lassesen 7:48 pm on February 20, 2024
Tags: Chronic Fatigue Syndrome ( 4 ), chronic-pain ( 4 ), health, microbiome ( 5 ), wellness

ME/CFS Books and MDs

In the family dealing with ME/CFS we were very fortunate in working with now retired folks, (links to MEPedia pages on them). It was 25 years ago.

Byron Hyde MD, Canada
David Bell MD. US – Created the Bell disability scale for ME/CFS
David Berg — I hosted several online chats with him. He is now retired

Also we had significant interaction with

Cecile Jadin MD, South Africa – by email. Still practicing
Garth Nicolson Ph.D. US – I was on a TV News Program with him

Many support groups provide lists of local MDs that are sympathetic to ME/CFS patients. Typically, they will attempt to do symptom relief, not remediate the underlying cause or do not test outside of their local standards of practice (i.e. testing for associated viral infection, Lyme or rickettsia infections) – independent of insurance coverage or the patient being will to pay.

For example:

For Washington State, Best Chronic Fatigue Syndrome Doctors in Seattle, WA. The heathgrade site covers most US states.
- Note: the grades tend to indicate friendliness, not effectiveness of treatment.
Chronic fatigue – Internal medicine specialists – Edinburgh

The family was extremely fortunate to be covered by the old Microsoft Medical insurance that covered everything that the MD wanted with no deductibles; and we had a MD that was willing to learn and explore.

My recommendations for books are:

Understanding Myalgic Encephalomyelitis, Byron Hyde MD
The Clinical and Scientific Basis of Myalgic Encephalomyelitis – Edited by Byron Hyde, M.D.
Free Download eBook (PDF) This is a collection of a massive number of early research papers — most still relevant.
Other publications worth a review: https://www.nightingale.ca/publications

Other books can be found here:

Goodreads: Me Cfs Books, I would exclude books not written by a MD or published before 2020.

Note that the better books are often difficult or impossible to understand due to brain fog (and sometime lack of sufficient education is specific areas)

Determine a Model and if possible, see if there is evidence that the model works

I went with two models for ME/CFS: A hypercoagulation condition (David Berg) and an “occult rickettsia like infection” (Cecile Jadin); today we could call it “post Infection Fatigue Syndrome”. Both were testable (by lab or by reaction to low risk drugs, i.e. an antibiotic often prescribed for Acne) and actionable.

Today, my thinking is that the simplest model is a persistent microbiome dysfunction. This is very testable with direct retail tests; and actionable (using Microbiome Prescription). Often the antibiotics suggestions from Microbiome Prescription mirrors the Jadin approach. The treatment plan works for her models and my microbiome model!

Going with a hypothesis that is not both testable and actionable is not recommended. Take action today incase it works! Leave speculations to researchers trying to get grant money for their special interests.

For examples using my model: see Analysis Posts on Long COVID and ME/CFS

Symptoms and Bacteria appears to be strongly related

It is typical that Microbiome Prediction correctly predicts 80-100% of a person’s dominant symptoms from their microbiome. This implies that the bacteria shifts are causing the symptoms; thus correcting the bacteria shifts may reduce or eliminate symptoms.

A follow up ME/CFS Analysis

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

24 Years of ME/CFS with Mouth Microbiome

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

Comparison of Microbiome Samples

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

Criteria	Current Sample	Old Sample
Eubiosis Index	62.8% 🙂	59%
Lab Read Quality	4.3	8.4
Outside Range from JasonH	8	8
Outside Range from Medivere	20	20
Outside Range from Metagenomics	10	10
Outside Range from MyBioma	8	8
Outside Range from Nirvana/CosmosId	18	18
Outside Range from XenoGene	42	42
Outside Lab Range (+/- 1.96SD)	9 🙂	16
Outside Box-Plot-Whiskers	38 🙂	98
Outside Kaltoft-Moldrup	56 🙂	139
Bacteria Reported By Lab	494	752
Bacteria Over 90%ile	20 🙂	82
Bacteria Under 10%ile	66 🙂	232
Shannon Diversity Index	1.465	1.701
Simpson Diversity Index	0.035	0.028
Chao1 Index	7474	17093
Shannon Diversity Percentile	28.5	61.4
Simpson Diversity Percentile	30.2	21.5
Chao1 Percentile	28.9	87.7
Lab: BiomeSight
Pathogens	18 🙂	39
Condition Est. Over 90%ile	4	4
Kegg Compounds Low	969 :-)	1242
Kegg Compounds High	5 🙂	23
Kegg Enzymes Low	272	284
Kegg Enzymes High	17 🙂	75
P or P Chi2	.9999245	.999999999

