Click for appointments or call (707) 927.5622 Home header

The Microbiome and Celiac Disease: A Bacterial Connection

The Microbiome and Celiac Disease: A Bacterial Connection

The gluten-free diet may not be all that is needed to treat celiac disease.

I was diagnosed with celiac disease twelve years ago. 10056375_sIt was quite a journey to arrive at the diagnosis, as it is for so many. When I finally found the answer, the sense of relief was overwhelming. I was additionally comforted by the fact that my treatment was a diet and not medication. Like most celiac patients, I was told to start a gluten-free diet and all would be well. Unfortunately, it wasn’t that easy. The diet was manageable, and my symptoms improved dramatically, but many persisted.

It is a common misconception that all celiac patients get completely well with only the gluten-free diet as a treatment. Many do, but many do not. A 2003 study found that celiac patients on a gluten-free diet have twice as many gastrointestinal symptoms as the general population. For many patients, continued gluten ingestion is the cause of their persistent symptoms. When patients strictly adhere to the gluten-free diet and symptoms persist, however, the answer may lie within.

A Finnish study published in the American Journal of Gastroenterology evaluated celiac patients suffering from persistent symptoms while adhering to a strict gluten-free diet. The subjects had been on a gluten-free diet for at least three years. Their lab results and biopsies had normalized, but they still had symptoms. What the researchers found is of potentially great significance to the future of celiac disease treatment. While the paper did not receive the attention in popular media that many gluten-related articles receive these days, the findings of the study are vitally important to anyone with celiac disease.

The microbiome defined

Before I explain further, it is important to talk about the microbiome. The term refers to the trillions of bacteria that inhabit our bodies in our gastrointestinal tract, our skin, hair, etc. These bacteria are vital to our existence. We need them. They also significantly impact our health. The genetic material they contain may be as important as the DNA we inherit from our parents and may be influencing our predisposition to certain diseases.

Just as we have our own genetic make-up, we also have a unique microbiome. The health  of our microbiome appears to play a pivotal role in our overall health. The study of the microbiome is so important that the National Institutes of Health initiated the Human Microbiome Project in 2007  to determine its overall impact on health and disease.

The amount of research on this topic is expanding rapidly, and alterations in the microbiome have been correlated to conditions such as obesityinflammatory bowel disease, other autoimmune diseases, and cancer. The information resulting from microbiome research is changing the practice of medicine.

Celiac disease and the microbiome

Several studies have reported imbalances in the microbiome in people with celiac disease, and another showed the bacteria we have may affect what symptoms we display. This may explain why some celiac patients experience headaches, while others have joint pain; the type of bacteria they have in their intestine may be playing a role.

Results of a 2014 Finnish study 

The 2014 study from Finland found less bacterial diversity (fewer different types of bacteria) and an imbalance in certain types of bacteria in celiac patients with persistent symptoms.  The bacterial make-up of people with ongoing symptoms resembled that of untreated celiac patients. Why this occurs in some people is not known, but may be related to a delay in diagnosis and a “resetting” of what is a normal microbiome. The microbiome stays relatively stable in healthy people, but when illness or antibiotics upset the balance, the microbiome is altered. In theory, the longer this occurs, the higher the risk of a new microbiome “set point.”

How this may affect the treatment of people with celiac disease and other autoimmune disorders

This is exciting news for people with celiac disease. If we can learn to optimize and balance the microbiome in addition to following a gluten-free diet , persistent symptoms may be alleviated. If we can modulate the microbiome with targeted probiotics or even fecal transplants, the potential for optimal health is improved.

Since a correlation is also being found between bacterial imbalance and autoimmune diseases, balancing and optimizing the microbiome may also decrease the risk of other autoimmune diseases, such as thyroid disease, that occur more commonly in people with celiac disease. And perhaps by modulating the microbiome, we can even decrease the risk of cancer. The possibilities are exciting.

Optimizing your microbiome

Effective treatments to modulate the microbiome are in development, but until then there are things we can do to optimize it on our own.

