Category Archives: Gut Dysbiosis

Using Bacteria to Recover My Child from Autism

Learn from yesterday, live for today, hope for tomorrow. The important thing is not to stop questioning.- Albert Einstein
Last weekend, my 3-year-old daughter and I were grocery shopping. She busied herself narrating a vegetable monologue, while I bagged up some bananas. Another shopper stepped between us, and my daughter lost sight of me. I silently watched to see how she would react. Her eyes darted around to find me, and then she hurried over to stand nearby.

A giant smile spread across my face.

Less than 18 short months ago, my daughter would have happily gone home with any stranger in that store. She did not know who I was. She did not know who her father was. And we cared for her 24/7.

If you look closely at my daughter’s bed, you will notice adhesive residue all over the frame. At 8 months of age, I found her in bed with a black eye. That same day, my husband taped foam pipe insulation around each bar of her crib. We were trying to protect her – from herself.

She was fearless, and seemed almost immune to physical pain. Her hyperactivity was extreme. She had a constant and relentless nervous energy that bordered on seizure-like behaviors. An MD specialist told us that her fixation on tiny objects, and repetitive physical movements, were early signs of Autism.

Then there were the developmental delays. Sitting up, rolling over, standing, walking, talking – she was significantly delayed on every milestone.

Along for the ride were the medical issues. Food sensitivities to EVERYTHING, GERD, a primary immune deficiency, epic insomnia, bacterial imbalances, appetite loss, failure to thrive, and vitamin and mineral deficiencies. That’s just what I can remember.

TODAY- she is unequivocally one of the happiest, healthiest, most loving and charismatic 3-year old’s you will ever meet. The journey between then and now has been epic, and life changing. I would not wish what we have been through on my worst enemy.

It was years spent poring over research studies, and learning from other parents on a similar path. I sought out doctors who understood the source of my daughter’s issues. We used lab work to identify vitamin/mineral deficiencies, and supplements to fill those gaps. We rotated nutrient dense foods, to prevent her immune system from reacting to them. We identified and eliminated any foods and food chemicals that provoked acute reactions in her. As much as possible, we reduced exposure to toxins from food, water, household cleaners, detergents, soaps, lotions, fragrances, cookware, vaccines, medications, and electrical devices.

And I prayed, pleaded, screamed, swore, cried, and begged. Some days were better than others.

But everything helped, and she recovered. Slowly. But as the months went by, we hit a wall. She was better – much less violent and self-injurious. I fought to convince myself that this might be as good as it would get. And I continually reminded myself how much worse it used to be. But, I could not shake the feeling that we were still missing something.

I heard a gentle, yet constant message: “This is not your daughter.”

So, I continued my infinite quest for answers. Soon after, a book showed up in my recommended feed. It was titled “Brain Maker: The Power of Gut Microbes to Heal and Protect Your Brain-for Life”, and it was ranked #1 in the category of Autism.

From the very first page, I could not put it down. It was like reading my own personal medical history. Heavy childhood antibiotic use – check, poor nutrition – check, frequent illness – check, food/chemical sensitivities – check, frequent GI distress, anxiety, insomnia – check, check, check.

And more importantly, were the parallels between the author’s patients and my daughter. The stool analysis of a young Autistic patient revealed he was missing an important strain of beneficial bacteria. Chills immediately shot up and down my spine. My daughter’s stool analysis lab results were identical to this child’s. The author suggested the patient’s mother try introducing probiotics with the missing strain(s) directly to his colon. Long story short, that child is no longer Autistic.

I was intrigued. Our integrative MD had suggested a probiotic suppository in the past, but it had been lost in the sea of our treatment trials. Now armed with the knowledge of how it might help my daughter, I was compelled to try. I contacted my colonic hydro-therapist for advice on how to administer a liquid suppository to my toddler, and probiotic dosage recommendations.

