The Journey Begins with your microbiome

Thanks for joining me!

This is a companion site to the analysis site at: https://microbiomeprescription.com/

The intent of this site to assist people with health issues that are, or could be, microbiome connected. There are MANY conditions known to have the severity being a function of the microbiome dysfunction, including Autism, Alzheimer’s, Anxiety and Depression. See this list of studies from the US National Library of Medicine. Individual symptoms like brain fog, anxiety and depression have strong statistical association to the microbiome. A few of them are listed here.

The base rule of the site is to avoid speculation, keep to facts from published studies and to facts from statistical analysis(with the source data available for those wish to replicate the results). Internet hearsay is avoid like the plague it is.

The Microbiome as a Key to Health

Continue reading “The Journey Begins with your microbiome”

ME/CFS Continues Improvement + Lab Read Quality Issues

Prior Posts

Analysis

A summary of his seven results are below. The Lab Read Quality bounces around, and with that, other values may echo these shifts (i.e. up to 20% shifts for some measures). A low read quality means less bacteria are reported, for example, when it was low, the Outside Kaltoft-Moldrup has low, when it was high, the value became high.

Another way to view it is this: If 10% are out of range and 400 are reported then we have 40. If we have 660 in another report then we would expect 66. This could be misread as a 66/40 or a 65% increase in out of range bacteria when the same percentage is out of range. Technically, it is more complicated but that should explain the problem.

Looking only at high read quality ( 1/22/2024, 2/22/2023, 8/31/2021) we see improvements where there are 🙂 below. This is an unfortunate aspect of 16s tests.

I have added at the bottom Forecast Symptoms compared to actual.

Criteria1/22/20249/12/20232/22/20238/11/20223/25/202212/3/20218/31/2021
Eubiosis56.41003710010068.167.4
Lab Read Quality7.93.59.75.56.23.67.8
Outside Range from GanzImmun Diagostics16161515171720
Outside Range from JasonH7777446
Outside Range from Lab Teletest20 🙂202424222225
Outside Range from Medivere16161515151519
Outside Range from Metagenomics7799778
Outside Range from Microba Co-Biome2277111
Outside Range from MyBioma5 🙂577778
Outside Range from Nirvana/CosmosId20202323181821
Outside Range from Thorne (20/80%ile)198 🙂198223223217217246
Outside Range from XenoGene24 🙂243232363639
Outside Lab Range (+/- 1.96SD)5 🙂1510119914
Outside Box-Plot-Whiskers54564236425942
Outside Kaltoft-Moldrup123 🙂70139567859140
Bacteria Reported By Lab511399666478613456572
Bacteria Over 90%ile20 🙂542624265746
Bacteria Under 10%ile108418248442999
Shannon Diversity Index1.3681.181.0381.2871.5610.8950.903
Simpson Diversity Index0.1150.0630.050.0420.0580.0220.02
Chao1 Index760350571253480531323455639209
Pathogens26 🙂253023392430
Condition Est. Over 90%ile0000000
Actual Symptoms in top 10 Forecasted581088109
Max Forecast Symptom Factor38.522.325.316.915.826.433.1

Explaining the new Symptom Forecast Algorithm

This algorithm is similar to the Eubiosis algorithm. We compute the expected number of matches to bacteria shifts associated with the symptoms. The expected theoretical threshold by randomness is 16%. A higher number indicate increased odds, a lower number decreased odds. This is based on the existing annotated samples uploaded. It is not definitive and often there can be multiple subsets of bacteria associated with a symptom. The match is on too much or too few of a collection of bacteria

The checkmarks are the entered symptoms, the list are the predictions from most likely to lesser.

This data actually clarifies that the ideal 16+ for a factor is dependent on the Lab Read Quality and that 16 may apply to shotgun results but for 16s results, some flexibility with the 16 is warranted.

As a general FYI, hitting 80-100% correct prediction of symptoms implies that the algorithm performs well and the change of algorithm was appropriate.

It also implies that we are successfully identifying the bacteria associated with the symptoms..

The drop of matches with this sample is difficult to clearly interpret. It was not intended to be an indicator but a tool to correctly identify the bacteria of concern. Getting suggestions solely from the symptoms have been added. See the video below.

Going Forward

Again, using Just give me suggestions include Symptoms is how we are going to proceed. And then add in the two Special Studies. This results in 7 packages of suggestions.

Thresholds: High is 524 thus 260 or higher, Low is -346 this -170 or lower

For our first pass, we are going to look items that all 7 agrees upon, the list is very short

The two take list is very short. Prescription items dominates the list with metronidazole (antibiotic)s[CFS] at 524(the TOP), followed by amoxicillin (antibiotic)s[CFS], ciprofloxacin (antibiotic)s[CFS]. The top NOT-PRESCRIPTION is 232, so we will drop the threshold to 116

The avoid list is much bigger

For myself, I would try to obtain and rotate the antibiotics listed above and use Splenda where practical.