  1. Diet:  A plant-based diet, free of processed foods and low in meat has been shown to improve microbiome diversity. Including cultured or fermented foods may also improve intestinal health by providing natural forms of probiotics
  2. Exercise:  Exercise has been shown to positively correlate with improvement in the diversity of our microbiome. Set a goal of 30-45 minutes daily.
  3. Sleep:  Improved sleep may improve the microbiome composition. Conversely, an altered microbiome can worsen sleep.
  4. Stress management:  An altered microbiome has been shown to contribute to anxiety and depression, and higher stress levels correlate with an alteration in the microbiome. Improve your microbiome by using your favorite stress reduction technique on a daily basis.
  5. Weight management: Maintaining a healthy weight will help promote a healthy microbiome.
  6. Probiotics and prebiotics: These can be used to manipulate the composition of the microbiome and targeted or specific formulations for specific disease states may be an important part of the future of medicine.

Popular articles on the microbiome:

You Are Your Bacteria: How the Gut Microbiome Influences Health” by  Veronique Greenwood, Time Magazine, Aug. 29, 2013

Some of My Best Friends Are Germs“ By Michael Pollan, The New York Times Magazine, May 15, 2013


Past columns by Dr. Burkhart:

April/May 2016: Reasons People Follow a Gluten Free Diet: 7 Types of Gluten Free Dieters 

March 2016: Ten Positive Aspects of a Celiac Disease Diagnosis

February 2016: Gluten Causes Keratosis Pilaris (a.k.a. “Chicken Skin”): Fact or Myth?

January 2016: Fingernail Changes in IBS,Gluten Disorders and Celiac Disease “A window to health”

December 2015: 20 Gluten-Free Gift Ideas: From Budget to Luxury, Sentimental to Practical & More

November 2015: Cold Sores, Canker Sores and Gluten

October 2015: Celiac Disease and Gluten Sensitivity Research: Snippets from ICDS 2015 (Part 2)

September 2015: Celiac and Gluten Sensitivity Research: Ten Snippets from ICDS 2015

July/August 2015: A New Home Test To Monitor Gluten Exposure

June 2015: Six Reasons to Test for Celiac Disease Before Starting a Gluten-Free Diet

May 2015: POTS, Celiac Disease and Gluten: An Undiscovered Connection?

February/March/April 2015: Arsenic in the Gluten-Free Diet: Facts and Tips

December 2014/ January 2015: The Microbiome and Celiac Disease: A Bacterial Connection

November 2014: Celiac disease and gluten sensitivity: The doctor-patient disconnect

October 2014: Should You Trust Gluten-Free Labels?

September 2014: Triggers for celiac disease: One possible answer

July/August 2014: Ten Tips for a Healthier Gluten-Free Diet

June 2014: Back Pain and Gluten

May 2014: Self-Diagnosis of Gluten Sensitivity: Four Alarming Trends

April 2014: Update on Restaurants and Gluten-Free Dining

March 2014: Histamine Intolerance: Could it be causing your symptoms?

February 2014: Celiac Disease and Non-Celiac Gluten Sensitivity (Reprinted with permission from Sonoma Medicine)

January 2014: Four Vitamin Toxicities on a Gluten-Free Diet

December 2013: Move Over Gluten-Free, Low FODMAP is Next

November 2013: SIBO, Gluten and IBS: What Is The Connection?

October 2013: Pesticides, Wheat and Gluten Sensitivity: What is the Connection?

September 2013: Is gluten really the culprit in gluten sensitivity?

August 2013: Clarifying the Gluten-Free Labeling Rule

June/July 2013: No such thing as Mild Celiac Disease

May 2013: Magnesium Deficiency

April 2013: Six Reasons to test for celiac disease before starting a gluten-free diet

March 2013: Why am I having migraines?

February 2013: What is fructose malabsorption?

January 2013: Educating doctors about celiac disease

December 2012: Are supplements to digest gluten safe and useful?

November 2012: Top 5 reasons for persistent symptoms after Going Gluten Free

Photo by


“I have been a patient of Dr. Amy Burkhart for several years. I suffer from Crohn’s disease and was having difficulty in my daily life. After visiting many doctors, all of whom were unable to help me, Dr. Burkhart took the time and patience to create a plan which brought me back to health. I still follow her plan to this day and have been living a normal healthy life. Dr. Burkhart listened to my symptoms along with listening to me, she took her time in preparing a plan which led me to the road for recovery. I cannot thank Dr. Burkhart enough, and I would recommend her to anyone.”

8 months ago

Stone Brewing company Stone Brewing - Napa opened recently in Napa in an historic building adjacent to the river. A great venue to enjoy life! The gluten free menu options are coming (per the manager ) but please visit and inquire about GF options. The more people who show interest and discuss cross contamination the more likely they are to get it right! Wine is available. Maybe they will even consider a GF beer! . ... See MoreSee Less