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Celiac and bacteria: strange breadfellows

While managing celiac disease for the last three years, I repeatedly hear the same question – “Why?” Millions of stomachs are growling for answers. Sit down for a gourmet dish on an epidemic that hits close to home.


Celiac disease is the presentation of a deeper, self-destructive autoimmune condition experienced by 2 million people and lurking within millions more. It is estimated that 75-90% of the celiac population in Western countries remains unrecognized. Even worse, undiagnosed celiac disease has been associated with a nearly 4-fold increased risk of death. People with celiac disease cannot digest any amount of gluten, the protein found in wheat, rye, barley and many other grains. Symptoms can range from nothing to severe intestinal distress and chronic pain. The major damage occurs in the villi of the duodenum portion of the small intestine that normally absorbs nutrients, provides enzymes for digestion, and protects against harmful pathogens. Self-destructive activity is common to autoimmune diseases like type 1 diabetes, inflammatory bowel disease, and allergic asthma.

Think you’re safe? Research has discovered that many people have latent or silent celiac disease with antibodies to gluten but few or no symptoms. Some doctors group this into the category of gluten sensitivity. Gluten sensitivity, like celiac disease, can affect intestines, connective tissue, lungs, skin, and nervous systems depending upon the type. With this condition, the intestinal lining does not increase in permeability as with celiac disease. Elderly patients who were tested as gluten-sensitive did not necessarily have celiac disease, but a majority of their biopsies showed intestinal inflammation. In a large study, intestinal inflammation in non-celiac patients linked to higher mortality rates than celiac disease. Swedish researchers believe this inflammation indicates early-stage celiac.

The symptoms of celiac sprue disease was noted since 250 A.D., but the link to wheat protein was only discovered in 1952. Gluten is now found in many food and body products, including soups, soy sauce, vitamins, shampoo, lip balm, and play dough. A gluten-free diet requires careful attention to product labels and restaurant practices. Celiac disease, like other autoimmune conditions, has no cure and the diet is required for life to avoid symptoms and further intestinal damage.

An official diagnosis of celiac involves an invasive intestinal biopsy requiring gluten ingestion and sedation. As damage to the lining may be patchy or minimal in early celiac, this procedure has its own limitations. Other antibody blood tests check for risks but can be affected by factors like IgA deficiency and diet. The endomysial IgA antibody test is gaining popularity and helped predict celiac among children with normal villi. The less expensive TTG test checks for tissue transglutaminase in the blood released when the intestines are damaged. Readily available ELISA-based IgG antibody tests can recognize a range of food sensitivities but do not directly associate with full-blown celiac disease. If you choose to avoid a biopsy, consider blood or genetic testing, health journaling, and elimination/challenge diets for best evaluating your symptoms under professional guidance.

Note: IgE testing through RAST does not measure gluten sensitivity or celiac disease. IgE refers to what most of us call “allergies” – more immediate, intense reactions like itchy skin, hay fever, and anaphylaxis. Identifying and removing IgE allergens are helpful in reducing inflammation associated with autoimmune conditions.

My unique set of symptoms included pain, bloating, fatigue, weight gain, depression, and hormone imbalances that slowly increased for years, baffling dozes of doctors before one discovered high IgG gluten antibodies, TTG antibodies, and probable celiac disease. I tested my family for food sensitivities with home-based blood testing kits (US BioTek lab) available from an online Florida doctor ( My entire family tested highly positive for IgG antibodies to gluten, dairy and eggs, and elimination of these foods resolved symptoms of their fatigue, ADHD, and digestive trouble. Interestingly, the gluten and egg antibody levels remained high when we retested after a year of complete elimination. I continue to experience intense autoimmune reactions after accidental exposure to allergens.

Unfortunately, throwing out the bread can put out the fire but not the embers. Even a strict gluten-free diet doesn’t resolve inherent bacterial imbalances, oxidative damage, and related malabsorption common to celiac and celiac-prone individuals. Research is showing how celiac sufferers are primed for these struggles from birth, and various triggers seem to hasten symptoms and severity.

Predicting the perfect storm

Wired for autoimmune challenge

Celiac disease features a strong, strategic adaptive immunity that programs our cells for attack of certain pathogens for the long-term. A more primitive, shotgun-type approach to fighting invaders is called innate immunity. Both types of immune responses are involved in celiac disease, triggered by a charged biological and environmental climate.

The DQ2 gene haplotype appears to be one of the biggest risk factors for celiac disease. 25% of Americans carry the riskiest DQ2.5 isoform that also associates with juvenile diabetes. Europeans in Ireland, Northern Spain, and islandic regions have the highest frequency of DQ2.5 while areas of Russian, Japan, and China have the lowest. Native American tribes from Central and Eastern America carry the DQ8 haplotype which, combined with DQ2.5, correlates with diabetes type 1 and 2.

Studies showed that even non-celiac first degree relatives of celiac patients have altered gut flora. It is not yet clear if and when genetically susceptible people should avoid gluten or take other precautions.

Gluten exposure from infancy through adulthood

Celiac disease, as currently understood, requires gluten consumption as a trigger. Both the DQ2 gene and per capita wheat consumption affect the prevalence of celiac disease in many countries. With a continued rise in the global consumption of wheat, there is an extreme urgency to understand celiac and prevent additional health risks.

If someone unknowingly has celiac disease and continues to consume gluten, they increase intestinal damage, malnourishment, and risk of many crippling diseases. More obvious symptoms of celiac include bloating, cramping, and diarrhea of varying degrees. Adults may experience vague symptoms like fatigue, joint pain, headaches, canker sores, rashes, anemia, depression, numbness, and miscarriages. Doctors do not routinely test for celiac, and proper diagnosis can take an average of 4 years.

The European Society for Paediatric Gastroenterology, Hepatology and Nutrition recommended avoidance of gluten introduction before 4 months and after 7 months in children, and encouraged introduction of gluten while children are still breastfed. Timing appears crucial in developing tolerance to gluten while establishing a diverse gut bacteria. Constipation in 2-year olds was also associated with gluten introduction prior to 6 months of age. As with other autoimmune diseases, breastfeeding shows some protection in the long term, though data is limited.

In addition to timing, the amount of gluten consumption may also correlate with risk as shown in regional Indian celiac rates as well as regional European celiac rates.

Bacterial imbalances

Bacteria is proving to play a monumental role in driving celiac disease, even prior to symptoms. Celiac patients have dramatic differences in gut bacteria populations. A lower diversity of lactic acid bacteria (LAB) and Bacteroides was found in patients with active celiac disease, and there were fewer populations of Bacteroides uniformis and Bacteroides ovatus. A new study on infants corroborates some of this data, revealing that breast-fed infants with low genetic risk for celiac had higher populations of Bacteroides uniformis, Bacteroides ovatus, and Bacteroides plebeius. Infants with high genetic risk for celiac showed a higher prevalence of B. vulgatus. The research indicates that both the type of milk feeding and genotype affect bacteria populations which may influence the risk of celiac disease. Similar gut dysbiosis has been shown in infants with cow’s milk allergy.

While scientists have not yet been able to identify or culture all of the bacteria in the gut, they have found too few gram positive bacteria and too many gram negative bacteria in celiac biopsies. Probiotics are primarily composed of gram-positive, lactic acid-producing species, and probiotics show some support for immune-mediated disorders. In one study, gram-positive Bifidobacterium actually inhibited inflammatory mechanisms normally caused by exposure to glutenPrebiotics are also helpful to support the growth of probiotics like Bifidobacteria. Prebiotics include inulin and oligofructose found in bananas, asparagus, artichokes, onions, and garlic.

Interestingly, gut microbiota is being linked to other complex conditions like obesity and type-2 diabetes.

Increased intestinal permeability

The intestinal lining is the door to our castle. When our intestines become increasingly permeable, we absorb harmful bacteria, fungi, and viruses. Celiac patients have linings that become highly permeable when exposed to gluten, even in trace amounts. The increase in permeability is driven by the release of an intestinal protein called zonulin that is excessively produced in celiac disease and type 1 diabetes. Intestinal permeability is appearing to play a lead role other autoimmune diseases like Crohn’s, H. pylori infection, liver disease, and food allergies.

While research has not been able to answer the question of whether intestinal permeability causes allergy and intolerance or the reverse, we do know more about how to improve intestinal permeability through diet. Intestinal permeability is dramatically increased by alcohol, aspirin, and anti-inflammatory drugs (NSAIDs). In one study of alcoholics, even periods of sobriety did not improve permeability results.

