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Unknown's avatar lassesen 1:26 pm on February 26, 2023  

A Microbiome Trek Continues thru the land of ME/CFS

This is a continuation of prior blog posts. For other related posts see: Analysis Posts on Long COVID and ME/CFS.

The earlier posts for this person are:

Largely recovered. Post exertional malaise (PEM) persists selectively,

  • I am ramping up my workouts. Weights 10 -15 minutes even if I’m lifting close to max , I have no problems.
  • Basketball is the kicker. 

Using a fit bit watch to monitor found a threshold that impacts severity heart rate. generally tried to stay at 110.  Keeping it lower I think netted a less sever crash, but still happened.

  • My PEM crash starts exactly 5 hours post work out  for 24 hours. I played basketball till 5pm, these stats are reflective of me in a crashed state through the night till the following morning. 

Experiment: I got the Gammacore vagus nerve stimulator earlier this week and seeing some positive results. Body feel calmer overall. HRV looks better and balanced by fight or flight. My ANS almost always showed as sympathetic dominant . The Gammacore tvns device does seem to help push me to balance a little bit. I feel more social . Have to be careful not to overdo it, I feel like it flares up my allergies. If I hit the sweet spot, I feel more social/chatty and relaxed.   

PEM starting to think it could be MCAS. I feel flushed in the face at the 5 hour post workout. I crash , but also  get a stuffy nose and then disrupted sleep. Seems allergy like. 

  • Zyrtec and reservatol hasn’t stopped it.
  • Going to try the cromlyn spray you mentioned. I read it could take weeks  to work though?

Dec, 2022 Unfortunately I was unsuccessful and caught the stomache plague . Had to take a couple zofran. 

It took me 3 ombré tests to get one that didn’t get rejected. So strange!

Sample Comparison

The past 16 months of samples is shown below. Some general observations:

  • The number of different bacteria detected is reducing (while sample quality is improving — thus likely a true reduction)
  • Number of pathogenic bacteria is tending downwards
  • Bacteria patterns are starting to match some of the patterns from PubMed (i.e. moving into “normal” patterns)
  • Less Enzymes are at low levels
  • More Enzymes are at high levels
  • His catching “the stomach plague and taking Zofran (ondansetron hydrochloride,(prescription)  – 300 bacteria impacted listed)” is an hiccup for trending.

Remember that there is variability from time of day that the sample was taken (see Changing your Microbiome Results by when you take your sample!).

Criteria2/1/202312/9/202210/29/20228/22/20224/30/202211/22/2021
Lab Read Quality5.65.15.153.64.2
Bacteria Reported By Lab434476472657506468
Bacteria Over 99%ile1071000
Bacteria Over 95%ile1829101562
Bacteria Over 90%ile255232382512
Bacteria Under 10%ile1086016016891187
Bacteria Under 5%ile442182844890
Bacteria Under 1%ile321824222
Rarely Seen 1%1723170
Rarely Seen 5%162712983116
Pathogens343036494641
Outside Range from JasonH554477
Outside Range from Medivere141415151818
Outside Range from Metagenomics998877
Outside Range from MyBioma444433
Outside Range from Nirvana/CosmosId151520202222
Outside Range from XenoGene343447473636
Outside Lab Range (+/- 1.96SD)81071672
Outside Box-Plot-Whiskers2758681356929
Outside Kaltoft-Moldrup9182791559870
Condition Est. Over 99%ile600000
Condition Est. Over 95%ile701210
Condition Est. Over 90%ile1013310
Enzymes Over 99%ile1000201
Enzymes Over 95%ile118929486116
Enzymes Over 90%ile6475111299193103
Enzymes Under 10%ile150119217175291354
Enzymes Under 5%ile7559125101151154
Enzymes Under 1%ile121527202129
Compounds Over 99%ile1003831313129
Compounds Over 95%ile463228227131244233
Compounds Over 90%ile606451365371358347
Compounds Under 10%ile59948286212259264
Compounds Under 5%ile5801915454154163
Compounds Under 1%ile569928234641

US National Library of Medicine Studies

As shown above, we now have some matches, he does not have any of the following

  • Liver Cirrhosis 100%ile 47 of 170
  • Atherosclerosis 100%ile 25 of 105
  • Hashimoto’s thyroiditis 92%ile 7 of 16
  • Ankylosing spondylitis 92%ile 26 of 133
  • hypertension (High Blood Pressure 85%ile 13 of 40 –clearly does not have
  • Obesity 57%ile 32 of 107 – clearly does not have

Looking at ME/CFS co-morbid, we find 17-20% overlap for Hashimoto’s thyroiditis [Src]; for Atherosclerosi see Effects of Post-Exertional Malaise on Markers of Arterial Stiffness in Individuals with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome); Chronic Fatigue is associated with Ankylosing spondylitis (Src) as is Liver Cirrhosis. Both hypertension and Obesity are not associated with ME/CFS.

