A Complex Microbiome Situation

Foreword – and Reminder

I am not a licensed medical professional and there are strict laws where I live about “appearing to practice medicine”.  I am safe when it is “academic models” and I keep to the language of science, especially statistics. I am not safe when the explanations have possible overtones of advising a patient instead of presenting data to be evaluated by a medical professional before implementing.

I cannot tell people what they should take or not take. I can inform people items that have better odds of improving their microbiome as a results on numeric calculations. I am a trained experienced statistician with appropriate degrees and professional memberships. All suggestions should be reviewed by your medical professional before starting.

Dr. A.I. is not a person ,it stands for Artificial Intelligence – a compute program that takes facts (in this case, well over 10 millions) and use logic to come up with suggestions based on probability.

Back Story

I’ve had severe gastric symptoms for about 15 years (unstoppable daily acid reflux, severe bloating and food sensitivities/very reduced diet, upper digestive pain, chronic UTI, chronic tender lymph nodes), and milder related symptoms my whole life (recurrent sore throat, allergies, eczema, psoriasis, vitiligo, depression, anxiety, fatigue ). Since I haven’t been able to fully resolve them, I’ve also developed comorbidities (Hashimoto’s, thyroid microtumor). I’ve found your website and have gotten a bit better and have hope to keep improving. I’m trying to understand your videos and instructions on how to use your AI the best I can.

I did a number of Ubiome tests in its day, unfortunately I only downloaded the raw data for two of them, which I uploaded to your website. I am attaching other gastro tests that I believe I cannot upload since there’s no raw data, they may be useless. I also have uploaded my recent  thryve test, and I plan on having more tests done to monitor progress. I have been going back and forth with microbiome labs to try to get the raw data, we’ll see. I’m “hooked” to herbals, taking bidens for UTI for years, and tied to foods like cabbage and meat, and my microbiome shows signs that it needs a wider variety of foods as well as a rotation of probiotics, herbal antibiotics, and foods. I react very strongly to prebiotics. I can eat cruciferous veggies, meats, fish, low-carb, low oxalate NO: starches, grains, cereals, fruits, sugars, eggs, milk, legumes. Neem helped a bit with oxalate sensitivities. A few probiotics helped with mood. Then I get stuck in needing these things, the flora develops resistance.

My husband and I are both following your sites. Thank you again for all you do.


Sending the first draft results in the following information, see Addendum Discussion at the bottom.

I am thankful you have taken my sample to analyze. This is an incredible amount of work and very illuminating on how you approach the tools on your website. I agree, my situation seems to be a bit contradictory and difficult to approach. Here are some comments and reactions to your ideas—I am not suggesting these should be included or modify your post, that is up to you…

Firstly, I would like to say, that I have already been implementing a few of the top probiotic and flavonoid suggestions for a couple of weeks and I do feel that many of my symptoms have either improved some or changed and are changing, which, for at least a decade seemed unmovable. Other are unchanged. I do not think I mentioned this before, but in general I have less hepatic region/upper digestive discomfort and when I do have some, it’s less aggressive and I recover faster. I have related this symptom in the past to oxalate intolerance. My UTI feels much better, though it is not fully gone and my reflux has more frequently better days, though these come and go. My mood has improved and I tend to be more hopeful. I’m a bit less fatigued.

The things I have so far implemented are:

  • Before I implemented any of your website suggestions, I used bidens and neem which helped a lot.
  • When I took the Ombre sample I had been doing high doses of reuteri, plantarum, longum, casei for a couple of weeks… I wonder if these have anything to do with the high Kegg.
  • I have been taking P. acidilactici as a base…
  • I did 2 courses of Symbioflor 2 (2 bottles) and Enterogermina, which I think helped. I think some results suggest I may be low in good strep too.
  • I am now on a run of B. coagulans and Equilibrium (this last one because I test low in alpha diversity)
  • I am planning a run of L. sakei and Enterogermina again next…  The prescript assist folks refuse to share an updated CoA with me.
  • I am taking artemisia, planning to alternate with neem, bidens, cryptolepis/sida

Regarding dietary recommendations, these are mostly non-negotiable at this point due to intolerances and allergies. One single pistachio a week ago gave me more bloating and worse symptoms for a couple days, so it is unlikely that nuts will be part of the solution initially. Rice bran is a big question, I have been searching for a brand that has low heavy metal analysis, but generally, I do not tolerate prebiotic fibers well at all. This is subject to change, for instance neem did help minimize a bit oxalate intolerance.

I have been using quercetin and I am waiting for a full-spectrum cannabinoid extract to arrive to try. I have had a complicated relationship with licorice in the past, but I am willing to try again. 

I do not think I can do oats yet, starches and cereals are too challenging.

The foods I eat that contain choline are salmon (once a week), beef daily and cruciferous vegetables which are the bulk of the veggies I eat because I tolerate them well, probably because of low oxalate content.

I think some killing is necessary along with the rest. The Mircobiome FX people recommended their B. subilis strain for this purpose (in their test C. difficile and B. fragilis were high) but it’s not recommended by the AI.