Bottom Line

This analysis has been both challenging and informative. We see that 16s Lab Read Quality can confuse analysis because it will alter many measures significantly. Care must be taken when comparing two or more samples with different Read Quality. Additionally, having the top suggestions full of prescription items means that we needed to adjust the threshold based on the top non-prescription item.

On the positive side, we see that the revised symptom forecasts appear to perform well, actually better than I was expecting.

Postscript – 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 result 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.

The answers above describe my logic and thinking and is not intended to give advice to this person or anyone. Always review with your knowledgeable medical professional.

A Youth’s Microbiome with Marfan

This is the son of a person with issues: Bad Diet and Antibiotics? ME/CFS like symptoms. As I have often cautioned, young people’s and children’s microbiomes are different than adults and we do not have appropriate reference ranges. We will do best efforts.

  • Tired all the time
  • Cannot gain weight (very skinny)
  • Diagnosed with Marfan syndrome (a genetic disease he has since birth)
    [editor] About 1 in 5,000 people have Marfan syndrome
  • Stomach pain
  • Disgestion issues (yellow stool and fat in stool)
  • Joint and Muscle pain
  • Dark circles around the eyes

Analysis

There is no available literature on microbiome shifts with Marfan syndrome. Marfan syndrome (MFS) results from heterozygous mutations in the fibrillin-1 gene (FBN1; OMIM #134797), located on chromosome 15 at band q21. 1 (15q21. 1), which encodes for the glycoprotein fibrillin. [MedScape]. Coagulation plays a major role in Marfan syndrome. Both procoagulation and bleeding disorders participate in the disease. Platelet function abnormalities, compatible with von Willebrand syndrome or congenital thrombocytopathies, have been identified in 29% of patients. [2014].

 FBN1 is the causative gene for Marfan syndrome, an inherited disorder of connective tissue whose major features include tall stature and arachnodactyly, ectopia lentis, and thoracic aortic aneurysm and dissection. More than one thousand individual mutations in FBN1 are associated with Marfan syndrome, making genotype-phenotype correlations difficult. [2016]

At a high level we see potential issues. [NOTE: The Eubiosis value changed for many people after a defect was detected in how percentile was computed for some bacteria – often 100% dropped, which how agrees with people symptoms ].

However, there were no statistically significant matches (this page was just updated to use the latest algorithm). This algorithm is similar to the Eubiosis algorithm. We compute the expected number of matches to bacteria shifts associated with the symptoms. The expected number by randomness is 16%. A higher number indicate increased odds, a lower number decreased odds. This is based on the existing annotated samples uploaded data. It is not definitive and often there can be multiple subsets of bacteria associated with a symptom. The match is on too much or too few of a collection of bacteria associated to symptoms.

We will still check the matching symptoms. The top one is a match for symptoms but not a match for the typical bacteria seen for this symptom. We have to hope that there is sufficient matches to be worth while.

First, looking at all of the common, popular measuring sticks –

  • General Health Predictors has a low number (just 8) with only one of possible concern: Veillonella atypica 
  • All of the usual ratios are between 20%ile and 80%ile
  • Anti inflammatory Bacteria Score is at 89%ile — very good
  • No Potential Medical Conditions Detected detected
  • Histamine issues are a potential health issue
  • Bacteria deemed Unhealthy: Bacteroides fragilis and Parabacteroides merdae are the only one, both are potentially infectious bacteria.
  • Dr. Jason Hawrelak Recommended Levels came in at 94%ile

So, everything looks like a reasonably healthy person.

Going Forward

With no clear issue associations, we are going to do two runs: One with symptoms and one without.. Using the standard ‘Just give me Suggestions’ The list below are for the items at a priority of 50% or more of the highest priority [506] [Symptoms: 440]. This limit has no rationale apart from reducing the volume of suggestions.

Suggestions

Let us look at AVOIDS, given the general healthy state, just try reducing if taking,

At this point, I attempted to do cross validation: Are there any literature of items suggested (or avoid) on improving Marfan syndrome. This is done to test the suggestions – for other conditions with lots of literature, we have usually seen 90-95% agreement. For ME/CFS, I know the literature well — for this condition, not. I found only symptom treatment (Mayo, NHS). Since this is a DNA condition and I know DNA can influence the microbiome (and the reverse), then trying to improve towards typical this youth’s microbiome is a reasonable (and low risk) approach.

Because of the platelet function abnormalities that could be present, as well as thick blood (procoagulation) — both areas that I am familiar with from ME/CFS. I checked suggestions for possible items that could be related to coagulation:

Questions and Answers

Q: Do you know why it suggest gluten Free diet? Could he have gluten intolerence/celiac maybe?

  • The why is because of that type of diet impacts on bacteria that are off balance. We cannot detect  gluten intolerance/celiac. Only the impact of that type of diet on different bacteria. Some source papers to illustrate:

Bottom Line

The thing that strikes me most about the suggestions, the items to avoid are prebiotics and probiotics; the opposite of common advice for anyone with health issue, especially digestive issues. There are no studies on PubMed for probiotics and this condition which infers to me (given the popularity of trying probiotics) that there were studies with no effect or negative effect. In the sparse literature, we did have one of the take suggestions computing matching the literature.