This type of matches is not intended to predict, rather, if you have these conditions then these are the bacteria shifts that may likely contribute to the severity of symptoms.

Going Forward

I am going to build a consensus using the 4 ME/CFS or Chronic Fatigue associated items above in addition to my usual ones – thus 7 sets of suggestions.

The top suggestions:

Going over to KEGG, we do NOT see Escherichia coli at the top of the list (often seen with ME/CFS). We see Bacillus subtilis near the top of the list, Lacticaseibacillus casei further down the list and Lactobacillus gasseri still further down. pediococcus acidilactic (probiotic) was not listed. Of special interest was the absence of B-Vitamins at the top of the list which is typical of people with ME/CFS.

My preference is usually to go with the most consensus (the best odds). So the short probiotic list would be:

He has started doing cited in Interesting Successful Clinical Trial for Long COVID and ?ME/CFS  which is available on Amazon for $40.

OverTime_ConsensusDownload

OverTime-SimpleSuggestionsDownload

Speculation on ongoing Post Exertional Malaise issue

One of my dark fears with ME/CFS is that it will cause epigenetic changes. Epigenetic means that parts of your DNA is turned on or off. Reprogramming such a DNA change is outside of my focus.

There are some interesting studies on MCAS and epigenetics

  • “In TET2-deficient mast cells, chronic activation via the oncogenic KITD816V allele associated with mastocytosis, selects for a specific epigenetic signature characterized by hypermethylated DNA regions (HMR) at immune response genes” [2022]
  • Hypoxia modulates human mast cell adhesion to hyaluronic acid. [2022] – this is of special interest because cellular hypoxia is often seen with ME/CFS and FM
    • “Hypoxia-mediated regulation of mast cell adhesion to extracellular matrix components might be involved in the pathogenic accumulation of mast cells observed in the course of certain diseases including rheumatoid arthritis and cancer.”
  • “In this manuscript, we investigated the ability of mast cells primed with different stimuli to respond to a second stimulation with the same or different ligands, and determined the molecular and epigenetic drivers of these responses.” [2022]
  • “This study confirms that epigenetic changes are involved in mastocytosis, and suggests that allergy may be an important epigenetic modifier of the disease. ” [2021]

My current most probable hypothesis is that the higher level of activity with basketball than weight lifting results in more hypoxia (low oxygen levels) when then triggers a histamine cascade which takes some time to clear.

  • ” the secretion of the prestored mediator histamine was increased under hypoxia alone.” [2017]

The logical testing would be taking the following pre-basketball and then at hour 4, to see if they alter the pattern:

Going down the hypoxia path, my favorite experiment to suggest would be:

Using the New Artificial Intelligence Dietician on the Internet

No, it us not Chat_GPT — it uses a very different branch of AI. For more information see: Microbiome Menu Helper — The AI Dietician

In this case the top items look very reasonable (with 4,183 items listed):

The avoid items included:

Postscript – and Reminder

I am not a licensed medical professional and there are strict laws where I live about “appearing to practice medicine”.  I am safe when it is “academic models” and I keep to the language of science, especially statistics. I am not safe when the explanations have possible overtones of advising a patient instead of presenting data to be evaluated by a medical professional before implementing.

I cannot tell people what they should take or not take. I can inform people items that have better odds of improving their microbiome as a results on numeric calculations. I am a trained experienced statistician with appropriate degrees and professional memberships. All suggestions should be reviewed by your medical professional before starting.

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

Unknown's avatar lassesen 9:30 am on February 23, 2023  

Two new Microbiome Review for ME/CFS

Another ME/CFS after 19 years

Another ME/CFS person has gone to Firmicutes!. 

for more see Analysis Posts on Long COVID and ME/CFS

Unknown's avatar lassesen 5:16 am on January 25, 2023  

Bacteria are very very rarely bad or good

A reader messaged me this

hello I do not want to bother, I have a question in the laboratories of my country, in the microbiota tests they put veillonella as virulent, but in a recent publication of microbiome prescription I saw that it could be a solution, why do the laboratories attribute virulence to it?

