Autism and the Microbiome

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.

  1.  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.
  2. 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.
  3. 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.
  4. This is remarkable proof of the strong association between microbiota and human behavior.
FMT Capsules

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:

  1. 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.
  2. Be in harmony with bacteria in your environment: this includes consuming ferments.
  3. 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:

  1. SIBO (Small Intestinal Bacterial Overgrowth)
  2. Intestinal Permeability
  3. 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!

Allergies: Take the long cut via Functional Nutrition- 1

Allergies: Take the long cut via Functional Nutrition- 1

You have heard this:The functional nutrition approach to allergies tells us that the way to achieve victory in the long term is by hitting it at the root (literally).

However, when an allergy sufferer wants to kick allergies, they want it NOW. In fact, they want it yesterday. The misery of staying with a runny nose, watery eyes, unable to breath at times is so overwhelming that good health is really not as much as a priority as comfort. I get that, I am like that, in fact, with headaches. A short cut isn’t unfortunately always the best cut, for any chronic health affliction.

Chronic: Persisting for a long time or constantly recurring

Acute: Of short duration but typically severe

Quick fixes (pill popping, fad diets, etc.) are designed for acute conditions. When a condition repeats every year, it needs root-cause remedies. This is the learning that functional nutrition imparts for all chronic conditions.

The number 1 influencer of your immunity is your gut health, and I include the microbes living in your large intestine. Did you know that a vast signaling network has been discovered between bacteria living in your gut, on your skin, in your nose, etc.
Disruption of this signaling by antibiotics, hand sanitizers, eating diets with refined foods, high in sugar, serve to either under-feed bacteria, feed the wrong bacteria, or feed them in the wrong place, all of which lead to chronic health conditions.

Check out this article for more information on bacterial signaling and the immune system.

5 things you can do to optimize your child’s microbiome (to heal your allergies of course):

  1. Feed the bugs. There are schools of thought that say that prebiotics, the food that bugs eat are more important than probiotics. These predominantly include soluble fiber.Have your root vegetables and rotate them. Eat whole grains and legumes, and alternate them.
  2. Eat a diverse diet. You may have noticed the emphasis on rotating grains and vegetables in the previous point. This is because we have a dazzling variety of bacteria in our gut and they all eat different food.
  3. Serve your family ferments every day. Food is of no use if there is no one to feed. Every traditional 

    culture has a history of a variety of fermented foods. Sauerkraut, buttermilk, and a variety of fermented vegetables exist. Buy them raw, or better yet, make them at home.  Store bought brands are often pasteurized (killing all the bacteria), or have very low bacterial counts.

  4. Encourage your child to play in the (organic) dirt.
  5. Look at alternatives to antibiotics. Don’t get me wrong here. If your child is sick and needs antibiotics, by all means, don’t avoid them like the plague! But most conditions that necessitate antibiotics are preventable, or can be treated through gentler means, eg. ear infections. In fact, points 1-4 will actually make point 5 easier.

A healthy immune system is like a healthy plant. You need to water the soil, provide it nutrients so there are no weeds, but not make it sterile. You need the earthworms, and the naturally occurring symbiotic organisms to help your plant grow. And it takes time.

Check out my previous blog on bacteria, ear infections, and signs of a disturbed microbiome here

Bacteria, Fungi and Ferments: Rock your digestion and immunity with your inner bugs!


A story of bacteria, ferments, immunity, aggression, and how to avoid ear infections.

Most of us realize that our job as humans is to exist in harmony with other beings without destroying native civilizations, their habitat and without making it impossible for them to survive.

Where do we draw the line? We conserve endangered species, you know, tigers, dodos (should have), and the like… But somehow the rules have completely broken down in the realm of our own body.

If you didn’t, you know now that your intestines contain trillions of bacteria, fungi, viruses AND parasites. Their population density vary (increasing) from the stomach to the large intestine. But they are there and they are important.

And most of them need to be there. Even the ones that don’t, that are “gate-crashers” are not always evil. There are some that are disease causing, and this is why we need a healthy population of “good” bugs to keep balance. To list everything that our microbial guests do for us is almost impossible. But they include:

  • Improving digestion
  • Crowding out and protecting against pathogenic (bad) organisms
  • Regulating the immune system
  • Even possibly reducing tumors and protecting against cancers.

Perhaps you have heard of Helminths. If not, you have certainly heard of parasites. In certain situations, people ingest parasites to increase their parasitic load (of course), to reduce internal inflammation. Yes, this is a well-established scientific fact. I say this to emphasize the role of our gut-microbes in modulating the immune system [1].

It would stand to reason that sterility is likely the worst thing for us. Yet, as a culture, we have strived for external sterility for years now.

What are the signs that you don’t have a healthy and diverse microbiome? I’ll list a few:

  1. Frequent ear infections 
  2. Frequent cavities, despite good care
  3. Eczema [2]
  4. Immune Dysfunction 
  5. Digestive issues, and actually most chronic issues you see around today.
  6. Severe aggression and behavioral issues.

How do you fix it? While the answer to this isn’t the most straightforward, for one I would say stop being manic about avoiding germs. For most people, eating fermented foods is a fantastic way of at least trying to increase the effects of microbial diversity. [If you are bloated or feel worse, there may be more work to do in healing your digestive/immune system before you can tolerate probiotics.]

5 ways to optimize and hold on to your precious microbial treasure:

  1. Use Antibiotics with extreme awareness and only when really needed. Did you know that extensive antibiotic use results in fungal overgrowth and that knowledgeable doctors will prescribe a mild anti-fungal and probiotics along with the antibiotic!
  2. Ear Infections are the most avoidable of infections. If you are jumping from infection to infection with multiple courses of antibiotics, pause and seek help. Though giving complete care details for ear infections is not in the scope of this particular post, a few are:
    1. check food sensitivities,
    2. see a chiropractor to help with natural fluid drainage,
    3. Ingest probiotics/ferments regularly [3]
    4. use garlic/mullein oil in the ears as a preventive and as a local anti-microbial in the early stages of an infection [4].
  3. Play in the dirt (as long it is not infested with fertilizers and pesticides), do some gardening, get some worms, all of that!
  4. Get started on fermentation in your kitchen. Even making ferments increases the bacterial diversity in your home and on/in your body.
  5. Look up Fecal Microbial Transplants! They sound radical but can work wonders in situations that are dire.

If your problems are more chronic, get help from someone who knows the interaction of the gut, the microbiome and immune health.

Note that this is not a complete list of references on everything mentioned above. I have included key references for topics that I thought the reader may be interested in. Do post a comment if you need more sources or detail.

  1. “Suppression of inflammation by helminths: a role for the gut microbiota”
  2. “Prenatal antibiotics and atopic dermatitis among 18 month old children in the Danish National Birth Cohort”
  3. “Specific probiotics in reducing the risk of acute infections in infancy–a randomised, double-blind, placebo-controlled study.”
  4. “Efficacy of naturopathic extracts in the management of ear pain associated with acute otitis media.”