If this was my own child, I would likely follow the items in suggestions above. There is low risk in following them and one suggestion does cross-validate with the available literature (which has almost nothing published in this area).

I work off the axiom that a disease or conditions modifies the microbiome to be favorable to the condition. Undoing those shifts have a reasonable change of slowing, and in some cases, reversing the condition. I have had antidotal reports of this approach speeding cancer treatment.

Postscript – 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 result 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.

The answers above describe my logic and thinking and is not intended to give advice to this person or anyone. Always review with your knowledgeable medical professional.

ME/CFS + 3 times COVID + food poisoning

This is part of a continuing series of analysis for ME/CFS or/and Long COVID.

Background

I am contacting you as you may provide a microbiome analysis for you has cfs – long Covid 19.
I have been struggling for years with cfs-me. I also have Covid 3 times (the last one was in December 2023). When I did the test, I just had few days before a food poisoning that led me to ER.
I did a GI map last year because I wanted to have more information after failing to cure a methane SIBO with herbs. I have a very bad infection (enterohemorrhagic e choli).
I was suggested by the functional doctor whom I ordered the test some thyme and probiotics but obviously it had no impact. I redid a stool test (biomesight) but I am really overwhelmed by the results.

Would you mind give me some insight on those tests ?

  • joint pain, neck pain, TMJ, migraines
  • hypothyroidy, insulin resistance, low cortisol,
  • possibly Lyme (low nk57 but negative test)
  • possibly mold intoxication 
  • heavy metal intoxication 
  • brain fog
  • Attention-Deficit/Hyperactivity Disorder (ADHD)
  • skin issues on the face and eczema on my hand 

Analysis

We have some dysbiosis (i.e. Eubiosis is not 100).

Looking at reported symptoms, we see a number of matches to reported symptoms over 16%ile, with one of the unchecked,  inability to focus eye/vision , being a potential missed item. There are 67 symptoms entered with 58 of them above 16% (the threshold)

Explaining the new Algorithm

This algorithm is similar to the Eubiosis algorithm. We compute the expected number of matches to bacteria shifts associated with the symptoms. The expected number by randomness is 16%. A higher number indicate increased odds, a lower number decreased odds. This is based on the existing annotated samples uploaded. It is not definitive and often there can be multiple subsets of bacteria associated with a symptom. The match is on too much or too few of a collection of bacteria

Looking at Health Indicators

  • General Health Predictors: 11 items, with Veillonella atypica being the greatest concern
  • Potential Medical Conditions Detected: None. I double checked, and there were no significant matches.
  • Dr. Jason Hawrelak Recommendations: 94%ile

Going Forward

Doing just give me suggestion with symptoms gives the following suggestions for items to add (50% of 516 or hgh

The Avoid List

The lowest value was -550, so items below -275 should be the highest priority.

Comparing to Suggestions from GIMAP

The data transcribed is below. Our consensus report above picked 67 bacteria of concern

As expected (See this post) there was agreement and disagreements between these reports on what is high or low, and some agreements. For example,  Faecalibacterium prausnitzii was at the 81%ile on Biomesight data and very low above.

Suggestions will always be different because of the much smaller set of bacteria being used. We do note the following agreement in suggestions:

Many suggestions are not found at all in the GIMap suggestions because there is no literature for those substances and the bacteria reported.

Questions and Answers

Q: Would you have any specific recommendations about enterohemorrhagic e coli (ehec) ?

Q: Another question about the antibiotics protocol for me/cfs (in case I succeed to convince my GP). Dr Jardin suggests : 1 week on with one antibiotics then 3 weeks off, then another cycle with another antibiotics. Is it right ? 

  • Correct for Jadin.  One week on and 3 weeks off… and then change antibiotics.  This comes from old clinical experience at the Pasteur Institute.  I have read studies dealing with sewage plants that found this pattern works better.

Q: On your blog, it also says to pick one of the 4 suggestions of supplements and switch every week during 8 weeks and retest. Does it mean I must choose 4 supplements, take 1 supplement during 1 week then switch to another 8 times and so on. Am I right ? (I am not English fluent so I struggle a little to understand everything)

  • 4 SETS of supplements…. so each week you change sets.  This again is suggested to prevent dysbiosis adapting. I have too often heard “It works for 3 months and then stopped working” . As an analogy, think of cops setting up cameras to stop people speeding, their existence improves traffic — but once people learn that they are always at the same place … bad behavior returns.

Q: Last question : could symbioflor1 help for my enterrococcus faecalis overgrowth? Or is it the opposite?

