microbiome free of disease-causing bacteria appeared to protect mice against inflammation. Notably they lost their protection after receiving a bacterium from a human celiac disease patient.

While these studies indicate bacterial associations, research has yet to prove that an altered microbiome causes celiac disease in humans.


Sanz says, “We know that exposure to microbes makes the immune system maturate, but we don’t know the type of interactions between the microbiome and gluten in the diet” and how they together might lead to celiac disease.

beyond simple genetics

The microbiome can also profoundly influence how the host interprets its own genetic code. While human DNA contains the entire library of functional tools that pass from parents to their children, many genes remain silent. Environmental factors can switch them off or on, and these switch positions may also pass from one generation to the next. Fasano says this field of study, called epigenetics, may explain why a previously rare inheritable disorder like celiac disease has become an epidemic.

“We thought that we had everything straight with celiac disease,” explains Fasano. “We knew a lot of the genetics. We know that the environmental trigger is gluten. For many years, we’ve been under the impression that there were two necessary sufficient conditions to develop celiac disease. Then, over the years, we learned that that’s not true, that there are people who eat gluten for 50 years and they stay healthy, and then at a certain point they lose the [ability] to tolerate it and develop celiac disease.”

The rapid increase in cases pointed to some environmental factor at play. Doctors speculated that changes in breastfeeding behavior and infant nutrition might be to blame, but extensive research has ruled these out.

Now Fasano is turning attention to what he calls “cross-talk between us and this parallel world [of gut microbes].” Changes in the microbiome likely alter gene expression, causing the immune system to behave differently, he says. Instead of defending the body, it begins attacking the lining of the gut, marking the onset of celiac disease.

Fasano is one of the principal investigators in the Celiac Disease Genomic, Environmental, Microbiome and Metabolomics (CDGEMM) Study through Massachusetts General Hospital for Children. It aims to follow 500 children at risk for celiac disease from birth until age 5. Participants will provide stool samples, allowing investigation of the bacteria and metabolites produced in the gut. Further, the study will explore interactions between genetics and environmental factors such as diet, infections and antibiotic use.

Fasano says a study such as CDGEMM is necessary because it follows a group of people over time, ideally from birth. It will compare the microbiome before and after onset of celiac disease, shedding light on changes when they occur. This data will help predict why an individual took the wrong turn rather than stay the course and maintain tolerance to gluten.

Eventually doctors may be able to prevent celiac disease by manipulating the microbiome to “bring it back to the right course,” Fasano says.

supporting microbiome health

While experts are still looking for evidence, they can offer advice on how to support a healthy microbiome. One of the most important practices is to avoid overuse of antibiotics.

Karp says, “There are times when antibiotics are absolutely essential, and they’ll save you from a life-threatening disease. You have to use them then.” However, in the United States, the average person receives antibiotics many times during the course of childhood. Antibiotics “totally upset the composition of your microbiome,” he says.

Research suggests that dietary fiber also supports a healthy microbiome, he adds. “Probably the best way to maintain a healthy microbiome is [through] a healthy diet, also good exercise, a good amount of sleep and try to decrease the level of stress. Laugh a lot, because that helps to boost the immune system and therefore helps the microbiota to keep us healthy.”

Van Waffle has a Bachelor of Science degree in biology and lives in Waterloo, Ontario, Canada. He is research editor for Gluten-Free Living. He blogs about nature, gardening and local food at


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