The Microbiome

The scientific literature claims that the human microbiome should be considered an organ or possibly a superorganism.

It wasn’t until the 1990s that it was even discovered and now believed to have an overwhelming impact on human health.

The term microbiome is referred to by the experts as ‘the collection of the genomes of microbes in a particular ecosystem’.

The term ‘microbiota’ is referred to as the ‘collection of organisms’.

In other words, the entire digestive tract is a living ecological community of microorganisms – over 100 trillion bacteria – which we call the microbiome.

What is even more astonishing is that 80% our immune system is created by the enteric bacteria or gut flora found in the microbiome of the intestines of the gastrointestinal tract.

There is a very intrinsic connection and complex interaction among the gut, the immune system and even the brain!

The Gut, the Brain and the Immune System

The gut and the brain are both part of the body’s autonomic nervous system that not only communicate with each other, but also with the immune system.

You might have heard the terms ‘gut/brain connection’, ‘the second brain’, and the ‘gut-brain axis’.

These all refer to the communication between the central and enteric nervous system, the emotional and cognitive centers of the brain with the gastrointestinal system.

95% of the body’s serotonin and 50% of the body’s dopamine are produced in the gut.

Just as neurons are found in the brain, they are also found in the gut.

Consequently, if there are alterations in the functioning of the microbiome, then this connection is going to be disrupted and will affect not only the gut itself, but the brain and the immune system.

Nowhere is this more obvious than in children with autism spectrum disorders who clearly show behavioral abnormalities, cognitive deficits, developmental delays, sensory issues and immune dysregulation.

What’s in the Gut?

Derrick MacFabe MD, PhD, a Canadian researcher, was actually the first researcher to scientifically prove this gut-brain-immune connection through mouse studies.

He discovered how gut bacteria can alter behaviors in children with autism.

Dr. MacFabe found that children with autism had a history of antibiotic exposure or hospitalization, GI symptoms, abnormal food cravings and unique intestinal bacterial populations that were related to the severity of their symptoms.

His research on the role of enteric short-chain fatty acid fermentation products, in particular one strain called proprionic acid (PPA), a toxic metabolite of Clostridia difficile (C. diff), was found in the GI tract of children with autism.

PPA is a compound of many gastrointestinal bacteria and a common food preservative.

It causes neurochemical changes that are all consistent with autism findings, such as:

  • Neuroinflammation
  • Oxidative stress
  • Mitochondrial dysfunction
  • Glutathione depletion
  • Altered phospholipid/acetylcarnitine levels

The results from laboratory studies showed that rats treated with PPA developed behaviors similar to autism such as repetitive, perseverative, antisocial behaviors and seizures.

What is clear about PPA is that many systems within the body are affected such as:

  • Neurotransmitters
  • Intracellular acidification
  • Calcium release
  • Fatty acid metabolism
  • Immune function
  • Alteration of gene expression

Environmental triggers maybe the etiology behind PPA, but it is quite clear that the role of the microbiome has an effect on metabolism, immune, mitochondrial function and gene expression in children with autism.

How Can Diet Help?

Diet also plays a big role in the elimination of PPA in the GI tract.

A typical modern-day acidic diet of refined sugars, high fructose, simple carbohydrates, gluten, casein, transfatty acids, fast foods with chemical preservatives and all refined foods increase PPA in the GI tract and affect the brain and the immune system.

If your child is eating a high carbohydrate and rich food diet, then the likelihood of PPA is much higher.

PPA increases acidity and creates more behaviors associated with autism.

To lower levels of PPA, give your child a diet rich in:

  • Fermented foods and vegetables
  • Kefir non-dairy yogurt
  • Organic vegetables, fruits and protein
  • Good quality fats
  • Lots of prebiotics and probiotics.

These will help heal the microbiome by alkalizing the gut and creating more butyrate in the gut which is necessary for healing.

Restoring gut integrity and rebalancing the gut microbiota by healing the microbiome will improve brain functioning, reduce behaviors and keep the immune system stronger.

