Missing_Microbes Over the years I have read many half baked and even dangerous theories about why there is an autism epidemic in this country. There are a lot of interesting correlations, but none of the hypotheses held up to further scrutiny.

Until now.

Missing Microbes explores the link between the human microbiome and obesity, food allergies, ADHD, celiac disease, increasing height, and autism. It is written by a former CDC epidemiologist who has dedicated his life to understanding microbes.

The hypothesis is simple. In our legitimate quest to eliminate pathogens we have overused antibiotics, hand sanitizer, c-sections, and even soap and water and that the combination of these factors has killed off too many strains of very necessary gut bacteria, and overgrown others thereby causing a whole host of problems.

What makes this hypothesis so elegant and horrifying is that all the weird correlations that have been noted about autism, correlations that have no causal or predictive value on their own, can be explained with this theory.

Allow me to demonstrate.

The next section of this post contains correlations around autism that I have seen in five years of reading and research. Each one is followed by an explanation of how it could, theoretically, be caused by a gut flora imbalance.

At the very end I list several scholarly peer-reviewed studies that indicate this link. Now normally, one has to pick through studies. Some are badly designed and get odd results. This time, every single study on gut flora and autism showed a link.

All of them. Kind of like every study on cyanide says it kills mammals.

Let’s begin.

Why does autism risk increase with maternal age?
The older mom has had more courses of antibiotics in her life and is more likely to have survived serious infections (any meaningful immune response causes gut bacteria to change).

Why is there a correlation with affluence?
Middle class and upper middle class parents are more likely to have health insurance and to take their young children to the doctor for ear infections before the age of three.

Why is there a correlation between colder, wetter, climates and autism? Damper colder climates = more sinus infections = more ear infections = more hand washing and more antibiotics.

What about the link between parental education and autism?
Educated parents use antibiotics and they wash their babies a lot. They keep their babies in nice clean childcare settings. They use antibacterial soap and hand sanitizer.

Why do autistic kids have trouble with metals or eliminating mercury? The gut flora eliminate toxins and mercury. That is how it leaves the body…in the poop. If those bacteria are no longer present they can no longer do that job.

Why do so many autistic kids have constipation?
You cannot trigger IBS in a mouse model without intentionally messing with the mouse microbiome.

Why do autistic kids with high fevers sometimes seem to come out of the autistic trance and then go back in when the fever breaks?
Because any strong immune response (like a high fever) changes the microbiome at least temporarily.

Why do autistic kids sometimes respond very well and strongly to vitamin B12 shots but then it doesn’t last?
B12 injections bypass the digestive system. Oral B12 requires breakdown by the intestines and is made bioavailable with the gut flora.

What about the link to Lyme disease? Or PCBs?
That causal relationship has been debunked. If you mean why are rates so high in Minnesota, Massachusetts, New Jersey, Maine, Connecticut and Vermont? These states have sinus infection weather, affluent parents, and most important of all, they had less than 10% of the population uninsured even before Obamacare (which means parents here can get c-sections and…antibiotics).

Why are rates so low in Louisiana, Nevada and New Mexico?
These states are warm. Fewer sinus infections mean people don’t feel the need for antibiotics. Also they had 20% or more of the population uninsured before Obamacare. Uninsured people are less likely to take a child to a doctor for every ear infection.

If you want to see the source of those numbers about insurance rates by state they are available here

What about the genetic link?
Genetic diseases are consistent generation after generation. Tay-Sachs, PKD, sickle cell anemia or any other true genetic disorder follows a predictable pattern with children impacted at a consistent rate. Autism is an epidemic. It keeps rising. It seems to run in families because families have similar microbiomes.

Why do some children seem to heal after antifungals, enzymes, and a special diet while others do not?
Gut bacteria produce the enzymes that digest your food. Your gut bacteria control gene expression. They control how much of the caloric value of a food gets stored in your body. They control what nutrients you absorb and they neutralize some of the toxic defenses put up by plants. They make Vitamin K and some B vitamins.

Diet can change gut flora composition rapidly, as can antifungals, as can antibiotics.

A drastic change in diet, plus enzymes, plus drugs that kill off pathogens, plus probiotics is going to radically change the microbiome. Hence the “die-off” and subsequent recovery in certain children.

I know a mom who didn’t change anything in her kids diet and he got better anyway. Explain that!
Theoretically gut bacteria can grow back just like any other locally extinct species. They also evolve. This may be why some kids “outgrow” food allergies, but most do not. This may be why they “outgrow” certain ones (like eggs or dairy) more often than others (like nuts).

Why so many more boys than girls?
Girls have a vagina. In theory this may be acting as a safe harbor for a few critical strains of fecal microorganisms. Until girls are potty trained really really well, some gut flora may hide out in the vagina and get passed back and forth to the anus and repopulate the colon. Boys would have no such protection from cleanliness.

I never rely on one study, one book, or one researcher to support a theory. The following links will take you to other studies that all show a link between abnormal gut flora and autism. If you are interested in more support for this let me know. It exists.


The single most encouraging study was done with ten children who have autism. The good news was that 8 of 10 total children improved, some to the point of becoming neurotypical within six weeks of starting an antibiotic therapy using vancomycin (which is an extremely strong antibiotic). The bad news is that they all reverted to their prior levels of autism when the therapy (which cannot be done long term) was stopped.

If we can find a way to maintain the new microbiom

The following link is to the actual paper about the study.

The following quote, which is not written for lay people comes from pages 6 and 7.
“A clinical trial was carried out to assess the bowel and behavioral impact of anti-microbial therapy directed against these abnormal clostridia species (69). Oral vancomycin was used for 6weeks. Behavioral measurements were carried out before and after, as well as clinical assessment of bowel symptoms. The numbers were low but the response to intervention was reported as statistically significant. 8 of the 10 patients studied improved in terms of behavior and bowel symptoms with some scoring within the neurotypical range. Discontinuation of vancomycin after the 6-week trial period led to a gradual regression in bowel and behavioral symptoms in all participants (69) suggesting that gut environment gives preference to these abnormal species. As yet, there has been no investigation of the combined approach of anti-microbial therapy and other interventions targeted at altering microbiota composition.”

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