The results were nothing short of miraculous. Of all the treatments we have used, none have had the dramatic effect this did. Almost exactly 48 hours after the first treatment, she slept 14 hours through the night. And she woke lethargic. I thought something was wrong, that she must be sick. She was not sick. Her physical body was simply exhausted. This poor child’s nervous system had been operating on hyper-drive for nearly 2 years of her life. And now, it had finally downshifted.

Two weeks after the first treatment, she hugged me for the first time ever and soon began calling me ‘Mama’. A week later, she saw something that startled her on the television and came running to us for comfort. She took a minor fall on the kitchen tile, hit her head and began to cry. These might sound like normal childhood behaviors, but they were all new to her.

Within a month of starting the treatment, her hyperactivity reduced dramatically. She could sit with me long enough to read a short book, or watch a television program. And she continued to sleep a solid, uninterrupted 10-13 hours. Every. Single. Night.

Her energy, pain, and fear thresholds all normalized. She began to exhibit empathy and caution. Her epic tantrums subsided, and her extreme mood swings were replaced with a calm complacency that I didn’t even know was possible. There were countless subtle changes in her, too many to remember and list.

In short, I met my daughter for the first time when she was about 19 months of age.

I cry tears of happiness every time I share our experience with someone, and as I’m writing about it now. It still feels completely unreal that a teaspoon of probiotic-rich water – gave me back my daughter. I don’t know that this treatment will work the wonders for anyone else that it did for us. But I want to tell our story, if it means it may help even one more child.

With Peace & Love,

Curing Recurrent Ear Infections

“I keep treating my child, but their ear infections continue to reoccur.”

The number one question that I believe gets missed too frequently and is critical to stopping chronic ear infections is: Why?
Your provider does a great job of identifying the ‘What’ –type and severity of ear illness. This article provides resources to tackle ‘How’ to treat, but figuring out the ‘Why’ is going to require detective work on your part.
Chronic ear infections are caused by two things:
•structural abnormalities (i.e. babies with Down Syndrome or other genetic disorders have small ear structures that may be inverted and poorly move fluid out)
•environmental triggers that create inflammation resulting in increased fluid
I am going to discuss environmental triggers. An Audiologist and/or ENT would be the professional to diagnose structural abnormalities as a potential cause of recurrent ear infections.
But how can a food allergy cause an ear infection?
Eating an offending food will create inflammation in the body. One way inflammation is expressed is an increase of fluid and congestion. This can look like recurrent ear infections, puffy eyes, frequent runny nose, allergic shiners under eyes, excess phlegm, etc. snot bubble

“The middle and inner ear are immunologically responsive and this includes responsiveness to food hypersensitivities. Both chronic otitis media with effusion and Meniere’s disease can improve with treatment of food allergies.” ¹ Other common signs of inflammation include eczema, rashes, and asthma. Symptoms sounding familiar?
In a study that looked at the association between recurrent otitis media with effusion and its association to food allergies, “the most common food found to be associated was milk, egg, beans, citrus, and tomato.”²  They removed the food(s) for a few weeks; symptoms resolved. They added the suspected offending foods back in; symptoms returned. This practice is commonly referred to as an Elimination Diet.
So Milk and Eggs are top causes of recurrent ear infections in this study. They are also on the Top 8 Food Allergens list for the world.

topeight  Allergy to milk is THE most common food allergen in the entire world! This is not rare. So, why aren’t parents being advised to eliminate milk for 30 days as a Least Invasive, evidence-based approach to chronic otitis media?

This is how I observe it usually play out…
Ear infections begin around age 1. Round(s) of antibiotics resolves. Next month, new ear infection occurs. Repeat same antibiotics treatment. Following month, same thing again. Professional assures you that if it happens again your child is a candidate for PE Tubes (Do they expect us to start cheering?). Next month, guess what? Yep, ear infection again. PE Tube surgery is scheduled and completed under general anesthesia. You are relieved that this is over… Unless you have one of the thousands of children that go on to have continued drainage issues sometimes resulting in the surgically-placed tube falling out. No problem. They will surgically put the tube right back in under general anesthesia. Repeat the cycle of most invasive, symptom-focused treatment…
This story is far too common. As an early interventionist and a Hearing Specialist I can tell you that this same story is told to me monthly. Every time I ask the parent, “What did the professional say is CAUSING the ear infections?” ***crickets***
“They never talked about a cause…”

So I begin asking basic, non-medical questions.

