Mankind does not have an ideal Microbiome

One of the common misconception is that there is a “normal” microbiome that can be used as a reference.  Below is a chart from “Metagenomic sequencing of fecal DNA“. Diet makes a major impact on the distribution and volume of the bacteria.

  • “In a study of gut bacteria of children in Burkina Faso (in Africa), Prevotella made up 53% of the gut bacteria, but were absent in age-matched European children.”[2010]

The chart below is for healthy individuals in 12 different countries.  In some cases neighboring very similar countries (Sweden [SE] and Denmark [DK]) have very different compositions.

world

This great variation means that testing the microbiome can only be done as group of individuals living in the same area with similar eating habits…. An individual result without reference from people with the same eating habits and possibly ethnic background is very fuzzy to interpret. Yes, highlights may be common — like low E.Coli, Lactobacillus and Bifidobacteria….  but they likely apply to no more than 80-90%, others may have different shifts based on things like being gluten free and other diets.

For more information see: The gut microbiome of healthy Japanese and its microbial and functional uniqueness [2016]

Then we also find that DNA also impacts the microbiome,

Host genetic variation drives phenotype variation, and this study solidifies the notion that our microbial phenotype is also influenced by our genetic state. We have shown that the host genetic effect varies across taxa and includes members of different phyla. The host alleles underlying the heritability of gut microbes, once identified, should allow us to understand the nature of our association with these health-associated bacteria, and eventually to exploit them to promote health.

Human genetics shape the gut microbiome , 2014

People have asked me, “Did you get your microbiome done, what was it?” My honest answer was “No, such testing was not available when I last had CFS. I simply assumed that my pattern would be an appropriate match to that reported from the 1998 Australian studies”

Age changes the microbiome

” DNA of the Clostridium leptum group and pathogenic Enterobactericeae increase in the gut microbiome with age and can be detected in the same individual’s coronary plaques along with pathogenic Streptococcus spp., associating with more severe coronary atherosclerosis. ” [2019]

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The presence of the BifidobacteriumFaecalibacteriumBacteroides group, and Clostridium cluster XIVa decreased with age up to 66-80 years of age, with differences reaching statistical significance for the latter group. Interestingly, the levels of some of these microorganisms recovered in the very old age group (>80 years), with these older individuals presenting significantly higher counts of Akkermansia and Lactobacillus group than adults and the younger elderly

Age-Associated Changes in Gut Microbiota and Dietary Components Related with the Immune System in Adulthood and Old Age: A Cross-Sectional Study. [2019]

Latitude changes the Microbiome

Latitude means the distance from the equator. This may be due to sunlight-vitamin D levels.

Geographical variation of human gut microbial composition , 2014

If you exercised recently impacts the microbiome

Underlying these macro-level microbial alterations were demonstrable increases in select bacterial genera such as Veillonella (+14,229%) and Streptococcus (+438%) concomitant with reductions in Alloprevotella (-79%) and Subdolingranulum (-50%). To our knowledge, this case study shows the most rapid and pronounced shifts in human gut microbiome composition after acute exercise in the human literature. 

Rapid gut microbiome changes in a world-class ultramarathon runner. 2019

Some Population Studies

“We analyzed the combined microbiome data from five previous studies with samples across five continents. We clearly demonstrate that there are no consistent bacterial taxa associated with either Bacteroides– or Prevotella-dominated communities across the studies. By increasing the number and diversity of samples, we found gradients of both Bacteroides and Prevotella and a lack of the distinct clusters in the principal coordinate plots originally proposed in the “enterotypes” hypothesis. The apparent segregation of the samples seen in many ordination plots is due to the differences in the samples’ Prevotella and Bacteroides abundances and does not represent consistent microbial communities within the “enterotypes” and is not associated with other taxa across studies.” [2016]

” All Egyptian gut microbial communities belonged to the Prevotella enterotype, whereas all but one of the U.S. samples were of the Bacteroides enterotype.

  • The intestinal environment of Egyptians was characterized by higher levels of short-chain fatty acids, a higher prevalence of microbial polysaccharide degradation-encoding genes, and a higher proportion of several polysaccharide-degrading genera.
  • Egyptian gut microbiota also appeared to be under heavier bacteriophage pressure.
  • In contrast, the gut environment of U.S. children was rich in amino acids and lipid metabolism-associated compounds; contained more microbial genes encoding protein degradation, vitamin biosynthesis, and iron acquisition pathways; and was enriched in several protein- and starch-degrading genera.
  • Levels of 1-methylhistamine, a biomarker of allergic response, were elevated in U.S. guts, as were the abundances of members of Faecalibacterium and Akkermansia, two genera with recognized anti-inflammatory effects.
  • The revealed corroborating differences in fecal microbiota structure and functions and metabolite profiles between Egyptian and U.S. teenagers are consistent with the nutrient variation between Mediterranean and Western diets.” [2017]

“This suggests that similarities between the Inuit diet and the Western diet (low fiber, high fat) may lead to a convergence of community structures and diversity. However, certain species and strains of microbes have significantly different levels of abundance and diversity in the Inuit, possibly driven by differences in diet.” [2017]

Bottom Line

IMHO: There is no clear definitive benefit from doing an individual microbiome testing — there is no reference that is reliable for it on an individual basis at a fine level of details. On the other hand, having results showing abnormalities help in several ways:

  • It encourages you to make changes in eating which will usually be for the better
  • It confirms that you have significant shifts and supports the concept that the gut is causing your symptoms.

” This work supports that sex is a critical factor in colonic bacterial composition of an aged, genetically-heterogenous population. Moreover, this study establishes that the effectiveness of dietary interventions for health maintenance and disease prevention via direct or indirect manipulation of the gut microbiota is likely dependent on an individual’s sex, age, and genetic background. ” [2019]

The shortfall in available probiotics

The source of this blog comes from SCIENCE,VOLUME 377|ISSUE 6612|16 SEP 2022, , pp. 1328-1332 DOI: 10.1126/science.abm7759, Codiversification of gut microbiota with humans

 An awareness of differences in gut microbial strains between populations has already led to the notion that probiotics for treating malnutrition should be locally sourced (38).

From Bifidobacterium infantis treatment promotes weight gain in Bangladeshi infants with severe acute malnutrition. Sci. Transl. Med.14, eabk1107 (2022).

I have held to the hypothesis that a person DNA and their microbiome evolved thru their ancestors and their ancestors’ diet together. This study demonstrated that the strains diverge .

