
Autism and the Microbiome
-And why aren’t we targeting this in every child?
This question comes with an answer: It is not that straightforward.
But it should be done. Most of the nutrition/ biomedicine based interventions you are doing to help your Autistic child’s regulation, anxiety, diarrhea, constipation, pain should focus on diversifying and “normalizing” their microbiome.
Q. What is the microbiome?
A. The trillions of bacteria (but also yeast, parasites and viruses) that coexist with your body and directly or indirectly affect almost every biochemical process in your body.

Q. What is wrong with the microbiome in children with Autism?
A. There are numerous studies that correlate a disrupted microbiome (altered ratio of bacteria when compared to non-autistic controls) with autistic symptoms. We also have both anecdotal and published data that shows that attempts to correct this imbalance often results in a reduction in severity of both GI and behavioral symptoms.
This past month itself, there have been (at least) 3 landmark studies / clinical trials that have talked about the role of the gut-microbiome in children with Autism. The combination of these three papers is remarkable but not a completely new paradigm. We have known for close to a decade about this strong association.
- Microbiota Transfer Therapy : This is a remarkable trial where 18 children with “severe” autism symptoms were given a fecal microbiota transplant (along with some other facilitating procedures) and 44% of these kids no longer qualified for an autism diagnosis. 90% of the children involved had a 70-100% improvement in their symptoms!
Here is an excellent summary by Gita Gupta. - Genetic Mutations in the Gut and the Brain could cause Autism. We know that a majority of kids with autism suffer from severe gut issues. This study isolated a gene mutation that causes impaired digestion, lower motility (movement through the digestive tract).
To me, this mutation seems like an invitation for SIBO (Small Intestinal Bacterial Overgrowth) which co-occurs very frequently with people with gut issues, and therefore in autistic children. - Human Gut Microbiota from individual with Autism induced “hallmark autistic behaviors” (in this case the authors mean reduced social interaction and repetitive actions) in mice.
- This is remarkable proof of the strong association between microbiota and human behavior.

But impacting our microbiome is something we do on a daily basis.
So why aren’t we doing anything about it?
While a Fecal Microbiota Transplant is the most effective way to change your microbiome, these methods and their variations such as Microbiota Transfer Therapy are methods generally done under close supervision of an expert.
Eating pesticide laden food, exposure to chemicals from plastic, synthetic hormones, antibiotic usage are all well known ways to damage the diversity of your microbiome.
You don’t have to wait for a study to impact your gut microbiome. In the meantime you can:

- Eat a diverse variety of prebiotics or fiber containing foods. Different foods with different lengths and types of fiber feed different bacteria.
In fact, prebiotics are the single most effective way of increasing diversity of the microbiome after a Fecal Transplant. It is also the easiest way to maintain diversity. - Be in harmony with bacteria in your environment: this includes consuming ferments.
- Avoid pesticides. Avoid frequent antibiotics by addressing root cause [unless being used therapeutically for a specific reason].
In short, avoid constant exposure to things that are designed to kill bacteria, given that you ARE made up of bacteria!
If you have tried (1) or (2) already and have not seen results, it may be because they often will not work in a child with:
- SIBO (Small Intestinal Bacterial Overgrowth)
- Intestinal Permeability
- Weak upper digestion
Healing is not linear. We don’t proceed step by step. We converge upon it from many sides simultaneously. Check out this radical blog on the 3-step model for optimal health.
More on prebiotics later.
Things not clear? Still need to chat about the microbiome? Drop a comment, let’s chat!