Health Analysis Comparisons

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

	Current	Prior
General Health Predictors: Flagged Bacteria	8 🙂	10
Anti inflammatory Bacteria Score	14.4%ile 🙂	13.3 %ile
Lactate (controls many bad bacteria)	33.1 %ile 🙂	20 %ile
L-Lactic Acid (controls many bad bacteria)	47.1 %ile :-)	25.2 %ile
NADH (Typically low with ME/CFS)	26.5 %ile :-)	13.7 %ile
Hydrogen peroxide (controls many bad bacteria)	17.3 %ile 🙂	5.8 %ile
D-Lactic Acid (Associated with brain fog)	6.5 %ile 🙂	7.9 %ile
Potential Medical Conditions Detected	2 🙂	7
Bacteria deemed Unhealthy	7 🙂	22
Jason Hawrelak Criteria	56.4 %ile	75.8 %ile

Going Forward

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

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

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

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

And the to avoid list is more typical.

Let us go over to viewing the consensus for the latest microbiome sample to get some suggestions.

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

Foods
1. whole-grain barley
2. lauric acid(fatty acid in coconut oil,in palm kernel oil,)
3. Vegemite (with apologies — it’s an acquired taste)
Diet Style
- Only gluten-free was in positive range
- Avoids: animal-based diet, high beef diet, ketogenic diet
Herb or Spice
Prebiotics and similar
- Nothing in take
- Avoid: inulin (prebiotic),xylan (prebiotic),Psyllium (Plantago Ovata Husk) etc
Probiotics
1. lactobacillus kefiri (NOT KEFIR) — only available in Italy
2. lactobacillus casei (probiotics)
3. bifidobacterium breve (probiotic)
4. bifidobacterium longum bb536 (probiotics)
5. AVOIDS: lactobacillus plantarum (probiotics), lactobacillus rhamnosus (probiotics), bacillus licheniformis,(probiotics)
Sugar and similar- Effectively LOW SUGAR DIET
1. sucralose
2. chitosan,(sugar)
3. Avoid: stevia, saccharin, galactose (milk sugar), sugar, polydextrose
Vitamins, Minerals and similar
- The typical ME/CFS ones: Vitamin B1, B3, B6, B7, B9, B12 and Vitamin C
Amino Acid and similar
1. melatonin supplement (it helps with sleep but also can improve the microbiome)
2. Taxifolin
3. Avoid most of the other ones
Antibiotics (limited to those used for ME/CFS)
1. metronidazole (antibiotic)s[CFS]
  - “Metronidazole/Flagyl is reported to have 75% of CFS patients improving according to some surveys.”
2. amoxicillin (antibiotic)s[CFS]
3. dapsone (antibiotic)[CFS]
4. lymecycline (antibiotic)[CFS]
5. azithromycin,(antibiotic)s[CFS]

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

Postscript – and Reminder

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

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

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

lassesen 6:08 pm on January 31, 2024
Tags: food ( 2 ), gut-health ( 6 ), health, mushrooms, nutrition ( 6 )

Beta-Glucan and ME/CFS: The Microbiome Fixer

A reader that does microbiome analysis of her ME/CFS daughter ‘s microbiome using Microbiome Prescription expert system sent me this note with some literature.

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

β-Glucan is a nonstarch polysaccharide having documented health benefits and industrial applications. It can be extracted from various sources, including cereals, bacteria, molds, and fungi. The chemical nature of extracted β-glucan from these sources differs slightly. This variation in chemistry defines its industrial uses and health benefits.
Biopolymers for Food Design, 2018

Literature

There is not much literature available for ME/CFS.

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

Some literature for Autism

Many Sources of Beta Glucan

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

“The primary sources of food β-glucan for humans are cereals (especially oats and barley), fungi, algae, and yeast ” [2023] A table from this article is below

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

Bottom Line

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

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

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

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

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

Among those, mushrooms feature a particularly high level, so it’s no exaggeration when we say “for beta glucans, look to mushrooms!” The amounts of beta glucans found per 100 g of raw mushroom include 2.3 g (maitake), 2.0 g (bunapi), 1.9 g (eryngii), 1.8 g (bunashimeji) and 1.5 g (shimofuri hiratake) (Hokuto data).
https://www.hokto-kinoko.co.jp/lang/en/kouka/jiten/jiten06/

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

Celiac and Gluten Sensitive Issue

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

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

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

lassesen 7:40 am on December 15, 2023
Tags: bacteria ( 2 ), gut-health ( 6 ), health, microbiome ( 5 ), Probiotics ( 5 )

Tool for getting suggestions for your specific ME/CFS Symptoms

After I posted List of Bacteria significant for ME/CFS from the shared samples uploaded to Microbiome Prescription, several readers asked “How do I use this”. This took me a few days to come up with, code and implement an answer.

