Autism and the Early Bacterial Microbiome

Last month, a review paper[i] came out on the implications of the disruption of the  bacterial microbiome in autism.  I was hoping to find something new in it and was not disappointed.

A few highlights.

  1. As the bacterial microbiota are crucial for the production of many important vitamins, they “…can exert an important influence over systemic antioxidant status.” In 2015, a study was done comparing germ-free and conventionally raised mice, and the results showed that the latter group  had lower numbers of the genes involved in the production of glutathione (the body’s biggest antioxidant and detoxifying agent).   Glutathione has been found to be so significantly decreased in the autism population, that autism can be diagnosed 97% of time by checking these levels.
  2. GI symptoms have been found in at least half the autism population, and the severity of autism symptoms is directly “… related to the occurrence of problems in the GI tract.” A 2012 study of over 14,000 people with autism found a markedly higher percentage of inflammatory bowel disease than in the typical population, and the presence of “…abnormal permeability, inflammation and different composition of intestinal microbes.”
  3. Children with autism have a less diverse microbiome composition, and, in fact, “…the severity of the autistic characteristics correlated with the diversity and prevalence of some specific gut microbes such as Firmicutes. ” In 2017, a study showed an increase in the Firmicutes/Bateroidetes ratio because of a reduction in the latter abundance.  Also, the prevalence of the yeast, Candida, was more than double in the autistic population compared to controls.
  4. Of particular interest to me – as my son was put on antibiotics intravenously for 5 days at 36 hours old – was the section on early use of antibiotics.   “Antibiotics decrease the ability to absorb iron, to digest certain foods and to produce essential molecules…Even a relatively short course of antibiotics can lead to alteration in gut microbiota, which in turn can lead to severe consequences such as inflammation, immune dysregulation, allergies, infections, cardiovascular diseases, diabetes, metabolic issues, GI disease such as Crohn’s, IBD,  yeast overgrowth, chronic constipation and diarrhea.”  For 2 decades plus, well before it was documented in the medical literature, I held that those antibiotics formed the autism snowball that continued to run downhill, unchecked, gathering autism severity, until I put Alex on the Specific Carbohydrate Diet when he was 9 years old.  In fact, the article goes on to say,  “The age of first exposure to antibiotics is very important for the future overall health of many individuals.  Early colonization of healthy, beneficial gut bacteria is vitally important to maintain gut homeostatsis, but the use of antibiotics during infancy can drastically alter the microbiome…..”  (It’s not like I didn’t know this but…it always hurts reading it again.)
  5. A disruption in the gut biome can lead to low levels of serotonin, as 90% of serotonin is produced in the gut. “A deficiency of serotonin levels leads to many symptoms that most individuals with autism exhibit, such as anxiety, poor sleep, inability to focus, agitation, mood swings, and depression.”  Tryptophan is the primary amino acid needed for serotonin production and “…tryptophan metabolism has shown to be reduced in patients with autism and the commensal bacterium, Bifido infantis, which is a probiotic, has been shown to be involved in tryptophan metabolism in a rat model.”  I wish we’d known that 22 years ago.
  6. Many, if not most, individuals with autism have been shown to have mitochondrial issues.  The mitochondria are the energy-producing generators of each cell.  When they do not work properly, the cell is under-powered which has tremendous negative implications on health…especially proper brain functioning as the brain requires an enormous amount of energy.   Apparently, certain antibiotics cause mitochondrial dysfunction, including tetracycline, minocycline, chloramphenicol and aminoglycosides.  Several studies have shown that antibiotics, and the antibiotic-resistant microbes left after their use, negatively impact the ability of the mitochondria to produce energy.   This, of course, affects brain development.

There’s more gems in this paper, but I think this is enough to give you a good feel for what we currently know.  If there was one thing that always struck me throughout the years, it’s the number of children with autism who were given antibiotics in the first two years of life.  I have no idea if anyone has ever compared a large cohort of those with autism to controls to see if the former have a greater incidence of use.  If I ever do come across any statistics, I’ll be sure to let you  know.


[i] Eshraghi, RS, Deth, RC, Mittal,, R, Aranke, M, Kay, SIS, Moshiree, B, Eshraghi, AA. Early disruption of the microbiome leading to decreased antioxidant capacity and epigenetic changes: implications for the rise of autism.  Frontiers in Cellular Neuroscience. 2018. 12:256.

2 Comments on “Autism and the Early Bacterial Microbiome

  1. Pingback: Early Life Exposure to Gut Bacteria: The Timing Matters – THE BIOME BUZZ

  2. Pingback: Nutritional Treatments and Autism: Too Little Research but…Here’s Some of What We Currently Know – THE BIOME BUZZ

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