Suzuki et al. noted that the global distribution of some human gut microbial strains mirrors historical human migration patterns out of Africa … However, within a species, some strains can show remarkable population specificity. The question is whether such specificity arises from a shared evolutionary history (codiversification) between humans and their microbes.

Evolutionary history of someone from the Hebrides Islands produces a high incidence of red hair. Evolutionary history of someone from the South Africa will be black haired, and  low and high curl individuals [2017]. Similarly, their microbiome will be different and reflect the DNA inherited by their host.

This was nicely illustrated in a series of diagrams in the above article. In the middle of each circle, you will see how the different strains branched from each other:

Branching for Bidifbacterium Breve — Colors represent Regions of the world

I noticed the following in the article:

 For mother-child pairs, strain sharing is often interpreted as vertical transmission, but acquisition of strains from a shared environment cannot be excluded (8). Indeed, our data also support strain sharing between community members: Within sampling locations in Gabon and Vietnam, we observed instances of the same strains in the microbiomes of mothers and unrelated children

Mother passing bacteria on to the children — breast feeding is the likely mechanism

We hypothesized that species that codiversified with their hosts are better adapted to the host environment than those that did not….together with the observed functional attributes, such as smaller genomes and oxygen and temperature sensitivity, codiversified species likely evolved host dependency.

This means issues such as diet and environment (hot, cold, humid, dry) impacts the evolution of the bacteria in the microbiome

Bottom Line

Probiotics should be sourced locally/from same genetic heritage. This is very technically feasible — just isolate the bacteria from stools of a suitable population, sequence it to insure no undesirable genetics, culture it and produce a local version.

Personally, I chuckle because the probiotic that I have responded best to was one that was one obtained from Germans in 1917, which in a match for my ancestry (Duchy of Slesvig, and southern islands of Denmark).

If you are of East Indian Descent (perhaps living in the US), you may wish to obtain probiotics from India and not your local health store. IMHO, you should contact the distributor of any probiotic that you use to obtain the provenance of the strain being used. Demand it!

To rephrase for some:

  • If the probiotic kosher?
  • If the probiotic halal?

Unfortunately, many probiotics being sold out there are not even from human sources, little more appropriate (regional) human sources for the consumers.

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

There is no Normal or Ideal Microbiome!

Son and Daughter with Autism Analysis

The parents provided rich information:

  • OmbreLab results
  • OmbreLab results processed thru BiomeSight (preferred because of Special Studies)
  • OATS

Both children are in the same household, so diet will be similar.

The Son

 Our son is 14 and weighs 90 pounds and is Autistic.  It’s amazing that he sleeps well (10 hours) although the minute he gets up he is not stop moving, spinning, stimming, etc.  He can be redirected and can follow directions and can slowly progress is school although if we could calm him down I think he could learn a ton.  He understands everything we say and can ask for things if he slows down although he is not conversation.  Every 6-8 weeks he seems to have face flair (although hasn’t been that bad the last 6-10 months although we don’t know if it’s yeast, bacteria, etc.  Once he has it his OCD kicks in and he can’t stop putting lotions and creams on it.  He’s a skinny kid with not much muscle although can ride a bike, run a mile or two, etc.  

The Daughter

Our daughter is almost 16 and is not verbal although uses a device.  She has the autism diagnosis as well although also has a genetic mutation of the WDR45 gene (BPAN) which can create iron accumulation in the brain.  We spend a lot of time with supplements, organic nutrition, gluten free, time on the treadmill and sauna and more to make sure her body is detoxing the best it can.  She understands everything you say just can’t speak back.  Where my son is not stop she would cuddle all day and be 100% content.  She also  has fine and gross motor delays and in general is just cautious in her physical movement.  We’ve treated for SIBO several times, etc. although we’ve obviously never solved the problem.  She isn’t necessarily constipated although 95% of the time needs assistance with a small suppository for her to go the bathroom.  The stool is always there it’s just like she doesn’t have the urge to release it. 

High Level Comparisons

Below are summaries of the two children for comparison

DaughterSon
Biomesight Gut Wellness77.3785.89
Potential Medical Conditions Detectednonea few fuzzy issues
Bacteria deemed Unhealthy77
Dr. Jason Hawrelak Recommendations98.8 %ile99.7 %ile
KEGG Enzymes – Low LevelsOver reported (18.5)Over reported (158)
Percentile RepresentationHigh in rare bacteriaHigh in rare bacteria
Special Studies: Autism49 matches63 matches
Special Studies: Constipation28 matches19 matches
Probable SymptomsNothing
High Anxiety
85
Depression
85
ME/CFS with IBS
72

Comments on the above

Going thru the above, we see little difference between the two on may ways to evaluate the microbiome. However, there were a few where we see a great contrast:

  • Enzymes at both extremes are very much higher for the son (4x higher at both top and bottom 1%iles)
  • Bacteria under 1%ile is much higher with the son
  • Box-Whisker and Kaltoft-Moldrup are much higher with the daughter
  • Having profiles matching predicted symptoms, son only has significant matches

Daughter Action Plan

For the daughter, build up a consensus report from:

  • Special Studies Autism (49 all low)
  • Special Studies Constipation (28 all low)
  • PubMed Autism (6)
  • Box-Whisker (all were high)
  • Kaltoft-Moldrup (17 low, 72 high)

Obtain Probiotics from:

  • OATS
  • From KEGG Computation
  • From Consensus

Son Action Plan

For the son, build up a consensus report from:

  • Special Studies Autism (49 all low)
  • Special Studies Anxiety (30 all low)
  • Special Studies Depression (39 all low)
  • Special Studies ME/CFS with IBS (49 all low)
  • PubMed Autism (6)
  • Box-Whisker (5 too low, 44 too high)
  • Kaltoft-Moldrup (36 low, 39 high)

Obtain Probiotics from:

  • OATS
  • From KEGG Computation
  • From Consensus

This looks like a lot of work!

Actually, it’s not — I have done a video doing the son to illustrate the steps better.

Son Consensus

My person picks from the list are below. I was not overly happy with the To Take suggestions.

Looking at the avoid items, I would be inclined to try shifting these items out of his diet (if it is in it)

Son Probiotics

See video for details, the key items that occured at the

Daughter Consensus

Some of the items may please the daughter.

On the avoid side, we see also:

Daughter Probiotics

The consensus probiotics were much different than her brother

Daughter’s Consensus Probiotics
Son’s Consensus Probiotics

Looking at the OATS results, we see Bifidobacterium dominating it. This is not a surprise because Human milk oligosaccharides usually shows up when Bifidobacterium needs good encouragement. Please note: the list below did not use any microbiome data — just the OATS results.