Me: You said ear infections began monthly around age 1. What else changed around age 1?
Parent: I can’t think of anything. She wasn’t in daycare yet, no illnesses.
Me: What did she eat or drink around that time?
Parent: We switched her over from Breastmilk/formula to cow’s milk after her 12 month checkup. **ding ding ding**
Me: Does anyone in the family have food reactions?
Parent: Well I am lactose intolerant, but she hasn’t showed any negative reactions to dairy thankfully.

And this is the problem. Intelligent, well-intentioned, loving parents have ZERO clue that the #1 Allergen in the whole wide world can CAUSE ear infections. And they are led on a journey of pharmaceutical and surgical interventions, many times without any discussion of there being a  cheap, easy, and less invasive solution for the vast majority. And all the literature that clearly demonstrates the association is never discussed even with high risk families such as parents with a history of food intolerances.

Here is what I wish would occur…
12 month check up:
Pediatrician: Many kids start cow’s milk at age 1. Do you or anyone in your immediate family have a history of food allergies/intolerances, eczema, allergies, or asthma?
Parent: Yes, I am lactose intolerant, have asthma and allergies. My other child has eczema and allergies.
Ped: Well, dairy is the #1 Allergen and with your family history you may want to either wait to introduce dairy or observe for the following signs that a reaction is occurring…

Ear Infection Appointment:pediatrician-2
Pediatrician: Here is a list of Ear Infection treatment options. If there are no signs of other infections in the body, let’s pursue a Least Invasive to Most Invasive approach. This means we will save antibiotics as a last resort.


Recurrent Ear Infection Appointment:
Pediatrician: What new foods or environmental triggers has your child been exposed to?
Let’s try 6 weeks of an Elimination Diet of the Top Allergens to see if food is a factor. Let’s also review the treatment options so we can pursue a Least Invasive to Most Invasive treatment path. Read my other article, Treatment Options for Ear Infections: A Least Invasive to Most Invasive Approach.

I used examples citing cow’s milk as the culprit because it is the most common. However, any food can cause an inflammatory response. We are all individuals with individual responses. There are a variety of ways to identify food culprits. To read about Why and How to do an Elimination Diet to identify food triggers read Dr. Axe’s article.
Remember to assess your child’s environment for other environmental triggers as well. The Top 6 Environmental Allergies list.
Check products that you put on your child by using an app like Skin Deep to see the Environmental Working Group’s toxicity rating on skin products, foods, cleaning products, and more.

The most important focus of this article is empowering parents to ask Why questions and Cause questions. These are the questions that will Heal Our Little Ones.

  1. The role of food allergy in otolaryngology disorders. Ramakrishnan, JB. Curr Opin Otolaryngol Head Neck Surg. 2010 Jun;18(3):195-9.$=activity
  2.  Recurrent otitis media with effusion and food allergy in pediatric patients.  Arroyave CM. Rev Alerg Mex. 2001 Sep-Oct;48(5):141-4.

The Autism Intensive – Expert Interview Series

38 functional medicine experts expose the latest science about the gut microbiome, immunity, and methylation.
The Autism Intensive

And be sure to check out Dr. Thomas’ newly released book for additional tips on keeping your family healthy and protected.
The Vaccine-Friendly Plan: Dr. Paul’s Safe and Effective Approach to Immunity and Health-from Pregnancy Through Your Child’s Teen Years

A Reflux Revelation

Gastroesophageal Reflux Disease (GERD)

