Vaccinations and the Microbiome

This post was triggered by the email below. They included a Biomesight microbiome test, Mosaic Organic Acid Test and a Gastric Tissue report. My expertise is solely the microbiome as a statistican so I will ignore all except the microbiome test.

Key Question: Is “vaccine injury” is a permanent condition?

  • Answer: No, the most probable cause of vaccine injury is a vaccine response triggering or worsening a microbiome dysbiosis. See the literature below.
    • A microbiome dysbiosis may self-resolve for some people (i.e. people feel off for a few days or weeks after the shot) or become stable — requiring sophisticated intervention.
    • There can be other speculated mechanism (autoimmunity induced, molecular mimicry or bystander activation) but they lack clear evidence, and are often based on ideological beliefs. I keep to Osler Principle and the simplest explanation supported by evidence.
    • Followup from reader: H1N1 Influenza Pandemrix vaccine which caused narcolepsy (autoimmune disease) due molecular mimicry, which is my worst fear..
      • Correct: Narcolepsy Associated with Pandemrix Vaccine [2018]. This is one specific vaccine, not for all vaccines (my scope). The researchers who found this in the data would have reported all vaccines with similar side effects if there was data supporting it. [Studies] It seems to be associated to H1N1 vaccines.

I wanted to give you a rundown of what’s been going on with me. On January 6, 2023, I got the third dose of the nonavalent HPV vaccine, Gardasil 9. Immediately after the shot, I felt wiped out and weird, but my symptoms subsided only to come back with vengeance two weeks later.

The symptoms I experienced were all the classic ME/CFS ones, specifically POTS, tachycardia, panic attacks, brain fog, blurred vision, shortness of breath, trouble finding words, fatigue, PEM, fasciculations, neuropathy, pins and needles, Raynaud’s phenomenon, joint pain and joint cracking, food intolerances and food malabsorption, yellow mushy stools, and some more alarming sensations: like feeling that my body was heavy, like it was made of concrete, a sensation of electric shocks in my arms, and tingling in my feet that moved to my hands a couple of times.

Since then, some symptoms have disappeared, but others remain and new ones pop up. Right now, the symptoms I still have are joint pain and joint cracking, fasciculations, malabsorption and yellow stools, what I think is Raynaud’s phenomenon (my hands are red most of the time), and, at the moment I’m writing this message, heavy drowsiness and a general feeling of malaise, which is discouraging, since I felt better earlier this month and thought I was finally getting out of this nightmare.

A reader on CFS Remission

Overview

This is a two-sided discussion exploring the interaction between vaccinations and the microbiome from both perspectives:

  1. How vaccinations may alter the microbiome
  2. How the existing state of the microbiome may influence the effectiveness of a vaccination

To be transparent, I want to share that I personally experienced an adverse side effect following a series of vaccinations. The side effect involved severe gingival (gum) recession, causing the roots of my teeth to become fully exposed. Unfortunately, the condition progressed to the point where dentures became necessary due to the extent of gum loss.

At a high level, interactions in both directions are not only possible but expected. Vaccinations stimulate the immune system, similar to a natural infection — and any shift in immune function can, in turn, affect the microbiome. Conversely, the microbiome plays a key role in shaping immune responses, meaning it can directly influence how the body responds to vaccines.

It’s important to remember that the primary goal of any vaccination is to safely prompt the immune system to build protection against a specific infection. However, because the microbiome and immune system are deeply interconnected, this process can be more complex than it first appears.

Vaccination to Microbiome

A few studies of interest:

Growing evidence shows that the composition of the intestinal microbiota, which is known to play an important role in the development and regulation of immune responses7, influences responses to vaccination8,9,10. Studies which have investigated this have shown that a higher relative abundance of the phylum Actinobacteria is consistently associated with higher vaccine responses and a higher relative abundance of Bacteroides with lower responses, while the association between the relative abundance of the phyla Firmicutes and Proteobacteria and vaccine responses varies for different genera and species11,12,13,14,15,16,17,18.

The immunological interplay between vaccination and the intestinal microbiota [2023]

A recent study using metagenomic sequencing, reported that the intramuscular administration of an inactivated and an mRNA SARS-CoV-2 vaccine was associated with lower bacterial diversity, an increase in the relative abundance of Bacteroides caccae and a decrease in the relative abundance of Clostridiales (Coprococcus comes, Dorea longicatena and Ruminococcus obeum) in the intestinal microbiota one month after vaccination

… a total of 15 bacterial species in the baseline gut microbiome were identified, of which Bifidobacterium adolescentis was enriched in high-responders while Bacteroides vulgatus, Bacteroides thetaiotaomicron and Ruminococcus gnavus were more abundant in low-responders

Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events [2021]

Microbiome to Vaccination Effectiveness

Not only do pathogens exert immunomodulatory effects, but the microbes that populate a healthy human host, known as the microbiome, can also influence the immune response.4,11

Influence of the microbiome on response to vaccination [2015]

When facing respiratory syncytial virus (RSV), mice supplemented with Lactobacillus showed an enhanced immune response 

Lactobacillus johnsonii supplementation attenuates respiratory viral infection via metabolic reprogramming and immune cell modulation. [2017]

One of these factors seems to be the microbiome differences among individuals (101, 102). A growing number of studies suggest that the microbiome can modulate immune responses induced by vaccines (103, 104). Huda et al. (105) studied infants’ microbiomes to evaluate how their microbiome composition influenced the response to oral PV and hepatitis B virus vaccines. They found that Actinobacteria species prevalence may increase the vaccine response, while Enterobacteriales, Pseudomonadales, and Clostridiales were associated with lower response to the aforementioned vaccines. Hagan et al. (106) showed that differences in the microbiome can alter the responses of humans vaccinated against IAV.

The Interplay between the Host Microbiome and Pathogenic Viral Infections [2021]

Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events

Analysis

My model is that ME/CFS is a microbiome dysbiosis. A vaccination is a microbiome disruptor — for most people, they recover. If you start with dysbiosis, then recovery may be a bit less likely.

Urban Legend in some ME/CFS groups is that people with ME/CFS do not catch things. There may some truth to it — virus friendly to the typical microbiome may find the dysbiosis of the ME/CFS patient very unfriendly. Secondly, (with a little tongue in check humor) how can they tell!!!

It turns out that virii often requires specific species to infect a person.

 certain microbiome can be essential for a virus to infect its host. Jones et al. (82) showed that human norovirus needs Enterobacteria spp. to successfully infect B cells, as this bacterium aids in the attachment of the virus to the host cell. Norovirus infection in mice requires the microbiota to be persistent (83): mice with a depleted microbiome prevented persistent norovirus infection. 

The Interplay between the Host Microbiome and Pathogenic Viral Infections

Going Forward

The phrase of “Vaccine Injury” is very misleading and implies that the body is somehow injured in potentially a permanent way. I believe that “Vaccine Dysbiosis” is a better and more accurate term.

We find a mountain of literature associating a vast array of different virii to ME/CFS. A few examples are:

  1. Epstein-Barr Virus (EBV)
    EBV, which causes infectious mononucleosis, is one of the most frequently implicated viruses in ME/CFS. Studies show that 8–15% of people who develop infectious mononucleosis go on to meet ME/CFS criteria, and a subgroup of ME/CFS patients show evidence of EBV reactivation or immune response abnormalities related to EBV5 7.
  2. Human Herpesvirus 6 (HHV-6)
    Reactivation of HHV-6, another common herpesvirus, has been hypothesized to contribute to ME/CFS symptoms, particularly in combination with EBV reactivation7.
  3. Enteroviruses
    Historical and contemporary evidence links enteroviruses (a group that includes polioviruses, coxsackieviruses, and echoviruses) to ME/CFS. Outbreaks of ME/CFS have coincided with enteroviral epidemics, and some researchers consider enteroviruses a likely culprit, especially in cluster cases1.
  4. Influenza Viruses
    Influenza infection has been associated with a more than two-fold increased risk of developing ME/CFS in the years following infection17.
  5. SARS-CoV-2 (COVID-19)
    Many individuals with long COVID meet criteria for ME/CFS, and SARS-CoV-2 is recognized as a trigger for ME/CFS in some cases67.
  6. Other Herpesviruses
    Varicella zoster virus (which causes chickenpox and shingles) and other herpesviruses have also been reported as potential triggers7.
  7. Ross River Virus
    This mosquito-borne virus has been linked to ME/CFS onset, likely through immune system dysregulation3.
  8. Retroviruses (e.g., XMRV)
    Early studies suggested an association between the retrovirus XMRV and ME/CFS, but this link has been discredited by subsequent research and retraction of the original findings2.

The goal of vaccines is to trigger enough of a response to set up the body to fight the target infection. Unfortunately, it also has a risk of triggering ME/CFS in some cases. If the person has ME/CFS, it may trigger cascades like reported above.

Going Forward

Forget about trying to “repair the injury”, the ‘injury’ is dysbiosis. You want to correct the dysbiosis. He did not have a prior to vaccination test to use for reference 🙁 .

Looking at the forecasted symptoms and the symptoms he marked we see a lot of matches at a high level (> 85%)

Looking at the bacteria that the above picked, we have one that is in the literature is associated with norovirus above.

Looking at the shifts reported for COVID, we see 64 matches to reported bacteria shifts from the literature.
 

