Microbiome Analysis of a 11 y.o. boy with Autism

Most of the analysis is done in the video. I captured a few highlights here

Some notes from the mother

  • Diagnosed at age 18 months
    • Given antibiotics at 3 months
  • Improved with removing gluten and dairy •Positive lab tests for Lyme Above reference levels for Coxsackie and EBV and HHV6.
  • Focus issues and lot/severe OCDs and tantrums and lot of rigidity and not conversational
  • No social skills and gets head pain all of a sudden which might be PANS will last for few minutes and will be fine again.
  • Failure to thrive (low weight), lot of Gut issues, started having Acid Reflux issues

(Chronic) Lyme, Coxsackie, EBV, HHV6 are extremely common with people with Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). These people also show some neurological symptoms like with autism: emotional fragility, loss of executive decision making, slowness of thought, sound intolerance (which can be perceived as not wishing to socialize). I view ME/CFS as generally being a microbiome dysfunction.

The positive for infections may be due to the microbiome being sufficiently jacked by the microbiome dysfunction that latent low level infections are not longer being well controlled.

Ken’s initial impressions

Video (90 Minutes)

Steps covered

  • Review “to go” solutions
  • Supplements and vitamins that may be deficient
  • Review end products produced by bacteria
  • Review Modules (processes) produced by bacteria
  • Review Enzymes produced by bacteria
  • Identify any probiotics that could theoretically help
  • Review bacteria with unusual shifts (may have no idea of role/function)
  • Creating diet modification suggestions


  1. Bifidobacterium : Too High 78% of the microbiome, I have seen similar in other children with autism (up to 85%).
  2. Bacteroides vulgatus : Too High
  3. Ruminococcus gnavus : Too High
  4. Veillonella dispar : Too High
  5. Dorea longicatena : Too High
  6. Streptococcus sanguinis : Too High
  7. Erysipelatoclostridium ramosum : Too High
  8. Bifidobacterium bifidum : Too High
  9. Streptococcus marimammalium : Too High
  10. Streptococcus dentapri : Too High
  11. Streptococcus danieliae : Too High

We have agreement with published studies on the microbiome of autism for:

  1. Bifidobacterium : Too High
  2. Bacteroides vulgatus : Too High
  3. Ruminococcus gnavus : Too High


Take the following

Take none of the following

To avoid that agrees with mother’s observation (child improved)

Bottom Line

Use this video with the site to walk thru the same process. If you have a TV (which can stream YouTube) and a laptop, put the video on the TV and step thru on your laptop.

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