  • Sixty percent of the adult population will experience some type of gastroesophageal reflux disease (GERD) within a 12 month period and 20 to 30 percent will have weekly symptoms. 1
  • Approximately seven million people in the United States have some symptoms of GERD. 2
  • In 2004, approximately 20 percent of the United States population reported reflux symptoms that occurred at least weekly. 3
  • Primary or secondary GERD diagnosis increased by an unprecedented 216 percent or from a total of 995,402 individuals diagnosed in 1998 to 3,141,965 in 2005. 4
  • Children with GERD symptoms who were hospitalized with a primary GERD diagnosis increased by 42 percent in infants and 84 percent in children between the ages of two and 17. 5
  • There are approximately 64.6 million prescriptions written for GERD medications in the United States on an annual basis. 6
  • It is estimated that worldwide, approximately 5 to 7 percent of the total population has symptoms of GERD, which is most commonly reported as heartburn that occurs on a daily or frequent basis. 7

Ask the average person what they think causes heartburn, and they will probably tell you it’s stomach acid. While largely unproven, this conclusion has been widely accepted and likely derived from the ‘burning’ sensation, and success with treatment using proton pump inhibiting (PPI) medications like Nexium, Prevacid, and Prilosec. PPI medications reduce gastric acid by blocking the gastric pump of stomach parietal cells, so one would naturally assume the reduction in acid is to credit for the relief in our associated ‘burning’ GERD symptoms.

However, what most people don’t realize, is that PPI medications can also serve as powerful anti-inflammatories. 8 In fact, a published study review concluded that PPI medications potentially have beneficial effects in any number of inflammatory diseases, gastrointestinal or extra-intestinal, in which acid has no role, and a positive clinical response to PPIs should not be interpreted as proof of an underlying acid-peptic disorder. 9 The review goes on to suggest that patients may be mistaking their symptom improvement on PPI medications as acid reduction, when in fact it is a reduction of inflammation within their gastrointestinal tract. 10

And there is further compelling evidence bringing into question the presumed etiology of GERD, from a recent study done on 12 patients being treated with PPI’s for their reflux esophagitis. 11The study concludes that the damage done to each patient’s esophagus was not caused by stomach acid, but by an inflammatory immune response. 12

So, let’s review: For some of us, the pain we know as ‘heartburn’ potentially has nothing to do with the gastric acids produced by the stomach, and instead is the result of immune inflammation and aggravation within the upper gastrointestinal tract/esophagus. PPI medications are anti-inflammatories so they are potentially reducing the inflammation, thereby eliminating the associated pain. Sounds like the perfect treatment solution, right?

That is, until you consider the risk of side effects – especially with long term use of PPI medications. Adequate stomach acid is a necessary and relevant part of the metabolic process, and there are adverse consequences to habitually reducing/eliminating it. PPI use has been linked to the predisposal of certain infectious diseases, dementia, kidney disease, heart attacks, stroke, vitamin deficiencies, bone fractures, and gut dysbiosis – just to name a few. 13 14

But there is an alternative option: Determine what is triggering the immune inflammation in your GI tract and eliminate it. It will cost you nothing, except some time and effort, there is no risk of any adverse side effects, and you may end up eliminating other cryptic inflammatory symptoms you did not even realize were associated to the exposure.

My advice? Start by removing some of the top allergen offenders from your diet one at a time, and see if you notice a difference in your GERD symptoms. And start paying attention to what you’ve been exposed to recently when your symptoms are at their worst. Did you suffer with heartburn all night after eating a bowl of ice cream? That should raise dairy up to the top of your suspect list. With time and practice, your allergen detective skills will improve, but try to keep it simple initially. And bear in mind that there may be multiple allergens contributing to your symptoms, and the sources may potentially include environmental triggers (lotions, detergents, soaps, pollen, cat dander, etc.), in addition to food or medication.