The revised KEGG Probiotic had two items that tend to be frequent:

If there are any Lactobacillus probiotics being taken, I would eliminate them.

Bottom Line

Everything in this post is created by modelling data and nothing has been validated clinically. The advantage with modelling is that it is usually better than than a MD tossing an idea out in frustration.

All suggestions should be reviewed by a qualified medical professional before starting.

Cromolyn Spray for Histamine and Mast Cell Issues, etc

This is an old drug with most of the studies in 1970-1990. It is very different in action from antihistamines (i.e. it is NOT an antihistamine) with an awesome safety record. A reader asked me to assemble and review the literature. Mast cell and histamine issues are often reported with other conditions; the domination of other symptoms may mask the mast cell issues.

Conditions Often Comorbid With Mast Cell Diseases

• Chronic inflammatory response syndrome (CIRS)
• Fibromyalgia syndrome (FMS)
• Ehlers-Danlos Syndrome (EDS)
• Gulf War Illness (GWI)
• Interstitial cystitis/bladder pain syndrome (IC/BPS)
• Irritable bowel syndrome (IBS)
• Kounis syndrome
• Multiple chemical sensitivity syndrome (MCSS)
• Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS)
• Post-Lyme syndrome
• Postural orthostatic tachycardia syndrome (POTS)
• Post-traumatic stress disorder (PTSD)
Recent advances in our understanding of mast cell activation – or should it be mast cell mediator disorders? [ 2019]

Cromolyn sodium is a medication used to manage bronchial asthma, allergic rhinitis, and certain allergic eye conditions such as vernal conjunctivitis, keratitis, and keratoconjunctivitis. It is a mast cell stabilizer. 

Cromolyn Sodium – Continuing Education Activity – StatPearls [NIH site – 2022]

Notes from the above:

  • Derived from Mediterranean herb called Ammi visnaga
  • Cromolyn sodium metered spray is used to prevent and relieve nasal symptoms of hay fever and other nasal allergies like runny or itchy nose, sneezing, and allergic stuffy nose.[7]
  • Cromolyn sodium is off-labeled used for preventing serious reactions to foods.[8]
  • The effect of cromolyn sodium on mast cells lasts for approximately 6 hours
  • Cromolyn sodium inhibits immediate and late reactions.[15][12] 
  • Adverse reactions reported with the inhalation solution were throat irritation and hoarseness, esophagitis, laryngeal and pharyngeal edema, drowsiness, dizziness, bronchial irritation, pulmonary infiltrates, and cough.[19]
  • Given its safety profile and current evidence, its use is likely most favorable for those who cannot tolerate intranasal corticosteroids or require short-term prevention before known exposures.6,7 

I was unable to find any generic clinical studies for Cromolyn with Myalgic encephalomyelitis/chronic fatigue syndrome or ASD (despite mast cell issues being associated with inflammation of the brain.

Availability

In the US available at retail (Walmart etc) from several brand,

The Herb Ammi Visnaga (Visnaga daucoides )

Used for over 2000 years

  • “it is used in modern medicine to treat many aliments such as renal colic and coronary insufficiency, and is used as an antioxidant, antifungal, and antibacterial, with a larvicidal effect on mosquito larvae…. A.K.A. Khella Baldi or toothpick weed, In Arabic countries Avisnaga has many common names such as Khella baladi, Khella, Khellah, Khellakl, Chellah, Kella, Gazar sheitani, Kammon habashi, Bizer Al-Khilla, Kulla, and Swak Al-Nabi. In Turkey, it is known as disotu, kilir, and hiltan.” [2020]

Headaches — likely a spray symptom

A study of this spray against a placebo was found “The most common adverse events in both groups were headache and rhinitis, and there was no significant difference in the rates of such events between groups.” [2002]. This suggests that the spraying is a more likely cause, not the cromolyn nasal spray.

Literature

Bottom Line

Given its awesome safety record, I would suggest a discussion with your medical professional on doing a course of over-the-counter nasal spray (done before each meal and at bed time – because it effects lasts only 6 hours). A single bottle should last for 50 days.

A History of Several 16s Tests and Suggestions

With regular testing and following suggestions, Hawrelak’s criteria out of range items went from 9 , to 7, to 4. Suggestions appear to work (slowly). This is a follow up of prior posts, the bottom line is that with

I am going to start with the same comparison as I did in the prior post above, and then move on to do an analysis using the latest tools available.

Why Follow Up Posts are important

The first item is simple, does the model and suggestion appear to work. Everything is theoretically computed, not based on clinical practice or clinical studies. The second item is that these posts encourages people to try suggestions, or to do “self-serve” with the site.

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 appears to 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.

Comparisons between Samples

We have the latest test processed through both Ombre and Biomesight. This analysis will use Ombre because that is what was used in prior; latest one will use Biomesight so we can use the new special studies for suggestions

The high lights are:

  • Sample quality is better than the prior samples, we see more bacteria reported
    • Ombre is reporting more (as we saw in a prior post)
  • Improvement in the critical bacteria identified by Dr. Jason Hawrelak, we are down to just 4 bacteria outside of range for both (from prior 7 and 9)
  • Similar with Medivere, MyBioma,Nirvana/CosmosId, and XenoGene ranges
  • On the opposite side, we have more outside of Box-Plot-Whiskers, Lab Range (+/- 1.96SD) and Kaltoft-Moldrup – this is not unexpected because we have a lot more bacteria. The criteria improved are the criteria with a fix set of bacteria that are usually there in most samples.
  • The number of extreme enzymes levels (using Ombre) have been significantly reduced. Compounds have no clear shift
Measure 8/22/2022
BIOMESIGHT
8/22/2022
OMBRE
6/15/20225/16/20223/15/202211/21/2021
Lab Read Quality554.84.83.64.2
Bacteria Reported By Lab657765515669593473
Bacteria Over 99%ile090101
Bacteria Over 95%ile1545422219
Bacteria Over 90%ile388222404821
Bacteria Under 10%ile16835431122387
Bacteria Under 5%ile84161860546
Bacteria Under 1%ile2430902
Lab Read QualityBiomeSightOmbreOmbreOmbreOmbreOmbre
Pathogens474337423833
Outside Range from JasonH447799
Outside Range from Medivere151517172020
Outside Range from Metagenomics888877
Outside Range from MyBioma44881010
Outside Range from Nirvana/CosmosId202023232222
Outside Range from XenoGene44881010
Outside Lab Range (+/- 1.96SD)16142762
Outside Box-Plot-Whiskers13511842717225
Outside Kaltoft-Moldrup15520911314814391
Condition Est. Over 99%ile000000
Condition Est. Over 95%ile000000
Condition Est. Over 90%ile000010
Enzymes Over 99%ile289148535
Enzymes Over 95%ile4878599305182147
Enzymes Over 90%ile99154719629438458
Enzymes Under 10%ile17575707138169
Enzymes Under 5%ile101331928478
Enzymes Under 1%ile2032000
Compounds Over 99%ile313669314319
Compounds Over 95%ile13126518627719089
Compounds Over 90%ile371380303435220118
Compounds Under 10%ile212282321528333133
Compounds Under 5%ile54186195378310100
Compounds Under 1%ile2362011826742

