Category Archives: Conditions

Unknown's avatar lassesen 5:29 am on November 2, 2021  

Hypoperfusion in the CFS/ME and Long COVID brain

To me, this keeps getting reported in the literature over the last 30 years, with the latest excitement being this August 2021,

Limbic Perfusion Is Reduced in Patients with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)

Hypoperfusion or reduced perfusion means simply reduced oxygen gets to the brain. There can be many causes, for example (with convention causes first, then likely ME/CFS/LC causes:

  • Low blood pressure
  • Heart Issues
  • Loss of blood volume
  • Hypercoagulation (thick blood)
  • Sticky blood
  • Inflammation of blood vessels (due to chronic low grade infections — often secondary infections and not primary infections)
  • Issues with hemoglobin (iron) due to things like chemical pollutants, including carbon monoxide

Each one of these impair oxygen to the brain and thus can cause many symptoms: inability to concentrate, memory issues, mood swings / irritability, light intolerance, noise intolerance, and many many more. Hypoperfusion also occurs with many neurological conditions and forms of dementia.

To add a personal note, during one relapse of ME/CFS my SPECT scan showed significant hypoperfusion which the radiologist read as “possible early onset Alzheimer’s disease”(due to my age) – it was not, I fully recovered (as evidence by some 1500 blog posts on this site and it’s sister site, Microbiome Prescription Blog.

ME/CFS Literature

When patients deal with MDs, having a rich collection of studies often persuade them to take something serious instead of dismissing it as something from the internet rumor-mill. So, I have assembled prior studies below. Note that POTS has been a hallmark of ME/CFS and is associated with hypoperfusion.

In 20+ years reading literature on ME/CFS, the following issues (or a combination) appear to be dominant causes:

There are a few subsets, like those that suffered organophosphate pesticides exposure (2003). Prolonged ME/CFS reduces the size of the brain (I suspect due to prolonged oxygen starvation)

COVID Literature

The above was the result of 30+ years of investigations, Long COVID is less than 2 years.

Putting it all together

First, try to get an Appropriate Brain Scan depending on the method of scan, abnormalities would be be found from 14% to 80% of the time. You want the 80% scan — or else you MD will say “it’s in your head” in the alternative meaning 😦 .

Second, it is very unlikely that you can be tested for each and every candidate item above. In some cases, there may not be the expertise available or the testing deemed experimental/for research purposes only — this can be ignored/dismissed by a treating physician (or their supervisor). For myself, I had coagulation testing with Berg (their test suite is available in a few locations). There are almost a dozen makers examined — most MDs and even specialists — will only test for a few.

I have put together a collection of researched pages dealing with various issues:

The secondary infections are harder to deal with — often they can become occult (using Jadin’s term from the Pasteur Institute for Tropical Medicine), that is, they may not be seen in the blood (an oxygen rich environment) but in the tissue (lower oxygen, and even more when they produce metabolites (toxins) to inflame blood vessels (further reducing oxygen) and cause fibrin barriers to block oxygen from red blood cells getting into the tissue. They may also persist in the gut microbiome and never enter the blood system — instead their metabolites enter the blood system.

Personally, I favor the microbiome alteration approach. The goal is to make a hostile environment for these bacteria by starving them of their preferred food and flooding them with what they do not like. I did the Jadin’s antibiotic protocol (multiple rotating specific antibiotics for months) with earlier relapse — but I have been just as successful with microbiome manipulation with later relapses (and an apparent shorter time to recovery).

There is Hope

Given the number of issues, challenges with MDs, etc, I realize that most patients will likely get zero traction from the conventional medical establishment — unfortunately. I view that there is a viable alternative treatment approach because of the availability of direct-to-retail 16s microbiome tests. We know that there are pattern of bacteria shifts seen in CFS/ME and Long COVID. It is likely (at least from personal experience) that correcting these shifts result in reduce symptom severity and number (and even complete elimination). See my personal experience here.

The key is really simple — alter diet and supplements –NOT WITH A FORMA COOKBOOK MODEL from Internet ramblings of others — but explicitly based on your personal microbiome. The suggested changes are generated (for free) by artificial intelligence on Microbiome Prescription using almost 2 million facts harvested from the US National Library of Medicine. The suggestions are unique to you — but should always be reviewed by your medical professional before starting.

Unknown's avatar lassesen 12:12 pm on October 17, 2021  

Update on a ME/CFS patient

The patient has been under a lot of family stress. Stress is known to flare ME/CFS and to also alter the microbiome. One of the typical symptoms seen is an increase of brain fog.

