A Detail Analysis using the new tools

A reader pinged me after my last post on the new microbiome comparison tools to look at their results. I usually avoid digging into readers results because I really do not have the time. Her summary and the pair of results looked like a good opportunity to do a detail walk thru of where the site logic should take a reader.


  • Female – born and raised in Russia, mid twenties
  • Living in Canada since 2010
    • Eating raw vegan from 2010-2017, modified paleo afterwards
    • 2016 took sick
    • SIBO, Rifaximin did not help
    • Mast cell issues

Compare Summary

We see multiple concerning changes:

  • Number of bacteria matches has dropped by 12% (less selected diversity)
  • Number of matches to known symptom patterns has increased by 20%
  • Number of high condition matches has increased by 73%

Reader Notes

The last one which I uploaded on your site is 9 month ago ( sept 2018) :2-3 weeks after teeth infection and 10 days of antibiotics, which actually along with long berberine supplementing made me feel better ( bloating) but put me at 71% of diversity (from earlier 96.4%). 

We see a match of diversity loss above.

What to Alter?

Looking at the data clicking Eureka, we see a shift to high levels of:

At this point, we hit a decision point — do we go with changes of high and low OR do we focus on bacteria eureka matches that also match the symptoms. Since our real concern is reducing or eliminating the symptoms then filtering by symptoms where the bacteria pattern matches seems the most productive approach to do first.

For the latest sample (where she had entered symptoms – (here is REAL IMMEDIATE VALUE to you and the community to get symptoms entered!), we see:

+’ve is overgrowth, -ve is undergrowth


All of the high items are at the genus or species level — so we can get very targeted suggestions by picking:

The suggestions (excluding drugs and antibiotics) are below. We are lucky with a nice set of matches of bacteria to symptoms to known modifiers.

Back to Reader’s Notes

Even through I would still have a brain fog after canned food but I just ate everything like when I was living there (Russia) , lots of fermented dairy, sourdough bread, histamine fruits  and had no constipation and absolutely clear skin. Here in Canada fruits is a driver for my acne- when I was on raw vegan food(2010-2017) I did not have constipation but I was all over in acne. I don’t think it was from a native food I ate since I had a constipation and acne when I was living there years ago, but from probiotics?! And I ate a lot of food I can not afford to eat here:.

How does this experience compared to the suggestions? First item is that we have probiotic species matches for when you improved! Second, item that jumps out is an apparent contradiction between the lists — we have take high fat diet and avoid high red meat diet. Are they not the same? Actually eating meat in Russia (higher fat) will have a very different cut than in Canada or the US (lean, low fat). In the west, style has shifted to lean (low or no-fat) meat.

There has been a shift towards beef only in the west, “white beef” (as it is referred to in Israel), a.k.a. pork consumption has decreased. In Russia, I greatly suspect that meat is higher in fat content and was more likely to be pork, especially for the former peasant classes.

The issue of being a vegan is interesting, because we see almost all of the B-vitamins listed as suggestions. She took sick while a vegan and low B-vitamin levels would be expected then. The overgrowth identified above are associated with various low vitamin B levels.

There is a large amount of literature about nutrition and vegan, for example, “Nutritional Considerations for the Vegetarian and Vegan Dancer.[2018]”. This situation may actually be reflected in the high level of bacteria that attempts to consume the B-vitamins from food… unfortunately if food with B-vitamins are not consumed, the bacteria net result may be little B-vitamins. The site report is shown below.

Where the table below is produced

B vitamins are bacteria that extract from food, NOT natural producers.

My own take on being a vegan is simple — the microbiome is inherited and has been tuned to work with traditional food that your ancestors ate – very well. My ancestry is heavy coastal regions where a high fish intake was normal. On occasion I have needed to supplement with iodine — I suspect that my efficiency in uptaking iodine is diminished because my ancestors was exposed to abundance of iodine in fish and there was no need to be more efficient. A close friend is from India and is a strict vegan (and her ancestors has been for likely centuries). Her westernizing son started to eat meat when he started University (Pizza with friends lead him astray!) etc and then to “beef up for the gym”. It resulted in psychological and physiological issues — his inherited gut bacteria was not suited (I did a post on the best diet earlier, that may be worth reading).

Choosing to become a vegan is often a philosophical choice that ignores the reality of the inherited microbiome and even DNA. All bodies are not created equal.