The data suggests further improvement with the latest sample — in terms of numbers, dramatic!

Going Forward

We are going to use the Special Studies to generate the next set of suggestions. Remember that the numbers below are sensitive to the number of bacteria detected (i.e. lab quality). The latest sample had the highest quality which means that percentages may increase due to that alone.

Percentage Matches8/22/20227/21/20224/20/20222/22/202211/22/2021
1Alcohol intolerance or Medication sensitivities5234363639
1Allergic Rhinitis (Hay Fever)3331353536
0Allergies And Food Sensitivity3032323234
0Autism3828313144
1Bloating2422242432
2Brain Fog2832393926
2Chronic Fatigue Syndrome (CFS/ME)3330282830
0Cold Extremities3136292931
0Constipation1718151529
2?COVID19 (Long Hauler)3936313139
0Depression4030333335
0Easily irritated2831242427
2General Fatigue2626282828
1High Anxiety2826252526
1Histamine or Mast Cell issues2824272732
0Inflammatory bowel disease4348283843
0irritable bowel syndrome3130262636
1Intolerance of Extremes of Heat and Cold3230242436
0ME/CFS with IBS3124242427
2ME/CFS without IBS3025232328
0Poor Gut Motility2537313135
2Post-exertional malaise2224232326
0SIBO3836272734
0Tinnitus (ringing in ear)3234242428
2Unrefreshed sleep3727262629

What surprised me, and delighted me, was the relative consistency of the numbers for the same person over time for many symptoms. This time, because of the special studies, we are going to focus on generating suggestions specific to the issues of greatest concerns (2) above.

  • Brain Fog
  • Chronic Fatigue Syndrome (CFS/ME)
  • COVID19 (Long Hauler)
  • General Fatigue
  • ME/CFS without IBS
  • Post-exertional malaise
  • Unrefreshed sleep

Having high IBS or IBD values does not equate to ME/CFS with IBS — prior to my latter flares, I saw no gut issues at all.

The top Items are similar to each other:

The top of the avoid list are many B-Vitamins. In prior posts, I speculated that the low vitamin B-levels seen in the blood of ME/CFS patients etc is because of greedy gut bacteria that prevents it being absorbed. I just did some literature browsing and this speculation appears to agree with some research.

Now, Wexler et al. show that some gut microbes may be able to pirate vitamin B12 from us as it passes through the digestive tract. Wexler et al. showed that a protein called BtuG on the surface of a type of gut bacteria called Bacteriodes grabs onto vitamin B12 with extraordinary strength. In fact, these bacterial proteins bind to vitamin B12 so strongly that they can even pry it away from our own vitamin B12 collecting protein.

Human gut Bacteroides capture vitamin B12 via cell surface-exposed lipoproteins [2018]

This means that to avoid B-vitamins via food or supplements, despite having low blood level may be a rational approach. Getting Vitamin-B injections bypassing the gut bacteria may be a more effective approach to dealing with low vitamin-B. Choline is connected with B-Vitamins, see The B Vitamins and Choline: Overview and Methods [1998], hence the reduce choline suggestion above.

Probiotics

Escherichia coli was the top probiotic on the consensus. Using Ombre reading of the sample and the Kyoto Encyclopedia of Genes and Genomes, Escherichia coli is the top suggestion with items like Bacillus subtilis being 1/3 of contribution. The same results appear with the BiomeSight processing.

The top probiotics which were never recommended to avoid

For flavonoids and polyphenols — it seems that supplementing with any should be avoided. The very few with a positive value has ‘equivalents’ being negative values. For amino acids: Conjugated Linoleic Acid, l-citrulline and proline (amino acid) are the top choices. Diet choices are low animal protein (which agrees with avoiding b-vitamins) and high fiber (which agrees with pulses above)

The top Vitamins and Minerals
Herbs and Spices tend to be East Asian

Bottom Line

Remember, these are not generic suggestion for anybody with ME/CFS. These are specific to this person’s microbiome. We see that the numbers for his microbiome has improved, but some items are still of concern. Our method of getting suggestions shifted over to using the Special Studies because he had a number of symptoms that were significant which were covered by the special studies, as well as his data being processed thru BiomeSight which we are using for special studies (apples to apples comparisons).

Again, the computations are based on the odds of items helping the microbiome to shift in the desired direction. Odds are just that, some will work, some will not — but ideally more will work than not. For the suggestions, remember ROTATION (Rotation — Essential for Changing the Microbiome), and pick items that work for you and your medical professional. The suggestions can be viewed as a series of dresses on a rack, you do not need to buy all of them to be fashionable. Use the ones that work for you.

Rotation — Essential for Changing the Microbiome

Rotation as a key facet of fixing or keeping a microbiome healthy was first introduced to me in 1999 by Cecile Jadin, MD (Surgeon in South Africa) with the Occult Rickettsia Protocol from the Pasteur Institute of Tropical Disease (where her father worked). I have written about this prior, Rotation and Pulsing: Herbs, Probiotics, Antibiotics [2017], Rotate, Rotate, Rotate and Curcumin [2016], Continuous or Pulse Supplements? [2015]

Some literature on it:

The Microbiome is not a Mechanical System

Think in terms of societies. Think about a gang that steals quality goods at a store. The antibiotic may be having a store detective. Issue solved – no more crime! Wrong, the gang will change to a different crime, they will adapt. It will become a continuous battle and escalation by both sides. Many people view the microbiome as a simple mechanical system unfortunately, bacteria continuously mutate (think of COVID mutations). If the antibiotic kills off 99% of the bacteria, the remaining 1% likely has a mutation that allowed it to survive. Give this 1% a few weeks and we are back to old levels with the antibiotics making no difference.