The last sample was taken on Aug 20, 2021 with 20 symptoms entered.

My Usual Flow for Analysis

With the addition of “Consensus Suggestions” getting suggestions become easier. I can do several analysis and then work off the consensus report. This means less mental exertion for ME/CFS patients

Typically I will start with the top two shown below, but since ME/CFS is included. I have 3 to use

After getting three sets of suggestions by different paths

Takes from Consensus (highest values), there are 130 positive items. I will just pull the highlights.

odifierTake Net
trametes versicolor(Turkey tail mushroom)28.62
cinnamon (oil. spice)25.34
thyme (thymol, thyme oil)18.93
anise16.37
polymannuronic acid15.26
galacto-oligosaccharides (prebiotic)13.02
chitosan,(sugar) – Probable19

At lower values (and still good to take), are many typical ME/CFS supplements including:

The AVOID list

The flip side — the avoids — often this is hard for ME/CFS to implement. Often they are limited to choices due to available income or other issues (for example histamine issues). Occasionally, they have been convinced to need a specific type of diet.

Adding the new tools to the Analysis

First, I checked the medical conditions from the new site, GMRepo, and ME/CFS is not listed. This means that any researcher who have done a study, had not contributed their data there 😖. Going to the full list and seeing if anything sticks out for the latest sample there was nothing, there was a weak possibility for (Obesity, Morbid and Clostridium Infections).

Next, I looked at Symptom Forecasting

The predicted symptom really looked like ME/CFS, as shown below

Consensus Prediction of Symptoms

Reducing Salicylates in the diet would be an additional suggestion. I clicked on the top item, DePaul University Fatigue Questionnaire : Difficulty following things especially since the person reported more severe brain fog recently.

This takes me to a page showing the bacteria involved. We have 44 out of 49 bacteria having a strong or better match.

We then create an additional sample profile by clicking the [Create Other Samples Profile…] , view the suggestions and returned to the consensus page (which now uses all 4 suggestion list)

The rest of the lists are similar. The number of absolute takes did drop down by 30%.

KEGG Suggestions

KEGG works off the genetics of the bacteria involved (genus and species) and not the mechanisms used above. We get the following suggestions:

For possible supplements, we see the following that appears supported by the literature.

  • Magnesium – which helps many with ME/CFS and also stress related [Magnesium and stress]
  • D-Ribose – used by Dr. Jacob Teitelbaum [The use of D-ribose in chronic fatigue syndrome and fibromyalgia: a pilot study]
    “D-ribose significantly reduced clinical symptoms in patients suffering from fibromyalgia and chronic fatigue syndrome.”
  • beta-alanine – which appears to be execrated more in ME/CFS [1996]
    “Increased excretion of beta-alanine was found in a subgroup of CFS patients, indicating that there may be a link between CFS and beta-alanine in some CFS patients.” [2007]
  • Cysteine – i.e. N-Acetyl Cysteine (NAC) on the take list above
  • Proline — “The disorder of arginine-proline metabolic pathway is detected in CFS middle school students before exercise intervention.” [2018]

There were also some items that I could not find any suitable literature on and thus I am ignoring.

Bottom Line

This has been a pro-forma walkthru of how to analysis the microbiome of a person with ME/CFS. We used several different approaches to get multiple sets of suggestions which we viewed in the Consensus Report. Each way used a different model of which bacteria to select (since no one knows the right one that works for everyone!).

Looking at the items above, my personal high priority choices would be to go hard on stress reducers:

Then add in at the next level

  • Thyme Oil
  • Anise Oil
  • B Vitamins
  • Probiotics

And then the appropriate items on the above lists.

REMEMBER — do not ignore the Avoid list. Doing so will reduce or eliminate the benefits from the Take list.

As always, this is not medical advice — all suggestions should be discussed with a knowledgeable medical professional before starting. This is a walkthru of using an academic model (not based on clinical experience) to model what may improve the microbiome examined. Every microbiome is unique and the contents of this post cannot be applied to other people.

Unknown's avatar lassesen 8:41 pm on August 7, 2021  

Monitoring watch for CFS and other Conditions

This is a follow up from a previous thread to show what type of information is available.

The $45 watch

The store is BangGood and the price varies. Today it’s $44, I had gotten it on sale for $32 earlier this year

This is not “medical certificed”, but the numbers are good for on going monitoring. This watch can be set to record every 10 minutes of the day. Usually I need to recharge every 4 days with these constant readings

Example from the day that I got cellulitis

My watch was removed in the E.R. when I arrived at hospital, so only a half day was recorded. The charts illustrate the progression.