I wanted this to go beyond just ME/CFS because there is a huge variety of symptoms and co-morbidity seen with ME/CFS. After testing and tuning the algorithm, I am pleased with the current results.

The process is show below.

The Steps

First get a suitable microbiome test done (See this list of supported tests)
Transfer or upload your results to Microbiome Prescription
An email will be sent to you to login
Login in.
Enter your symptoms

Return to “My Profile”
A new button will appear

Clicking it will move to the page below. YOU MAY FIND THAT IT TAKES UP TO A MINUTE (We are doing a massive number of computation)

This will show a tree of the bacteria involved. The Species are under the genus they below to. In the example below we see the ENTIRE phylum that Bifidobacterium is in are low (none found) of 9 species whose presence would likely reduce your symptoms.

Elsewhere you may see highs with certain bacteria species desired to higher. Often the symptom key is at the species level.

At the bottom you will see a button to get suggestions

The next page shows the symptoms being targeted to and choices of what you want to consider.

Make any changes desired and click show suggestions

REMEMBER these are suggestions for ONE person using their Symptoms and their microbiome profile. It is intended for them only. Your own suggestions may be very different with many items exchanged between ADD and REMOVE.

Technical Methodology Details are described here Technical Note: Prevalence, Average and Not Reported.

Post-Script

This approach sidestep the proforma process often drilled into researchers (you must have a healthy control group and a verified, criteria matching target population). I kept to rigorous statistical analysis while ignoring these constraints which are philosophical in nature. We used the available data and set our significance level to P < 0.005; instead of the typical research level of P < 0.05. In other words, we are 10 times more certain about our results.

lassesen 6:50 am on December 12, 2023
Tags: agriculture, antibiotic-resistance, bacteria ( 2 ), benefit, food-microbiology, food-science, health

List of Bacteria significant for ME/CFS

This is from donated samples on microbiome prescription that have been annotated with diagnosis or symptoms. See this post for how these were calculated. All items are with P < 0.005 (10 times more significant than many published studies).

Bacteria Name	Rank	Shift
Deferribacteres	phylum	Seen too often
Thermodesulfobacteria	phylum	Seen too often
Hyphomicrobium aestuarii	species	Seen too often
Rhizobiaceae	family	Seen too often
Gluconobacter	genus	Seen too often
Erwinia oleae	species	Not seen as often as expected
Actinobacillus porcinus	species	Not seen as often as expected
Prevotella micans	species	Not seen as often as expected
Prevotella oulorum	species	Not seen as often as expected
Prevotella shahii	species	Not seen as often as expected
Thiocapsa	genus	Seen too often
Pediococcus argentinicus	species	Seen too often
Peptostreptococcus stomatis	species	Seen too often
Streptococcus mutans	species	Seen too often
Sporosarcina pasteurii	species	Seen too often
Lactobacillus acidophilus	species	Seen too often
Erysipelothrix inopinata	species	Seen too often
Bifidobacterium angulatum	species	Not seen as often as expected
Bifidobacterium catenulatum	species	Not seen as often as expected
Bifidobacterium ruminantium	species	Seen too often
Bifidobacterium catenulatum subsp. kashiwanohense	subspecies	Not seen as often as expected
Corynebacterium glucuronolyticum	species	Seen too often
Haploplasma	genus	Seen too often
Acholeplasma hippikon	species	Seen too often
Propionigenium modestum	species	Seen too often
Levilactobacillus	genus	Seen too often
Pediococcus	genus	Seen too often
Roseospira	genus	Seen too often
Caloramator indicus	species	Seen too often
Caloramator viterbiensis	species	Seen too often
Hyphomicrobium	genus	Seen too often
Prosthecobacter fluviatilis	species	Seen too often
Tetragenococcus halophilus	species	Not seen as often as expected
Acidaminobacter hydrogenoformans	species	Seen too often
Thermodesulfobacteriales	order	Seen too often
Deferribacterales	order	Seen too often
Heliorestis baculata	species	Seen too often
Parapedobacter	genus	Seen too often
Mogibacterium vescum	species	Seen too often
Collinsella tanakaei	species	Seen too often
Absiella	genus	Seen too often
Pseudomonas viridiflava	species	Not seen as often as expected
Finegoldia magna	species	Seen too often
Sphingobium abikonense	species	Seen too often
Anaerococcus tetradius	species	Seen too often
Cetobacterium ceti	species	Seen too often
Peptostreptococcus	genus	Seen too often
Thermodesulfobacteriaceae	family	Seen too often
Thermodesulfatator	genus	Seen too often
Deferribacteraceae	family	Seen too often
Deferribacteres	class	Seen too often
Thermodesulfobacteria	class	Seen too often
Cetobacterium	genus	Seen too often
Propionigenium	genus	Seen too often
Prosthecobacter	genus	Seen too often
Roseobacteraceae Pujalte et al. 2014	family	Seen too often
Desulfonatronovibrio	genus	Seen too often
Thermodesulfatator atlanticus	species	Seen too often
Aminiphilus circumscriptus	species	Seen too often
Olivibacter terrae	species	Seen too often
Parapedobacter koreensis	species	Seen too often
Acidaminobacter	genus	Seen too often
Bifidobacterium kashiwanohense PV20-2	strain	Not seen as often as expected
Aminiphilus	genus	Seen too often
Haploplasma cavigenitalium	species	Seen too often
Prevotella copri	species	low in ME/CFS
Prevotella	genus	low in ME/CFS
Sporolactobacillaceae	family	low in ME/CFS
Sporolactobacillus putidus	species	low in ME/CFS
Sporolactobacillus	genus	low in ME/CFS
Prevotellaceae	family	low in ME/CFS
Firmicutes	phylum	high in ME/CFS
Blautia	genus	high in ME/CFS
Cetobacterium ceti	species	high in ME/CFS
Cetobacterium	genus	high in ME/CFS
Bifidobacterium tsurumiense	species	low in ME/CFS
Propionigenium	genus	high in ME/CFS
Propionigenium modestum	species	high in ME/CFS
Phocaeicola plebeius	species	low in ME/CFS
Eubacteriales	order	high in ME/CFS
Clostridia	class	high in ME/CFS
Catonella morbi	species	high in ME/CFS
Catonella	genus	high in ME/CFS
Bifidobacterium gallicum	species	low in ME/CFS
Bacteroides rodentium	species	high in ME/CFS
Cerasicoccus	genus	low in ME/CFS
Gallionellaceae	family	low in ME/CFS
Gallionella	genus	low in ME/CFS
Aggregatibacter aphrophilus	species	low in ME/CFS
Cerasicoccus arenae	species	low in ME/CFS
Filifactor alocis	species	low in ME/CFS
Desulfotomaculum defluvii	species	high in ME/CFS
Collinsella intestinalis	species	high in ME/CFS
Anaerolineae	class	high in ME/CFS
Bifidobacterium bifidum	species	low in ME/CFS
Clostridium frigoris	species	low in ME/CFS
Desulfotomaculum	genus	high in ME/CFS
Hahella	genus	low in ME/CFS
Desulfovibrio	genus	low in ME/CFS
Megamonas	genus	low in ME/CFS
Lachnospiraceae	family	high in ME/CFS
Bifidobacterium angulatum	species	low in ME/CFS
Acinetobacter antiviralis	species	low in ME/CFS
Syntrophomonas sapovorans	species	low in ME/CFS
Pseudomonas viridiflava	species	low in ME/CFS
Chloroflexi	phylum	high in ME/CFS
Puniceicoccaceae	family	low in ME/CFS
Oribacterium	genus	low in ME/CFS
Geobacter	genus	high in ME/CFS
Geobacteraceae	family	high in ME/CFS
Terrabacteria group	clade	high in ME/CFS
Campylobacter concisus	species	low in ME/CFS
Fusobacteriaceae	family	high in ME/CFS
Opitutae	class	low in ME/CFS
Fusobacteriales	order	high in ME/CFS
Fusobacteriia	class	high in ME/CFS
Fusobacteria	phylum	high in ME/CFS
Emticicia oligotrophica	species	low in ME/CFS
Emticicia	genus	low in ME/CFS
Megamonas funiformis	species	low in ME/CFS
Puniceicoccales	order	low in ME/CFS
Thiorhodococcus	genus	low in ME/CFS
Granulicella	genus	low in ME/CFS
Allohahella	genus	low in ME/CFS
Allohahella antarctica	species	low in ME/CFS
Spirosomaceae	family	low in ME/CFS
Gallionella ferruginea	species	low in ME/CFS
Oribacterium sinus	species	low in ME/CFS
Granulicella tundricola	species	low in ME/CFS
Prevotella paludivivens	species	low in ME/CFS
Legionellales	order	high in ME/CFS
Caldilinea tarbellica	species	high in ME/CFS
Caldilineales	order	high in ME/CFS
Caldilineaceae	family	high in ME/CFS
Caldilinea	genus	high in ME/CFS
Caldilineae	class	high in ME/CFS
Moorella	genus	low in ME/CFS
Cytophagaceae	family	low in ME/CFS
Legionellaceae	family	high in ME/CFS
Anaeroplasmataceae	family	low in ME/CFS
Anaeroplasma	genus	low in ME/CFS
Anaeroplasmatales	order	low in ME/CFS

CFS Remission

Striving for true remission of CFS, chronic Lyme, FM, IBS etc

Tag Archives: health