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The Microbiome & Autism

The microbiome is the term for the collection of microorganisms that live in and on the human body, a large proportion of which are bacteria that live in the gut.  Once considered simply as free-loaders that helped humans digest food, this view has been replaced with a more modern view that increasingly recognizes the microbiome’s role in regulation of the immune system and metabolism.

Thanks to modern molecular techniques, we know that the microbiomes of children with autism are different than those of typically developing children.  But even before such findings were made, parents had been reporting significant GI issues frequently occurring in their children with autism which could have been a clue.  Some had also reported changes in their child’s autism symptoms (positive and negative) in response to various antibiotics, another clue. (Want to help follow these clues)  Unfortunately, these clues were not followed by the medical community until a parent in Chicago, Ellen Bolte, pieced clues together from her own child’s case history which led to a ground breaking study that provided the first clinical evidence of a link between bacteria in the gut and autism.

In a story that has been explored in the documentary film, The Autism Enigma, and most recently in Spectrum, Bolte theorized that adverse changes in gut bacteria following multiple courses of antibiotics had contributed to her son’s rapid regression into severe autism.  Working with gastroenterologist, Richard Sandler MD, at Chicago’s Rush Children’s hospital, they watched her son’s autism symptoms rapidly recede while taking an antibiotic, vancomycin, that works primarily against some forms of anaerobic bacteria found in the gut.  Encouraged by their success, they organized a clinical trial that demonstrated similar improvements in 8 out of the 10 boys, with similar case histories of regression, who participated in the trial.  The trial was published in 2000, but despite its surprising success, the researchers were unable to secure funding for additional studies (Want to see more studies like this?) because the findings did not fit the conventional “genetics-first” view of autism at the time.

Recognition (Ascendency) of the Microbiome

In 2008 the National Institute of Health (NIH) initiated the Human Microbiome Project an attempt to characterize the microbiome across individuals.  The microbiome is speculated to play a role in many chronic diseases including, diabetes, asthma, and rheumatoid arthritis.  More recently the theory of the gut/brain axis has emerged which considers the microbiome a player in many behavioral conditions.  In the past decade, researchers began applying newly developed tools to characterize the gut bacteria of children with and without autism.  Their findings can generally be grouped into the following observations:

  1. Children with ASD typically have less bacterial species diversity than typically developing children

  2. The overall composition of certain key species of gut bacteria tends to differ in children with ASD vs. typically developing children

  3. Several studies have found rare bacterial species in children with ASD, although these findings have not been consistent

  4. No single bacterial species has been identified that occurs only in children with ASD

N of One Is On The Case

In 2012 the Founder of N of One also saw a dramatic improvement in his son’s symptoms when taking a common antibiotic for the first time and published his observations in a scientific journal as a case report.  He soon began hearing from parents all over the world who had seen similar improvements.  Frustrated that the vancomycin study cited above had not been followed up on and motivated to get better answers for his son, he founded the N of One: Autism Research Foundation in 2014.

Since its inception, N of One has been at the forefront of encouraging researchers to focus, on and better understand, the link between autism and the microbiome.  Within months of its inception, N of One sponsored the first ever scientific conference on Autism and The Microbiome at Arkansas Children’s Hospital.  Additionally N of One has been vocal in trying to gain media coverage of the potential links and are pleased that last year mainstream media publications like the New York Times and the Atlantic ran feature pieces about the microbiome that both discussed autism.

In 2016, N of One announced a new clinical study in collaboration with Baylor College of Medicine to gain more insight into understanding the antibiotic response in some children.  This study is ongoing. Despite the momentum, this continues to be an under-studied, under-funded area. 


If you are frustrated at the lack of answers in this area and would like to contribute to help accelerate efforts in this field.  Please consider making an annual donation to N of One.

N of One's Microbiome Team:

Emma Allen-Vercoe, PhD

Ruth Ann Luna, PhD

Ellen Bolte

If you are interested in following N of One's efforts in this field or participating in our upcoming study.  Please sign up for updates.

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