Analysis of an atypical Crohn’s Microbiome

After the last post on Gene base probiotic selection, another friend asked me to look at her results. I will follow the same pattern as my last post doing an analysis of a ME/CFS person.

The sample was done by Thryve (721 taxonomies identified) and the FASTQ file also processed by ( 523 taxonomies identified). This is in the middle range of samples processed there.

Why did I double process? Many people will ask, “Which one is right?” The answer is neither and both. For the technical details see this post from a year ago, The taxonomy nightmare before Christmas… alternatively, see the story of Blind men and an elephant. The description of each gives a better overall understanding.

The most probable predicted symptoms from the microbiome samples are below — they are very correct except for age.

Step 1 – Enzymes Issues

As in the prior post, we will show both processing of the data.

From this we click the button on the bottom and get the two lists below. For one item we have 5 items —lactobacillus paracasei has a count of 5 indicating that it helped 5 of the 15 enzyme aboves. In other words, this is the highest priority probiotics.

In comparing the two sets of suggestions, we see some similar items with a count of 3/3 or 15/15. These are probiotics that produces all of the low enzymes

Clostridium butyricum and streptococcus thermophilus are also the ones we had strongly recommend in our last post for a ME/CFS patient (which has some symptom overlap with this person).

Using Quick Suggestions, we see that the probiotic containing b.pumilus was rated as a should be take

Comparing Core Supplements

This is based on the end products data (similar to enzymes but done by manual review and entry — so more incomplete).

This a interesting:

Remember: In no aspect do we have complete knowledge — only fragmentary information.

Advance Suggestions – Filtered by Crohn’s

As we did with ME/CFS, we filter to the official diagnosis

The above settings is not to find all that is wrong, rather just the most significant to give a focused target.

Again, we will do side by side analysis with a threshold of 0.5, rounded (to be consistent with the last post)

I extended this to lower numbers to show the overlap of suggestions created by both samples

We see this probiotics is tied with 3 others for first choice.

Probiotic Suggestions

Again, we have overlap — often with the same impact estimates seen


Here, we almost have identical lists with Flaxseed, meal on both, and Cumin – on just one

Bottom Line

The reader can go to the site and make the same advance suggestions pick shown above. I could go off into more complex analysis approaches, but this gives a solid starting protocol.

What we have discovered is that there is general convergence of suggestions from the two different processing of the same sample. Neither is clear better. A user has two main paths: go with items that only both processing are suggesting, or go with the super-set (merge combination).

One path is to do the items in agreement for 3 weeks and then add in the superset items for 3 more weeks. After 6 weeks, I would usually recommend a new sample to see what has changed.

Looking at common outliers

This person has multiple samples processed by biomesight (most are from ubiome), and we can see persisting commonality

The results are similar to those seen for the last sample.

Looking at this sample versus the prior samples, we see some changes. For example, L-lactate dehydrogenase has decreased which implies lactic acid increases (and thus cognitive issues — which agrees with reported symptoms).

We also note an increase is a few items, like diadenosine hexaphosphate hydrolase (ATP-forming). This increases production of ATP (adenosine triphosphate). As often happens, our knowledge of these enzymes is often limited and evolving (Work on ATP resulted in a Nobel Prize in 1997), so we are still on the learning curve. We can identify issues but may not know the meaning or consequences of the issues.… IMHO, we should strive to reduce abnormal enzyme levels.

I have a concern — the microbiome, especially in terms of enzymes, has not changed that much. This may be due to lack of consistency, or the dosages being too low to alter the status quo.

Dosage Problem

In general, dosages / amount of supplements needed is unknown. For ME/CFS, I have tracked down some dosages from human studies but in general, ideal dosage is a mystery. This is compounded by some people almost taking a homeopathic attitude. “Well, all of the items listed are in my one-a-day vitamin. The suggestions did nothing for me!” The same person’s lab test for Vitamin D will show very low (instead of being around the 95%ile, the level I advocate for ME/CFS patients) and they will cite that “I drink milk with Vitamin D, and my one-a-day also have it! I take Vitamin D !!!!!!!”

The reality is that the absorption of Vitamin D depends on gut bacteria and decreases with age. Studies have shown that to get up to mid-range for people in care homes, often 15,000 IU/day is needed. Mayo cites an RDA of 800 IU/day at present, twice the earlier RDA.

This issue can become even more complex. They may take a B-100 because it has all of the Vitamin B recommendations — unfortunately, many of the fillers in it are in the not recommended list. This happens very often with probiotics: people focus on a mixture having most of the recommended probiotics and assume that the others included and the prebiotics included will do nothing or be helpful.

For the person above, look at their avoid list!