Exercise can increase permeability when fluids are restricted. Type of fluids can also have an effect; researchers found that athletes consuming regular milk before exercise had nearly double the increase in intestinal permeability compared to consuming colostrum milk.

Not surprising, chronic stress appears to increase permeability and inflammation in the gut, lasting for up to 7 days after psychosocial relief in rats.

Legumes, sweet peppers, mushrooms, paprika, L-tryptophan, linoleic acid, chitosan, medium chain fatty acids and surfactants can increase gut permeability. Cooking by roasting, grilling, broiling, or frying in moderate to high temperatures increases the production of toxic advanced glycation end products that are associated with increased permeability.

Foods that reduce permeability include oily fish, gamma-linoleic acid, nutmeg, and black pepper. Glutamine supplementation decreases permeability in animal studiesLactobacilli probiotics also help counteract increases in permeability. Another study described how certain bacteria levels affect intestinal permeability, suggesting that they might trigger celiac disease.

Trauma or infection

Symptoms of gluten sensitivity can precede intestinal damage and celiac disease, though the duration and type of symptoms vary greatly. I recall being sensitive to gluten for decades before experiencing the signs of irreversible celiac disease. My condition expanded to include chronic pain, fatigue, and depression after an oral surgery with subsequent mystery infection and antibiotics. Daily consumption of gluten fueled a constant flow of inflammation in my gut until I was tested over two years later.

Reports indicate that physical trauma, surgery, childbirth, viral or bacterial infection, antibiotic treatment, and severe stress can mark the onset of celiac disease in susceptible people. All of these triggers appear to share bacteria imbalances which pave a path to celiac and other autoimmune disorders.

Why is this happening?

Genetic shifts may offer benefits with risks

Our ethnicity and ancestry determine our genetic composition and shape our susceptibilities. European ancestry associates with celiac-prone DQ alleles as well as Type 1 diabetes. It would seem that our genes would have evolved to better protect us over many thousands of years. Yet genetic diversity appears to reduce as populations migrate from regions. Perhaps we are experiencing some consequences as our bodies race to catch up with dramatic shifts in diet and lifestyle over the past several generations.

Scientists are tracking how our genes are changing with cultural innovations as well. The lactase gene has mutated to support lactose tolerance in completely separate populations in the Middle East, Europe, and East Africa and where cattle domestication and milk consumption established. Some cultures that are not lactose persistent can digest fermented milk products such as yoghurt, cheese, and kefir which are low in lactose and take longer to pass through the intestines.

This information might help us understand our DQ gene, how it may be struggling with our modern gluten-based culture, and how we could alter gluten for better digestion. Genetic research is proposing the alteration of wheat proteins to remove allergenic properties. A less sophisticated approach by food scientists explored how sourdough (fermented with lactic acid bacteria) dramatically reduced gluten and enhanced available nutrients in a bread recipe! Here again, bacteria plays a role in moderating gluten.

Wheat crops have changed in genetic composition

The rate of celiac cases in the US has increased 5-fold since 1974. Scientists theorize that the disease may relate to agricultural changes to crops that affect the protein. A recent study confirmed that the genetic composition of wheat crops has changed in the past century. The celiac-sensitive Glia-α9 epitope in gluten was higher in modern crops, suggesting the possible link and encouraging alternate breeding for future crops. In fact, lab tests have found that the toxicity of gluten proteins can be eliminated by creating mutations with amino acid substitutions.

Other research explores the influence of modern sanitary lifestyles on the underlying bacterial imbalance. A fascinating study on genetically similar populations of people found that lower economic status and inferior hygiene associated with reduced rates of celiac disease. These results may support the popular idea that exposure to a wide variety of bacteria may provide protection against autoimmune disorders like celiac.

Fluoride-based fumigant insecticides taint wheat and eggs

Most of us are unaware that many foods like grains, nuts, coffee, cocoa, and dried fruits are stored in silos and warehouses for many months before going into production. During this period, mills and bakeries use fumigant insecticides for controlling pests, and foods do not need to be labeled for this treatment. Earlier this year, the EPA called for a phase-out of insecticide sulfuryl fluoride after new research has confirmed our excessive exposure to fluoride. Most notable is that the two foods with the highest “allowable” limits of fluoride residue are dried eggs and wheat. Heat treatment has been known to disinfest organic material for a century, but it is now being reconsidered by means of radio frequency.