Adlercreutzia – genus : Low 21
Adlercreutzia equolifaciens – species : Low 14
Aeromonadaceae – family : Low 2
Akkermansia – genus : Low 12 15 16 22 24
Akkermansia muciniphila – species : Low 10 13
Anaerococcus – genus : Low 13
Bacillota – phylum : Low 14
Bacteroides – genus : High 1 4 11 13 14 24 25
Bacteroides stercoris – species : High 13 14
Bacteroides uniformis – species : Low 13 14
Bacteroidia – class : High 9
Bacteroidota – phylum : High 9 14
Blautia – genus : Low 5 6 12 13 16
Blautia obeum – species : Low 8 13
Clostridia – class : Low 23
Clostridiaceae – family : Low 14
Collinsella aerofaciens – species : High 7 14
Coprococcus – genus : Low 12 13 14
Coprococcus catus – species : Low 14a
Dorea formicigenerans – species : Low 8 13
Enterobacterales – order : High 18
Enterobacteriaceae – family : High 2 13 14 16 17 19 20
Escherichia – genus : High 3 14 17
Escherichia coli – species : High 14
Eubacterium – genus : Low 11 13 21
Faecalibacterium – genus : High 1 4 12
Finegoldia – genus : Low 13
Flavobacteriaceae – family : High 14
Gammaproteobacteria – class : High 14
Haemophilus – genus : High 16
Lachnospiraceae – family : Low 3 11 14 21
Moraxellaceae – family : Low 2
Oscillospira – genus : Low 24
Ruminococcus – genus : Low 6 12 13 16 24
Ruminococcus bromii – species : Low 13
Spirochaetia – class : Low 14
Spirochaetota – phylum : Low 14
Verrucomicrobiota – phylum : Low 22

The top results are very typical for ME/CFS: specific antibiotics used with the Jadin Protocol for ME/CFS. I know that both getting specific antibiotics off-label and often human reluctance to do them(valid from many horror stories of them being arbitrarily selected by MDs and making people worse) — makes that a path rarely travelled.

Looking at the R2 model for making probiotics do the work, the top ones (that are commercially available)

  1. In Research — not for sale
    • Anaerobutyricum hallii – rank: 998
    • Christensenella minuta – rank: 888
    • Roseburia intestinalis – rank: 882
    • Blautia wexlerae – rank: 823
    • Blautia hansenii – rank: 748
    • Faecalibacterium prausnitzii – rank: 697
  2. Top Recommendations
    • Enterococcus faecium – rank: 687
    • Lactococcus cremoris – rank: 558
    • Akkermansia muciniphila – rank: 547
    • Lactococcus lactis – rank: 331
    • Leuconostoc mesenteroides – rank: 282
    • Levilactobacillus brevis – rank: 236
  3. Fall backs – very small impact.
    • Segatella copri – rank: 189
    • Bacteroides uniformis – rank: 137
    • Parabacteroides goldsteinii – rank: 136
    • Ligilactobacillus salivarius – rank: 127
    • Latilactobacillus sakei – rank: 111
    • Bacteroides thetaiotaomicron – rank: 106
    • Streptococcus thermophilus – rank: 89
    • Lactiplantibacillus plantarum – rank: 88
    • Bifidobacterium adolescentis – rank: 67

All of the items listed in 2 above are available from one or more of my usual sources except for Akkermansia which does have several providers today:

The next item are other suggestions which are listed below and high in herbs. As a FYI, Enterococcus faecium is actually the top probiotic using PubMed literature (and not R2 infererence) – I do like that type of convergence of different paths.

Suggested Methodology

  • Get the probiotics in 2 above.
    • Start the first and keep taking for 4 weeks (then 2 week break)
    • Every week, add in one more probiotic for 4 weeks followed by 2 week break
  • Do a lot of teas with different ones of the above herbs — if it is liquid, it should be a tea!
  • Wheat bread are all avoids, so do 100% Rye bread which is on the above list (not wheat-rye mixtures)

Go through the consensus list for more information. Do a retest about 2-3 months after starting the above. The retest will show the next course correction (often there are many).

Questions and Answers

  • The vaccine I got (HPV vaccine) is documented to cause ME/CFS and is one of the vaccines with higher number of reported adverse reactions compared to others. Why would you say is this?
  • I see you highlight the family Enterobacteriacea but ignore others like Bacteroides 
    • I picked Enterobacteriacea for purpose of illustration of one virus-microbiome interaction, there is not sufficient literature on HPV vaccine. We have extremely sparse data in this area.
  • Microbiome Prescription also told me that I probably had lactic acid acidemia and biofilms but I didn’t understand it very well. Can you explain which implications have this and what bacteria may be causing it?
    • Lactic Acid Acidosis means too much lactic acid. It is very common with ME/CFS and typically associated to brain fog. This is also associated with the following symptoms:
      • Nausea and vomiting.
      • Exhaustion and fatigue.
      • Fast, deep breathing (respiratory compensation).
      • Muscle cramps and body aches.
      • Increasing weakness and drowsiness.
      • Delirium and confusion.
      • Ataxia.
      • Oliguria (low urine output).
      • Low body temperature.
      • Low blood pressure.
      • Fever.
      • Jaundice (a yellow tint to the skin and whites of the eyes).
    • Biofilms include dental plaque and often acts as “bullet proof vests” to bacteria that we want to change. See Wikipedia for more.
  • Regarding the antibiotics, I was terrorized when I saw Ciprofloxacin at the top of the recommendations as it’s infamous for injuring people and causing a ME/CFS like condition, even being sold with a black label warning in the US. It seemed ironic to me and I am frankly hesitant to try it.
    • The system does not consider these risks — that is for your medical professional to evaluate.
    • I strongly favor Cecile Jadin’s approach. One course (7-10 days) of one antibiotic, 3 weeks off, rotate to another appropriate one. the ones marked with [CFS] have been use with some success for ME/CFS. I believe the issue cited was for continuous use of this antibiotic for more than one course. See this video for her experience. She has never seen in 20+ years of using it, adverse interactions. This also details her process (to be reviewed by your medical professional).
  • The top two suggested probiotics, I haven’t heard of them in my life and haven’t seen them sold anywhere. Will they even still work? 
    • Enterococcus faecium – rank: 687 and Lactococcus cremoris – rank: 558 are likely not available at your local health food store. Enterococcus faecium Source, Lactococcus cremoris source
    • They are computed to work — and my experience using the above sources for other probiotics is they work for me. One factor may be the freshness or the probiotics.
    • Followup:  I see Lactobacillus reuteri at the top of my probiotics suggestions list and don’t see Lactococcus cremoris at all. Are we look at the same screen?
  •  I am coming out of a 14-day Rifaxamin cycle which I think caused my current neuropathy and I wonder if it altered my microbiome enough so the results of the Biomesight are no longer accurate. Is my suspicion of the neuropathy being caused by Rifaxamin accurate? It started on the very last days of the cycle and I also have neurological symptoms again after a long time without having them. 
    • Rifaximin are your current sample is listed as an avoid. Your neuropathy may have been contributed by it.
    • I suspect that the suggestions will not be dramatically altered, so I would suggest implementing the top suggestions that you are comfortable with. Also, eliminate as many of the AVOIDS as is practical.
  • I am also still taking Saccharomyces Boulardii, Lactobacillus Plantarum, Lactobacillus Gasseri and will be adding Colostridium Butyricum, Bacillus Coagulans and the mix of Bifidobacterias “Seeking Health ProBiota Bifidobacterium.” All of them suggested by ChatGPT o3 model after feeding it my Biomesight, OAT, and a wide array of conventional medical tests.
  • I find some of the recommendations given by Microbiome Prescription weird, like whole milk and camel milk. Didn’t Biomesight said that my lactose processing was low? Or walnuts. What kind of walnuts they need to be? Can they be pecans or indian walnuts? 
    • Microbiome Prescription will differ from Biomesight see Why sites suggestions disagree on the same data. In short, MP uses over 7,431,437 facts to compute decisions as of today. I do not know the number BS uses, I suspect very few. All suggestions can be traced back to studies. The names of suggestions are based on the terms used in studies.
    • I do not know how many studies they based “lactose processing was low”, I see lactose as a significant positive value in your results (400).
  • Also most of them are herbs like you said or non foods like spices and other odd things. Is this common for other microbiomes?
    • I view every microbiome as different. The suggestions that I see are similar to others with ME/CFS, see other analysis here.

Followup: As I am not doing well economically and looking for ways to save, I feed ChatGPT o3 model the Microbiome Prescription suggestions table and told it to look for probiotic mixtures with the most amount of recommended strains and the least of strains to be avoided, Seeking Health ProBiota Bifidobacterium was the result.

I was aware of the wrong strains on the mixture and asked ChatGPT about the impact they would had. It told me that even then, it was still worth the risk as the strains to avoid had relatively low impact (Bifidobacterium bifidum -132.8) compared to the recommended strains on the mix (Bifidobacterium Longum 540.3).

You see this as an accurate analysis from ChatGPT or you would still recommend to avoid them?

In case that you say yes… Can I take all the probiotics I previously told at once or they antagonize each other? Is doing this risky?

ChatGPT and other Large Language Model are sophisticated Hearsay-Engines. The lack the expertise of a fuzzy logic expert system. If I was a judge, I would strike hearsay evidence from consideration. The issue of risk is a question for your medical professional. All that I can say is that it was decreased odds of helping and may have some risk of hurting.

5.- “I see lactose as a significant positive value in your results (400).”

A = I am talking about the lactose degrader shown as LOW (0.11%) under the food intolerances section on the Biomesight report.

There are some other findings here that disturb me, like butyrate producers LOW, colibactin producers HIGH, D-Lactate producers HIGH, gram negative bacteria HIGH and gram positive bacteria LOW.

Would you say that I fit on the classic ME/CFS profile? Anything else that stands out about my microbiome?

Thank you and I hope this format is easy to understand but if not, please let me know.

I avoid comment on any provider individual reports, i.e. Biomesight report, beyond what the US National Institute of Standards and Technology has stated. I will comment on methodologies, the usual comment is they “went cheap” and do not use sufficient data — MP consider 7,431,520 facts in computing suggestions.

Your sample have strong statistical associations to may symptoms of ME/CFS and Long COVID. “Fitting a profile” is question more suitable for a medical professional. I am a statistican.

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.

Also, I note that many people will make inferences (often based on influencers opinions) that are not supported by the evidence. Often people want absolute certainty and will deem things proven if they find a single case study supporting a hypothesis; this is not how science and statistics work… it is all odds.

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.

Family Convergence of Microbiome

A reader wrote me saying:

I have 5 Biomesight samples uploaded to my MP.com account, of which 3 are mine and 2 are my kids.  

When I choose a different sample from the dropdown list, the ‘Suggestions’ change as I would expect them to, however, the commercially available Probiotic recommendations do not change. So the Priobiotic ‘weighting’ is the same on all 5 samples, which I included a screenshot of.  

Any idea why this is happening and how I can get accurate commercial Probiotic suggestions for each different sample?