“White Coat Hypertension”

At my last checkup, the nurse reported high blood pressure… the BP chart agreed at the time she took my B.P. BUT it also showed that my BP is not high most of the time…..

Unknown's avatar lassesen 4:56 am on July 13, 2021  

A German CFS Patient Experience and Analysis

A reader had initial success from modifying the microbiome but it did not persist.

The reason I ended up at your website doing research into the connection microbiome and ME/CFS was that firstly I tried Miyarisan and it turned out to be one of the best things I ever tried, MY headaches and brain fog were early completely gone and I had a lot more energy. Unfortunately this wonder only lasted about 6 weeks till I overdid it and crashed and with that crash Miyarisan lost it’s effect on me.

The other thing was Nystatin, which I was given for the candida found in my gut last year and right on from the first pills I took, it gave me more energy ( so I doubt it had anything to to with the candida, but rather must have changed something else in my gut for the better). This lasted about 10 weeks and then pooped out and was not reproducible. 

But these two times that I felt I got energy because of some changes in my gut, were very rare in the way the they just generally provided a relief in all symptoms, as I was just overall feeling better and had more energy, but without crashing. Most of the times I have trouble, because I am easily overstimulated and most things that give me energy give me instant fatigue rebound, so Miyarisan and Nystatin really were different and made me try to work on my gut. 

She attached her tests and summarized them as “As to my tests, I guess the most notable things are my low TH1(Interferon Gamma), my low glutathione, high TGF beta, my decreased SOD activity.”

Reminder that recovery is a journey

In an earlier youtube review of another ME/CFS patient, I used the graphic below

I used this model for my last flare and can be seen by the list of posts below on CFS Remission. Each report was associated with a new microbiome test and a change of supplements etc to address the changes that the prior changes caused.

  • Report #1
  • Report #2
  • Report #3
  • Report #4
  • Report #5
  • Report #6
  • Report #7
  • Report #8

I have been busy adding features that exposes more information about the microbiome. We shall see if these feature helps with the analysis.

Pro Formula Analysis

My usual starting point is to pick the low hanging fruit — identify outliers.

Bacteria Outliers

I quickly saw some massively high ones. I will focused on those. Note that  Firmicutes is massively overrepresented.

End Products

Only two items were suggested, none available as a supplement (a-Galactosidase , Phosphoamidase)

KEGG Bacteria Products Out of Range

A short list, as above none available as a supplement

KEGG Modules out of Range

Only one item (M00570) Isoleucine biosynthesis, threonine => 2-oxobutanoate => isoleucine

KEGG Enzymes Out of Range

A longer list — all being low. We hope over to KEGG Computed Probiotics and get the following list

Because this person is in Europe, they may be able to get lactobacillus kefiri which is described more in my post of 2017 and sold by online Italian sites. This is a researched probiotic. Also AOR, Probiotic 3 is a sweet one — all of the researched probiotic species in it, are on the above list. For the bifidobacterium, see Researched Probiotics list for recommended choices.

Predicted Symptoms – Citizen Science

At this point we get some very interesting results. First, the bacteria by themselves do not match any symptoms.

But when we go over to the KEGG components that the bacteria produces, we see the type of predictions that we would expect

Conclusion: She does not have the typical ME/CFS bacteria shifts but she has the typical jacked metabolites imbalance seen in people with ME/CFS. Same crime — different crime family!

Action Plan

At this point, we have identify major items of concern.

Hand Picked Suggestions

I am going to run it two ways — first with the extreme outliers shown above, then including Firmicutes (which I rarely do)

Without Firmicutes

Remember we need to set Precision to the kitchen sink to have Firmicutes included in the calculations for the suggestions

If you do not change — the suggestions will be the same as above.

What about the two strange strains?

These bacteria do not ring any bells with me, so over to pubmed.

Proposed Plan for next cycle

Rotate every 2-3 weeks:

  • Triphala (we usually buy organic and make our own capsules) – 2000+ mg/day (source)
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  • Licorice (I prefer the Italian products — not teas or powders) . Dosage used in clinical studies are 24-32 grams/day
Amarelli - Spezzatina liquorice with its and unmistakable taste - 100 gr
Amarelli – Spezzatina liquorice with its and unmistakable taste – 100 gr from Amazon.De

If your physician is willing to prescribe “off-label” also do alternating every two weeks between a PPI and atorvastatin (prescription). PPI is over the counter in some places and includes:

  • omeprazole (Prilosec, Prilosec OTC, Zegerid)
  • lansoprazole (Prevacid)
  • pantoprazole (Protonix)
  • rabeprazole (Aciphex)
  • esomeprazole (Nexium)
  • dexlansoprazole (Dexilant)

For items from the suggestions above, I would suggest going with handpicked suggestion list without firmicutes.

