Child with Autism, etc Microbiome Tool

This technically can be used for any microbiome dysfunction when there are multiple people living in the same house that are related.


You will see in my earlier post There is no normal or reference microbiome! illustrates that a “typical” microbiome varies greatly by many factors. This makes it extremely difficult to know if there are atypical values in a microbiome.

Known factors that can shift the microbiome includes:

  • Diet
  • Age
  • Gender
  • Longitude (distance from the equator)
  • DNA (thus race and ethnic group)
    • Epigenetic changes should be included here
    • For example FUT2, see this post.

When dealing with conditions known to be microbiome responsive, that is a change of microbiome can improve or deteriorate symptoms, we prefer not to be chasing a bacteria/taxa that is actually irrelevant to the condition because the shift was due to other factors described above.

About a year ago I worked with a mother with an autistic son, and put up my first attempt to doing a family analysis. Over the last year, the site and my understanding has evolved. I have just updated this feature to be closer to what a useful tool may be. I have a personal interest because I am a high function autism spectrum individual. Some prior posts.

The purpose of the tool is attempt to control for as many known variations of the microbiome as possible. The ideal solution would be a child with some condition, say autism, that have two same gender siblings — one older and one younger. With this combination we have restricted DNA impact, diet impact, longitude impact, gender impact, and age impact. Any aspect of the microbiome that is shifted away from the siblings are suspect.

Unfortunately, such families have become rare. With a single child family, we end up needing mom’s and dad’s as the best available control for DNA.

The Tool

At the top of the sample page there is a compare between family members button which will be there if you have two or more samples.

On the next page you will see the samples available. You can only compare samples that have been processed in the same manner. uBiome and Thryve are not compatible (see this post for why). You can select the source at the top (and only those from that source are listed).

In this case, we know that we are dealing with autism, so we include information about what published studies have reported. Our page before we view the taxonomy data may look like this:

You can only pick one Unhealthy and as many healthy as you wish.

Now we are ready to click the button at the bottom of the page.

On the next page you will useful information. Under Direction are letters for a few taxa. This come from published studies.

We have Alphaproteobacteria being reported as “High”. We see that the middle 50% are between 277 and 20493, Dick is way above this range with 31826. This looks like a good match. On the left, by the bacteria name is a checkbox. Check it.

Continuing down the page you may see further agreements. Put checkboxes on all of them.

This one should not be checked, because it looks like the household diet results in low for everyone. Thus Dick’s values (none) are not unusual.
This should be checked, because everyone has some and Dick has none AND low values have been reported in studies.
Rest of family is in the normal range, Dick is high and studies report high

When you are done, click the button at the top of the page.

Why are there duplicates with different values?

Each published study is a line. Some found high and some found low. There are many reasons why studies may differ. It is up to you to include or exclude.


This will return you to the sample page and a golden row of buttons will appear.

Clicking “View Hand Picked Taxa” will show the bacteria picked

Getting suggestions that may improve

Clicking the gold suggestion button, takes you to a screen that shows groups of microbiome modifiers that you wish to consider. I have covered these in previous videos.

In this case, we see the following suggestions:

Looks like all of the sugar replacements are bad.
And a list of recommended probiotics

Bottom Line

This tool can be used in many ways — for example a mother has a condition and eats close to what the family does. She would be the unhealthy one and the husband and kids for be the healthy one.

The goal is to create a ‘familial microbiome’ reference to compare to. We also use information from published studies to try focusing on the most probable bacteria involved.