Child Autism microbiome over time – Part 3

In my last post, End Products and Autism, etc, I looked at the end product shifts seen in autism patients uploaded to my analysis site. In this post, I am going to look at the significant ones over time for this child.

The process is simple, go to compare samples, select the desired ones and click [EndProduct Time Line], as shown below.

I will do all of those reported in the post above and on the page cited.

Watchout for Normal for Age!

We are dealing with a child, and should first look at the pattern seen for children. We do not have enough samples at the moment to be able to drill down into children with autism (as stated on the page).

Similarly, we cannot drill down further into autism until we get more samples.

A fishing expedition

The end products identified are the most likely involved with autism. More probable – not a certainty. Going thru the many charts below, I noted:

  • Between Feb 14 and April 26, 2019 there was major changes visible on many charts that cascaded onwards.
  • It may have been triggered by an increase in Acetate or Lactic Acid shown on the Feb 14 sample
    • DAO and GABA jumped massively on Apr 26, dropped down but slowly increasing afterwards
    • GABA
  • Formic acid, Thiamine and Urolithins kept increasing after that

April 26th Notes: Diet: up to this date still eating mainly soups and all organic home cooked meals and healthy snacks fruit and nuts. Taking full set of recommended supplements tho experiencing nose bleeds.
Feb 14 Notes: After Sample started probiotic L.reuterei and camel milk. Stools consistency soft, solid. Diet: consisted of vegetable soups and also had introduced celery juice in the mornings.
Addendum ” we stopped for a week because I started seeing more irritability as result. ” resumed.

I would suspect that Lactobacillus Reuterei

From 8 bins and 16 bins


The data driving end-products is not as complete as I would like it (if you know of a good source of end product to taxa, please email to me!). I refer to it as experimental because of the lack of solid data. Many of the taxa reported to produce some end products are not reported on by 16s labs.

For this person, we see that Lactobacillus Reuteri appears to have triggered significant changes. “Role of Lactobacillus reuteri in Human Health and Diseases“[2018]. It would account for the increase of Lactic acid and periodic courses may be advantageous. Also with L. Reuteri, “acetate is produced at much higher concentrations 76.” 

The production of formic acid is a little concern. This does not mean you will find high levels in the body; you may find some very fat bacteria that feeds on it and it’s salts ( Formate) .

As a result, I want to identify the bacteria that is causing this. First a Visual:

Then I added a new page,

Clicking and then selecting the End Product
We see what the high producers are.. child and parent (a double count scenario)
We can see that almost every sample is sky high

Going over to Peter D’Adamo Data Punk site, we see that this bacteria inhibits a lot of things:

At this point we have several choices – we could click on Eubacteriaceae or Eubacterium and pick up items to add or remove from the menu. Instead, recall in my Child Autism microbiome over time – Part 2 post, we had a hand picked taxa. I am going to add it to that existing mixture:

Doing it on the already selected taxa
Just click the two, and click Create a custom
Our new collection of bacteria taxa that we wish to modify

We now have similar, but also different suggestions then before. The artificial intelligence engine attempts to find the optimal combination for the above bacteria

Note that we have contrary results for the species lactobacillus rhamnosus (probiotics) versus a specific strain lactobacillus rhamnosus gg (probiotics)

Explicit manipulation of end produces is beyond my comfort level. Formate is water soluble, so this may be a moot issue apart from changing pH. I will leave that speculation to medical professionals.

Bottom Line

This is my first detailed end product analysis connected to a symptom or medical. I ended up writing two more analysis page with the final results being interested. This autism child has one bacteria extremely high and because of using end products we discovered that it would end up with a high amount of formic acid altering the gut and from the literature, also see that it would alter the gut pH — causing more changes of gut bacteria. I have seen another “out of control bacteria (top 2% of values)” in another child with autism (but totally different bacteria) after a different probiotic was started. This may be just two unusual cases, but I thought that it should be mentioned.

We ended up combining several parts of this analysis into one hand picked taxa to adjust and have a good list of changes to consider in consultation with your medical professional.

P.S. One more sample result arrived and was uploaded. The predicted symptoms are matches to earlier ones. I will leave it to the mother to inspect the updated charts shown above.

The microbiome of autistic children is challenging because of several factors:

  • Medical studies (over a dozen) do not replicate each other (see Technical Study on Autism Microbiome)
  • Not many samples to work with using citizen science
  • There is a feeling of “instability”

On the positive side, by this series of post – we can make logical deductions of experiments that may be worthwhile. With regular 16s testing (always the same lab please!!!) you can actually see if something made a difference (for better or worst).

A big KUDO to the mother for keeping detailed daily detail notes and granting permission to use the child’s microbiome results.

Feed Back

I feel I got to keep thanking you for all your observations regarding the data. These give me huge clues in which I can find more bread crumbs in how to better help my daughter.

In you 3rd part of your observations on end products you mentioned that Formic acid was increasing, so from studies that is linked to inflammation in the large colon and increase in bad bacteria.  But I also found an interesting study that indicates the following:

“ This study was conducted to explore the in vitrofermentation characteristics for different ratios of soluble to insolubledietary fiber in pig fecal microbiota. The fermentation substrates consistedof inulin and a non-starch polysaccharide mixture and were divided intofive groups according to different soluble dietary fiber (SDF) to insolubledietary fiber (IDF) ratios (SDF 25, 50, 75, and 100%). With the increasedSDF ratio, the total gas production increased, and the pH in the substratedecreased as the fermentation proceeded. The concentrations of lactic acid,formic acid, and acetic acid increased in the high SDF ratio group, whereasthe concentrations of propionic acid and butyric acid increased in the lowSDF ratio group. The genera Clostridium_sensu_stricto_1, Ruminococca-ceae_NK4A214_group, Christensenellaceae_R-7_group, and Rikenella-ceae_RC9_gut_group were enriched in the high SDF ratio group.Correlation analysis indicated that these differential bacteria had thepotential to degrade polysaccharides. These results revealed that high SDF ratios could stimulate the proliferation of fibrolytic bacteria, which in turn degrade fibers to produce organic acids and monosaccharides. Collectively, these findings add to our   understanding of the mechanisms responsible for interaction the rational use of dietary fiber.”

This is also giving me a clue on the type of food that may be contributing to the increase of Formic acid..  as I explore the type of diet I had changed to e.g. no wheat  I reduced the intake of insoluble fiber, then I furthered explored what level of IDF vs SDF foods I have been giving my daughter.  I’ll be looking at my food logs to see the trend.  

THANK YOU!  As I continue in my search.