Thanks much,

Step #1 Reproduce the issue

First item was checking that there was not duplicate uploads – there were not. I then got suggestions from each sample and list them below: I also included the top suggestion to verify that different suggestions were made.

There were duplicate suggestions between some samples:

  • Two the same (2024-12-17, 2024-03-10)
  • Three the same ( 2023-12-15, 2024-01-08, 2023-12-15) 

One item was on all of the recommendation: L.Gasseri.

I also did Experimental Probiotics Suggestions using Taxa R2 Site. I find that I trust R2 suggestions more than the default suggestions. The differences are:

  • Default is based on available studies — most have not been duplicated and have small sample size. Small sample size means only things that really stand out are reported. Most are done with 16s testing which is much less accurate than shotgun. We have 4,625 data points.
  • R2 is based on 1000 shotgun samples and based on statistical associations ween between probiotic species and other species. There are no clinical studies showing that they work. We have 2,446,755 data points.

So the decision is trusting limited clinical studies, or trusting statistics with 529x more data points. My personal experience is that I have noticed more benefit from R2 suggestions than the default suggestions.

Sample 2025-06-29

Top amoxicillin [CFS] 1444

R2 Suggestions for Available:

Step #2 2024-12-17

Top Item: metronidazole [CFS] 1434

R2 Suggestions for Available:

Step #3 2024-03-10

Top Item: metronidazole [CFS] 584.5

R2 Suggestions for Available:

Step #4 2023-12-15

Top Ferrum {Iron Supplements} 1013

R2 Suggestions for Available:

Step #5 2024-01-08 

Top imipenemL 932

R2 Suggestions for Available:

Step #6 2023-12-15

Top Cichorium intybus {Chicory} 839

R2 Suggestions for Available:

Bottom Line

The reader did report correctly that the same suggestions were being made. The default probiotics were likely correct based on the sparse data from clinical studies available. I would suggest that this user try the top 3 probiotics suggested by the novel R2 algorithm; I suspect they will have a greater and more targeted impact.

I am not surprised that given the limited palette of probiotics from clinical studies that we have convergence because the microbiomes have convergenes.

Key findings from published studies include:

ME/CFS after EBV in Competitive Athlete

Background:

35 y/o male. Previously very healthy. Competitive endurance athlete (Ran a 2:46 marathon in 2024). For reference, normal resting heart rate was in the low 40’s bpm. “Easy” running pace (HR < 130 bpm) was ~8:00min/mi.

  • Contracted EBV in November 2024. Acute infectious mononucleosis (fever, sore throat) lasted ~2weeks. Confirmed first-time infection via EBV antibody panel. (Not a reactivation)
  • Fatigue persisted through January – February 2025, but other than not being able to train, lived essentially normal life. (40+ hour work week, family and social activities, gardening, etc.) Went on a few easy jogs 9:00 min/mi, HR 130-140. No issue recovering and performing daily activities post run. But could tell I was not back to 100% and did not want to push it.
  • Fatigue worsened in March. Continued to work and perform family/social activities. No running at all.
  • On 3/31/25 had EBV antibodies re-tested. Showed elevated IgM, IgG, EBNA, EA-D. (IgM should have disappeared by this point). 
  • Deteriorated further in April. Hospitalization after waking with full body tremors one night.
  • Continued decline throughout May and June. Have seen multiple specialists to no avail. Seems like I may be rapidly progressing to developing full blown ME/CFS. 

Current Symptoms:

  • Elevated resting HR (compared to my baseline) – now consistently in low 50’s while sleeping; 60’s laying supine awake; 70’s sitting upright — This confuses doctors because they see these numbers as “normal.”
  • Tachycardia on minimal movement (110 bpm getting dressed)
  • HR 170+ with 5min of light walk/jog – HR still 130 an hour later (no recovery) – heavy lactic acid build-up and DOMS. This is much more than would be expected due to just “de-conditioning” (as some uninformed doctors have wanted to suggest).
  • Heart arrhythmias – developed since April. 
  • Fatigue that does not improve with rest.
  • Post exertional malaise – sitting upright in a chair for several hours one day leaves me in bed the next day.
  • Tremors, Night sweats, Heat Intolerance, numbness/tingling in hands & feet, burning sensation on skin (intermittent).
  • Intermittent mild hypoxia (93-94 O2 sat) and air hunger.
  • Abnormal lab values: Low WBC, High RDW%, Low MPV, Low BUN, High CO2 (repeated in multiple tests over the last 6 weeks) .. Misshapen RBC’s – “dacrocytes” noted on manual smear in June. (none were present in mid-April)
  • EBV panel in mid-June still showed elevated IgM, IgG, EBNA, and EA-D. Started taking Valacyclovir 1g x 3/day.

What you have written about ME/CFS and coagulation makes a lot of sense with what I am experiencing. My Thorne microbiome test appears to present lots of opportunity for improvement as well… 

I look forward to your insights and analysis.

Thank you for your time and consideration of my case,

Given EBV Involvement …

My wife had EBV and EBV-Specific Transfer Factor was highly effective for her. The problem is that it appears to be no longer available. This gives some background: Transfer Factor: Myths and Facts [2020]

Immunization of donor animals: Animals are immunized with an EBV antigen, such as recombinant EBNA-1, a nuclear antigen of the Epstein-Barr virus. The antigen can be introduced via injection. The milk from the animal is then processed. [More Info]

There are Transfer Factor products on the market — but none appears to be EBV specific (which is what my wife used). It may be worth trying some of them — the apparent lack of specificity of these products is a concern. My memory is that the hosting animal is critical for its effectiveness. There are notes on it’s use on Hemex Protocol and Dave Berg, unfortunately the website selling the version they used is no longer there.

I did a quick search for chronic active EBV (CAEBV) treatment and nothing stands out as being very effective [more info]. It is an area of active research.

Trying to support the immune system to deal with CAEBV by Microbiome Manipulation

Premise: An infection (including virus) alters the microbiome to be optimal for it survival. Correcting the dysbiosis, weakens the infection (i.e. you may starve it of essential metabolites)

From other samples reporting EBV, we have many associations (different bacteria for different test unfortunately: Why this is expected). Thorne tests was not one of those that we had sufficient data (uBiome, Ombre/Thryve, Biomesight). Thorne also gives percentile ranking which opens a backdoor. I went into the data and found only 5 samples marked with EBV.

The following were found out of range consistent across these sample, all extremely low ( < 5%ile)

  • Faecalibacterium genus
  • Faecalibacterium prausnitzii species
  • Eubacteriales order
  • Clostridia class

To my delight, these collapses into one bacteria linerage: Bacillota; Clostridia; Eubacteriales; Oscillospiraceae; Faecalibacterium; Faecalibacterium prausnitzii   

 This makes suggestions very easy:

  • Go to Faecalibacterium
    • for linerage, you want the second from the left.
    • The information included it’s children and its parents modifiers,
      • i.e.  Oscillospiraceae; Faecalibacterium; Faecalibacterium prausnitzii )  
  • Sort and filter the long list of items to increase it.

CAUTION: Faecalibacterium is not listed in the above EBV association page using other labs, nor is it reported in any published studies.

In terms of probiotics we have this list (based on number of studies reporting — not impact):

Fortunately a recent addition allows us better information, including relative impact! Going to Microbiome Taxa R2 Site, we see the probiotics ranked by impact that increases this bacteria:

This is the core set of probiotics to try. I would suggest 1-2 weeks of each and then rotate to the next one. After the third one, do one of the X for a week and then repeat.

More relaxed patterns of 80% of samples showing consistent highs across 4 of the samples. There is a clustering around Corynebacterium, so we want to pick items to decrease it. As above, we should go to Corynebacterium

  • Negativicoccus massiliensis species
  • Peptoniphilaceae family
  • Tissierellia class
  • Corynebacteriaceae bacterium ‘ARUP UnID 227’ species
  • Staphylococcus lugdunensis species
  • Tissierellales order
  • Corynebacterium simulans species
  • Corynebacterium jeikeium species
  • Corynebacteriaceae family
  • Methylobacterium genus
  • Corynebacterium singulare species
  • Corynebacterium genus
  • Corynebacterium striatum species
  • Trichosporonaceae family
  • Trichosporonales order
  • Corynebacterium segmentosum species
  • Methylobacteriaceae family
  • Peptoniphilus harei species
  • Anaerococcus genus
  • Tremellomycetes class
  • Staphylococcus genus
  • Staphylococcaceae family
  • Corynebacterium camporealensis species

And for lows:

  • Bifidobacterium breve species
  • Muribaculum genus
  • Lachnospiraceae bacterium KM106-2 species
  • Roseburia intestinalis species
  • Blautia obeum species
  • Pseudobutyrivibrio xylanivorans species
  • Pseudobutyrivibrio genus
  • Chitinophaga genus
  • Coprococcus sp. ART55/1 species
  • Lachnospiraceae bacterium species

This adds one more probiotic: Bifidobacterium breve which I would include in the #X rotation above.

EBV and Coagulation

Epstein-Barr virus (EBV) infection can be associated with significant coagulation abnormalities, particularly in the context of hemophagocytic lymphohistiocytosis (HLH) and EBV-associated lymphoproliferative disorders. [more info]

If practical, I would suggest the Hemex Panel which is a very complete test of the many vectors of coagulation. The other aspect is checking for genetic variations — often some are not clinically significant for a healthy person. When the immune system and/or microbiome is dysfunctional then they may “flare”. For myself, it was Prothrombin G20210A (Factor II Mutation) which may present itself as a cramp or Charley horse . I was lucky because selected supplements (piracetam and turmeric) was able to mitigate it.

There can be a problem because specialists may deem these issues to be “sub-clinical” (i.e. not worth intervention — i.e. not a stroke or visible Deep Vein Thrombosis). This same issue may be devastating for quality of life – physical or mental impairment.

For myself, I was reckless and took the highest daily dosage of aspirin for 10 days. The change that it caused convinced my MD that coagulation testing was warranted (perhaps to stop my reckless taking more aspirin!).