  • There is nothing that I could find for  symbioflor1 impact on enterrococcus faecalis overgrowth in the 13 studies I have processed. So we are again into the “fuzzy knowledge area”, in general (especially the EU), probiotics are not troubles strains and thus can be used to shift related bacteria.
  • From https://link.springer.com/article/10.1007/s11259-024-10324-0, we see that it is hard to treat. BUT Curcumin is better than 2 antibiotics tested.

Postscript – 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.

The answers above describe my logic and thinking and is not intended to give advice to this person or any one. Always review with your knowledgeable medical professional.

Fifth Analysis of IBS/Long COVID/ME/CFS

We have a varied history with some storms blowing us off courses. Here’s a list of the tests and prior blog posts:

This is one of two set of ongoing samples from readers that “have appeared to almost stalled”. The other reader sent me this note at the same time (and another sample) “I have to say, symptoms are pretty dead on accurate to what I’m experiencing like all but one box. PEM is my highest ,”

This implies strongly that the association between symptoms and bacteria shifts are strong. The microbiome is just stubborn.

Feedback

He has 49 different symptoms checked and unusually, have a friendly MD in terms of antibiotics.

I would say some small subjective improvements since last time, but no major changes. Also I increased squats from 14 to 15 and push-ups from 9 to 10 at the time of the sample. (I also increased walking distance a little, but only after the sample was taken. I probably could have increased them by more, but I wanted to start really slowly with increasing those things.)

Between the last test and this sample, Amoxicillin was the only antibiotic I did. I also did some of the top herbs and probiotics (B. infantis, Mutaflor and L. Kefiri).

Also anxiety is a bit of a problem, but only sometimes, not every day. I’m not really sure what the cause is. I think it might be connected with winter, cold, rarely seeing the sun, maybe piracetame, people around me coming to me with suggestions on what I should do, maybe noise. (Noise has been a problem for me since the beginning of CFS. I really can’t endure noise well.) But those all don’t have to be the cause, they can also just be triggers or be connected to it. (Eating might also be connected to it. It seems to me that on the days I eat bacon for breakfast and a large portion of potatoes and beef for lunch (like once a week), it is better. On the days I eat sth. made from corn flour for breakfast (like every four days), it is worse. But I cannot eat the same things multiple days in a row because I quickly develop food intolerances if I do that, so I have to eat alternating things that I tolerate.) I am just wondering whether something can be done to help with that (anxiety).

Analysis

The eubiosis index is a recent addition and I am curious on how it behaves compared to other measures. Having a magic number to indicate health is an ideological goal, my gut feeling is that there is no such magic — rather many aspects need to be examined.

SampleEubiosis (balanced) gut.Unhealthy Bacteria
2021-11-1899.68
2022-05-2048.512
2023-06-2238.512
2023-09-0410012
2023-11-2310012

The traditional analysis

Criteria11/23/20239/4/20236/22/20235/20/202211/18/2021
Lab Read Quality5.44.77.28.15.5
Outside Range from GanzImmun Diagostics1211111515
Outside Ran ge from JasonH79966
Outside Range from Lab Teletest2522222020
Outside Range from Medivere1115151616
Outside Range from Metagenomics87799
Outside Range from Microba Co-Biome33311
Outside Range from MyBioma66655
Outside Range from Nirvana/CosmosId2223232020
Outside Range from Thorne (20/80%ile)235241241231231
Outside Range from XenoGene3335352929
Outside Lab Range (+/- 1.96SD)2 🙂21786
Outside Box-Plot-Whiskers31 🙂58423769
Outside Kaltoft-Moldrup47 🙂51929448
Bacteria Reported By Lab508568582674527
Bacteria Over 90%ile17 🙂41243852
Bacteria Under 10%ile835014717736
Shannon Diversity Index1.591.2721.5561.8531.826
Simpson Diversity Index0.0470.0870.090.0560.038
Chao1 Index6986100619016147447390
Shannon Diversity Percentile43.812.74081.878.2
Simpson Diversity Percentile45.377.578.654.833.6
Chao1 Percentile2548.941.479.427.8
Pathogens2223293220
Condition Est. Over 90%ile50934

At first look, there seem to be little change. Looking at specific items, there is improvement (highlighted in red above), namely less bacteria with extremes levels. For all of the reference ranges from 3rd party labs, there is no effective change.

Going Forward

Since symptoms were also entered, we proceeded with [Just give me Suggestions Include Symptoms]. The results surprised me a little; the top items were CFS antibiotics and whole-grain barley (likely a proxy for beta glucan — see this post: Beta-Glucan: The Microbiome Fixer; ß-glucan is on the to take list). The following was sorted by Take Count descending (which means that all five sets agreed)

Personally, given the slow progress, I would be inclined to try talking a medical professional into prescribing one of these.

Let us do the usual breakdown by types, most are below 1/2 of the highest value.

Further analysis

I did a second run, but excluded symptoms, there was no significant shifts. The top items were the same but other antibiotics shifted position.

From the early draft, this reader responded with more information:

  • He has started nicotine patches which has a significant positive score of 113

I used the ability to do a double sort (Descending Take Count, Descending Priority) to get a double conservative list.