Excessive fluoride exposure causes problems with oral and gastrointestinal health which overlap symptoms of celiac. The kidney and its antioxidant system is highly vulnerable to the toxicity of fluoride as demonstrated in a recent study on rats. While [sodium] fluoride may inhibit certain harmful bacteria in the mouth, we may be doing more damage to our gut bacteria by ingesting it in drinking water, fumigated foods, and fluoride toothpaste.

Associated conditions

Other autoimmune conditions

Celiac disease associates with many other autoimmune conditions like rheumatoid arthritis, asthma, eczema, Down, Turner, and Williams syndrome, Type 1 diabetes, and multiple sclerosis. Gluten sensitivity also associates with Sjögren’s syndromeStudies show that both schizophrenia and bipolar disorder associate with gluten sensitivity but through different immune mechanisms. There is a six to seven fold increase of celiac disease in autoimmune thyroid disease. There is an increased risk of psoriasis with celiac disease both before and after diagnosis, and psoriasis patients showed antibodies indicating active or latent celiac. The incidence of autoimmune disorders seems to relate to the duration of exposure to gluten.

A rare condition called Refractory Celiac Disease (RCD) involves persistent symptoms and intestinal epithelial damage despite a gluten-free diet. RCD type I is usually treatable, and RCD type II is considered a malignant stage between celiac disease and lymphoma.

Oral health

Dental enamel defects and canker sores are associated with celiac disease. A recent study revealed the genetic link between these dental enamel defects and celiac in children. Interestingly, the dental enamel defects were more prevalent in atypical or silent forms of celiac than typical forms of celiac. It is crucial for dentists to become educated about celiac disease and aware of these signs to help alert patients of underlying disease.

Low bone density with risk of fracture and back pain

Celiac patients have a higher risk of fractures prior to diagnosis. Treatment of celiac disease reduces this risk, indicating the importance of early detection. Further research suggests that both calcium malabsorption and inflammation play a role in bone mass loss seen with celiac disease and inflammatory bowel diseases. Unless a very strict gluten-free diet is followed, children and adolescents with celiac disease continue to have high risk for low bone mass density. Meeting recommended calcium and vitamin D intake is crucial for these individuals.

Vitamin/mineral malabsorption and deficiency

“With celiac disease mostly affecting the proximal small intestine, iron, folic acid, calcium, and fat-soluble vitamins are malabsorbed leading to iron deficiency, folate deficiency, and reduced bone density that is often not seen until adulthood.

Vitamin K deficiency in celiac patients can also lead to problems with coagulation. Vitamin K2 is linked to reduced risk of cancer and heart disease.

Iron deficiency links celiac disease with Restless Legs Syndrome, and it may be resolved with a gluten-free diet.

Fat malabsorption

Celiac patients show reduced levels of arachidonic acid, docosapentaenoic acid, and docosahexaenoic acid even after following a gluten-free diet.

Abnormalities in the colon

Even on gluten-free diets, celiac patients following a gluten-free diet showed microscopic and macroscopic abnormalities of the colon. The amount of eosinophils were much higher in the right (ascending) colon in celiac patients.

Risk of irregular heart rhythm

Patients with celiac disease are at higher risk for atrial fibrillation.


A study of 28,000 patients with celiac disease showed an increased risk of cataracts. Vitamin deficiency and malabsorption may play a role in this condition as well.

Hearing loss

Pediatric hearing loss was associated with celiac disease in a recent study. Similar associations were found in a small study of adults.

Epilepsy and ataxia

Neurologic symptoms like ataxia – lack of coordination – associate with the anti-TG2 antibodies that indicate celiac disease in mice. Similar associations are being discovered with epilepsy and peripheral neuropathy.

Abnormal response to hepatitis B vaccine

Researchers have recently discovered that children with celiac disease showed a significantly low immune response to the HBV (hepatitis B virus) vaccine. Incidentally, all of the subjects showed a low response to the pertussis vaccine. (See previous blog entry “Pertussis: know the vaccine, the epidemic and your rights“)

Parts of both the gluten protein (gliadin peptide) and the hepatitis B virus (HBsAg) bind to the DQ2 gene. This binding competition may affect the immune response, suggesting new concerns for vaccines and undiscovered disease susceptibility.