Back to addressing Microbiome Dysfunction …

My preferred approach is to use Symptoms with statistical association based on the lab. This is not available for Thorne. In this case, my approach is to use the generic (that works off high and lows alone)

  • Novice: Just tell me what to take or avoid

This gives 220 target bacteria. This is a high number, but given your back story — not shocking.

Clicking on the bottom link, takes us to the Microbiome Taxa R2 Site looking at all of these shifts. We get the following probiotics recommendations (with almost 2 dozens to avoid):

We have 60% of them matching the above list. At the end of each line, I included the Priority from the consensus (– not listed, likely because of no studies). Remember, no one knows the right way, I try different logical algorithms and look for items that everyone agrees on.

For completeness, let us look at the other items suggested:

IMHO – We have probiotics nailed!

Let us look at other vectors from the consensus list. Order by priority. Emphasis should be on ones that are around 500 or higher (1/2 of highest priority)

At this point, I will leave reviewing other items on the consensus report to the reader.

Bottom Line

I must confess, this post blew me away — we got key bacteria identification from just 5 annotated samples – still uneasy about that. The number of bacteria shifted was huge with key suggestions being items known to be effective for treating EBV.

I think we have enough to set a course of action. I would suggest trying for 2 months (one probiotic cycle) and then doing a retest. If finances can afford it, repeat Thorne (to allow comparisons) and also do a Biomesight test (to allow taxa filtering by symptoms).

For a list of more documented items that help EBV infections, see Treatment of Epstein-Barr virus (EBV) in ME/CFS Context

Questions From Reader

Thanks, Ken. That is a lot of information to take in. I’ll try to summarize my takeaways and questions:

  • – Transfer factor: How did your wife receive the EBV-specific? Was it through a medical facility, or did it used to be available as a supplement? ..  Does not seem like there is much actionable for me to do on this other than consider trying one of the non-specific bovine supplements. 
    • It was available for order on the internet from a company in the eastern US. I recall it was mare( female horse) based. Thus likely high overheads and then the FDA became concern about transfer of other infections. Sterilization of the Transfer Factor likely killed it.
  • – Coagulation: Hemex panel no longer available. The Dedimed lab in the linked post appears it might be closed. (website down, last social media post was in 2023) .. Aware of any alternatives?
    • I am sorry to see that it is gone. It means that you may have to fight with the specialists for each test done. I asked perplexity on best DNA test
      “Blueprint Genetics provides the most comprehensive DNA testing for inherited coagulation factors among the providers in the search results. Their Bleeding Disorder/Coagulopathy Panel covers 71 genes, including all major and many rare genes associated with inherited bleeding and coagulation disorders. This panel assesses both coding and non-coding variants, which increases the likelihood of detecting clinically relevant mutations”. [More Info]
      Site: https://blueprintgenetics.com/
  • – I have read of your aspirin experiment – not sure I am that brave. I am considering trying with some combination of Bromelain, Natto, Lumbro, Serra, Bosweilla, etc. … Based on your fibrinolytics and half-life posts. Thoughts on a strategy?
    • Conceptually it’s good. A reasonable shot in the dark. This page shows the coagulation cascade. One or more of the arrows shown below may be defective. Each of these substances affects one or more of the arrows. Watch out for “overdoing” some part of the cascade and you became an easy bleeder and the bleeding takes a long time to end.


– Probiotics:  I’m struggling a bit here trying to combine the lists from two sections in the article to get a 2-month rotation:

What should be #3? Still a “mixture of Baccillus” or one of the single strains below

– After 2 months retest with both Thorne and Biomesight – Yes, Biomesight allows you to use discovered associations and thus focus solely on the (likely) causal bacteria. Thorne to allow comparison of changes.

– Vitamins: – Understood. Already doing most of these. – Double check the to Avoid List, often people forget that step.

– Diet: – My high level takeaway from trying to use the tools on the report was “high fiber, less fat.” But that was just based on the “just tell me what to take or avoid” with no attempt to nuance for EBV. Not sure how to do that?

Good question: no attempt to nuance for EBV. Not sure how to do that?  — classic issue of sparse data,,,,  I asked Perplexity and got https://www.perplexity.ai/search/are-there-any-diet-changes-fou-psucBMISRi2DEBw_.VFddA#0 Most appear to be based on speculation… This is the best of the citations: https://journals.sagepub.com/doi/10.1177/2150131915573472  “However, after adjusting for potential confounders the results for both dietary factors and food insecurity were no longer statistically significant. ” so no data to work from.. 🙁

Thanks again for the effort you’ve put into this already. I’m quite amazed at how quickly you’ve put it together.

Postscript and Reminder

As a statistician with relevant degrees and professional memberships, I present data and statistical models for evaluation by medical professionals. I am not a licensed medical practitioner and must adhere to strict laws regarding the appearance of practicing medicine. My work focuses on academic models and scientific language, particularly statistics. I cannot provide direct medical advice or tell individuals what to take or avoid. My analyses aim to inform about items that statistically show better odds of improving the microbiome. All suggestions should be reviewed by a qualified medical professional before implementation. The information provided describes my logic and thinking and is not intended as personal medical advice. Always consult with your knowledgeable healthcare provider.

Implementation Strategies

  1. Rotate bacteria inhibitors (antibiotics, herbs, probiotics) every 1-2 weeks
  2. Some herbs/spices are compatible with probiotics (e.g., Wormwood with Bifidobacteria)
  3. Verify dosages against reliable sources or research studies, not commercial product labels. This Dosages page may help.
  4. There are 3 suppliers of probiotics that I prefer: Custom Probiotics , Maple Life Science™, Bulk Probiotics: see Probiotics post for why

ME/CFS from UTI Treatment?

Back Story

In 2021, at age 28, I developed an upper respiratory infection while working in a hospital (tested negative for Covid repeatedly). The URI persisted for over a week so I was prescribed a course of Augmentin thinking it might be a sinus infection. On day two of antibiotics, brain fog, headache, orthostatic intolerance, and fatigue began and never went away. I would go on to develop PEM and sleep disturbances and I was eventually diagnosed with ME in 2023. 

I have two tests that have been uploaded. The first is from 2023, at which point I was Mild/moderate and still had some bfido/lacto left but was also dealing with a dysbiosis. The second is from 2024 and am now very severe. Probably unsurprisingly, I have had a decrease in levels of desired bacteria and also changes in the dysbiosis. 

There seems to be conflicting suggestions between new UI and the cross validated items to add. If I was considering an antibiotic for example, the new IU weights specific floroquinolones highly and lists macrolides as items to aovid, while the cross validated suggestions say to add specific macrolides. Diet styles and some specific supplements also seem to conflict. What do you recommend when there are conflicting suggestions between the two?

Additionally, within the new UIs suggestions,

 the individual probiotics in items to add list list don’t always match the recommended probiotic products. (Ex. L. Sakei and L. Hellveticus are listed under to avoid/decrease column, but are also listed in the commercial probiotics section with a relatively high weight.)

I am wondering if you can help me better understand the specific bacteria that have changed as my ME had gotten worse, how to potentially optimize them, which suggestions to follow, and how I might apply all that to Dr. Jadin’s protocol? 

I apologize for my lack of understanding and for all that you’ve already explained and that I’ve missed. I’ve spent a lot a time on your site but am very limited in what I can do and process at the moment and want to make sure I’m approaching this the right way. 

You have my permission to use the above information for a blog post. 

Review of Concerns

Microbiome Prescription does best efforts and without dedicated staff to do checking — a variety of errors can occur. I depend on people like the above person to ask questions.

Conflicting Suggestions

Above there is the subjective report of getting worse, this is objectively seen with predictive symptoms where the number exploded and the agreement with self-reported was significant

2023-01-232024-11-23

The first question is which methods were used in both the simple UI and the old UI. Different choices result in different suggestions. Suggestions are based on which bacteria were selected to be significant and the type of modifiers. You can get some items flipping from take to avoid with different choices. No one knows the right way to select which bacteria and their significance. Microbiome Prescription tries to give a variety of choices (so people can follow their beliefs on what is significant).

For the New UI suggestions, I will use: Beginner-Symptoms: Select bacteria connected with symptoms . Despite the large number of symptoms, we ended up selecting only 24 taxa, with 12 genus being significant:

The suggestions are below

Old UI

The old UI gives many different ways of getting suggestions. These choices allow users to follow their beliefs for better or worse. A few choices are below

I tried Critical Bacteria Associated to Symptoms. This seems to be the closest equivalent to the Simple UI. We got just 16 bacteria selected with only 4 genus. 1/3 of what we got above. Why? When I wrote the Simple UI, I incorporated a different way of weighting and filtering bacteria as a result of more recent research and observations. Also, I also incorporate multiple algorithms in the Simple UI (which is why it takes much longer to get suggestions).

I checked the top few items from the Simple UI and they were on this to take list, just with a lower value. The additional bacteria shifted the order.

Q: Why did I not revise to make them agree?

  • Answer: I do not know which is the best. I intentionally avoid changing algorithms that have been in use for any time (unless there is a gross error). When I did that in the past, I got a flood of email asking for explanations. The Simple UI captures my best current thinking when I added it.

Probiotics Question

From the Beginner-Symptoms: Select bacteria connected with symptoms we have

Looking at the KEGG computations on the Simple UI we have those on the KEGG Compound / Enzymes Lists Suggestions

We have apparent good agreement.

Looking at Critical Bacteria Associated to Symptoms suggestions, we see a short list

Looking at the KEGG computations on the Simple UI we have those on the KEGG Compound / Enzymes Lists Suggestions

Bottom Line for Probiotics

I do not see either L. Sakei and L. Helvetius in the above list, so I will assume that a different filter was used to get them.

Antibiotic Question

Unlike probiotics, we do not have 2 additional scales to evaluate suggestions (i.e. KEGG Compounds and KEGG Enzymes)

Simple Suggestions

The — numbers below are from the OLD UI

So, what we see is that with the smaller genus count, antibiotics are of a much lower value. When the other genus are added, they become more important.

Bottom Line

I wish that I was omniscient on the microbiome and how to adjust it. I am not. I have listened to people on what they believe is the right way and implemented it. For the Simple UI, I did my best attempt to compute suggestions. With the suggestions computed from PubMed studies and the suggestions computed from KEGG’s data being in general agreement (at least for the top items), I fell confident that they are reasonable. The same core algorithm was used for Suggestions Cross Validation using PubMed where we had an average of 86% agreement.