Tudca is Tauroursodeoxycholic Acid and available as a supplement. Based on this clinical study: Safety, Efficacy and Pharmacokinetics of Doxycycline Plus Tauroursodeoxycholic Acid in Transthyretin Amyloidosis, I would suggest that it be taken concurrently with the metronidazole. There are 34 clinical studies using it. It is interesting that metformin (a diabetes drug) is suggested at the same time we see avoid all natural sugars in our suggestions – there is an interesting symmetry here. Teicoplanin is also interesting and very suitable (literature here). Literature for Ceforanide is here.

My prescription model to be discussed with the MD would be:

  • Week 1:A course of metronidazole with Tudca
  • Week 2-4: metformin (possibly with Tudca)
  • Week 5: Teicoplanin with Tudca
  • Week 6-8: metformin (possibly with Tudca)
  • At end of week 8 do another sample
  • Week 9: Ceforanide with Tudca
  • Week 10- new report: metformin (possibly with Tudca)

Barley porridge and similar alternating with beta-glucan supplements (since food sensitivities appear to develop quickly). Perhaps consider a diabetes-like diet (to keep the natural sugars low).

For Tudca, we read about some possible adverse effects in this paper Pharmacokinetics, Safety, and Tolerability of Orally Administered Ursodeoxycholic Acid in Patients With Parkinson’s Disease—A Pilot Study [2021] namely ” gastrointestinal discomfort, rated by subjects as mild to moderate“. It has a half-life of 2.1 ± 0.71 hr, so taking 4 staggered 500mg dosages per day should be considered.

Speculation: monitoring blood glucose levels (like what diabetics do) may be a waste or time OR may provide insight. I have a smart watch that monitors blood glucose ($30 from Banggoods to Temu). There are also more professional monitors.

Question:  I ate cornflour for breakfast, which I wrote about in my first mail. On those days anxiety is worse

Large Language Model vs Expert Systems for Medicine and the Microbiome

I tried out a new medical Large Language Model (LLM) API, https://www.drgupta.ai/ to see what it would suggest for a simple microbiome shift compared to what the Expert System(ES) (NOT LLM) AI system does on microbiome prescription. The first significant one Expert System for Medicine was called MYCIN and was written by Stanford University in 1972.

The main business differences between LLM and ES are costs. LLM run heavy computer costs, ES runs heavy human costs. An ES often require article by article review with suitably skilled reader (or example, a grad student). LLM are easy targets for getting venture capital funds — often based on pie-in-the-sky beliefs of how easy it would be to do that is sold to venture capitalists. Earlier I had several sessions with folks at the The Allen Institute for Artificial Intelligence exploring machine analysis of the literature. Their conclusion was that existing AI is still incapable of good analysis of medical and clinical studies.

LLM Report

I tossed a simple, three taxa problem at the API. Reality is that typically we are seeing 40-80 taxa of interest.

Expert System Response

Compared to:

We do not have vague “probiotics” but provide their specific names and dosages. We also include probiotics to avoid.

With information on suggested dosage for probiotics with links to sources.

As well as the names and links to studies used to make these suggestions.


Nothing in the LLM indicates that Pectobacteriaceae was considered. The Expert system does consider it:

And provide background

Bottom Line

This post intent was to contrast the difference between LLM and ES systems. Both can have data entry/text interpretation issues. With a suitable ES system, the suggestions can be audited and issues addressed. With LLM, this does not seem to be available with common code bases.

The table below from PubMedQA shows that accuracy is barely over 80% for the best models out there. Expert systems can exceed 95%. Is 80% “good enough” for treating patients especially if the ability to audit the logic is missing? By Audit, I mean provide links to all source studies).

A follow up ME/CFS Analysis

This is a follow up on the prior post below. The reader’s comments are “I am feeling much better but still very fatigued and lately been quite achey.  The recommendations have changed significantly except for whole grain barley.”

For more analysis see: Analysis Posts on Long COVID and ME/CFS

Comparison of Samples

Let us first do the simple numbers. A lot of values are the same (typical) but many of them show improvement. 😃 indicate significant reduction is out of range values See Technical Note: Lab Quality Versus Bacteria Reported We would expect a 15% drop from lower lab quality, the drops shown are well below that).

CriteriaCurrent SampleOld Sample
Eubiosis Index62.8%😃59%
Lab Read Quality4.38.4
Outside Range from JasonH88
Outside Range from Medivere2020
Outside Range from Metagenomics1010
Outside Range from MyBioma88
Outside Range from Nirvana/CosmosId1818
Outside Range from XenoGene4242
Outside Lab Range (+/- 1.96SD)9😃16
Outside Box-Plot-Whiskers38😃98
Outside Kaltoft-Moldrup56😃139
Bacteria Reported By Lab494752
Bacteria Over 90%ile20😃82
Bacteria Under 10%ile66😃232
Shannon Diversity Index1.4651.701
Simpson Diversity Index0.0350.028
Chao1 Index747417093
Shannon Diversity Percentile28.561.4
Simpson Diversity Percentile30.221.5
Chao1 Percentile28.987.7
Lab: BiomeSight
Pathogens18😃39
Condition Est. Over 90%ile44
Kegg Compounds Low969😃1242
Kegg Compounds High5😃23
Kegg Enzymes Low272284
Kegg Enzymes High17😃75
P or P Chi2.9999245.999999999
Percentages of Percentiles Chi2 is a proxy for severity of abnormality, it has decreased.

