Buyer Beware: Lab provided “normals”

BE VERY CARFUL ACCEPTING Lab ranges for “normal” or if they show an “average” and leaves you to interpret (more likely misinterpret).

One of the things that I have discovered is that often the numbers are NOT a normal curve or a bell curve. Averages and ranges using standard deviations are… well.. the same as saying that the earth is flat. (That use of averages and standard deviation is the standard process for many lab tests – it does not work for the microbiome)

Look at Statistics and Distribution for Prevotella(genus)… It calculates ranges using the KM algorithms…YOU SHOULD NAG THE LAB TO DOCUMENT HOW THEY CALCULATE THEIR RANGES AND THE JUSTIFICATION FOR SHOWING AVERAGE…

You may need a respirator for the amount of smoke that they send your way 🙂

Determining D-Lactic Acid free probiotics

For literature on D-Lactic Acidosis see these posts: [2019] [2015] [2019] or

Increased D-Lactic Acid Intestinal Bacteria in Patients with Chronic Fatigue Syndrome [2009] “This study suggests a probable link between intestinal colonization of Gram positive facultative anaerobic D-lactic acid bacteria and symptom expressions in a subgroup of patients with CFS. Given the fact that this might explain not only neurocognitive dysfunction in CFS patients but also mitochondrial dysfunction, these findings may have important clinical implications.”

There are two approaches that could be used to make this determination:

  • Growing the probiotic is a mono-culture environment and measuring it. This is the traditional approach.
  • Examining the genes and see if any contain d-lactic acid producing enzymes

I favor the second approach because there can be issues with the reliability of the first one. Some bacteria shift production of metabolites, such as d-lactic acid, based on the availability of food, supplies, other metabolites in the environment (look up quorum sensing) etc. To give a human analogy, a human blacksmith will make iron ploughs but in a war situation, they may switch to guns, spears or armor.

Using the genes approach, we know what they are capable of making (not necessarily what they are making in a specific environment). In the case of the black smith above, his shop may be incapable of casting cannons.

How do I find out data on the second approach? You could go to KEGG: Kyoto Encyclopedia of Genes and Genomes and search there. I have added that information to my Researched Retail Probiotics by Strains page.

On the far right column, you will see that some have a special link under Details.

Clicking this link will take you to the detail page where a link to KEGG data is shown

This page has four sections, two are important for this question: Produces and consume

Just enter lactic acid in the filter box to see whether it is included.

Example of a D-Lactic acid CONSUMING probiotics — likely good for the brain fogged (Lactobacillus helveticus R0052)

That is it. Remember this will only list bacteria that:

  • Have studies on PubMed with this specific strain
  • Have their gene sequence on
  • Be available as a retail product somewhere in the world.

Infrared Sauna and the Microbiome

Some 3 years ago, in this post I update my earlier post from 2013 and cited “, it is my hypothesis that this alters the microbiome — how, has still to be reported. “. There has been no objective impact on the human microbiome reported yet :-(.

Assuming that depression is partially microbiome caused (see this list of bacteria shifts seen with depression) then we have circumstantial evidence that they are changes (but do not know the details in humans). We do have information from one study on mice (see bottom of post)

From Far infrared radiation induces changes in gut microbiota and activates GPCRs in mice [2019]
D1 – is Day 1, D25 is Day 25

Needless to say, the later information has been added to suggestions algorithms.

Picking Probiotics from OATS results

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

A reader of that page presented me with a challenging question: “Which probiotic would reduce ….. ?” I checked the US National Library of Medicine studies — nothing. I am a lateral thinker (read Edward de Bono since I was a teenager) and it occurred to me that, theoretically, we can use data from KEGG: Kyoto Encyclopedia of Genes and Genomes because they have the gene sequence of many probiotics and thus their enzymes. Enzymes are mini-factories that consumes some metabolites and produces other metabolites. There are 5200+ different compounds reported on KEGG.

Since I have all of the data in a friendly (to me) datastore, it was just a matter of constructing a few complex queries and creating some web pages. The result was this page: Probiotics to Change KEGG Compounds

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

IBS + BioNTech COVID Vaccine -> ME/CFS?

A reader request a review of his results:

I am a 26 year old male living in Germany. I have a M. Sc. iIn 2018, I did a semester abroad in St. Petersburg, Russia, and during the exam period got IBS. I think stress and/ or vegan diet, which I only tried for a few months, played a role. Extremely low Vitamin D was found, but nothing else.