Post Script

I went and used Strict PubMed Cross Validated Suggestions, with  Inflammatory Bowel Disease and Chronic Fatigue Syndrome. This uses a different approach to filtering and thus different suggestions are expected.

The Genus flagged were the 8 below (midway between the 4 and 12 above):

  • Bacteroides – genus : High
  • Bifidobacterium – genus : Low
  • Clostridium – genus : Low 
  • Faecalibacterium – genus : Low
  • Haemophilus – genus : Low
  • Lachnospira – genus : Low
  • Prevotella – genus : Low
  • Streptococcus – genus : Low
     

With the suggestions below (remember ONLY items showing positive effects in studies are included, items not reported in studies are excluded):

The “best” would be to use what all methods agree on. If there are conflicts, omit the items. Usually, there will be a significant list of items in agreement.

Postscript and Reminder

As a statistician with relevant degrees and professional memberships, I present data and statistical models for evaluation by medical professionals. I am not a licensed medical practitioner and must adhere to strict laws regarding the appearance of practicing medicine. My work focuses on academic models and scientific language, particularly statistics. I cannot provide direct medical advice or tell individuals what to take or avoid.My analyses aim to inform about items that statistically show better odds of improving the microbiome. All suggestions should be reviewed by a qualified medical professional before implementation. The information provided describes my logic and thinking and is not intended as personal medical advice. Always consult with your knowledgeable healthcare provider.

Implementation Strategies

  1. Rotate bacteria inhibitors (antibiotics, herbs, probiotics) every 1-2 weeks
  2. Some herbs/spices are compatible with probiotics (e.g., Wormwood with Bifidobacteria)
  3. Verify dosages against reliable sources or research studies, not commercial product labels. This Dosages page may help.
  4. There are 3 suppliers of probiotics that I prefer: Custom Probiotics , Maple Life Science™, Bulk Probiotics: see Probiotics post for why

Life Long Health Issues

Backstory

I have been suffering from various health problems almost all of my life (49 years old) starting at around age 7 with digestive issues, eczema, acne and multiple sensitivities. These issues have only escalated in the last 15 years causing me to have to resign from my position as a data analyst 6 years ago due to my health issues which are food sensitivities to gluten, dairy, soy, corn, sugar, MCAS, multiple chemical sensitivities and in the last 5 years electromagnetic sensitivities so that i have had to remove all sources of wireless and cell phones in my home. I have installed ethernet for my PCs and have had to resort to basically becoming a shut in because i cannot go out in public or drive for more than a few minutes before experiences various health problems like heart palpitations, shortness of breath, dizziness, etc. luckily i have been eating pretty healthy since 2010 (no gluten, dairy, soy, sugar, corn) and am able to at least survive in my home but it would be fantastic if i could get some guidance as to what seems to be causing these issues. I have had tests for mold and lyme and both have tested positive and i am so sensitive that i am unable to tolerate any supplements. This has obviously made it extremely difficult to make much progress. I have transferred my Biomesight report to MicrobiomePrescription If you could please find the time to help me with my biomesight report and feel free to use it anonymously for a blog post it would be greatly appreciated 😉

Analysis

I am not a health professional, I have built an academic model that generates suggestions that are expected to typically reduce symptoms; in some cases, I have gotten reports of full remission. All of the suggestions should be reviewed by a knowledgeable professional.

Looking at entered symptoms, we see a high agreement between forecast and reported symptoms.

This allows us to focus on the bacteria that are likely to be involved with this person’s symptoms.

I usually do a multiple step approach because there are no “correct” way to do analysis and get suggestions. The ways are:

  • Beginner Symptoms
  • Probiotics:
    • From KEGG Enzymes
    • From KEGG Metabolites
  • Browse through the Consensus

Beginner Symptoms

We have 20 bacteria identified:

The “kitchen sink” suggestions are below

With a “skinny” list (no prescription items) below. Remember, many people with do the take suggestions and skip the avoids …. and then wonder why progress is slow…..

KEGG Based Probiotics

The top probiotics that are relatively easy to get are (Metabolite / Enzymes) With ** being positive on consenus, and *** being very positive.

  • Bifidobacterium longum subsp. longum (45.1, 47.55)
  • Limosilactobacillus fermentum (42.5, 49.4)
  • Lactiplantibacillus plantarum (40.95, 55) **
  • Enterococcus faecium (40.65, 58.45) **
  • Bifidobacterium longum subsp. infantis (40.3, 46.5)
  • Lacticaseibacillus rhamnosus (39.45, 60.5) **
  • Bacillus subtilis (37, 61.6)
  • bacillus subtilis natto {B.natto} ( 32.75 ,60.65 ) ***
  • L. Casei (33.75, 55.2 )***
  • L. Gasseri (16.5, 37.5 ) ***

With B. natto being the highest I would start there — unfortunately, the main source is a Japanese food called Natto — a bit of an acquired taste and unfortunately soy.

The secondary way is using Nattokinase supplements. If the natto food causes problems, then go to Nattokinase.

Given the number of allergies, I would only suggests from these sources. Your reactions may be partially caused by additives,

  • Custom Probiotics :they list all of their strains — many are researched on the above list. No other ingredients just the bacteria.
  • Maple Life Science™: No strains yet, but shipments usually have manufactured date within 4 weeks of arrival (i.e. FRESH). Contains FOS
  • Bulk Probiotics: US based Newbie — but has some species not available at the other two sites. No other ingredients just the bacteria.

I would experiment with the following three (different genus) probiotics to see if any are tolerable after reviewing Probiotics – General Advice

  • Bacillus subtilis
  • Bifidobacterium longum subsp. longum
  • Limosilactobacillus fermentum

The rest, given your allergies and sensitivities, are likely having to do trial and errors on the suggestions to see what you react to.

Postscript and Reminder

As a statistician with relevant degrees and professional memberships, I present data and statistical models for evaluation by medical professionals. I am not a licensed medical practitioner and must adhere to strict laws regarding the appearance of practicing medicine. My work focuses on academic models and scientific language, particularly statistics. I cannot provide direct medical advice or tell individuals what to take or avoid.My analyses aim to inform about items that statistically show better odds of improving the microbiome. All suggestions should be reviewed by a qualified medical professional before implementation. The information provided describes my logic and thinking and is not intended as personal medical advice. Always consult with your knowledgeable healthcare provider.

Implementation Strategies

  1. Rotate bacteria inhibitors (antibiotics, herbs, probiotics) every 1-2 weeks
  2. Some herbs/spices are compatible with probiotics (e.g., Wormwood with Bifidobacteria)
  3. Verify dosages against reliable sources or research studies, not commercial product labels. This Dosages page may help.
  4. There are 3 suppliers of probiotics that I prefer: Custom Probiotics , Maple Life Science™, Bulk Probiotics: see Probiotics post for why

2022 COVID + Heart Racing

Back Story

I got COVID on 2022. Then my symptoms started like 6 months after the infection.

Pain at the base of the skull and nausea (I went to a neurologist who ordered an MRI and everything was normal).
One day, I was sitting at work when my heart started to race for no apparent reason, about 180 bpm, lasting for 5 hours. Since I thought I was having a heart attack, I went to the emergency room, where they performed an ECG and enzyme tests, all of which came back normal. I was prescribed medication for colitis.
Tingling in my arms and hands.
Metallic taste in my mouth during moments of alertness or high stress (e.g., when about to crash in a car).
Exaggerated reaction to situations that were previously normal, such as involuntary hand muscle shaking when I was about to start an F1 race. Feeling like I was going to faint after a huge emotion, like after my team scored a goal while I was in the stadium. Rapid heartbeats, shortness of breath, and rigid hands during a traffic jam (it would usually improve by drinking electrolyte solution). Rapid heartbeats when speaking in public (this didn’t happen before).
Afterward, I saw an internist, and he said my symptoms were due to vagus nerve irritation, prescribing Esomeprazole, Lunarium, and Cinitaprida. At that time, I didn’t have any symptoms of acid reflux or heartburn, but he suggested it might be silent reflux. I was on this treatment for 2 months, but the other symptoms didn’t improve. They did improve a little by taking Vitamin B complex and magnesium.

Subsequent symptoms:

  • When it’s very cold or hot, I start feeling disoriented and a little nauseous.
  • Burning sensation on the outer part of my left arm.
  • Shortness of breath with exertion.
  • Cold hands.
  • Epigastric bloating (I feel this is what causes me to not be able to breathe deeply). It has gotten so bad that when I breathe deeply, I hear a crackling sound in my sternum.
  • Nasal passages closing.
  • Acid reflux.
  • Pain in the center of my back, related to reflux.
  • After exertion, disorientation, weakness, a little dizziness (it was worse before, but not as much now).
  • Brain fog (this has improved over time, I feel more mentally clear).
  • If I skip a meal, I feel extremely bad, I get nauseous, and feel very disoriented.
  • Constipation (I used to go 3 times a day with normal consistency, now it’s only 2, with very variable consistency).
  • Slurring words when speaking (this doesn’t happen much anymore, but it was common at one point).
  • Belching (in the morning and during/after exertion).
  • Very fast heartbeat after eating, feeling dizzy while eating.

Recent symptoms that concerned me:

On a camping trip, we went to … for work, and after walking approximately 10,000 steps uphill and downhill according to my app, I started feeling short of breath and my epigastrium was very bloated. I was also burping a lot and regurgitating some food. My heart rate was extremely fast, way too rapid, and I felt weak. I started feeling disoriented. My extremities were freezing. I didn’t have dizziness, chest pain, or nausea, but it felt like I was about to faint at any moment. It was time for lunch, and I had no appetite, but I ate anyway. My pulse regulated about an hour later. Then my blood pressure was taken, and it was 138/80. Normally it’s around 110/70, I’ve checked it in the mornings, and it’s always close to that value. After that, the rest of the day, when walking, I felt short of breath easily. The next day I still felt very fatigued, maybe due to my lack of physical activity. On Saturday, I went to a wedding, and since we were running a bit late, I started feeling short of breath. I danced for about an hour, then sat down as my heart rate started accelerating. I felt disoriented for a few moments, but then my heart rate slowly regulated. The next day, I felt fine. Then, while driving, I had a lot of acid reflux, so I took TUMS. About two weekd after , after 10 minutes of walking, I started feeling very weak, so I checked my blood pressure, and it was around 90/60. Then it went up. This happened for about two weeks, and then stopped.