Health Analysis Comparisons

I have not created an automatic compare yet (on to do list). Many values were similar, some interesting ones with improvements are below. Jason Hawrelak Criteria got worse, but I have deep reservations on using his criteria on Biomesight tests (he based them on a very different test method).

RecentPrior
General Health Predictors: Flagged Bacteria8😃10
Anti inflammatory Bacteria Score14.4%ile😃13.3 %ile
Lactate (controls many bad bacteria) 📚33.1 %ile😃20 %ile
L-Lactic Acid (controls many bad bacteria) 📚47.1 %ile😃25.2 %ile
NADH (Typically low with ME/CFS) 📚📚26.5 %ile😃13.7 %ile
Hydrogen peroxide (controls many bad bacteria) 📚17.3 %ile😃5.8 %ile
D-Lactic Acid (Associated with brain fog) 📚6.5 %ile😃7.9 %ile
Potential Medical Conditions Detected2😃7
Bacteria deemed Unhealthy7😃22
Jason Hawrelak Criteria56.4 %ile75.8 %ile

Going Forward

A review of the Health Analysis was done above, with the two items: Mood Disorders and COVID-19 (a proxy for ME/CFS IMHO). A secondary review of all the items on [Changing Microbiome]/[US National Library of Medicine Studies] for high items not flagged. Nothing added.

Doing what is becoming a regular pattern: “Just give me suggestions” and then using given symptoms under Special Studies using these items:

Note: items like age and gender are omitted as well as any other symptoms that we do not have sufficient data.

First the filtered PDF suggestions. The list is much longer than usual:

And the to avoid list is more typical.

Let us go over to viewing the consensus to get some priorities


The highest value was 485 (so 240 for cutoff), lowest value was -574 ( so-287 for cutoff)

So in summary, shift a diet to low sugar, gluten free with moderation in meat (no guidance on chicken or fish). If your MD is willing, I would suggest reviewing Cecile Jadin📚 approach with antibiotics and rotate with those suggested above. IMHO Continuous on a single antibiotic is more likely to complicate the microbiome.

Postscript – 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.

The answers above describe my logic and thinking and is not intended to give advice to this person or any one. Always review with your knowledgeable medical professional.

Beware of false statements on sites: Jonas Health

A reader asked me to evaluate their offerings. Remember, I do NOT sell testing, I offer a free citizen science analysis on over 3 dozen different microbiome tests using Artificial Intelligence. One of the first thing that strikes me is false and misleading statements on some sites. The following is from Jonas Health for illustration purposes. A few are below, taken from their site in November 2023.

This is incorrect. They cannot identify ALL organisms, they can only identify the items in their reference library. For example, there are 30 new fungi species being added every year in 2004 ( Biodiversity of Fungi, 2004) and I would expect that rate to be increasing. NCBI currently lists over 2.5 million taxa. In 2012 it was just 235,000. That’s a 10 fold increase in 10 years.

It is unlikely to be “all”

Looking at their sample report we see numbers given with no scale.

As for research, we see two papers, neither titles suggests that lactose was the focus of the study. One seems focuses on Rice and oats. The article is here – the word lactose is never mentioned in the article. As this is a demo report, I would expect correctness. Also, the journal was Front Immunol. 2021; 12: 787797. and NOT Nature.

Next we see what may be correct per the sample, but no guidance on how to:

  • Increase Faecalibacterium Prausnitzii WHILE CONCURRENLTY Decreasing Faecalibacterium .

Bottom Line

Based on this sample report, I see ugly problems. Thorne Gut Testing is 40% of the cost and much more useful, especially if used with Microbiome Prescription. I attach a copy of their sample report below.

Low Dosage Naltrexone for ME/CFS, Mast Cells, FM

A reader asked me to assemble information from studies on Low Dosage Naltrexone. For conditions like Fibromyalgia, we have 49 studies with good or no effects.  I speculate that the effectiveness is dependent upon the microbiome prior to starting.

A lot of the published literature are case-reports (i.e. on individuals). My general impression from larger studies is that it is a 50-50 toss of the coin if improvement will happen. There is an absence of literature on its impact on different bacteria in the microbiome.

Beta-Glucan: The Microbiome Fixer

A reader that does microbiome analysis of her ME/CFS daughter’s microbiome using Microbiome Prescription expert system sent me this note with some literature. The daughter has Celiac Disease and ME/CFS.