Short stature in children

While it is not clear why celiac disease associates with short stature in some children, one theory points to the development of antibodies against the pituitary gland.

Sleep quality

Sleep quality appears reduced in celiac patients, but gluten-free dieting does not seem to improve results. Sleep quality was related to depression, anxiety, and fatigue.

Heart disease

A nationwide Swedish study showed an increased risk of heart disease in patients with asymptomatic celiac disease or small intestinal inflammation.

Cancer of the intestines

When celiac disease goes undiagnosed or ignored with continued consumption of gluten, there is a higher risk of intestinal lymphoma. The increased risk of cancer is limited through the first year after diagnosis. In general, the risk of cancer increases with multiple autoimmune diseases, and inflammation may play a role in the development. One study found the risk of non-Hodgkin lymphoma was increased fourfold in patients with gluten-sensitive enteropathy including celiac.

Is gluten-free guaranteed?

While most symptoms can be resolved with a strict gluten-free diet within months, studies are showing that the autoimmune programming remains abnormal for many types of cells. In addition, a gluten-free diet fails to improve the unhealthy imbalance of bacteria in the gut. While intestinal inflammation was relieved in celiac patients on a gluten-free diet, their beneficial Bifidobacterium and Lactobacillus bacteria counts remained low. One study observed that healing of damaged villi plateaued at only half of normal size after 6-12 months of gluten-free dieting. Furthermore, oxidative damage to some DNA appears to be the same in both treated and untreated celiac patients. According to these findings, antioxidant vitamins A and E might be important for celiac patients to reduce cancer risk.

Children and adolescents with celiac showed increased anxiety and depression while managing their condition by avoiding gluten. Studies showed that a week-long gluten-free camp helped remedy these symptoms. In children and adults, emotional adaptation to the diet may require many months to a year. Other research showed that asymptomatic celiac patients actually experienced reduced perception of health and well-being on the diet. As celiac disease education and awareness increases and food options expand, the associated emotions with gluten-free dieting may likely improve and encourage early detection and long-term adherence.

Some people try gluten-free dieting to lose weight or reduce mild symptoms. While the diet usually improves both overweight and underweight conditions, some studies found that a surprising number of overweight patients gained weight. In all cases of celiac or gluten sensitivity, long-term nutritional counseling is strongly recommended. This phenomenon underscores the importance of a broader treatment of autoimmune disease that includes diet, bacteria balance, and reduction of environmental triggers.

Friends don’t let friends eat gluten

In light of this latest research, I encourage early detection and strict dieting even for the mildest gluten-sensitive symptoms. Fatigue increases and quality of life diminishes in people with undiagnosed celiac disease. Our immune system is completely dependent on a healthy gut which can be irreversibly damaged with our modern diet and environmental toxins. Infections can precede autoimmune disease, so protection from bacteria and viruses may help reduce risk in susceptible individuals. As a general rule, daily probiotics can increase healthy bacteria levels while researchers scramble to identify which ones are most critical to celiac disease, diabetes, obesity, and other puzzling conditions. For people at risk or suffering from autoimmune disease, avoiding alcohol and NSAIDs may help prevent further damage to highly permeable intestines.

Fortunately, gluten-free diets are no longer a prison sentence of cardboard pizza and bean sprouts. Many gluten-free breads and baking mixes are just as good or better than wheat-based equivalents. Some of my favorite allergen-free foods are listed online with purchasing links. Gluten-free foods can usually be found at smaller health-conscious grocery stores, Whole Foods markets, and specialty retailers or manufacturers’ web sites.

The latest insights on celiac Disease can be found in the August 2011 issue of the International Reviews of Immunology that is dedicated entirely to Celiac Disease.

To good (gluten-free) health,

-Shari Cheves

2 comments to Celiac and bacteria: strange breadfellows

  • GoodBelly makes a non-dairy probiotic drink, but I recommend the non-dairy, high-potency, refrigerated probiotic capsules that are available in health food stores or markets such as Whole Foods.

  • Most probiotics readily available in supermarkets are milk based. This makes it difficult for a person sensitive to dairy products to access. Is there another way of taking probiotics ?

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