How does this apply to vitamins, amino acids, even food? The simplest explanation is that those items affect the growth of different bacteria. Different bacteria strains produces different compounds, including  bacteriocins (natural antibiotics). When you think about probiotics, remember that they often work due to their natural antibiotics (see above for literature).

Different Strains of Lactobacillus Reuteri [Reuterin is an antibiotics]
[From prediction to function using evolutionary genomics: human-specific ecotypes of Lactobacillusreuteri have diverse probiotic functions[2014].

To jump to the human body for an example, when you were 20 you likely drank a lots of pop, smoked.. ate a lot of fast food… and were “healthy” and fine. As you body ages (evolved), the same diet would worsen diabetes, weight, and a dozen other conditions that will evolve. The microbiome changes with time, in fact, it changes faster than your body. When you make one set of changes, like running 2 miles a day, the body may act up with structure damage as you age. Professional players in sports do not age well. Going on a specific type of diet may address one issue and trigger a different issue eventually.

What is the answer? All things in moderation. Instead of just one type of exercise, do a variety of appropriate exercises. Instead of a specific diet (which may deliver insufficient minerals or vitamins), rotate around different diets that addresses the issue you are trying to address. Every change you make, changes the microbiome– sometimes in unexpected ways.

In terms of suggestions from the microbiome prescription site, rotating suggestions is desired — usually there are many suggestions so it should not be hard.

What is the Ideal Rotation?

I do not know, I have inferred from the typical duration of antibiotic prescription that 7-10 days is a reasonable guess. I will give a simple example of one rotation that I do (maintaining), alternating the various forms of gluten (the specific types are listed after each).

  • Oats – as porridge: avenin, C-hordeins, γ-hordeins, B-hordeins and D-hordeins
  • Rye – as German 100% rye bread: γ-40k-secalins and high-molecular-weight secalins
  • Wheat — as typical western baked goods: (ω5-gliadins, ω1,2-gliadins, α-gliadins, γ-gliadins and high- and low-molecular-weight glutenin
  • Barley – as porridge: C-hordeins, γ-hordeins, B-hordeins and D-hordeins

My stools will change every cycle – IMHO, there is no perfect stool.

From Isolation and characterization of gluten protein types from wheat, rye, barley and oats for use as reference materials [2017].

The goal is almost like trying to herd a group of cats.

And now for a different condition… Progressive Supranuclear Palsy

Most of the analysis that I have done recently has been either ME/CFS, Long COVID or Autism. If you look at the page entitled Medical Conditions with Microbiome Shifts from US National Library of Medicine you will see a lot of different conditions that may be influence by microbiome manipulation..

Today I got an email asking “My mother in law has Progressive supranuclear palsy (PSP), and Diabetes  and is in a very bad state, there is no help from the mainstream medicine” with samples of her.

My first action is to see if there are any published studies on PSP and the microbiome. There was just one study: “Unraveling gut microbiota in Parkinson’s disease and atypical parkinsonism‘ 2018.

Progressive supranuclear palsy (PSP) is a less well-known neurodegenerative brain condition which is sometimes misdiagnosed as Parkinson’s disease or Alzheimer’s disease (or other forms of dementia). Because of the similarity to some Parkinson’s symptoms during the early stages of the disease, PSP is included in a group of diseases called Parkinson’s Plus Syndrome or Atypical Parkinsonism. However, PSP progresses much faster, causes more severe symptoms, responds very poorly to Parkinson’s medication, and has a significantly reduced life expectancy.

Parkinson’s Europe

At this point out a recent news story, Woman who smelled her husband’s Parkinson’s helps scientists come up with diagnostic test, Sky News, Sep 7,2022. When some ones gut bacteria changes, their smell change. On a little morbid note, in WW2, they could tell dead soldiers apart from their smell (he’s a German, he’s an Italian, he’s an American) [Story]. So avoiding scented products may have health benefits. In Vietnam war, it was different — the Viet Cong favorite smell was Old Spice, it means that there were Americans close by.

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.

Analysis

We lack any special studies nor any Medical Conditions with Microbiome Shifts from US National Library of Medicine(PubMed) which matches this person except for Diabetes. We do not have enough samples for Special Studies for Diabetes. For the PubMed, this person is sitting at the 95%, so a definite include. There is another PubMed that seem appropriate and which is at the 99%ile, Brain Trauma

Looking at data in detail, we see a definitely interesting microbiome. We have a high quality sample

CriteriaCurrent SampleComment
Lab Read Quality10.6High Quality
Bacteria Reported By Lab960Very high Count
Bacteria Over 99%ile237 is expected, so high
Bacteria Over 95%ile8548 is expected
Bacteria Over 90%ile15596 is expected
Bacteria Under 10%ile29696 is expected
Bacteria Under 5%ile26748 is expected
Bacteria Under 1%ile2427 is expected
Rarely Seen 1%56
Rarely Seen 5%182
Pathogens59
Outside Range from JasonH8
Outside Range from Medivere16Candidate
Outside Range from Metagenomics8
Outside Range from MyBioma7
Outside Range from Nirvana/CosmosId19Candidate
Outside Range from XenoGene5
Outside Lab Range (+/- 1.96SD)37Candidate
Outside Box-Plot-Whiskers194Candidate
Outside Kaltoft-Moldrup347Candidate
Condition Est. Over 99%ile3
Condition Est. Over 95%ile20
Condition Est. Over 90%ile29

Dr. Jason Hawrelak Recommendations are at 99.7% so no red flags from that. There is a huge number of PubMed matches, I will only use the best ones for what was reported for this person. The following sets of suggestions are going to be used for our Consensus Report

  • PubMed: Brain Trauma
  • PubMed: Type 2 Diabetes
  • Outside Range from Medivere
  • Outside Range from Nirvana/CosmosId
  • Outside Lab Range (+/- 1.96SD)
  • Outside Box-Plot-Whiskers
  • Outside Kaltoft-Moldrup

The consensus download is below

Probiotics

From KEGG, we see many of the Equilibrium and PrescriptAssist bacteria listed with the following further down the list (in descending order) (Remember : Lacticaseibacillus is the new name for Lactobacillus)

From the consensus we have (in decreasing order), a similar list.

My gut feeling is that the following products are likely a reasonable choice.

I would suggest starting with whatever arrives first, starting with a low dosage and increasing every second day. Remember to review with your medical professional.