I developed a lot of food intolerances since then.

In April 2021 I got a Biontech vaccination, and in the following days, noticed that I was tired all the time. It did not get better. I was barely able to finish my Masters Thesis as it was almost finished, but could not start working. Long story short, I now have a lot of the common CFS symptoms, additionally my hair fell out and low testosterone was found.

From a reader

Some technical notes: It cannot be diagnosed as CFS because it has not lasted long enough. It can be viewed as post-immune reaction syndrome. Second, I too have concerns about post-immune reaction syndrome this year, to explain why:

  • Three COVID 19 vaccinations
  • Tetanus vaccination
  • Pneumonia vaccination
  • Two Singles vaccinations

After each, I saw my system “act up”, Some measurable — such as a jump in blood pressure that took a couple of weeks to calm down. More often, i was dragging for a couple of weeks. Night Sweats. skin inflammation, etc.

To Vac or Not to Vac that is really not the question. It is equivalent to saying “I will not wear a seat belt in case the car plunges into a lake and traps me in the car” The risk of that happening is very low compare to the risk of not wearing a seat belt. There is no rationality that can supported by rational analysis.

Some studies showing that vaccination does alter the microbiome.

Human studies have likely not been done because they will be misused by “anti-vaccination” people. We can be confident that changes will happen. The nature of the change will depend on the prior state of the microbiome – an unstudied area. The change from each vaccine will likely be different.

I should mention that I have read several personal reports of major improvement of microbiome conditions as a result of vaccination. A percentage may go either way.

Where do we go from here?

We have 3 sets of microbiome changers – stress, IBS and vaccination. Food intolerance was something of interest — alas, I could not find anything on PubMed that identifies bacteria associated with it. Doing a quick scan of my Biome View, nothing really stood out.

Doing Due Diligence

Kaltoft-Moltrup Ranges

This produces a list FULL of unusual supplements… and a few familar. This is the first time that I have ever seen   lactobacillus bulgaricus appear in the to add list. Some of my personal preferences (from experience with ME/CFS) are there:   glycyrrhizic acid (licorice), Slippery Elm,triphala and quercetin,resveratrol

My general impression is that our list of usual suspects is really not there,

Time to Beat the Bushes

KEGG Generated Suggestions

The Weights were all below 20 — i.e. marginal, with Sun Wave Pharma/Bio Sun Instant, being the best of the short list

Similarly the supplement list was short at 10%ile and none at 5%ile

  • beta-alanine
  • D-Ribose
  • L-Histidine
  • Molybdenum

Compounds Produced and Consumed Page

Looking at the new Compounds Produced and Consumed, there were a number of items that had high ( > 99%ile) production – with 600 items listed, we would have expected just 6 (1%) not 41!!:

  1. ADP
  2. all-trans-Heptaprenyl diphosphate
  3. 5′-Deoxyadenosine
  4. 5-Phospho-alpha-D-ribose 1-diphosphate
  5. Acetaldehyde
  6. AMP
  7. CO2
  8. Diphosphate
  9. Fumarate
  10. Menaquinol
  11. NADH
  12. NADPH
  13. S-Adenosyl-L-homocysteine
  14. UDP
  15. Uracil
  16. Arsenite
  17. H+
  18. N-Acylsphingosine
  19. Xanthine
  20. Acetoacetyl-CoA
  21. Acyl-carrier protein
  22. D-Amino acid
  23. Protein lysine
  24. Protein-L-arginine
  25. (3S)-3,6-Diaminohexanoate
  26. 5-Methylthio-D-ribose
  27. Acetyl phosphate
  28. Alcohol
  29. D-Xylulose 5-phosphate
  30. Glycyl-tRNA(Gly)
  31. N-Formimino-L-glutamate
  32. Orthophosphate
  33. (S)-4,5-Dihydroxypentane-2,3-dione
  34. L-Sorbose
  35. N-Acetyl-beta-D-mannosaminyl-1,4-N-acetyl-D-glucosaminyldiphosphoundecaprenol
  36. 6-Deoxy-L-galactose
  37. Protoporphyrin
  38. tRNA
  39. D-Mannose 1-phosphate
  40. Spermidine
  41. Glycolate

In terms of consumers, the highest percentile was 75.3%ile, In fact most of the consumed items appear ‘balanced’

Proposed Model

Because events were recent, we have high volatility in the microbiome’s bacteria. I saw similar at the start of my relapse… the various clans of bacteria are fighting each other with short term victors of one group and then a reversal.

