The Surprising Cause of Food Allergies and How to Treat Them

Dr. Frank Shallenberger, MD

February 10, 2020



Food allergies can cause everything from auto-immune diseases to migraines to rashes to intestinal problems. But, what causes food allergies? And why do people who have never had food allergies suddenly get them?

The answer might surprise you. But the good news is that the surprising answer will also show you how to treat them.

Almost two decades ago, University of Chicago immunologist Dr. Cathryn Nagler began to suspect that the body’s intestinal bacteria played a role in food allergies. That was because a handful of studies in the 1980s and ’90s of germ-free mice had shown that certain bacteria in the gut and the compounds they produce are important in teaching the immune system not to overreact to the foods we eat. One of those compounds is lipopolysaccharide (LPS)

Dr. Nagler discovered a study in which researchers looked at mice that were genetically unable to respond to LPS. When the researchers exposed these mice to freshly ground peanuts they went into a severe and sometimes fatal allergy reaction called anaphylaxis. The mice could not respond to LPS because they lacked a protein that is activated by certain intestinal bacteria. This made Dr. Nagler wonder if the balance of bacteria in the intestines had anything to do with why some people get food allergies. So, she conducted an experiment.

She treated a group of mice with broad-spectrum antibiotics to kill off their intestinal bacteria, and found that they started having severe reactions to certain foods. According to the doctor, “That established a role of signaling by bacteria in the gut in regulating responses to food.” Since then, the information has been mounting that our intestinal bacteria have a big say in whether or not we will develop food allergies.

An estimated 6% of children and up to 10% of adults in the U.S. have an allergy to some food. And the numbers are steadily increasing. Scientists like Dr. Nagler are increasingly finding connections between a person’s intestinal bacterial balance and whether or not that person has a food allergy. Intestinal balance also determines which children will outgrow their food allergies and which won’t.

Engineering Food Allergies Is Possible

A few years ago, Dr. Nagler and her colleagues conducted an experiment on mice that had been treated with antibiotics to kill off all of their intestinal bacteria. They split the mice into three groups. They treated the intestines of one group with fecal samples from healthy human infants. They treated the intestines of the second group with fecal samples from infants with cow’s milk allergy. This had the effect of creating the same balance of bacteria in the mice that was present in the infants. The third group they left alone. The results were amazing.

The mice that received samples from the babies allergic to milk became allergic to milk. On the other hand, the mice that had received the samples from the healthy infants did not develop the allergy. When they examined the balance of the various bacteria in the mice, they discovered that the absence of one particular bacterium, Anaerostipes caccae, was responsible for the milk allergy. When they took this particular bacterium and transferred it to other mice it protected the mice from developing a milk allergy.

In another study, researchers at Boston Children’s Hospital had similar results with egg allergies. They divided a group of mice with severe egg allergy in half. They transplanted fecal material from healthy human babies into one group and found that it protected the animals against an allergic response. But, when they transplanted fecal material from babies with food allergies, the allergic responses persisted. They later discovered that feeding allergic mice a mix of Clostridium or Bacteroides bacteria or the single species Subdoligranulum variabile protected them from egg allergy. This study caught my because of something I learned in another study.

That study found that when the researchers gave antibiotics to mice without any other intervention, those mice go on to develop elevated levels of immunoglobulin E. That’s important because immunoglobulin E is the class of antibodies that causes food-allergic reactions.

All of this reminded me of the first experiment, the one in which Dr. Nagler and colleagues killed off the intestinal bacteria of three groups of mice. You might remember that one of the groups was not treated with any fecal material. What happened to them? They also developed milk allergies just like the mice who had received the fecal material from the allergic babies. Combine these two observations and you have to wonder if the amazing amount of antibiotics that we get exposed to from doctors and in the foods we eat may be why we see so many food allergies these days.

What About Probiotic Supplementation?

Probiotics influence the balance of intestinal bacteria. Perhaps they can help with food allergies. Good idea, but, not so fast. According to Rima Rachid, a co-author of the Boston Children’s Hospital study, “When it comes to probiotics, so far the studies done are not very definitive. The approach is worth pursuing further but nothing definite so far.”