I will follow up with another Ombre test soon.


Comparing results from different labs has risks. In this case, I thought it may be worth it. (I was debating about purging ubiome data since the data is stale and they consume a lot of space — I will keep them available).

I should note that I recently revised the code to use lab specific percentiles for ubiome, ombre and biomesight. This means that the numbers are more accurate despite the oddities of different labs.

05-08 Ubiome
06-29 Ubiome
2022 Thryve/Ombre

The ubiome samples had a over representation of bacteria that had extreme values (at 90% or higher). The Ombre sample had a better balance, but still with some overrepresentation of bacteria with extreme value.

Dr. Jason Hawrelak

Jason’s criteria was developed using uBiome data. And all of the samples are good. There were no significant potential medical condition on any samples. The same number of bacteria deemed unhealthy were seen on each report.

  • 05-08 – 98.8%ile
  • 06-29 – 95.6%ile
  • 2022 – 95.6%ile

The new Over and Under Population Experimental Feature

With this feature, we see much more difference between samples. The latest sample suggests that the issue may be related to too much being produced.

05-08 ubiome
06-29 Ubiome

The Road Forward

There are a lot of health issues. The site supports targeting of specific issues (because that is how some people wish to proceed). In general, I have been finding the consensus with perhaps 1 or 2 specialized set of suggestions appearing to give good results. We are dealing with fuzzy data everywhere and should resist temptations to over engineer suggestions.

I looked at the Taxon Hierarchy and selected items in Ombre. There was something odd with the data as shown below.

 Bacteroidetes is part of Bacteroidetes/Chlorobi group – so the parent should be the same or more than the children, not less.

The work around is to keep choices to the family, genus and species level. Picking items with a count of 2000 or more only. The selection is shown below

The result of the hand picked is shown below, I usually truncate the list to 0.4 and higher. Both lists are relatively small!

I usually stop at 0.4 or .5

Doing the pro forma consensus building next

The consensus Report download is below.

The top items on the consensus report are similar to the hand picked results (in decreasing priority)

The avoid list:

Looking at Grains

  • Take: Oats (porridge each morning?)
  • Avoid: Barley, Rye, Wheat (a bit fuzzy, different types are on either side)


The top ones selected using KEGG may be hard to find in many places: enterogermina, Sun Wave Pharma / Spor Sun. The weight give them is light, so likely not much impact would be expected.

The top ones appears to be:

Again, they appear to be light in potential impact. With too high production of many things found above, probiotics may be adding wood to the fire.


Vitamin b7 biotin (supplement) and Vitamin C (ascorbic acid). A B-Complex has both good and bad items, so be specific to B7.

Bottom Line

This is a sample which I term “on the border of what we have knowledge about”. We can see the issues, but lack studies that we can use to correct the issues. I have encountered one like this before and after doing the first set of suggestions, the microbiome moved into a state where we are able to get a normal number of significant suggestions from. I hope this is the case here. Samples like this are a bit frustrating to me..

  • I would suggest stocking up on Spezzatina (perhaps even do what we did, buy a whole kilogram (2.2 lbs) of Amarelli Spezzatina [note: no sugar at all!]) and using them through out the day.
  • We had the space and purchased our own infrared sauna a few years ago (on sale at Costco). If you follow that path, remember lots of water and slowly work up duration. For water in the sauna, we use Gerolsteiner Natural Mineral Water (available from Trader Joe’s) because of it’s high mineral content.
  • Reduce the foods high in choline in your diet (see the list here)
  • Keep nuts (Costco/Trader Joe’s?) handy for snacks. Remember peanuts are NOT nuts.

Addendum Discussion

First, and most important: items are suggestions only. People should do only what works for them. Each item increases the odds of a positive shift a little, key word is a little. Occasionally, I will get emails from people who experienced awesome changes from a single item (Neem and Tulsi are often cited). If something is not mentioned and it helps — keep doing it!.

  • a complicated relationship with licorice in the past” In follow up email, the cause appeared to be licorice oil being used. For licorice, I strongly favor the Italian Spezzatina. This person had no problem with the Spanish equivalent… when there is an item with a suggestion, before discarding entirely, consider the following:
    • If in an oil, you may be reacting to the carrier and not the substance. On occasion, it can be preservatives in it. For example Mountain herbs is 35-45% alcohol
    • The dosage may be too high to start, I always advocate starting low and slowly increasing
    • For capsules, read Study: Herbal Supplements Full Of Contaminants, Substitutes, And Fillers [2013]
      • We rarely buy prepared capsules, instead we buy organic bulk and make our own capsules. It is both cheaper, organic sourced (very few supplement bottles cite organic) and less likely (but not impossible) to have the issues cited above.

Concerning salmon, etc. Remember everything is odds. Nothing is guaranteed. You want to shift your odds where practical.

One item that may be worth trying is Akkermansia Probiotic (link with 30% discount). Both my wife and I have, and are, using it — it has definitely made changes (I had almost the same amount that he has – 52%ile, and there was a change). The link is for by subscription — of course, once you get your first bottle, you can just suspend the subscription.

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