When I clon Ed stairs, about 3 flights at a normal pace, when I reach the top, I feel short of breath, I burp, and feel disoriented. Normally, it takes about 1 hour for me to feel okay again. When I’m worried about something, I feel like I’m about to faint.

Today, I am bedbound and can hardly think. I cannot walk more than 3 minutes. I would like your help to improve, thank you, god bless you. 

Analysis

Looking at forecasted versus entered symptoms, we see many matches. We will use this as one of our collection of suggestions. The other two are Cross Validated for Long Covid and KEGG Enzymes/Metabolites. No one knows the perfect solution, I look to where we have the greatest agreement as the best pathway forward,

From the above, we get just 25 critical bacteria. The top suggestions are very familiar from other analysis:

  • Inulin
  • Wheat Bran
  • Wheat
  • Dietary Fiber
  • Barley
  • Maize

The list is below

The top probiotics appear to be Limosilactobacillus reuteri {L. Reuteri}, bacillus licheniformis {b. licheniformis},Saccharomyces cerevisiae var boulardii {S. boulardii} and L. Gasseri . Unlike most people with Long COVID, only a single antibiotics appears in the top list.

Going to Cross Validated Suggestions, we see a smaller number of bacteria flagged as significant.

With the suggestions having some overlap with the above:

  • minocycline
  • Propolis {Bee glue}
  • ß-glucan {Beta-Glucan} i.e. Barley etc

In general. these same items often appear further down the list on the consensus list. The list above lacks priority.

KEGG Enzymes and Metabolites

The top suggestions are:

ProbioticCompoundEnzymesConsensus
Lactiplantibacillus plantarum41.6533.85292.7
Escherichia coli (Mutaflor)38.6551.6563.2
Limosilactobacillus fermentum36.630.95314.8
Bacillus subtilis36.549.580.6
Limosilactobacillus reuteri 34.8534492
bacillus licheniform33.9548.6422
L. Gasseri17.615.8574.6
Saccharomyces cerevisiae ——366

My suggestion for probiotics to be used in rotation (1-2 weeks of each and then move to the next) are:

  • L. fermentum
  • L. plantarum
  • L. Reuteri
  • Bacillus subtilis
  • Mutaflor

See Probiotics – General Advice for more information.

My recommendation for a regular breakfast is porridge (Barley, Oats) as well as a high fiber diet (see How much fiber is best/ideal? ).

Postscript and Reminder

As a statistician with relevant degrees and professional memberships, I present data and statistical models for evaluation by medical professionals. I am not a licensed medical practitioner and must adhere to strict laws regarding the appearance of practicing medicine. My work focuses on academic models and scientific language, particularly statistics. I cannot provide direct medical advice or tell individuals what to take or avoid.My analyses aim to inform about items that statistically show better odds of improving the microbiome. All suggestions should be reviewed by a qualified medical professional before implementation. The information provided describes my logic and thinking and is not intended as personal medical advice. Always consult with your knowledgeable healthcare provider.

Implementation Strategies

  1. Rotate bacteria inhibitors (antibiotics, herbs, probiotics) every 1-2 weeks
  2. Some herbs/spices are compatible with probiotics (e.g., Wormwood with Bifidobacteria)
  3. Verify dosages against reliable sources or research studies, not commercial product labels. This Dosages page may help.
  4. There are 3 suppliers of probiotics that I prefer: Custom Probiotics , Maple Life Science™, Bulk Probiotics: see Probiotics post for why

Long COVID + UTI + ME/CFS

Back Story

Back story: I have probably been infected by Covid since Nov 2021 and developed post Covid. In mid 2022 I got many urinary tract infections and took many antibiotics including ciprofloxacin. After another infection in End of 2022, I developed MECFS in early 2023 and was diagnosed with viral myocarditis in 2024. I have had problems with medication intolerances (bile issues: losartan, clopidogrel; pain, breathing: prednisolon, ketotifen, LDN) since 2023 and develop biliary pain every time I take them, which has persisted since the first time I took clopidogrel and is made worse again by the abovementioned medications. Everything has been checked many times with ultrasound, bloodwork, faecal examination, MRI and the like, including the pancreas. Nevertheless, the potential medical condition worries me. Can I counteract it?

It has been confirmed that I am dealing with chronic myopericarditis. Additionally, I have been suffering from constant gastritis since July 2024, which has caused ongoing issues. In the first half of 2024, I tried new medications. Ivabradine works well for me, and I continue to take it. However, I could not tolerate Prednisolone and Losartan due to side effects. Losartan, like Clopidogrel previously, caused biliary pain. Prednisolone led to severe muscle and joint pain, likely due to FQAD (following Ciprofloxacin use), which has had long-term effects on me.

Currently, my main symptoms are:

  • Chronic gastritis, likely triggered by Pentoxifylline, turmeric, or possibly diet.
  • Persistent biliary pain, worsened by fatty meals (extensively checked by gastroenterologists with examinations including bloodwork, MRI, ultrasound, and tests for the pancreas and gallbladder – all results were normal).
  • Severe fatigue and lack of energy.
  • Muscle pain. (feels like lactic acid. Tested after a lot of sugar/carbs on christmas)
  • Persistent tiredness.
  • Anxiety and nervous system overstimulation.
  • Medication reactions (possibly MCAS).
  • Reactions to carbohydrates/sugar, resulting in heart palpitations and autonomic nervous system overstimulation.
  • Concentration difficulties.
  • Angina Pectoris symptoms.

I am currently housebound and feel that I need to rebuild my stomach health to heal the gastritis and regain energy. Unfortunately, I had to take Pantoprazole, Gaviscon, and slippery elm for a long time due to the gastritis.

I have already purchased all the probiotics from your list and created a 4-week plan (attached) based on your PDF. However, I recently read your December 2024 post about the potential dangers of Lactobacillus, which has left me feeling uncertain.

Analysis

First, the lactobacillus probiotics issue is mainly a caution. There are lactobacillus probiotics that will produce significant amount of d-lactic acid that will worsen brain fogs etc. This is compounded by both species mis-identification issues on retail probiotics and that different strains of the same species may produce different compound. Avoiding lactobacillus is the safest (simplest) course for many.

Chronic myopericarditis has no explicit literature on microbiome shifts. I suspect Heart Failure is the closest match for what I have gathered data on. My expertise is assembling “the facts” from studies on the microbiome and the mathematical application of these facts. So proceeding with my skill sets and available data, let us look at your data.

Quick Health Review

Most of the other measures are questionable in their usefulness given your back story.

Predicted Symptoms that matches back story

A few of the clear matches are below.

  • General: Fatigue – [88.5%]
  • Neurocognitive: Brain Fog – [88.2%]
  • Official Diagnosis: COVID19 (Long Hauler) – [87.6%]
  • Comorbid: Histamine or Mast Cell issues – [86.9%]
  • DePaul University Fatigue Questionnaire : Anxiety/tension – [86.5%]
  • Comorbid: High Anxiety – [86.2%]
  • Immune: Sensitivity to smell/food/medication/chemicals – [86%]
  • DePaul University Fatigue Questionnaire : Abdomen pain – [86%]
  • Autonomic Manifestations: palpitations – [85.9%]

These are checked and use to generate suggestions. Because of the existing use of prescription drugs, those are included in the suggestions.

Some 66 bacteria were picked from the matching patterns

Checking substances tried or taking (where we have information). The goal is to see what helps or hurts the microbiome. I have switched to % of highest or lowest value below

  • ciprofloxacinm, LDN, around 61 ( -20%)
  • losartan, clopidogrel, ketotifen, clopidogrel, Ivabradine, Prednisolone, Losartan, Gaviscon, Pantoprazole – no listed (i.e. no effect on microbiome or balanced effect)

Alternatives to clopidogrel likely include:

  • aspirin, resveratrol:  -30% which are likely worse choices.
  • slippery elm: -30%
  • Ginkgo biloba {Ginkgo}: +80%

So no major hurt and no apparent better with the exception of these antibiotics that are round +30% positive (lincosamide, kanamycin, paromomycin, ofloxacin) and a potential discussion point with your MD.

Prescription items high on benefits are:

  • proton-pump inhibitors (prescription): +100%
  • metformin (prescription): +85%

Cross-Validated Suggestions

I went to the old UI to see what shows up with cross validation.

The algorithm is slightly different (no one knows the right answer — and I have implemented multiple “reasonable” approaches across the site. We see that with this alternative algorithm, the slightly negative for LDN above is now positive. Similarly with Prednisolone.

The preferred pattern is to always discuss with your MD, try items in isolation (i.e. one new item a week) and taking notes for response.

Postscript and Reminder

As a statistician with relevant degrees and professional memberships, I present data and statistical models for evaluation by medical professionals. I am not a licensed medical practitioner and must adhere to strict laws regarding the appearance of practicing medicine. My work focuses on academic models and scientific language, particularly statistics. I cannot provide direct medical advice or tell individuals what to take or avoid.My analyses aim to inform about items that statistically show better odds of improving the microbiome. All suggestions should be reviewed by a qualified medical professional before implementation. The information provided describes my logic and thinking and is not intended as personal medical advice. Always consult with your knowledgeable healthcare provider.