Reminder: The suggestions are based on studies done in isolation. It is vegetarian versus control, or high fat versus control. With the locations and base diet of ‘control’ likely being different in each study. Suggestions is a list of alternative paths. Almost all studies controlled for just one item only, not combinations.

Probiotics sensitive to inherited regional microbiome?

This reader also appears to confirm the human population base sourced for probiotics being significant:

I was along prescribed local probiotics in liquid active form. They believe this form is much more effective than a dried powder/tablets. Human strains ( they don’t show strains numbers) : Lactobacillus  Acidophilus, Lactobacillus Rhamnosus, Lactobacillus plantarum, Bifidobacterium Bifidum and Bacillus Subtilis…. I ordered the same name probiotics from custom probiotics – don’t see the same result even though the BCFU count is higher.

Russian girl using probiotics extracted from human sources in Russia does not do as well on same species sourced from US human sources!?! See this post for more discussion.

This suggests that she should try to get probiotics shipped over from Russia. Alternatively, I would try Seed probiotics for a month (which conforms to the recommendations) and if no significant impact, get their refund. It is very interesting to note that the probiotic strains that caused her to feel better in Russia — are on the to-take list!

L. Keferi vs Commercial Kefir

Lactobacillus Keferi LKF01 (DSK 32079) is on the list, this is explicitly the one isolated and available in Italy from hundreds researched (see this post). Whether an arbitrary kefir product contains it is very questionable – they likely contain L. kefiranofaciens  – a different strain. This reader improved with russian made Kefir (done in the traditional way I suspect). Commercial “kefir products” are very different, see this 2015 article for some history or this pdf. L. Keferis are often in dominant in Russian kefir which typically does not have L. kefiranofaciens. This latter one is often seen in western Kefirs.

I am not sure about how strict Canada is for importing probiotics from overseas for personal use. In the US, there has been no issues for me getting them from Germany, Japan or Italy. There has been issues finding sources willing to ship.

Is the DNA of food the same between countries?

This was an interesting question that she asked. The truthful answer is no if you comparing western supermarket food to a region-specific heritage food. Let us look at a simple stable: potatoes!

There are about 5,000 potato varieties worldwide. Three thousand of them are found in the Andes alone, mainly in Peru, Bolivia, Ecuador, Chile, and Colombia. They belong to eight or nine species, depending on the taxonomic school…. Around 80 varieties are commercially available in the UK.[35]  … variation in the comparative ratio of two different potato starch compounds: amylose and amylopectin…. Different potato varieties contain different levels of glycoalkaloids.


In Russia, there are 113+ varieties [2017]. The same applies to just about every fruit and vegetable.

There are additional compounding issues, for example breeding for shelf-life, color and shape [Especially true in North America]. All of these have side effects on the nutritional aspects and metabolites in them. An article on the history of tomato breeding is informative. In some cases, there has been lost of flavor (and more) as this 2019 study reports in Nature emphasises.

Additionally, we have vegetable and fruit waxing which covers (contaminates?) the product with shellac wax or carnauba wax [see this article on some history]. Some people have allergies to these, or they may trigger mast cell issues.

The ideal solution would be to grow your own using seed stock from your home country. Unfortunately, this runs into problems trying to import them. As a child in Canada, I remember going with my dad to a farmer (a Dane, like my dad) and getting some of his potatoes that had been smuggled from Denmark. My dad always complained about canadian potatoes not having the right taste and feel.

Bottom Line

Her current state is almost the opposite of mine (major physical fatigue at present but no cognitive symptoms!). That is the nature of microbiome shifts – different shifts yields different symptoms. There is no one size fits all!

Most disturbing: adhd, brain fog, memory worsening, constipation,anxiety and joints problems. And I do NOT have a fatigue. 

Reader’s main concerns
Ken’s Current Suggestions — many items to decrease are on this reader’s increase list.

Suggestions going forward:

  • Therapeutic dosages of the B-vitamins,
  • Melatonin at bed time.
  • Resveratrol/grape seed extract
  • Russian made Kefir, if available
  • Have 3-4 servings of eel, fatty pork, lamb or goose a week (chicken, rabbit and fish are low fat)
  • Heritage fruit and vegetables ideally from organic farms.

After three weeks, redo ubiome to see what changes has happened.

There were enough items to change by working from microbiome + symptoms to identify a short list. There was enough material in the database of modifiers to give a reasonable size starting list of changes.