Your wonderful system recommended beta-glucans [also written β-Glucan] for my daughter,  and when I looked further, I found this. I’m trying her on them for a month-, after testing her for reactions for three days- the first week has been hopeful. Will keep you posted if you wish.

Reader

β-Glucan is a nonstarch polysaccharide having documented health benefits and industrial applications. It can be extracted from various sources, including cereals, bacteria, molds, and fungi. The chemical nature of extracted β-glucan from these sources differs slightly. This variation in chemistry defines its industrial uses and health benefits.

Biopolymers for Food Design, 2018

Literature

There is not much literature available for ME/CFS.

  • “The findings showed that the beta-glucan supplementation significantly improved cognitive fatigue (assessed with FIS-40 scores) after the 36-week treatment compared to the baseline (p = 0.0338). Taken together, this study presents the novel finding that yeast-derived beta-glucan may alleviate cognitive fatigue symptoms in ME/CFS.” [2023]
  • β-Glucan Improves Conditions of Chronic Fatigue in Mice by Stimulation of Immunity [2020] Reduces TNF-α (which is connected to mast cell issues)
  • Effects of β-(1,3–1,6)-d-glucan on irritable bowel syndrome-related colonic hypersensitivity [2012]
    “β-Glucan did not affect the pain response in general but specifically affects the visceral pain response.”
  • Serum concentrations of 2′,5′-oligoadenylate synthetase, neopterin, and beta-glucan in patients with chronic fatigue syndrome and in patients with major depression. [1994]
  •  the dosage of supplementation ranged from 2.5 to 1000 mg daily [of beta-glucan] for up to 6.5 months … The primary physiological outcome of the majority of the interventions was immunomodulation, which resulted in (a) strengthened immune defense that reduces the incidence and symptoms of cold, flu and other respiratory infections and (b) improvement of allergic symptoms.” [2021]
  • β-glucan attenuates cognitive impairment via the gut-brain axis in diet-induced obese mice [2020]

Some literature for Autism

Many Sources of Beta Glucan

Often the expert system on Microbiome Prescription comes up with Barley as a strong recommendation for ME/CFS people. Barley is an excellent source. Personally, I have oats or barley porridge a couple of times every week. The impact of the β-Glucan in the Barley may be the mechanism — we just do not have as many studies as we do for Barley.

  • “The primary sources of food β-glucan for humans are cereals (especially oats and barley), fungi, algae, and yeast ” [2023] A table from this article is below
  • β-glucans bind to specific receptors on immune cells and initiate immune responses…. In vitro study found that the fermentation of barley and oat β-glucan by human fecal samples show variations in SCFAs production and the bacterial populations of Clostridium histolyticum and the ratio of Bacteroides–Prevotella species. Absorption of these SCFAs by the gut epithelial cells helps in regulating cell differentiation, proliferation, apoptosis, and gene expression (210). Butyrate increases the protein expression of tight junctions such as ZO-1 and claudin-1, resulting in enhanced intestinal barrier function.”
    β-glucan is an essential food ingredient in controlling metabolic dysregulations linked to metabolic syndrome. β-glucans have a very minimal probability of having any unfavorable side effects and are reasonably inexpensive.” [2023]

Bottom Line

Real simple: Barley or Oats porridge for breakfast each day! Since there are some chemical differences between the β-glucans in these two grains– rotate between these (and different brands) at least monthly.

Using the generic suggestions for me/cfs we see both barley and B-glucan are positive (but oats are slightly negative). The more detailed citizen science suggestions are still be worked on, but I expect similar.

Reviewing Clinical Trials, my impression is 1 gram/day of β-glucans which translates to 20 grams of Barley or 40 grams of Oats per day.

“30g uncooked oats or barley will make a fairly small bowl of porridge whilst 70-80g will provide a particularly large serving for one person. Traditional porridge recipes tend to use oatmeal with approximately 200ml of water per 50g oats, and a pinch of salt.”

University of Aberdeen

Some people will advocate just eat mushroom. While correct that it contains beta-glucans, we need to be careful not to slip into homeopathic dosages!

Among those, mushrooms feature a particularly high level, so it’s no exaggeration when we say “for beta glucans, look to mushrooms!” The amounts of beta glucans found per 100 g of raw mushroom include 2.3 g (maitake), 2.0 g (bunapi), 1.9 g (eryngii), 1.8 g (bunashimeji) and 1.5 g (shimofuri hiratake) (Hokuto data).

https://www.hokto-kinoko.co.jp/lang/en/kouka/jiten/jiten06/

When we go to typical US mushrooms (i.e. Button), we drop to .75 g/100 grams [FDA]. So we are talking about 5-6 oz of mushrooms per day. That 3/4 of the typical mushroom package per day per person.

Celiac and Gluten Sensitive Issue

Most beta glucan supplements are produced from Saccharomyces cerevisiae (thus gluten free). For example the item below is about US$17.00 and gives 100 days at 1 gram per day.