The apparent issue is massive overproduction of compounds!!! How to address that may mean that I need to add more code to identify the key bacteria responsible and thus the page changed as shown below. This is a logical but experimental novel approach.

The result is shown below:

Next I checked the highest numbers to create a Hand Picked list

The result is show below. None were very high by themselves, Five were around 75%ile

I removed everything below 50%

From this hand pick selection, we proceed to get suggestions. The results are shown below

and the to-avoid

This looks similar to what I often see with ME/CFS people. That is, breakfast porridge made from barley with inulin and wheat bran with walnuts (which is my own regular breakfast!) with yogurt containing lactobacillus plantarum. There are some interesting studies in this area:

Additional Lab Results from User

After getting to this point, the reader reported some recent lab results. Some are of interest:

  • Vitamin D was just 28% into the normal range, so the vitamin D suggestion above is reasonable
  • His coagulation factor II (G20210A/G) was at the high end of normal — I have the same coagulation issue and found that turmeric with black pepper or piracetam helps greatly — especially with brain fog and slowness.
  • Protein S was low (barely in normal range), See Protein S deficiency

Issues causing hypercoagulation (thick blood) was shown to be common with ME/CFS by David Berg back in 1999, for articles and townhall transcripts (hosted by me!) see this page. This appears of part of this person’s causality.

Neither G20210A nor Protein S are likely to be deemed clinically significant, thus my personal preference (regular heparin taken sublingual, held for 1 minute and then spitted out) is unlikely to be prescribed.

For ways of addressing these, see my CFS Remission blog.

The COVID Vaccine Overtones

Prior to my getting my first COVID vaccine, I had concerns about it triggering coagulation – an ongoing ME/CFS risk. The reason was simple, vaccines triggers an immune reaction — milder than having COVID — but still an immune reaction. COVID was at that time, well known to produce coagulation issues (Abnormal coagulation parameters are associated with poor prognosis in patients with novel coronavirus pneumonia April 2020) so they was a risk. The severity would likely be far less than that of COVID, but still enough to push someone with borderline coagulation issue across into ME/CFS. This appears to be correct as shown by some studies, a few are:

This also is suspected with Long COVID,

Bottom Line

The microbiome is just a part of a health analysis, a significant part but far from being complete. We have a model for the tiredness. IMHO, non-prescription anti-coagulation treatments may eliminate it over a few months.

We are going to do two approaches that are connected.

  • Coagulation — which appears to be caused by the bacteria of concern (a topic that I cover on CFS Remission)
  • Bacteria — the ones that appear to be causing over production of many compounds

Reducing some of the bacteria cited above will likely also help, since many are known to cause coagulation:

  • “These results indicated that Bacteroides sp. and F. mortiferum can accelerate blood coagulation in vivo ” [1973]
  • “Bacteroides fragilis, Bacteroides vulgatus, and Fusobacterium mortiferum …. demonstrate that LPS of selected gram-negative anaerobes activate HF and thereby initiate the intrinsic pathway of coagulation.” [1984]
  • Interaction of Bacteroides fragilis and Bacteroides thetaiotaomicron with the kallikrein-kinin system [2011]
    • “Bacteroides fragilis and Bacteroides thetaiotaomicron, were found to bind HK and fibrinogen, the major clotting protein, “
  • Unhappy Triad: Infection with Leptospira spp. Escherichia coli and Bacteroides uniformis Associated with an Unusual Manifestation of Portal Vein Thrombosis [2021]

Some questions from reader:

  • The only probiotic I will add is lactobacillus plantarum. (Or also lactobacillus rhamnosus gg?) I will have to rotate that. Here is the question: I would also like to address IBS. I read on cfsremission that some probiotics, like Prescript Assist, could lead to IBS remission. Prescript Assist was also 2nd place on the KEGG recommendations, although you said the weights were marginal. Would it be not unreasonable to try Prescript Assist at some point, to address IBS?
    • Yes, I would suggest two-four weeks on a probiotic and then rotate to the other
  • Does this plan sound reasonable?:
    • Continue to take: D-Ribose, Vitamin D, Coenzyme Q10, Multi-Minerals, Magnesiummalate, L-Carnitine
    • Discontinue: VSL3, Citrullinmalate, Vitamin C, Vitamin B12
    • Add: As many of the recommendations as possible from the Kaltoft-Moltrup suggestions, the KEGG recommended supplements, and the novel approach. Add anticoagulants.
    • After 2 months test again.
    • Yes, if sound very reasonable – track objective measurements as much as possible
  • New results IgA 1 is at 4500 with normal range 500-2000. This may be related to the vaccination but IgA is associated with a lot of things.