Implementation Strategies

  1. Rotate bacteria inhibitors (antibiotics, herbs, probiotics) every 1-2 weeks
  2. Some herbs/spices are compatible with probiotics (e.g., Wormwood with Bifidobacteria)
  3. Verify dosages against reliable sources or research studies, not commercial product labels. This Dosages page may help.
  4. There are 3 suppliers of probiotics that I prefer: Custom Probiotics , Maple Life Science™, Bulk Probiotics: see Probiotics post for why

Chronic Lyme, Food poisoning, COVID

Backstory

  • 25 Year Old Female 
  • 2016: Experienced a concussion.
  • 2018: Diagnosed with chronic Lyme disease.
  • 2019: Dealt with chronic mold exposure 
    • all of the above diagnoses/symptoms improved by 2020.
  • 2022: Food poisoning led to IBS-D (Irritable Bowel Syndrome with Diarrhea).
  • 2024: Contracted COVID, resulting in hives, joint pain, and fatigue.
  • 2024: Chronic UTIs managed with Hiprex.
  • Current Symptoms:
    • Persistent diarrhea and stomach cramps.
    • Constant fatigue.
    • Occasional joint pain.

Analysis

First Thoughts

The constant UTI infection cause a knee-jerk suggestion for the following two probiotics:

Details

The reader does not appear to have added their symptoms, but the top current symptoms is cited under Current Symptoms. In fact, there are 245 symptoms forecasts at 80% or higher…

  • Lyme at 84%
  • COVID at 90.1%
  • Diarrhea at 90.7%
  • Joint pain at 87.9

I am just going to do  Novice: Just tell me what to take or avoid, to start. We have 43 bacteria identified as being too high or too low. The top suggestions are shown below

Typically I look at Probiotics first — mainly because of the common belief that they should be “cure all” In this case we have the following being usually available, I added some online stores after a few of them:

My usual suggestion is to do one at a time starting with a low dosage and then increase (double every second day) until you are at known effective dosages listed here. Keep at the maximum dosage for a week (or bottle is empty), and then proceed to the next Take notes on any changes seen (stool shape, farts, moods, etc). Some will have dramatic positive effects, others little.

The above were computed based on the complex interactions across the microbiome using literature from the US National Library of Medicine. An alternative approach for probiotic selection is using KEGG data to supplement with enzymes and metabolites that you appear to be low in.

Typical for Lyme, Long COVID and ME/CFS, Escherichia coli is the top choice (Mutaflor and Symbioflor2) at 109/293. With this method, {B. coagulans} and Clostridium butyricum would be the next choices.

Other Items

There were no strong diet suggestions to take, but avoid high carbohydrate diet and ketogenic diet. Foods to avoid are atypical items (cranberry bean flour, cranberry bean flour, {black currant},lychee fruit etc). Also to avoid: {Ginkgo}, a-Gluco-oligosaccharides {GOS}, Carrageenans {Carrageenan}, {Stevia}.

Cross Validated for Long COVID

This is a more restricted identification of bacteria to shift. The changes found that agreed with literature is shown below.

The suggestions are shorter and includes antibiotics.

Postscript and Reminder

As a statistician with relevant degrees and professional memberships, I present data and statistical models for evaluation by medical professionals. I am not a licensed medical practitioner and must adhere to strict laws regarding the appearance of practicing medicine. My work focuses on academic models and scientific language, particularly statistics. I cannot provide direct medical advice or tell individuals what to take or avoid.My analyses aim to inform about items that statistically show better odds of improving the microbiome. All suggestions should be reviewed by a qualified medical professional before implementation. The information provided describes my logic and thinking and is not intended as personal medical advice. Always consult with your knowledgeable healthcare provider.

Implementation Strategies

  1. Rotate bacteria inhibitors (antibiotics, herbs, probiotics) every 1-2 weeks
  2. Some herbs/spices are compatible with probiotics (e.g., Wormwood with Bifidobacteria)
  3. Verify dosages against reliable sources or research studies, not commercial product labels. This Dosages page may help.
  4. There are 3 suppliers of probiotics that I prefer: Custom Probiotics , Maple Life Science™, Bulk Probiotics: see Probiotics post for why

Professional Medical Review Recommended

Individual health conditions may make some suggestions inappropriate. Mind Mood Microbes outlines some of what her consultation service considers:
A comprehensive medical assessment should consider:

  • Terrain-related data
  • Signs of low stomach acid, pancreatic function, bile production, etc.
  • Detailed health history
  • Specific symptom characteristics (e.g., type and location of bloating)
  • Potential underlying conditions (e.g., H-pylori, carbohydrate digestion issues)
  • Individual susceptibility to specific probiotics
  • Nature of symptoms (e.g., headache type – pressure, cluster, or migraine)
  • Possible histamine issues
  • Colon acidity levels
  • SCFA production and acidification needs

Update on : Another ME/CFS person has gone to Firmicutes!

Backstory

I’m writing today to get your guidance.  I recently got back my 5th microbiome sample and I haven’t made significant progress.  I suspect it’s because of the food I eat, and I’m hoping you can help advise me of what to eat.

Earlier post: Another ME/CFS person has gone to Firmicutes! [Jan 2023]

My hypothesis as to why i’m not getting better results is that I haven’t followed the dietary recommendations very closely.

The recommendations are to basically eat a carnivore diet.  My main diet… Fruit, Oats, Rice, Potatoes, Nuts, Wheat and cheese are all hugely negative.  Thus, I think this is what’s holding me back.  It’s nice to identify the problem, but the solution isn’t easy.  

The only thing for me to eat on the recommendation list is Meat.  Even vegetables are mostly disallowed because I’m supposed to eat low fiber.  

Is that your understanding as well from the recommendations – that I should be nearly 100% meat (and possibly eggs), with some low fiber vegetables?  It’s hard for me because i prefer to be vegan.  But i’ll do whatever I need to fix my gut.

Note: 4 months ago I completely eliminated wheat and cheese and I started eating beef once a day.  That helped but it doesn’t seem to be enough, which is why I’m reaching out to inquire what to eat. 

 I  think I can withdraw my question.  I didn’t know what I would eat when meat showed up on my Suggestions list as basically the only option.  But I’m having miso or bone broth soup for breakfast, eggs for lunch, and meat for dinner… and that feels sustainable for me.  So far I think it’s working.  Time will tell.

Over the last 18 months i’ve had some good days and even a good week here and there, which has given me hope that your approach holds the solution i’ve dedicated a lot of my life to over the last 15 years.  However I always gravitate back to my baseline of feeling crummy.

I thought that taking all the top suggested pills, and cutting out the foods with very negative Priority score would be enough, but I now believe that my diet of mostly oatmeal, nuts, beans, (and previously wheat) has been holding me back.  All those items have a negative Priority scores, and my recommendation list very clearly points to red meat, low fiber, low carb.

First Step: Compare Last to First Sample

This immediately ran into issues with sample quality. One sample produced 723 bacteria versus 434, i.e. 66% more. It makes comparing the numbers very difficult.

CriteriaCurrent SampleOld Sample
Lab Read Quality11.84.3
Outside Kaltoft-Møldrup22086
Bacteria Reported By Lab723435
Bacteria Over 85%ile8466
Bacteria Under 15%ile26858
Lab: Thryve
Pathogens3320
Condition Est. Over 85%ile210
Kegg Compounds Low238331
Kegg Compounds High196309
Kegg Enzymes Low83479
Kegg Enzymes High322237

A second approach is to compare forecast symptoms

Current SampleFirst Sample

The surprising thing is how close both sets of forecasts are to each other, often with less than 1% difference. The reader’s “I haven’t made significant progress” appears to be right on. This is the first repeat analysis that there was not objective improvement all. The expert system is not perfect.

Going Forward — let us try getting religious on suggestions!

I am going to do three approaches to try helping this person:

  • Stock suggestions from the Expert System using the simplified UI. This used only studies on PubMed to try to shift the microbiome.
  • Using the Food Site – This use the nutrients identified as significant and tries to map them to a wide variety of foods (infer from nutrients to food)
  • Probiotics using KEGG – this uses no explicit studies, rather identify what substances that the microbiome may be starving for, then identify any probiotics that produces those substances. The reasoning is that the starvation contributes to the dysfunction.

Remember, everything are estimates of likely to help (or hurt). Estimates can be wrong. In some cases, it may be worthwhile to do a short term trial to see if there are any immediate changes. This applies especially to anything that is a mixture because the good may overpower the bad (or the reverse).

Simplify UI

We get 137 (out of 723, i.e. ) or 19%. The top diet types are shown below

We see high values for:

I had the same takeaway about inulin!  The basic form was super negative but the oligofructose enriched was very positive.  Not going to risk touching it.  

Similar thing with “low-fat high-complex carbohydrate” diet, which has a positive Priority score of 237.  However,  “Slow digestible carbohydrates” are negative 634  AND a “restricted-fiber diet” is hugely positive.   It would seem to me that eating low-fat high complex carbs is way too risky  🙂

Reader Feedback

The hard part – AVOIDS

The list contain many items that are often seen as to take.

Over to Food Helper

The food site, Microbiome Prescription Food And Nutrients is designed to bridge the gap between some nutrient tested in studies and foods it is found in. The food are often not tried in studies – so this is an inference because of sparse data. It should always be used with a grain of sodium chloride (salt).

The quick take list suggests:

The suggested nutrients are shown below

Take translates to American cranberry, raw black olives, a variety of fish

And these are the to avoid

Avoids translates to Vinegar, Almond, Red wine, chocolate

I will leave it to the reader to dig more on the food site. It may reveal what may have gone wrong.

KEGG Probiotics

This is an alternative way to determine probiotics working off compounds and enzymes produced (or not produced) compare to an estimated norm.

The results are shown below (first compounds and then enzymes). Suggestions are similar with the exception of the E.Coli probiotics. I would suggest these two:

Note: Prices include shipping anywhere in the world. These are typically manufactured weeks before shipping (have manufactured date) and thus alive. If you double the number of capsules, the costs usually go up by 20% only (see example below) and the price is awesome!!

$.29 per capsule$.20 per capsule$.15 per capsule

I just ordered the bacillus clausii and the bacillus mesentericus you recommended.  Thanks for making it so easy and linking it to an eBay seller!..

[Update] I just cancelled the bacillus mesentericus and the bacillus clausil you linked to.  They both contain fructooligosaccharids, which are a negative 193.

Question: Why did I skip Mutaflor?

