Using OATS test results to pick Probiotics

In a series of past posts, I walked thru the many pages of a OATS looking at each line in the context of Autism:

The thing that I kept finding is that while issues are identified, evidence-based treatment options are very sparse in the literature. Often none are found. For someone with brain fog, this is beyond possible.

The OATS tests from The Great Plains Laboratory, LLC is what I am referring to.

Typical OATS pages

One of the first challenges is the ‘biochemistry jargon’ on the page. Fortunately, every item is given a number which is what I used. If you are interested in Tartaric, then look for OATS6 – no need to try copying the name.

KEGG: Kyoto Encyclopedia of Genes and Genomes to the rescue!

Bacteria produces and consumes compounds, like organic acids. Probiotics are bacteria. There are two paths to connecting probiotics to organic acid:

  • Clinical Studies seeing what they actually change — there are almost none
  • Looking at the Genes in the probiotics and what they consume or produce. KEGG data covers almost all of the probiotics!

KEGG data is not friendly to most people. It is nerdy scientific speak which often require a master’s degree in the right areas to understand. An example page is below.

It contains genomic data on bacteria for some 6000 strains (out of over 10,000,000+ strains). When we look at probiotics, most retail probiotics do not list the strains in it, only the species (one species may have 400 different strains). Many mixtures also do not list the amount of each species.

The Kludge

The solution is to use the available information to give best estimates for species (by aggregating the values for each strain in a species that KEGG has) and to assume equal representation of each species listed for the probiotic. With these assumptions we can calculate what is produced and what is consumed.

The diagram below shows many of strains of L. Reuteri. We may see that 40% of the strains produce histamine and thus give it a weight of 0.4

From prediction to function using evolutionary genomics: human-specific ecotypes of Lactobacillusreuteri have diverse probiotic functions[2014].

The task of matching up the OATS compound to the KEGG compound is done. As would be expected, some that are on one list, may not exist on the other list. We do have 51 matches out of 76 listed on the OATS test. Going the other way, we have 3,184 compounds that retail probiotics produces or consume (i.e. 3,108 that are missing from the OATS test!).

The result was this page: Probiotics to Change KEGG Compounds

There are some challenges, For example: OATS report on Arabinose but not which type. KEGG provides both versions (What is the difference between D- and L-? It is which way that the molecule is twisted – to the Left or the Right (D – Droite from French) which impacts chemical interactions)

In the video below, I walk thru how we use OATS results and this page with the analysis post listed above. Other test results can be used. OATS happened to be inspiration for this feature.

Some of the items listed will be on the OATS tests, other may not. For example, you may have high Hydrogen sulfide which may be reported from a Small Intestinal Bacterial Overgrowth (SIBO) test.

Clicking on the left buttons will take you to a list of commercial probiotics:

If you are dealing with SIBO, you may wish to AVOID these probiotics!

OATS Specific Page

I have created a page that allows OATS data to be entered and then considered as a whole. Picking Probiotics From OATS results. The process is simple, check the boxes where you have high or low results on the OATS test.

At the bottom of the page you will see the results organized into 5 groups: