Follow up to: A German CFS Patient Experience and Analysis

The patient has done another sample and this continues the analysis. The original post, A German CFS Patient Experience and Analysis from July 2021. I am always interested in seeing changes that occur from the AI suggestions, they worked for me –I am as interested in them not working (to motivate improving algorithms).

What has changed?

There are a set of automatic comparison tools between samples, so I will check those first

I went to compare taxonomy outliers for the two samples and found just two items were on both. There was a lot of changes. We can ignore blues with no data besides – they were all likely what I term transitory bacteria that comes and goes. What we are interested

The two items of focus are VERY high on both:

Other component comparisons:

  • End Product — most were unchanged except for Polyhydroxyalkanoic acids which jumped from none to 98%ile
  • KEGG Bacteria Products nothing in common, on first sample we had only low values at risk, on latest sample only high values at risk
  • KEGG Enzymes — the same thing, earlier sample has all risks being low samples, latest high values
  • KEGG Modules — earlier sample had no risk items, latest had one high value
  • Medical Condition (PubMed) — nothing for either sample

The overall impression is that things have changed significantly. This does not say that the person is better — only that the suggestions have changed the microbiome

Non-Automated Comparisons

Next I will look at various aspects and do side by side comparisons. First, using Dr. Jason Hawrelak Criteria, shown below. The worst shift was for Blautia, the best shifts was for Roseburia and Faecalibacterium prausnitzii

LatestSampleEarlier Sample
TaxonomyRankLowHighYour ValueStatusYour ValueStatus
Bacteroidiaclass03538.369Not Ideal33.945Ideal
Akkermansiagenus130.21Not Ideal0.017Not Ideal
Bacteroidesgenus02025.986Not Ideal25.266Not Ideal
Bifidobacteriumgenus2.550.03Not Ideal0.021Not Ideal
Blautiagenus51011.557Not Ideal6.174Ideal
Desulfovibriogenus00.250.062Ideal0.091Ideal
Eubacteriumgenus0150.008Ideal0.004Ideal
Lactobacillusgenus0.0110.012Ideal0.017Ideal
Methanobrevibactergenus0.00010.020Not Ideal0.052Not Ideal
Roseburiagenus5105.166Ideal0.624Not Ideal
Ruminococcusgenus0152.848Ideal3.792Ideal
Proteobacteriaphylum0411.225Not Ideal5.753Not Ideal
Bilophila wadsworthiaspecies00.250.598Not Ideal0.848Not Ideal
Escherichia colispecies00.010Ideal0.022Not Ideal
Faecalibacterium prausnitziispecies101510.612Ideal3.415Not Ideal
Three improved, Two deteriorated

Health Status changes were a toss up, but appears marginally better

  • Latest: 0 Healthy, 4 unhealthy
  • Earlier: 2 Healthy, 6 unhealthy

KEGG Suggested Probiotics

  • Earlier Sample had 11 probiotics listed with a maximum weight of 12 (most of the time I see much higher weights indicating greater dysfunction)
  • Later Sample had 0 probiotics – this is actually a rare occurrence which hints at a better balance microbiome

KEGG Suggested Supplements

  • Earlier sample has 3 items suggested (using default percentile)
  • Later sample has 0 items suggested (using default percentile)

Pub Med CFS Profile

  • Earlier sample had 5 low matches, 5 high matches
  • Later sample has just 4 high matches

Citizen Science Models

  • Early Sample: Total Matching Bacteria :26. Very Strong: 15, Strong: 8, Weak: 2, Very Weak: 1
  • Later Sample: Total Matching Bacteria :24. Very Strong: 19, Strong: 4, Weak: 1, Very Weak: 0
  • Less matching bacteria (means some have disappeared), while strong/very strong are the same, the weak association have dropped

From looking at all of the available objective measures:

  • The microbiome has changed (our primary goal)
  • Many measurements show indicate that the microbiome is moving towards normal, none has a suggestion of things getting worst.

Remember our goal is not to attempt a one-step cure

Our earlier post used this diagram, we appear to have successfully moved along the path to recovery. We need to see what our next step is.

Symptoms Forecasts To Reported Symptoms

This reader was a good user and entered their symptoms – we have a 80% match rate. What is interesting is that one of the items not checked was a Keto Diet — this is interesting because a recent post dealt with a Keto diet resulting in Chronic Fatigue Like symptoms, with “Keto Flu” is some studies. A Keto diet is DEFINITELY NOT A SUGGESTION for this person, it will likely make things worst.

Updated Suggestions

For the earlier post, the consensus reports were not available. My intent is to run each of the matched predicted symptoms, the PubMed profile for ME/CFS and Citizen Science for ME/CFS – a total of 18 sets of suggestions will be merged. There are two ways of doing this:

  • Only the Auto Checked (which picks a few best items)
  • Auto Checked plus suggested one (marked with a light bulb).

This first pass is only with auto checked items (the most conservative approach) The bacteria selected are shown below, while there was some duplicates between symptoms, there was significant independence:

  • Acidobacteria Too Low
  • Anaerovibrio Too High
  • Anaerovibrio lipolyticus Too High
  • Bacteroides cellulosilyticus Too High
  • Bacteroides finegoldii Too High
  • Bacteroides salanitronis Too High
  • Bifidobacteriaceae Too Low
  • Bifidobacteriales Too Low
  • Bilophila Too High
  • Bilophila wadsworthia Too High
  • Candidatus Phytoplasma Too High
  • Clostridium malenominatum Too Low
  • Deinococcaceae Too High
  • Deinococcales Too High
  • Deinococcus Too High
  • Lelliottia Too Low
  • Lelliottia amnigena Too Low
  • Mitsuokella Too High
  • Oscillospira Too High
  • Parabacteroides johnsonii Too High
  • Rhodocyclaceae Too Low
  • Sphingobacterium bambusae Too High
  • Sutterella stercoricanis Too Low

I noted that many are atypical bacteria that I do not see usually in pub med studies.

Safest Takes is full of items that I often have seen on my own (and other ME/CFS results).

On the Safer Take, we find a regular pattern of 3 takes and 1 oppose.

Whey has historically been helpful to a subset of ME/CFS patients

The avoid list is relatively short and most are from a single suggestion (which suggests that it may be ignored). high red meat is the greatest avoid, with saturated fats variation being right behind.

Done with Secondary Suggestions

Since I have just implemented this feature, I am curious about it’s impact. The number of bacteria almost doubled with a variety. A lot of bacteria appeared multiple time.

  • Absiella Too Low
  • Acidobacteria Too Low
  • Acidobacteriaceae Too Low
  • Acidobacteriales Too Low
  • Acidobacteriia Too Low
  • Adlercreutzia Too Low
  • Adlercreutzia equolifaciens Too Low
  • Anaerovibrio Too High
  • Anaerovibrio Too High
  • Anaerovibrio lipolyticus Too High
  • Bacteroides cellulosilyticus Too High
  • Bacteroides finegoldii Too High
  • Bacteroides salanitronis Too High
  • Bacteroides vulgatus Too High
  • Bifidobacteriales Too Low
  • Bifidobacterium Too Low
  • Bilophila Too High
  • Bilophila wadsworthia Too High
  • Blautia hansenii Too High
  • Butyricimonas Too High
  • Candidatus Phytoplasma Too High
  • Clostridium malenominatum Too Low
  • Collinsella intestinalis Too Low
  • Coriobacteriia Too Low
  • Deinococcaceae Too High
  • Deinococcales Too High
  • Deinococcus Too High
  • Eubacterium dolichum Too Low
  • Eubacterium oxidoreducens Too Low
  • Finegoldia magna Too Low
  • Hymenobacter Too High
  • Lelliottia Too Low
  • Lelliottia amnigena Too Low
  • Leptospira Too Low
  • Leptospiraceae Too Low
  • Leptospirales Too Low
  • Megasphaera Too Low
  • Mitsuokella Too High
  • Oscillospira Too High
  • Parabacteroides johnsonii Too High
  • Peptococcaceae Too High
  • Porphyromonas Too High
  • Pseudanabaenaceae Too High
  • Pseudonocardiaceae Too Low
  • Rhodocyclaceae Too Low
  • Rickettsiaceae Too Low
  • Rickettsieae Too Low
  • Selenomonas artemidis Too Low
  • Slackia Too High
  • Sphingobacterium bambusae Too High
  • Streptococcus thermophilus Too High
  • Sutterella stercoricanis Too Low
  • Synechococcaceae Too High
  • Synechococcales Too High
  • Veillonellaceae Too High
  • Veillonellales Too High

As expected, the suggests are similar

The risk items are similar with saturated fats dominating

Bottom Line

Earlier today, I updated this post Ketogenic diet did not help a health issue, it created one where the person ended up with a ME/CFS like scenario. Many of these suggestions were very similar. The main items suggested are:

  • Fibre
    • Inulin like items (chicory, Jerusalem artichoke, inulin)
    • Fruit and legume fiber
    • Barley, Oats
  • Cacao (usually I suggest working up to 85% cacao or higher chocolate bars)
  • Apple
  • clostridium butyricum (probiotics)
  • rosmarinus officinalis (rosemary)
  • B Vitamins (classic CFS MD recommended supplements)
  • Vitamin D
  • Soy
  • Human milk oligosaccharides (prebiotic, Holigos, Stachyose)

In general, I favor “intact” fiber and herbs. I have seen several studies that the intact had a greater impact than the extract. Watch out for saturated fats — for example Pork is on the to avoid list

The excel file download (CSV) had only 291 items, less than other samples that I processed. I attached it as an example.

My usual advice is to take two weeks to sort out (and in some cases slowly move up to) the suggestions that are picked. It is helpful to check my Supplement Dosage page. That page is not numbers that I picked out of the air, but dosages used in various clinical trials (thus the dosages are likely safe, and more important, are sufficient to cause a change). Then at least 4 weeks for the microbiome to stabilize, then retest to find out the new status quo that will need to be adjusted.

For myself, I did notice a pendulum swing in my series of samples — an item was a take, then the next sample it was an avoid, then it became a take again and stayed as a take. The path is not always straight!

Nattokinase – Update for ME/CFS and Long COVID

This post was kick-started by a post to a study on a Spanish ME/CFS site shown below

This is extra relevant because Nattokinase is one of my personal favorite tools for dealing with hypo-perfusion (low oxygen to the brain), something that I have experienced during ME/CFS flares. It is also the subject of my last post. I have cited Nattokinase in prior posts, some 9 years ago, and it seems time to update what we know.

So what more has been added to our knowledge base. Nattokinase comes from Bacillus Subtilis Natto. This strain has been traditionally used in a Japanese dessert called “Natto” which you can buy is some Asian shops – it is a bit of an acquired taste (but I like it)

What Natto looks like in stores. This is a living bacteria.

Putting it together

Nattokinase seems to treat many conditions associated with western diet. The next question is simple, what are dosages used in studies?

Usually 100 mg = 2000 FU on most commercial products, so the range in trials is 1-7 100mg capsules per day.

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.

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.

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…..