My Answer

That is equivalent to saying “Italians are criminals”. Why would someone say that? “Some Italians belong to the Mafia”

Veillonella is a genus of gram-negative, anaerobic bacteria that are commonly found in the human oral cavity, gastrointestinal tract, and respiratory tract. While some strains of Veillonella can cause infections, particularly in individuals with compromised immune systems, the majority of strains are considered to be non-virulent or opportunistic pathogens. Some studies have suggested that Veillonella may play a role in certain disease states, such as periodontal disease, but more research is needed to fully understand the potential pathogenic mechanisms of this genus.

From https://chat.openai.com/chat

For a lab to creditably state that, the lab would need to identify the specific strain. Veillonella is a genus, composed of many species, each species is composed of many strains. In terms of our Italian allergy, Italians come from many regions of Italy (species), within each regions are many families (strains). There may be some of these families that tend to being Mafia, others may tend to be priests (and eventually Popes).

Yin-Yang

My attitude is that Yin and yang is a better way of viewing bacteria. Bacteria are out of balance. Too many poor people results in high crime rates (out of desperation), Too many rich people results in low class mobility (the only people that get ahead are their friends, “old school ties”). The “right balance” for a well functioning society varies by country — for example, Iceland versus Haiti. Similarly, your DNA and diet influences what the right balance should be.

This family’s favorite and most effective probiotic is Mutaflor, an Escherichia coli probiotic. All E.Coli is not bad, trying to eliminate all E.Coli is likely a very dumb choice.

Unknown's avatar lassesen 8:28 am on January 22, 2023  

Interesting Successful Clinical Trial for Long COVID and ?ME/CFS ?

A reader forwarded me this link,

A Randomized Controlled Trial of the Efficacy of Systemic Enzymes and Probiotics in the Resolution of Post-COVID Fatigue

The study concludes:

This study demonstrates that a 14 days supplementation of ImmunoSEB + ProbioSEB CSC3 resolves post-COVID-19 fatigue. The proposed supplement regimen significantly reduces the burden of both, physical and mental fatigue and is effective as an early intervention in the recovery of COVID-19 patients, many of whom continue to experience severe fatigue including muscle weakness and “brain fog” several months after initial infection. 

The substances used are very familiar to readers of my CFS Remission blog. They are:

  • Bacillus coagulans LBSC (DSM 17654)
  • Bacillus subtilis PLSSC (ATCC SD 7280)
  • Bacillus clausii 088AE (MCC 0538)
  • Serratiopeptidase,
  • Bromelain,
  • Amylase,
  • Lysozyme,
  • Peptidase,
  • Catalase,
  • Papain,
  • Glucoamylase
  • Lactoferrin

Some quick notes with citations for new readers:

This points back to the research and demonstration done by Dave Berg at Hemex Labs . “Berg and Joseph Brewer studied coagulation in CFS patients and concluded that approximately 85% of chronic fatigue syndrome patients had hypercoagulation, “[src].

My personal experience with the Hemex approach is good and put me into remission in 2000. Objective measurements showed coagulation in some parts of the coagulation cascade with piracetam and heparin being my favorite cocktail (both taken sublingual).

Reservations

The study ended at two weeks with no ongoing tracking of patients. My observations of ME/CFS people over several decades has been that short term remission is common with a slow regression back to fatigue. An excellent examples are ME/CFS in Australia doing Fecal Matter Transplants with remission within 48 hours and relapse in 4-8 weeks. Just as some bacteria (bacillus cited above) reduces coagulation, other bacteria triggers coagulation. If those triggering bacteria are not adequately suppressed then the fatigue and brain fog will return over time. Think of a leaking dike, you bring in the pumps and remove the water behind the dike, 3 weeks later the water is back — you need to fix the leak in the dike also.

A reader pointed out that the product is available on Amazon US for $40. So a cheap experiment to try! If you do try it– please add your experience as a comment on this post.

Unknown's avatar lassesen 8:31 am on January 15, 2023  

Samples over time of ME/CFS Spouse

This is the spouse of someone with significant ME/CFS. It is well known that bacteria is transferred between people in the same household unit.

This raises all sorts of questions — which I am not interested in exploring… “For better or worse, in sickness and in health”

My wink wink suggestion for microbiome issues has been “Snog a lot of pretty young healthy things as the best probiotic” — my wife does not agree…..

Comparison between Samples

The first step that I did was to verify that all samples used the same reference sticks. This means clicking this for each sample first.

This person has processed FASTQ data thru both BiomeSight and OmbreLabs. I am using OmbreLabs data below. Using reference tables uploaded in 2023.