Another way to lower PPA is to eliminate Clostridia difficile.

Vancomycin and Flagyl are two antibiotics used to eliminate C. diff., but many doctors have found that when taking these one of these two antibiotics the C. diff. disappears, it returns when administration of these antibiotics is stopped.

Supplements for Clostridia difficile include CD-Biotic (probiotic) by Kirkman Laboratories and Biocidin

To test for imbalances in the microbiome, have your physician order an Organic Acid Test (OAT) by Great Plains Laboratory.

Healing the microbiome can make many positive changes in your child, such as:

  • Reducing histamine and inflammation responses
  • Reducing the intensity of anxiety and depression (anger in many cases)
  • Reducing the self-stimulatory behaviors
  • Reducing head-banging and self-mutilating behaviors
  • Reducing hand-flapping
  • Reducing pacing and hyperactivity
  • Reducing the number of meltdowns
  • Reducing repetitive and obsessive compulsive behaviors
  • Improving sleep
  • Improving coping abilities
  • Strengthening and improving the immune system
  • Improving sensory processing


Sources & References

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Clark, J.A., et al. Intestinal crosstalk—a new paradigm for understanding the gut as the ‘motor’ of critical illness. Shock. 2007 Oct;28(4):384-93.

de Goffau, et al. Fecal microbiota composition differs between children with beta-cell autoimmunity and those without. Diabetes. 2013;62(4):1238-44.

Ganal-Vonarburg, S.C., et al. Microbial-host molecular exchange and its functional consequences in early mammalian life. Science. 2020 May 8;368(6491):604-607.

Grizotte-Lake, M., et al. Commensals Suppress Intestinal Epithelial Cell Retinoic Acid Synthesis to Regulate Interleukin-22 Activity and Prevent Microbial Dysbiosis. Immunity. 2018 Dec 18;49(6):1103-1115.e6.

Hanaway, P. Balance of Flora, GALT, and Mucosal Integrity. Alternative Therapies in Health and Medicine. Sep-Oct 2006;12(5):52-60; quiz 61-2.

Korpela, K., et al. Maternal Fecal Microbiota Transplantation in Cesarean-Born Infants Rapidly Restores Normal Gut Microbial Development: A Proof-of-Concept Study. Cell, 2020.

Liu, Z., et al. Tight junctions, leaky intestines, and pediatric diseases. Acta Paediatricia. 94 (2005): 386-393.

Moser, L.A. Astrovirus Increases Epithelial Barrier Permeability Independently of Viral Replication. Journal of Virology. 2007 Nov;81(21):11937-45.

Nankova, B.B. Nicotinic Induction of Preproenkephalin and Tyrosine Hydroxylase Gene Expression in Butyrate-Differentiated Rat PC12 Cells: A Model for Adaptation to Gut-Derived Environmental Signals. Pediatric Research. 2003 Jan;53(1):113-8.

Strauch, U.G., et al. Influence of intestinal bacteria on induction of regulatory T cells: lessons from a transfer model of colitis. Gut 54 (2005):1546-1552.

Vael, C., et al. Early intestinal Bacteroides fragilis colonization and development of asthma. BMC Pulmonary Medicine. 2008 Sep 26;8:19.

Wexler, H. Bacteroides: the Good, the Bad, and the Nitty-Gritty. Clinical Microbiology Reviews 20, no. 4 (October 2007): 593-621.

Williams, R.E.O., et al. The influence of intestinal bacteria on the absorption and metabolism of foreign compounds. Journal of Clinical Pathology. 1971; 5: 125–129.


Galland, Leo. The Effect of Intestinal Microbes on Systemic Immunity. Excerpted from Power Healing. Random House, 1998.

Lambert, Beth. A Compromised Generation: The Epidemic of Chronic Illness in America’s Children. Sentient Publications, 2010.

Sachs, Jessica Snyder. Good Germs, Bad Germs: Health and Survival in a Bacterial World. Hill and Wang, 2007.