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Attenuating My Patient’s Chronic Allergies by Altering her Microbiome

Understanding nutrition’s impact on the prevention of allergic diseases, to put it mildly, is biochemically complex and temporally dependent. For example, we know that even before conception, maternal consumption of polyunsaturated fatty acids, pre-, and probiotics have a protective role in preventing allergic diseases

In other words, if you really want to do all you can to prevent allergies, you would need to go back to before you were born. Of course, we can’t go back in time and change our mother’s diet to alter the critical macro- and micro-nutrients we needed during this period of our development. But it’s never too late to make strides with dietary and lifestyle interventions in the present.

Let me illustrate three important points about the gut and allergies and then discuss a patient who came to see me for chronic allergies.

  1. Specificity of probiotic strains matters. 

In a study by Luoto and colleagues (2010), high levels of the bacteria Lactobacillus rhamnosus GG and Bifidobacterium lactis Bb12 inside the gut were found to improve barrier function of the small and large intestines allowing reduced risk of common allergic diseases and intestinal infections. Supplements of these specific strains in children also led to long-term safety, unlike with most pharmaceutical drugs.  Other strains of L. rhamnosus and B. lactis did not improve health at all. Strain specificity of the bacteria is essential to improving gut function and preventing allergies.  

  1. Modulation of the microbiome in early life can attenuate allergic disease.

The protocol for developing a healthy gut microbiome is similar to the protocol for maternal nutrition:  eat a nutrient-dense fiber-rich diet with prebiotics, probiotics, and synbiotics (i.e. food sources that combine both prebiotics and probiotics), plus non-digestible oligosaccharides, human breast milk oligosaccharides and/or prebiotic oligosaccharides (Osborn & Sinn, 2013; Cuello-Garcia, et al., 2015; Chang, et al., 2016). 

Oligosaccharides are small but complex carbohydrates that, due to their chemical configuration, resist being broken down by salivary and intestinal digestive enzymes. While these sugar molecules may not be digested and absorbed by us, it is food for our friends in the colon, where the oligosaccharides are fermented by anaerobic bacteria (Roberfroid, 1997).

While the mechanism of microbial composition/activity on allergy development is not concrete, diversity of the microbiome appears to be the law of the land. Sjögren and colleagues (2009) observed that children who were eventually diagnosed with allergies were significantly less likely to be colonized with strains of L. rhamnosus, L. casei, L. paracasei, B. adolescentis and Clostridium difficile two months post birth. This would indicate that greater microbial diversity early in life, if balanced with beneficial strains, likely prevent allergy development.

  1. After being weaned from breast milk, expose, expose, expose!

Introduction of food (and pollen) is all about timing. It's the context in which this first introduction has the biggest impact on allergy development—the context (diet of the mother, breast or formula fed, rural or urban home environment, exposure to pets or no exposure, etc.) sets the stage for the allergic state of the individual. Context plays a HUGE role in whether a child will develop food allergies.

With each passing year, it’s becoming clear that the infant's microbiome has a direct effect on the person’s future risk of developing food allergies. Infants exposed to vaginal fluid during vaginal delivery dramatically helps create a healthy microbiome. Conversely, infants born via C-section are at higher risk for food allergies. When these infants delivered via C-section were exposed to their mother's vaginal fluid right after delivery, it dramatically increased their tolerance to their environment (i.e. food exposed to in the future). Adding plant-based prebiotics and probiotics, either through supplementation or milk formula, also showed benefit for the babies by decreasing their risk of developing new food allergies (Nowak-Węgrzyn & Chatchatee, 2017).

With this background information, see if you can guess what was wrong with a young student named Carmen who came to Advanced Health this summer for chronic allergies. 

One of the first things she told me was that she had felt anxious her whole life. By the time Carmen entered high school she had been started on an SSRI antidepressant.   SSRI’s are known to negatively impacted gut function and led to excess weight gain for Carmen.

A few years later, Carmen was diagnosed with Irritable Bowel Syndrome (IBS) as a result of her already damaged gut function.  Her symptoms of severe bloating, nausea, abdominal pain, and diarrhea were exacerbated during a trip to Latin America, and she was treated with multiple rounds of potent antibiotics. During this time, Carmen was diagnosed with a large benign thyroid mass and many food allergies (i.e., dairy, red meat, eggs, poultry, fish, wheat, potatoes, sweet potatoes).  Carmen had to do something to stop from getting sicker. 