Vitamins

A vitamin B complex and Vitamin C are recommended

Supplements

The top items are all available on Amazon and other stores:

Herbs And Spices

Diet Style

Bottom Line

This person wife also has issues, see And now for a different condition… Part 2. The suggestions are different but creating two different menus everyday would be challenging. See that post for a possible solution.

One of the items cited that I did not include above was dopamine (prescription). Looking at a treatment site for PSP in an attempt to do cross-validation, we see that dopamine is a factor, but things are more complex, see: Excessive dopamine neuron loss in progressive supranuclear palsy [2008].

When I started this project, I saw the potential of using the microbiome as a method to identify candidate treatments in the absence of successful clinical treatments. This is the first attempt of putting this into practice.

And now for a different condition… Part 2

Most of the analysis that I have done recently has been either ME/CFS, Long COVID or Autism. If you look at the page entitled Medical Conditions with Microbiome Shifts from US National Library of Medicine you will see a lot of different conditions that may be influence by microbiome manipulation..

In the same email I got an second challenge: “Father In Law – Diabetes, Heart conditions and High Blood Pressure” with samples of her.

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.

Analysis

In this case we have an even higher lab quality than the wife, but a lot less bacteria reported. This means that the microbiome is likely a lot less fragmented than the wife.

CriteriaCurrent Sample
Lab Read Quality11.5
Bacteria Reported By Lab628
Bacteria Over 99%ile4
Bacteria Over 95%ile27
Bacteria Over 90%ile48
Bacteria Under 10%ile330
Bacteria Under 5%ile295
Bacteria Under 1%ile237
Rarely Seen 1%12
Rarely Seen 5%41
Pathogens50
Outside Range from JasonH7
Outside Range from Medivere21
Outside Range from Metagenomics9
Outside Range from MyBioma4
Outside Range from Nirvana/CosmosId25
Outside Range from XenoGene6
Outside Lab Range (+/- 1.96SD)14
Outside Box-Plot-Whiskers54
Outside Kaltoft-Moldrup246
Condition Est. Over 99%ile1
Condition Est. Over 95%ile1
Condition Est. Over 90%ile8

Dr. Jason Hawrelak Recommendations has him at the 75%ile — so off, but not really bad. Following the same pattern of analysis as the wife (since we have no matching special studies):

  • PubMed: Hypertension (High Blood Pressure 
  • PubMed: Type 2 Diabetes
  • PubMed: Coronary artery disease
  • Outside Range from Medivere
  • Outside Range from Nirvana/CosmosId
  • Outside Lab Range (+/- 1.96SD)
  • Outside Kaltoft-Moldrup

The consensus download is below

Probiotics

From KEGG, we do NOT find Escherichia coli near the top of the list. We see the usual odd bacteria strains from Equilibrium and Prescript Assist then:

With microbiome labs/ megasporebiotic being a good match.

From the consensus we have (in decreasing order), a similar list.

I would suggest starting with whatever arrives first, starting with a low dosage and increasing every second day.

Prebiotics

Vitamins

Most of the vitamin B’s are to be avoided. Selenium, magnesium, vitamin a and folic acid,(supplement Vitamin B9) are the top items.

Supplements

The top items are all available on Amazon and other stores:

Herbs And Spices

Diet Style

Specific Foods

One item really jumps out — Burdock Root (Gobo in Japan)- which is available as a supplement if not available as a fresh vegetable. It is high in Inulin (but inulin is much lower, just 81 — so other components may be playing a significant role)

Bottom Line

The diet style is a major contrast with the wife — this creates the frustration of needing almost a double food preparation. To address this issue, I imported both consensus list into Excel, used a VlookUp function to display the values besides each modifier and then identified items that are positive for both and then order by the total of each.

This allows one menu to be used for both of them. Perhaps a little less effective, but likely a lot less frustrating (and thus better compliance). I attached it as an example.

Another ME/CFS Microbiome Followup

This is a follow up to a prior post:

This person did his tests using OmbreLabs.com and then transfer the data to biomesight.com. This allows us to use special studies to select bacteria. I am also, as part of my own learning (as well as the readers), going to do some comparison between the OmbreLabs and BiomeSight reports on the same data (i.e. FASTQ files).

I had another sample analyzed at Ombre, and there were already changes in my flora, even in a short amount of time. And they correlate with me feeling a bit better. So thank you. I’m still trying to crunch the data and make sense of the new results, and other than your great Dr. AI, I am using this new feature by Ombre which I find very clear (old sample first, new sample after)

Why Follow Up Posts are important

The first item is simple, does the model and suggestion appear to work. Everything is theoretically computed, not based on clinical practice or clinical studies. The second item is that these posts encourages people to try suggestions, or to do “self-serve” with the site.

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 appears to 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.

Comparisons between Samples

See this other review of a series of ME/CFS microbiomes from another person that I recently did, ME/CFS Follow Up Microbiome Samples. If you are new to this series, you may wish to review A new specialized selection of suggestions based on statistical significance for symptoms.

First, I do not know the best way to compare samples — what I usually do is put all of the numbers side by side. Special attention needs to be paid to Lab Read Quality. A poorer read quality results in less bacteria being identified.

Lab Quality is a measure of the total number of bacteria counted. The processing of a sample may detect just 30,000 bacteria or 300,000 bacteria. This impacts the number of bacteria detected and also the accuracy of the measures.

Also, Special Studies Percentage Matches is helpful to interpret these numbers better.

CriteriaBS 6/6BS 7/19OL 6/6O 7/19
Lab Read Quality2.15.42.15.4
Bacteria Reported By Lab280497365628
Bacteria Over 99%ile2756
Bacteria Over 95%ile24312724
Bacteria Over 90%ile49584951
Bacteria Under 10%ile17621860
Bacteria Under 5%ile5301028
Bacteria Under 1%ile01317
Rarely Seen 1%0409
Rarely Seen 5%418840
Pathogens15251928
Outside Range from JasonH4472
Outside Range from Medivere17171616
Outside Range from Metagenomics7777
Outside Range from MyBioma991414
Outside Range from Nirvana/CosmosId22222323
Outside Range from XenoGene661111
Outside Lab Range (+/- 1.96SD)6131014
Outside Box-Plot-Whiskers70846461
Outside Kaltoft-Moldrup70113112182
Condition Est. Over 99%ile1100
Condition Est. Over 95%ile2400
Condition Est. Over 90%ile5622
Enzymes Over 99%ile3101315
Enzymes Over 95%ile46326982
Enzymes Over 90%ile9051155411
Enzymes Under 10%ile10221955138
Enzymes Under 5%ile451322267
Enzymes Under 1%ile64752
Compounds Over 99%ile97104126
Compounds Over 95%ile5676385397
Compounds Over 90%ile292313533548
Compounds Under 10%ile72125183248
Compounds Under 5%ile3964109127
Compounds Under 1%ile5211617
Note: I just cut and pasted from “Multiple Samples” tab to Excel to make the above table.

What are the key things seen above (most of the numbers are similar):

  • Sample Quality are the same (expected from using the same FASTQ file)
  • Ombre reports more bacteria
  • Outside Range from Jason Hawrelak show a major improvement with Ombre Labs and no change with BiomeSight
    • As a historic notes, Jason’s numbers were developed using uBiome labs (adding more fuzziness to everything).
    • I view this major improvement per OmbreLab, to indicate the person’s improvement.
  • For Enzymes we see more high production rates and less low production rate with Ombre
    • Remember that enzymes are estimated based on the bacteria reported and is an estimate only.
    • The percentiles for both Ombre and BiomeSight are based on other samples from the same lab (they are NOT intermixed – I removed that earlier this year)
  • For Compounds, we see the same thing!

KEGG Computed Enzymes

I was curious what the top items were. Most of the bacteria are the bacteria only available in Equilibrium and PrescriptAssist, excluding those and looking at the top few — we see similar suggestions (and note E.Coli is not always #1 for ME/CFS people on all tests, just a frequent pattern what dates back to 1998 in some conference papers from Australia).

Special Studies Numbers

Only BiomeSight was used in the Special Studies (because of higher sample population). The person’s rating for each of the symptoms (2 – worst, 0 -none) is also added.

Why did the number increased so much? Look below at Lab Sample quality! We cannot pick a percentage match as being critical — because that percentage depends very much on lab quality!

BS 6/6BS 7/19PersonSymptom
2.15.4Lab Quality
13252 Allergies And Food Sensitivity
13202 Bloating
11242 Brain Fog
9342 Depression
13232 Easily irritated
8222 General Fatigue
11232 High Anxiety
12202 Histamine or Mast Cell issues
13231.5 Chronic Fatigue Syndrome (CFS/ME)
11201.5 irritable bowel syndrome
13231.5 ME/CFS with IBS
12301 Alcohol intolerance or Medication sensitivities
10231 Intolerance of Extremes of Heat and Cold
9171 Post-exertional malaise
21301 Small intestinal bacterial overgrowth (SIBO)
12281 Unrefreshed sleep
16280 Allergic Rhinitis (Hay Fever)
23280 Autism
12220 Cold Extremities
15200 Constipation
21290 COVID19 (Long Hauler)
26450 Inflammatory bowel disease
8230 ME/CFS without IBS
11210 Poor gut motility
8200 Tinnitus (ringing in ear)

Intrepretation

As cited in the introduction, the person reported feeling better. We also see a major improvement against Jason Hawrelak Criteria for a healthy gut (using Ombre numbers). With both labs we see an increased of rarely seen bacteria — which is open to many interpretations; statistically both increases looks like a move towards a typical gut. 5% of 628 bacteria is 31, we see 40.

Going forward

I am building a consensus report from the items marked 2 above using the Special Studies. The list is similar to other people with ME/CFS. We see 2 E.Coli probiotics (symbioflor 2 e.coli probiotics, colinfant e.coli probiotics) at the top with d-ribose (a sugar used by E.Coli). This is then followed by the earth based probiotics( General Biotics Equilibrium, Prescript Assist (Original Formula), Prescript Assist (2018 Formula)).

These suggestions agrees with the top KEGG suggestions (despite being calculated in a totally different way — one set used Genomics and one set used Clinical Trials)

The rest of the to take probiotics mainly fall into 3 groups: Saccharomyces boulardii (probiotics) bacillus (probiotics), bifidobacterium with bacillus coagulans (probiotics) being the top of this set. As is typical, lactobacillus is usually a negative.

Going over to vitamins, the strongest take is Ferric citrate. We have almost all of the B-vitamins being strong avoidthis is contrary to the conventional treatment wisdom which says vitamin B helps ME/CFS. I discuss this in a prior post and speculate that the reason that Vitamin B is low in blood test ME/CFS is that part of the microbiome dysfunction are bacteria that are greedy for vitamin B, hence it does not get to the body. Conceptually this speculation is testable with a lab reactor using the microbiome from a ME/CFS person.

Starving out bacteria that consumes B-Vitamins may be one path

Bottom Line

“This is too complicated” is what I can hear some people saying. This analysis digs into the nature of the data which is really not needed for most people. It is likely of interest to those treating microbiome dysfunctions as it illustrates many of the challenges in interpreting.

For most people, the process stays the same:

  • Upload the data
  • Try several different ways of generating suggestions
  • Look at the consensus

Why is consensus important? Simple, we have very incomplete data and also have limited accuracy with the microbiome tests. Going the consensus approach is similar to using a Monte Carlo Simulation, an appropriate approach to deal with complex processes with many parameters that are fuzzy.

ME/CFS Follow Up Microbiome Samples

This person has been using microbiome prescription to reduce the symptoms with success and with objective measurements of improved microbiome. His MD is willing to prescribe antibiotics and the top three items (from hundreds possible) are all used by ME/CFS specialist — indicating that the model is in agreement with clinical experience of ME/CFS specialist (a.k.a. Cross-Validation).

This is a follow up to these prior posts:

Why Follow Up Posts are important

The first item is simple, does the model and suggestion appear to work. Everything is theoretically computed. The second item is that encourages people to try suggestions

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.

Comparisons between Samples

First, I do not know the best way to compare samples — what I usually do is put all of the numbers side by side. Special attention needs to be paid to Lab Read Quality. A poorer read quality results in less bacteria being identified.

Lab Quality is a measure of the total number of bacteria counted. The processing of a sample may detect just 30,000 bacteria or 300,000 bacteria. This impacts the number of bacteria detected and also the accuracy of the measures.

Criteria8/31/202112/3/20213/25/20228/11/2022
Lab Read Quality7.83.66.25.5
Bacteria Reported By Lab461379479383
Bacteria Over 99%ile7533
Bacteria Over 95%ile20241113
Bacteria Over 90%ile32402123
Bacteria Under 10%ile283123237189
Bacteria Under 5%ile22266143107
Bacteria Under 1%ile16194423
Rarely Seen 1%32147
Rarely Seen 5%973314
Pathogens37304431
Outside Range from JasonH4477
Outside Range from Medivere15151515
Outside Range from Metagenomics6688
Outside Range from MyBioma7777
Outside Range from Nirvana/CosmosId18182323
Outside Range from XenoGene5577
Outside Lab Range (+/- 1.96SD)14968
Outside Box-Plot-Whiskers41583833
Outside Kaltoft-Moldrup211100123111
Condition Est. Over 99%ile0000
Condition Est. Over 95%ile4311
Condition Est. Over 90%ile9657
Enzymes Over 99%ile17193010
Enzymes Over 95%ile1058221968
Enzymes Over 90%ile139126296183
Enzymes Under 10%ile783369514645
Enzymes Under 5%ile542186264423
Enzymes Under 1%ile271374986
Compounds Over 99%ile33286247
Compounds Over 95%ile140127231254
Compounds Over 90%ile346307298338
Compounds Under 10%ile310227297308
Compounds Under 5%ile211111224173
Compounds Under 1%ile132476765

The next table is also very dependent of Lab Read Quality. The apparent improvement on 12/3/2021 is likely artificial because the counts are low due to low read quality.

8/31/202112/3/20213/25/20228/11/2022
PercentileGenusGenusGenusGenus
0 – 973245151
10-1915183224
20 – 2912131812
30 – 39410914
40 – 496893
50 – 594872
60 – 694493
70 – 79710710
80 – 897485
90 – 99141888
8/31/202112/3/20213/25/20228/11/2022
PercentileSpeciesSpeciesSpeciesSpecies
0 – 987295758
10-1924212924
20 – 2914152116
30 – 3910161414
40 – 4926143
50 – 591291710
60 – 69910107
70 – 7989147
80 – 8971554
90 – 991113109

So how to interpret this wall of numbers? People can cherry-pick the numbers to say improvement or no improvement. The difference of lab read quality is a big factor because they impact the count for most of the items above. The Outside Box-Plot-Whiskers numbers show continued improvement. In short, the changes shown were less than I was hoping to see.

There is one more method of comparison — using special studies. In this case we see the average matches. Doing a little math, the expected drop of percentage due to lab quality size between 8/31/2021 and 8/11/2022 is a 10% drop. Those that exceeded 20% are color with 😊 below. Nothing became 10% worse. Note that the 😊 also agrees with comparing to 3/25/2022 (the prior sample). Other items remained unchanged. Items reported by this person are 😧 – Strong issue, 😟 – a bit of an issue

Study8/31/202112/3/20213/25/20228/11/2022Average
Inflammatory bowel disease4932474743.8
Small intestinal bacterial overgrowth (SIBO) 😟51294834😊40.5
Allergic Rhinitis (Hay Fever) 😧 4127454138.5
Autism45344427😊37.5
COVID19 (Long Hauler)40244329😊34.0
Irritable bowel syndrome 😟40224430😊34.0
Alcohol intolerance or Medication sensitivities43233929😊33.5
Histamine or Mast Cell issues 😧 44174324😊32.0
Post-exertional malaise 😧 36234029😊32.0
ME/CFS without IBS 😟39223630😊31.8
Poor gut motility42214024😊31.8
Brain Fog 😧 3723333331.5
Depression3227323431.3
Allergies And Food Sensitivity 😧 38233625😊30.5
Cold Extremities 😧 42233322😊30.0
Intolerance of Extremes of Heat and Cold 😟38163927😊30.0
ME/CFS with IBS 😟3621362730.0
Bloating 😧 37223426😊29.8
General Fatigue 😧 3420313429.8
Unrefreshed sleep3122362829.3
Constipation37212925😊28.0
High Anxiety 😟3317332928.0
Easily irritated 😟32163423😊26.3
Tinnitus (ringing in ear) 😟2415292222.5
Chronic Fatigue Syndrome (CFS/ME) 😧 2521202322.3
Average37.822.437.028.931.5
Lab Quality7.83.66.25.5

What is my conclusion? Most of the measures above deteriorates into noise with the exception of data from Special Studies, where we seen improvement in many measures, but not all. In one real statistical sense this makes sense: many are based on common sense and the ones showing clear improvement on statistical significance.

Going Forward

For most of my prior posts used the logical reasoning and clinical studies (which used different labs and software than the samples that I was looking at). With the special studies, we have upped our game (potentially) – the bacteria deemed significant were determined by the same lab and software of our sample, plus the study sizes was much larger than published clinical studies — hence better detection.

To build the consensus I will use the special studies, I filtered to reported issues and high percentage of matches, namely:

Remember that most of the special studies found that infrequent bacteria with a low value was what was statistically significant. This is turning the usual logic on it’s head. As I state, this is all experimental but based on studies and statistics.

The top suggestions are below

Antibiotics

As expected, most antibiotics and prescription drugs are to be avoided. A few with positive impact includes:

In terms of generic suggestions, rifaximin (antibiotic)s is by far the top antibiotics, cited here on Health Rising: Rifaxamin – citing use by Dr. Teitelbaum, Dr. Peterson, De De Meirleir and Dr. Myhill (all ME/CFS specialists).

In short, all of the top suggested antibiotics are applicable. My personal approach would be do all three of them in a pulse manner a la Jadin, 10 days on, 20 days off and then move to the next one.

Both above and generic suggestions have proton-pump inhibitors (prescription) being the top choice for other prescription drugs.

Probiotics

The top probiotics list have the usual dilemma: both e.coli probiotics and lactobacillus probiotics. It’s a dilemma because they tend to be hostile to each other. My typical rotation resolution would be 2 weeks of each and then move to the next:

Probiotics to take

I should note that some are strong to be avoided (watch out for mixtures!!!)

Probiotics to Avoid

KEGG Suggestions

The KEGG suggestions top items were the bacteria found in Equilibrium and Prescription Assist, except for the top choice, Escherichia coli. A probiotic suggested by Dr. Myhill, a ME/CFS specialist in the UK. The next common conventional items are

Bottom Line

The suggestions above were done solely from special studies. The key question is are they reasonable? I would say yes based on the antibiotics suggestions — all of them have been reported to help ME/CFS patients. We also have agreement between KEGG probiotics and these suggestions.

There is a potential conceptual symmetry between the two approaches (working off extremes and using special studies that are often dealing with rare low bacteria). Bacteria influences each other in very complex ways.

The full list of suggestions is available above.