Criteria6/8/20228/4/20229/6/202210/26/2022
Lab Read Quality2.13.83.68.3
Bacteria Reported By Lab534774721775
Bacteria Over 99%ile10326
Bacteria Over 95%ile58272422
Bacteria Over 90%ile99534450
Bacteria Under 10%ile256848127
Bacteria Under 5%ile13281577
Bacteria Under 1%ile53116
Lab: Thryve
Rarely Seen 1%814912
Rarely Seen 5%43806073
Pathogens21343327
Outside Range from JasonH5577
Outside Range from Medivere13131717
Outside Range from Metagenomics9999
Outside Range from MyBioma7788
Outside Range from Nirvana/CosmosId23231919
Outside Range from XenoGene44444949
Outside Lab Range (+/- 1.96SD)38392622
Outside Box-Plot-Whiskers177202153118
Outside Kaltoft-Moldrup206257203292
Condition Est. Over 99%ile0000
Condition Est. Over 95%ile0000
Condition Est. Over 90%ile0000
Enzymes Over 99%ile1418523
Enzymes Over 95%ile11510559112
Enzymes Over 90%ile212192143320
Enzymes Under 10%ile6310693266
Enzymes Under 5%ile294527141
Enzymes Under 1%ile2208
Compounds Over 99%ile373631119
Compounds Over 95%ile289288275281
Compounds Over 90%ile372381361385
Compounds Under 10%ile288255235298
Compounds Under 5%ile192159136216
Compounds Under 1%ile3714431

General Impression

  • After the first sample, the next two had improvements but the last one went the wrong way.
    • Too high and Too low reduce for 2 samples and then increased
    • Too high or too low for Enzymes were the highest for the last sample
  • Most of the third party ranges were constant for the first two samples and most got worst for the last two samples.
  • Compounds are much less indicative of issues.
  • Special Studies are sensitive to lab quality,
    • 6/8/2022 4-14%, top items: ME/CFS without IBS, Poor gut motility, Cold Extremities
    • 8/4/2022 5-17%, top items: ME/CFS without IBS, Poor gut motility
    • 9/6/2022 4- 18%, top items:  ME/CFS without IBS,  Easily irritated
    • 10/26/2022 7 -22%, top items: General: Fatigue, ME/CFS without IBS

ME/CFS without IBS is a consistent top item and we see that the percentage is increasing.

Proposed Approach

Unlike many samples, we see distinct deterioration in several 3rd party criteria. For many samples, there is no change between samples. We will include those in the consensus, namely:

  • JasonH
  • Medivere
  • MyBioma
  • Xenogene

It is interesting to note that one 3rd part criteria improved: Nirvana. To this, we do our usual:

  • Lab ranges
  • Box-Plot-Whiskers
  • Kaltoft-Moldrup

The net result will be more bias to those in the 3rd party criteria cited above. Another way of stating that, we will emphasis more that which everyone agrees are most concerning.

The top suggestions (easily obtained):

The top avoids are:

The downloads are attached:

SimpleSuggestions_I-Download

I_ConsensusDownload

Food Suggestions

We mostly eat pastured meats and vegetables. No cereals and little in the way of carbs or even fruit. I used to eat linseed crackers in the USA, but here I eat buckwheat instead. Here in Spain we switched from wild Alaskan salmon, to seasonal, local, small blue fish, like mackerel, sardines, etc. Added Rabbit and can eat a lot more quality raw cured pork, if we want to. I have always enjoyed natural wine and Spain has plenty of it. Fresh made coffee and 100% cocoa. Raw goat, sheep and cow’s milk are also available and I do enjoy them with some regularity.

I used the latest sample with the Kaltoft-Moltrup Normal Ranges. The top suggestions are each because of different nutrients that appear significant with Fiber, total dietary and Magnesium, Mg being a common theme.

On the avoid list we have at the bottom:

Remember, foods are filtered to the nutrients that are above typical levels for foods containing the same nutrients. The goal is to reduce the intake of nutrients that have been identified to shift things in the wrong direction.

For most people, if you say reduce folic acid in your diet — most people will not have a clue. The purpose of the food suggestions is to translate a precise item into common foods.

Note: If a food in your diet is not in the list then we deem it as neutral. For example: there are 24 variety of rabbit in the food database, only one shows up in the suggestions from the sample, Rabbit, meat, raw, Oryctolaguscuniculus, (Nyama ya kalulu), which suggests to keep eating rabbit. Similarly for milk, the two that shows up are Milk with Cow’s blood (from Africa) of 626 entries for milk.

The video below may help understand Food Suggestions better.