I would suggest an initial retest at 4 weeks or so, a full cycle of a PPI and atorvastatin, at the same time a cycle of alternating licorice and triphala. We want to see if this has caused a downward movement of the two species of concern.

I am a strong advocate on doing alternative pulses. It is what C. Jadin does for antibiotics (changing them every month) and I also have read several modelling studies that found rotation had better success than continuous. The english explanation is simple: for anything you may take — 90% of the bacteria may be killed and 10% survive (resistant). If you keep up with the same, then that 10% slowly regrows as resistant to whatever you are using. Changing between two things that are 90% effective (and different), then it becomes 99% killed and 1% survive.

As you have witnessed, 6 weeks with one item and then the resistors recovered your dysfunction, for another substance it lasted 10 weeks. We want to keep to 2 weeks on and then rotate.

I checked the parent taxa on these two, and I see  Carthamus tinctorius L (Safflower) inhibits one of them – so using safflower oil may help. There is no simple parent for the other.

As always, consult with your medical professional before implementing.

Unknown's avatar lassesen 10:18 am on July 11, 2021  

Spouse of 35 year CFS Patient

This is a two goal post. First, to see if literature indicating that healthy partners of microbiome dysfunction reflect their partner’s microbiome. Second, just a look at his microbiome and any possible concerns.

There is a very significant difference between the two in terms of diet:

  • Patient has been eating gluten free for years, supplements. etc
  • Husband eats gluten and dairy and some junk food. Minimal supplements.  High lipids, possibly genetic.

Similarity between CFS and Spouse

Picking the two closest samples by date

End Products Outlier – CFS 11 x Husband 0

KEGG Enzymes Outliers: Wife 639 – Husband: 30 Common: 1 (but opposite extremes)

Scanning Bacteria

Items that are common

Items with stark differences:

Goal #1 Bottom Line

Contrary to some studies, there appear to be little similarity between these people microbiomes. The reason is likely that the shifts due to diet are so very significant. It does raise the issue of using uncorrected ranges for diet types (junk food, organic, gluten free, vegetarian, pork eater, chicken eater [Yes, studies have shown difference between people that eat pork mainly instead of chicken!], etc.). Similarly age is a factor How the microbiome ages [2019]

Goal #2 Husband Health

As I know first hand, a wife usually cares more about a husband eating habits than he does himself. The risk of a kiss on the spouse cascading microbiome changes is a technical possibility.

First I went to Expert consensus

On the resulting screen, I checked all of the genus and species that were out of range and create a hand-picked selection and then got suggestions for them, shown below. Given that they are in the sixties, I note with interest that the first suggestion is the type of sugars found in mother’s milk, it almost seems to be a collection of restoring a younger microbiome suggestions.


Next I checked the Nat.Library of Medicine Explorer. To my delight, there were only two items above 50.

The items are:

  • hypertension (High Blood Pressure) — at 60%ile — still fine and not unexpected since hypertension is age related (likely connected to aging of the microbiome) see Hypertension – What we know [2019]
  • NonCeliac Gluten Sensitivity – This may be a false positive. Let me explained, since the wife is Gluten free, the husband will likely eat more gluten free food than most people. It you starve the gluten consuming bacteria… the shift may look like gluten sensitivity.

Going over to citizen science, there were no matches for symptoms. Again, compared to most people that have uploaded samples — no concerns.

Standard Kaltoft-Moldrup Suggestions

The suggestions are similar to those above. Many of the items are not unexpected for someone in the 60’s — Vitamin D. There is one significant change from above — resistant starch is a to Add, above, a common source of resistant starch (broad beans, black beans, etc) were on the to avoid list. Personally, I would go for eating the beans and other sources of resistant starch (see  Resistant Starch Content in Foods Commonly Consumed in the United States: A Narrative Review [2020]).

High lipids – any known microbiome component?

I do not have lipids in the database yet, so the reader should review the following studies.

Bottom Line

The husband seems fine and has no apparent health issues associated with the microbiome. There are suggestions above which may help prevent microbiome issues developing.