Dehydration caused mast cell and histamine issues

A reader forwarded this 2019 study Dehydration affects exercise-induced asthma and anaphylaxis [Oct 2019]. Soem quotes:

 PubMed was searched from April to July of 2019 using predefined search terms “dehydration,” “exercise,” and “allergy responses.” Based on the reference search, more than one-hundred articles were identified
Also, numerous mast cells and eosinophils were recruited, therefore isotype switching to IgE antibodies occur, this hypersensitivity activates mast cell degranulation. After degranulation, proteases, leukotrienes, prostaglandins, and histamine lead to many kinds of allergy symptoms.

A few months ago, I wrote Hydration and the Microbiome which reviewed some literature.

The event that caused me to start looking at hydration, was a cheap home hydration device — a modern blue tooth scale, the one below. Currently $20.

Etekcity Scales for Body Weight Bathroom Digital Weight Scale [Amazon]

As a result, because I was definitely dehydrated (but did not feel dehydrated — because that had been my new norm!) and proceeded to work on increasing hydration. At the start, I was 45.4% and have slowly worked it up to the current 47.2%. My goal is at least 57%, the middle of the normal range (ideally over 65%). My significant other has mast cell issues and was sitting well below 45% and is working on this change. One of the challenges is finding alternatives for items she takes that are known to cause dehydration — including antihistamines.

  • Antihistamines, Blood pressure medicines, Chemotherapy, Diuretics, Laxatives. (U of Michigan)

So there is the appearance of a feedback loop: dehydration triggers mast cells, which result in the need for antihistamines, which then causes dehydration. The person is trapped!

A longer list from Oxford Medical:

  • Fybogel, Lactulose, Macrogol, Senna, Bisacodyl, Docusate
  • Antacids
  • Ibuprofen, Naproxen, Diclofenac
  • Loratadine, Cetirizine, Promethazine, Hydroxyzine
  • Lisinopril, Ramipril, Losartan, Amlodipine, Felodipine, Bendroflumethiazide

In terms of the microbiome environment, we can see the impact from this study

Dehydration was accompanied by cell changes in solitary lymphoid nodules and Peyer’s patches. The proportion between lymphocytes, macrophages, and mast cells in lymphoid organs depended on the stage of dehydration. The inhibition of cell mitoses, disappearance of mature plasma cells and mast cells (per field of view), significant decrease in lymphocyte count, 4-5-fold increase in the number of destructive cells, and low density of cells and lymphatic network of the small intestine (per unit area) were observed on days 6 and 10 of dehydration. Severe morphological changes were also revealed in other layers of the small intestinal wall (mucosa, submucosa, lamina propria, etc.).

Effect of dehydration on morphogenesis of the lymphatic network and immune structures in the small intestine [2008]

Bottom Line

Hydration plays a very important role for health. Drinking 6 liters of water/day is the classic health advice. This may be a over simplification. This area is still being studied. “As the most effective sports nutrition supplement, sports beverage has different ingredients and formulas, and also has various effects. To provide clues for the development of sports beverage, this article reviews the types, components, effects, and mechanisms of sports beverage currently used in post-exercise fluid restoration.”[Research Progress on Application of Sports Beverage to Post-exercise Fluid Restoration, 2021] So some sports drink may help, some may have little effect.

An unexpected side effect, I did not change my diet habits but with the shift of hydration, I also lost 12 lbs (6 kilos) over 7 weeks.

Picking Probiotics based on Studies

Several pages has been added that should help people pick and understand probiotic impact better

Picking Probiotics for a Condition


This page will search over 3000 studies on the US National Library of Medicine for studies that:

  • Used probiotic strains that are available as retail products
  • Mentions the word you search for in the study

We then add the name of the product containing it, with a link to a site selling it. There may be other products that also include it.

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Why I react to one probiotic but not the other

This does a cascade, from the probiotic mixture we look at all of the species/strains in it, then we go over to the KEGG: Kyoto Encyclopedia of Genes and Genomes and lookup the enzymes being produced by these bacteria. From these enzymes, we look up the products being produced.

When you compare two probiotics mixtures, you may not that one produces a lot more of some products than the other. These are likely candidates for why you have a different response.


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