InfantGERDThere is another chapter to this story we have not yet explored: Infant gastrointestinal reflux disease, and this is where things become slightly more complicated. There is no question that the use of PPI medications in infants and young children is skyrocketing. One large study of about 1 million infants revealed prescriptions for one of the PPIs, made in a child-friendly liquid, rose 16-fold between 1999 and 2004. In addition, there was an overall 7-fold increase in prescriptions for PPIs for infants, and of the prescriptions written for children under 1, about half of those were for infants younger than 4 months of age. 15

But – what exactly are we treating our infants for, with PPI medications? The clinical symptoms associated with infant GERD (depending on who you ask), can range from excessive/inconsolable crying, frequent vomiting/spit up, trouble latching and swallowing, loss of appetite, failure to thrive, diarrhea, blood/mucous in stool, gas, constipation, etc. Those hardly seem like a list of symptoms that can all be attributed to acid ‘burns’ resulting from regurgitation, and not all babies with GERD symptoms regurgitate (a condition known as ‘silent reflux’).

Not surprisingly, there is mounting evidence demonstrating that a wide range of gastrointestinal pain, motility and oral motor dysfunction symptoms, including those listed above, can all be attributed to various stages of gastrointestinal immune aggravation and inflammation. 16 17 18 19 20 21

In addition, there is plenty of evidence to suggest that identifying and eliminating food and environmental sensitivities is as effective as medications for treating gastrointestinal immune inflammation symptoms in children (with one particular study indicating cow’s dairy, soy, and wheat at the top of the list of offenders). 22 23 24

A few pointers regarding identifying and eliminating allergens in infants and young children.

  • You may find that most pediatricians will focus on cow dairy as the sole problematic component, and recommend a partially hydrolyzed (hypoallergenic) or fully hydrolyzed (super hypoallergenic/elemental) infant formula. However, nearly all powder infant formulas use corn as a sweetener so you may inadvertently end up replacing one potential allergen with another.
  • Given the extensive list of ingredients on the average can of infant formula these days, you will probably find a trial and error elimination of allergens from a breastfeeding mother’s diet to be easier and more accurate. (Not to mention, you get the added benefit of the immune modulating properties inherently found in breastmilk to potentially help battle the underlying hyper-immune conditions). 25 26 27
  • Research has demonstrated that gastrointestinal immune inflammation and activation can contribute to dysphagia (trouble swallowing), neuro-muscular dysfunction, intestinal motor abnormalities, and GI dysmotility. 28 29 Consequently, you may find that seemingly unrelated issues with latching, nursing, and the bowels may magically improve and/or resolve once the underlying immune inflammation is addressed.
  • Infant and young children’s metabolism is much faster than an adult’s, so you will typically see clinical improvement quickly once you identify and removing the offending allergen(s).

Allergen Sensitivity

  • According to the American Academy of Allergy, Asthma & Immunology, sensitization rates to one or more common allergens among school aged children are currently approaching 40%-50% worldwide.
  • One in five people in the U.S. currently have allergy or asthma symptoms.
  • 55% of Americans test positive to one or more allergens.

But for all our efforts to subdue the villainous stomach acid, the statistics are not getting any better. But perhaps that’s because we have been chasing the wrong villain. We know that This study, published just last month, strongly suggests that acid is not the underlying cause for the ‘burn’ in heartburn. Instead, an inflammatory immune response is. That’s right – your undiscovered dairy, gluten, corn, egg, or soy sensitivity may be entirely to blame for those pesky GERD symptoms you have been popping Nexium to treat. 30

But that does bring up an interesting point, if acid is not causing the burn then why are PPI (Proton Pump Inhibitor) medications like Nexium, Prevacid, and Prilosec so effective at treating the symptoms? We know that PPI’s reduce gastric acid by blocking the gastric pump of stomach parietal cells, so we would naturally assume the reduction in acid is to credit for the relief in our associated ‘burning’ GERD symptoms. However, it turns out that PPI medications have another, more relevant function in this scenario.