I should note that there are different forms of beta glucan, for example above it is the 1,3/1,6 forms. Another product has 1,3/1,4 and is derived from Oats (you will have to write the company to see if it is gluten free or low gluten).

The cost per gram is much lower as bulk powders than with pre-filled “premium” capsules – the same volume of beta glucan can be as high as $250 (12x more) with some products.

Severe ME/CFS from long COVID

Backstory:

I got COVID in Feb 2022. Over the next few months I developed long COVID symptoms. Within 6 months I was severe (bedbound), and within a year I was very severe (24/7 dark silent zero stimulation bed rest). About six months ago I progressed back to being severe and have stayed there. I’ve been officially diagnosed as having ME/CFS as well as long COVID.

I have basically all the symptoms but the worst are light and sound sensitivity, post exertional malaise, brain fog, fatigue, and cognitive and sensory processing issues.

I have severe episodes of d lactic acidosis when I eat dairy. D lactic acidosis was actually my very first long COVID symptom.

If it’s relevant – all “mitochondria boosters” make me significantly worse. Ubiquinol/CoQ10 is what pushed me into being very severe. [Editor note: We have limited information on Coenzyme Q10  and cannot propose reasons for this response – it was not listed in the suggestions]

A few months ago my GI symptoms (diarrhea, bloating, stomach pain, etc.) got more severe, I think as a result of taking Pepcid[Famotidine] daily for MCAS. I tested positive for H Pylori and was off the charts for methane and hydrogen SIBO. [Famotidine is a weak positive, but positive]

I did a GI Map before starting treatment, which is uploaded to my profile. I then did 2 weeks of metronidazole + doxycycline + pepto bismal to try to tackle the H Pylori. My histamine intolerance and d lactic acidosis got MUCH worse during treatment. I did my BiomeSight test a week after finishing antibiotics.

Then I did 2 weeks of Xifaxan + Nitazoxanide + PHGG for the SIBO. I just finished this. My bloating is a little better but my histamine intolerance and d lactic acidosis worsened even further and now my cognitive function is the worst it’s been in months.

I’ve just started Mutaflor and have also obtained Symbioflor-2, Miyarisan, and Equilibrium, and am planning on cycling through those (in addition to whatever recommendations pop up from my BiomeSight test).

Analysis

The Eubiosis index and percentages of percentiles show quite dramatic (and a typical) results. We have a large number of bacteria which I am inclined to described as “pedal to the metal”. These are all at extreme levels. Chao Index and Shannon Index are at 0%ile and Simpson Index at 83%ile.

Some of these extremes bacteria ( > 90%ile) with known health impacts are:

Morganella is a known extreme histamine producer (Histamine and biogenic amine production by Morganella morganii isolated from temperature-abused albacore [2000]) which accounts for the histamine issues. The KEGG estimate of histamine producers is up at 84%ile. Most of KEGG estimators are at extreme – for example Oxalate is at 100%ile and Oxalate degrading is at 0%ile [which indicates a risk of kidney stones developing over time]

The Bacteria deemed unhealthy is an impressive list.

Going Forward

The joy of using an expert system is that despite a very complex microbiome, the system will grind thru all of the data and produce a better results than a human doing so. A human will typically pick one or two bacteria to address “and see what happens”.

The person has marked their symptoms so we have five sets of suggestions going into our consensus.

The top suggestions have a few antibiotics but a lot of items are intermixed between them. In such a scenario I favor not doing antibiotics.

One item in the avoids really stand out, proton-pump inhibitors (prescription) at -637.

The following are items picked above 400 or below 300. The reason to do 50% of the extreme button is not to overwhelm the brain with too many suggestions. Check the site for dosages[Click here].

So, for breakfast every day: Barley porridge with soy milk with slices of bananas/apples?

One at a Time and Rotate

We want to identify items that help or hurts you specifically. Tossing everything in at once denies us this knowledge. My general guidance would be:

  • Spices and Herbs with meals
  • Probiotics at bed time

Break the suggestions into 4 groups and take them for a week at a time. After 8 -12 weeks (2-3 cycles) get a new microbiome test to see changes. Keep up this pattern until you have new test results.

Remember our goal is to destabilize a stable dysbiosis. We effectively want to do a guerilla war against it — constantly hitting it from different places.

Questions

  • Q: Question about herbs/spices. Is the recommendation to take them at the same time as probiotics? Or do a week of herbs, then a week of probiotics, and keep trading off? You’ve posted before about how some of the herbs can nullify the probiotics so I’m not sure how to stack correctly. 
    • Answer: If you click on one the herbs and spices you will be taken to a detail page where the first section is on the impact on probiotics. For the first item, we find that clove and clostridium butyricum have no interactions — so taking both on the same day is fine.

Similarly, for fennel we find that it actually enhances lactobacillus reuteri

So there is a manual process to identify what is neutral or helpful. If a herb or spice impacts every suggested probiotic, then either just do the herb, or keep 8-12 hours between them.