  • Items that are on both list are more likely (better odds) of having a positive impact. I am an odds-person (i.e. a statistician).
  • Also, Mutaflor has a large number of additives: The other ingredients include maltodextrin, talc, methacrylic acid-methylmethacrylate copolymer, macrogol, triethyl citrate, glycerol, titanium dioxide, iron(III)-oxide, white beeswax, carnauba wax, shellac, and purified water

Probiotics Solutions when additives are a problems

There are two providers with no declared additives that I know of:

Postscript and Reminder

As a statistician with relevant degrees and professional memberships, I present data and statistical models for evaluation by medical professionals. I am not a licensed medical practitioner and must adhere to strict laws regarding the appearance of practicing medicine. My work focuses on academic models and scientific language, particularly statistics. I cannot provide direct medical advice or tell individuals what to take or avoid.My analyses aim to inform about items that statistically show better odds of improving the microbiome. All suggestions should be reviewed by a qualified medical professional before implementation. The information provided describes my logic and thinking and is not intended as personal medical advice. Always consult with your knowledgeable healthcare provider.

Implementation Strategies

  1. Rotate bacteria inhibitors (antibiotics, herbs, probiotics) every 1-2 weeks
  2. Some herbs/spices are compatible with probiotics (e.g., Wormwood with Bifidobacteria)
  3. Verify dosages against reliable sources or research studies, not commercial product labels. This Dosages page may help.
  4. There are 3 suppliers of probiotics that I prefer: Custom Probiotics , Maple Life Science™, Bulk Probiotics: see Probiotics post for why

Sick since a child from contaminated water

My back story –

I’m now 35. As a child I contracted a bacterial gut infection from water that had cow poop in it (broken pipe through a field), and was unable to eat sugar without being sick. As a teenager I had relatively bad insomnia, acne and eczema. I was prescribed months of antibiotics as treatment and put on a contraceptive to address the acne. I also had a spinal injury that I was prescribed painkillers including ibuprofen and codeine, and a painkiller that’s no longer approved for distribution that I forget the name of. By the time I was 19 I was in a high stress job, sleeping well, but taking guarana and caffeine pills on top of coffee to stay functional due to fatigue. 

Doctors took blood tests, and everything was in the normal range so no diagnosis. 

At 22 I had sever food poisoning in the Netherlands. 

At 25, in 2016, I took a trip to California – I’m from New Zealand – and contracted giardia, during a heatwave, and ended up in hospital in hypovolemic shock. I was prescribed fluids which where intravenous and an anti-psychotic, which as a New Zealander I didn’t take. My sister flew over to help me get home. Once back in NZ, I was found to have irregular heartbeat, giardia, and neck injury from severe vomiting. I had an allergic reaction to the first antibiotic to treat giardia, was given a course of prednisone then a different antibiotic which killed off the giardia. 

During this time, I had extreme fatigue, brain fog, heart palpitations, insomnia, panic attacks, tension headache and the worst, internal vibrations or tremors that could not be seen. I developed a dependency on sleeping pills, which quickly stopped working all together. Doctors couldn’t find anything physically wrong with me, and eventually one decided to try b12 injections. This, along with osteopathy and rest, resolved most symptoms, leaving only tinnitus. I have had b12 injections 1-3 monthly ever since, and this mostly controls the vibrations. I resolved my dependence on sleeping pills by using natural sleep aids and pushing through several sleepless nights. I was left with an inability to eat gluten and dairy.

By 2021 I was in good health – able to regularly exercise and hold down a high pressure job. I had my first Covid vaccine no issues, the second vaccine I became violently ill for 48 hours with fevers, fatigue, and body aches. I took the recommendation to get the third shot, still Pfizer, and was bedbound for 2 days with fevers, rigours, vomiting, headache, weakness and fatigue. In December 2022 I contracted Covid. My symptoms included sore throat, swollen lymph nodes, vomiting, fevers, rigours, fatigue, elevated heart rate. By day 7 I was weak but recovering. On day 8, internal vibrations started with severity, followed by blurred and double vision (I required a new prescription following this), breathlessness walking across a room, heart palpitations, tension headache, brain fog, PEMS and extreme fatigue. I was diagnosed after 3 months with long Covid. 

I tried every treatment suggested by the internet and then some, from HBOT to magnesium floats to ozone sauna, thousands of dollars of supplements, osteopathy, massage, and more. After almost 2 years I’m working full time again, and most symptoms are managed enough to wake up, work, clean up a bit, and sleep again. However they are not fully resolved – I can’t exercise without an extreme energy crash, and I have to continually practise meditation and other calm down methods to regulate. It’s certainly not a life lived well, and one in constant fear of catching so much as a cold.

I am hesitant to accept a ‘long Covid’ diagnosis, despite it being the only thing on offer. This is because I experienced the same set of symptoms I after having giardia and dehydration, neither of which are viral so not a “post viral syndrome”. My lifelong battle with fatigue indicates to me that serious illness triggers a specific set of symptoms, and my Biomesight results strongly indicates a gut issue. I have tried various diets, each resulting in my becoming more fatigued – keto, Mediterranean, low carb, vegetarian, carnivore, low formal, and high protein. 

I find the microbiome prescription results a little overwhelming and difficult to sort through, so your advice would be so appreciate

Analysis

First, about “overwhelming”. I agree! Just like “No man can serve two masters”, “No site can server all users”. My primary focus has been correctness, depth of coverage and other technical (nerd) aspects. This came out of seeing failure after failure of simplified and naïve approaches. The “new UI” has been an attempt to simplify the process while maintaining a reasonable level of accuracy.

You have had a long history of microbiome insults causing dysbiosis. Some are known to cause ME/CFS, see IBS/CFS/Long Covid Insight from Bergen’s Giardia Infection [2018]. Rather than retracing past events, let us focus on your current state and go forward.

Looking at predicted symptoms versus reported symptoms, we see a high number of matches.

This usually indicate that “Beginner-Symptoms: Select bacteria connected with symptoms” is likely the best start, This will focus on the probable bacteria that are causing most of the symptoms (and ideally ignore bacteria shifts that are likely just noise).

Usually the number of bacteria identified is a fraction of the symptoms. In this case we have 63 bacteria identified for 55 symptoms. The suggestions are shown below. I usually suggest keeping to those above 50% of the highest weight (1706 x 50% =853) and avoiding to those below 50% of lowest value (-1375 x 50% = -865). The reason is that the higher (or lower) the weight, the more probable it will have an impact).

I retried checking all types of microbiome modifiers (usually overwhelming). Mainly to see if antibiotics often used for ME/CFS rank high. Going to the Consensus Report and filtering to antibiotics we see that none made it over the threshold – which means that they are likely to be really helpful.

At this point, I typically decompose suggestions into types, first with probiotics. VSL#3 is rarely a clean choice because there were changes in the formula and other issues.

I would go for the following probiotics (two weeks of one at a high dosage – 50-150 BCFU) and then rotate to the next. Given that you are “down under” , I would suggest getting them from my favorite Indian Manufacturer (usually manufactured just weeks before shipping and best prices) – I linked to the sight below. Note that doubling the capsules in a bottle often costs just 20% more and a lot cheaper than ordering two bottles!!

P.S. spirulina was a coding error – just fixed it.

Your inability to handle gluten or diary means that some suggestions must be excluded. I would be tempted to try an experiment with oats flakes, then barley flakes, then 100% rye bread — mainly to see if it is wheat gluten that is the issue (there are many types of gluten).

A handful of almonds and walnuts everyday is an obvious item. Do not do a B-Complex — some B vitamins will help and other hurt. Keep to Vitamin B7, B2. Hopefully you can tolerate dark chocolate (Cacao). Lime is suggested (as is Vitamin C).

The avoids should be pretty clear.

Alternative Paths

At this point, we branch into two additional paths — one by using Kyoto Encyclopedia of Genes and Genomes (KEGG) data on compound being produce and consumed by your microbiome. With KEGG we look for probiotics that can provide enzymes etc that you are deficient in. Why these alternative paths? Simple, there is not enough data available so we use inference.

The second path is going to the food site to identify foods rich in suggested nutrients. The foods may not have been used in studies, but the dominant nutrients in the foods may have been studied.

KEGG

The top suggestions are below. #1 item is common for ME/CFS, Mutaflor is available in Australia, I warn people that it may cause a major die-off / herx reaction. Symbioflor 2 is the same probiotic species but at ~ 1/100 of the BCFU and unlikely to cause die off. To the above list I would add these two

Foods

We see that you may be eating a lot of beans – they appear to be providing some of the nutrients that caused wheat to be suggested above.

Postscript and Reminder

As a statistician with relevant degrees and professional memberships, I present data and statistical models for evaluation by medical professionals. I am not a licensed medical practitioner and must adhere to strict laws regarding the appearance of practicing medicine. My work focuses on academic models and scientific language, particularly statistics. I cannot provide direct medical advice or tell individuals what to take or avoid.My analyses aim to inform about items that statistically show better odds of improving the microbiome. All suggestions should be reviewed by a qualified medical professional before implementation. The information provided describes my logic and thinking and is not intended as personal medical advice. Always consult with your knowledgeable healthcare provider.

Implementation Strategies

  1. Rotate bacteria inhibitors (antibiotics, herbs, probiotics) every 1-2 weeks
  2. Some herbs/spices are compatible with probiotics (e.g., Wormwood with Bifidobacteria)
  3. Verify dosages against reliable sources or research studies, not commercial product labels. This Dosages page may help.
  4. There are 3 suppliers of probiotics that I prefer: Custom Probiotics , Maple Life Science™, Bulk Probiotics: see Probiotics post for why

Professional Medical Review Recommended

Individual health conditions may make some suggestions inappropriate. Mind Mood Microbes. outlines some of what her consultation service considers:
A comprehensive medical assessment should consider:

  • Terrain-related data
  • Signs of low stomach acid, pancreatic function, bile production, etc.
  • Detailed health history
  • Specific symptom characteristics (e.g., type and location of bloating)
  • Potential underlying conditions (e.g., H-pylori, carbohydrate digestion issues)
  • Individual susceptibility to specific probiotics
  • Nature of symptoms (e.g., headache type – pressure, cluster, or migraine)
  • Possible histamine issues
  • Colon acidity levels
  • SCFA production and acidification needs

A knowledgeable medical professional can help tailor recommendations to your specific health needs and conditions.