Recent research has demonstrated that PPIs also serve as powerful anti-inflammatories, independent from their function of blocking acid production. A published study review concluded PPI medications potentially have beneficial effects in any number of inflammatory diseases, gastrointestinal or extra-intestinal, in which acid has no role, and a positive clinical response to PPIs should not be interpreted as proof of an underlying acid-peptic disorder. 31


  1. Gastroesophageal Reflux Disease (GERD) Hospitalizations in 1998 and 2005 – HCUP-US Home Page. Retrieved March 5, 2012, from:
  2. Gastroesophageal Reflux Disease (GERD). (n.d.). Office of Medical Informatics – College of Medicine – University of Florida. Retrieved March 5, 2012, from:
  3. Digestive Diseases Statistics for the United States – National Digestive Diseases Information Clearninghouse. (n.d.). Home – National Digestive Diseases Information Clearninghouse. Retrieved March 5, 2012, from:
  4. Gastroesophageal Reflux Disease (GERD) Hospitalizations in 1998 and 2005 – HCUP-US Home Page. Retrieved March 5, 2012, from:
  5. Gastroesophageal Reflux Disease (GERD) Hospitalizations in 1998 and 2005 – HCUP-US Home Page. Retrieved March 5, 2012, from:
  6. Gastroesophageal Reflux Disease (GERD) Hospitalizations in 1998 and 2005 – HCUP-US Home Page. Retrieved March 5, 2012, from:
  7. GERD Costs America Nearly $2 Billion Each Week in Lost Productivity – International Foundation for Functional Gastrointenstinal Disorders. Retrieved March 5, 2012, from:

Pay the Grocer, or Pay the Doctor.


Hot off the press of Current Microbiology journal’s March 2015 issue, a study evaluating the effects of glyphosate (trade name Roundup), a broad-spectrum systemic herbicide.  Thanks in large part to crops genetically engineered to be glyphosate-resistant (including corn and soy), glyphosate now makes its way into an estimated 75%-80% of the food lining grocery store shelves today.  But what effect does glyphosate have on us?

“In conclusion, glyphosate causes [gut] dysbiosis which favors the production of [neurotoxin] BoNT in the rumen. The global regulations restrictions for the use of glyphosate should be re-evaluated.” 1

Gut dysbiosis is effectively an imbalance of the microbiota within our gut.  But what are the health implications of this effect?  In a word:  Infinite.  We have an entire ecosystem of microbes outnumbering our cells 10 to 1, with a collective genome at least 150 times larger than our own.  This ecosystem exists primarily in our gut, specifically the large intestine.  Researchers are just beginning to uncover the many implications of the complex and intricate balance between ‘good’ and ‘bad’ microbes, especially in the context of our immune system. 2, 3  In order to properly frame just how rudimentary our knowledge is within this arena, a recent study has suggested that our appendix is responsible for producing microbes to influence our critical microbiota balance. 4  You may recall the long withstanding hypothesis for the appendix as a useless organ inexplicably left behind by evolution; supporting its frequent surgical removal in the case of inflammation.

GlutenFreeInternational research has identified a particular group of microbes that seem important for gut health and a balanced immune system, dubbed the ‘Clostridial Clusters’.  Of particular interest is the apparent direct relationship between certain members of this cluster and cells that prevent immune overreaction, called regulatory T cells, or Tregs.  Studies have demonstrated that without these Treg cells, mice are unusually prone to inflammatory disease.  Inflammation mediates and is the primary driver of many medical disorders and autoimmune diseases (including cancer 5), as well as many cardiovascular, neuromuscular, and infectious diseases. 6   One of the questions central to microbiome research is why people in modern society, who are relatively free of infectious diseases, a major cause of inflammation, are so prone to inflammatory, autoimmune and allergic diseases.  Many now suspect that society-wide shifts in our microbial communities have contributed to our seemingly hyper-reactive immune systems. 7

Given the recent and dramatic rise in chronic inflammatory conditions and the uncanny statistical correlation with the introduction of glyphosate, I would say it’s time to reconsider our position on the subject.  I know I have.

(Incidentally this is only one of additional published studies currently available on PubMed demonstrating the effects of glyphosate on the microbiota of animal models.)