The balance of bacteria we have in our intestines is determined by a lot of different factors, including our diets, stress, antibiotic use, and exposure to bacteria. Diets high in fiber produce healthier intestinal bacterial balances. Stress and antibiotics do the opposite. And this phobia that our modern culture has of bacteria with the resulting obsession with antibacterial soaps, mouthwashes, and wipes is also a problem. These sources of anti-bacterial chemicals undoubtedly affect intestinal bacterial balance.

Protecting Our Children

These habits can also affect children. We certainly don’t want our children to develop food allergies. But we often let our fears move us in the wrong direction. According to a recent study published in the Journal of the American Medical Association, there’s a 5.4% chance that a child will develop an allergy to eggs. And there’s a 2.5% chance of a peanut allergy. It’s easy to assume that the best way to avoid the possibility of developing an allergy to these foods is to delay feeding the foods to babies in their first year of life. But, surprisingly, that’s not what these researchers discovered.

The authors of the study were looking to see if the timing of when certain typically allergenic foods such as eggs, peanuts, gluten, and fish were put in an infant’s diet would influence the risk of subsequent allergies or autoimmune diseases. So, here’s what they did. They searched the published literature for any trials that examined this question that were published in the last 70 years. They were looking specifically for studies that evaluated wheezing, eczema, allergies, hay fever, food allergy, type-1 diabetes, celiac disease, inflammatory bowel disease, autoimmune thyroid disease, and juvenile rheumatoid arthritis. Here’s what they found out.

First of all, there was no connection in any of the studies that feeding babies various foods will somehow place them at risk for any autoimmune disease. That doesn’t happen. But the interesting thing was that the age that an infant is when you start adding eggs and peanuts to his diet can determine whether he becomes allergic to these foods.

The researchers found “moderate-certainty evidence from 5 trials (1,915 children) that early egg introduction at four to six months was associated with reduced egg allergy.” That’s right! When you give babies eggs at the four-to-six-month interval, they will be on average about 56% less likely to develop an egg allergy than if you wait until they are older to give them the eggs. They found a similar result with peanuts. Introducing peanuts to four-to-six-month-old babies made them 29% less likely to be allergic to peanuts as they grew up.

According to the lead author of the study, Robert J. Boyle, MD, PhD, of Imperial College in London, “In an infant whose family usually consumes egg and peanut, we can be reasonably confident that delaying egg and peanut introduction increases the infant’s risk for allergy to those foods.” He goes on to say, “As long as there’s no eczema or other sign of food allergy, then it seems reasonable to introduce egg and peanut when other complementary (solid) foods are introduced to the infant diet.” The timing of the introduction of the other foods studied (gluten and fish) was not associated with any allergy risk, just peanuts and eggs.

Eggs are certainly one of the best foods we can feed our kids. Next to breast milk, eggs are the most complete protein you can eat. And be sure to give them the yolk. Much of the nutritional value of eggs is in the yolk. Egg whites by themselves are virtually useless nutritionally speaking. Peanuts are also a great source of protein, vitamins, and minerals. So, don’t hesitate to give your babies these foods when they reach that age of four-to-six months and start taking in solid foods. The biggest concern with peanuts at this age is choking. So consider giving them small amounts of organic peanut butter.

If you or your parents didn’t have this information at the right time, you or your children might have developed an allergy. And, of course, food allergies are still possible even if you follow the best introduction timeline. This will just reduce your risk, not eliminate it altogether. So, if you are still plagued with food allergies, do your best to avoid antibiotics, foods treated with antibiotics, and GMO foods. Eat a diet high in fiber. And, just to be safe, take a good probiotic like Advanced Probiotic Formula two to three times a week.


Could Manipulating the Microbiome Treat Food Allergies? By Jef Akst. Jul 9, 2019

Microbiota therapy acts via a regulatory T cell MyD88/RORγt pathway to suppress food allergy.

Abdel-Gadir A, Stephen-Victor E, et al. Nat Med. 2019 Jul;25(7):1164-1174.

Bashir ME, Louie S, et al. Toll-Like Receptor 4 Signaling by Intestinal Microbes

Influences Susceptibility to Food Allergy. J Immunol June 1, 2004, 172 (11) 6978-6987

January 2017:

Ierodiakonou, D., V. Garcia-Larsen, et al. “Timing of Allergenic Food Introduction to the Infant Diet and Risk of Allergic or Autoimmune Disease: A Systematic Review and Meta-analysis.” JAMA. 2016 September 20;316(11):1181-1192.

“Preventing Food Allergies May Start in Infancy,” Medpage Today,

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