During my first appointment with Carmen her history alone indicated a low count of beneficial gut bacteria, and damaged intestinal cells. Urine toxicology tests showed extremely high levels of dangerous herbicide Round- Up (glyphosate), along with the carcinogen Acrylamide (found in plastics, agrochemicals, and when consuming foods and drinks cooked at high temperatures). Carmen also had extremely levels of toxins derived from multiple mold species (Chaetoglobosin A, Ochratoxin A, citrinin, sterigmatocystin, and mycophenolic acid).  These mold species are often found in foods which require a great deal of water for production and must be sprayed heavily in order to withstand their long journey from agriculture to marketplace. The most common foods rich in mold are coffee, wheat, corn, soy, animal protein (i.e., dairy products, all meats, poultry, fish, eggs), nuts, dried fruit, and wine.  

We shifted Carmen to a plant-based diet full of fresh produce, with limited to no consumption of GMO crops (i.e., corn, soy, wheat), alcohol, and coffee.  Within two weeks Carmen’s chronic allergies remarkably improved and she could stop taking daily oral antihistamines. 

Carmen also began drinking more warm water and becoming more mindful of how and when she ate.  As her allergies symptoms dramatically decreased, Carmen was sleeping better and feeling more energized during the day.  Her mood became more hopeful and happy allowing her to decrease her antidepressant dose in 3 weeks. Within one month of us working together Carmen was no longer experiencing daily allergy symptoms and chronic digestive problems. She was over-the moon happy to stop taking her 15+ “natural” supplements and start seriously contemplating discontinuing her SSRI for good.  It was the first time in Carmen’s adult life she could imagine being off of medications and feeling good!

Dr. Bhandari and her Advanced Health Team Are Here to Support Your Health. Dr. Bhandari, M.D. and her Advanced Health team of experts work closely together to help patients like Carmen dramatically improve their gut health. They’re always ready to share their expertise on optimal gut repair and healing. To book an appointment, contact Advanced Health or call 1-415-506-9393.




Chang, Y. S., Trivedi, M. K., Jha, A., Lin, Y. F., Dimaano, L., & García-Romero, M. T. (2016). Synbiotics for prevention and treatment of atopic dermatitis: a meta-analysis of randomized clinical trials. JAMA pediatrics, 170(3), 236-242.

Cuello-Garcia, C. A., Brożek, J. L., Fiocchi, A., Pawankar, R., Yepes-Nuñez, J. J., Terracciano, L., ... & Schünemann, H. J. (2015). Probiotics for the prevention of allergy: a systematic review and meta-analysis of randomized controlled trials. Journal of Allergy and Clinical immunology, 136(4), 952-961.

Luoto, R., Laitinen, K., Nermes, M., & Isolauri, E. (2010). Impact of maternal probiotic-supplemented dietary counselling on pregnancy outcome and prenatal and postnatal growth: a double-blind, placebo-controlled study. British journal of nutrition, 103(12), 1792-1799. 

Nowak-Węgrzyn, A., & Chatchatee, P. (2017). Mechanisms of Tolerance Induction. Annals of Nutrition and Metabolism, 70(Suppl. 2), 7-24.

Nurmatov, U., Devereux, G., & Sheikh, A. (2011). Nutrients and foods for the primary prevention of asthma and allergy: systematic review and meta-analysis. Journal of Allergy and Clinical Immunology, 127(3), 724-733. 

Osborn, D. A., & Sinn, J. K. (2013). Prebiotics in infants for prevention of allergy. The Cochrane Library.

Roberfroid, M. B. (1997). Health benefits of non-digestible oligosaccharides. In Dietary Fiber in Health and Disease (pp. 211-219). Springer, Boston, MA.

Sjögren, Y. M., Jenmalm, M. C., Böttcher, M. F., Björkstén, B., & Sverremark‐Ekström, E. (2009). Altered early infant gut microbiota in children developing allergy up to 5 years of age. Clinical & Experimental Allergy, 39(4), 518-526.

Dr. Payal Bhandari Dr. Payal Bhandari M.D. is a leading practitioner of integrative and functional medicine in San Francisco.

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