lassesen 7:40 am on December 15, 2023
Tags: bacteria ( 2 ), gut-health ( 3 ), health ( 9 ), microbiome ( 2 ), Probiotics ( 2 )

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 7:45 pm on December 14, 2023

Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Conference Videos

The following are a selection of informative videos to get better informed

Patient Movies

Chronic Fatigue Syndrome Advisory Committee

lassesen 7:22 pm on December 14, 2023

NIH Long COVID 19 Videos

The following are videos of talks on ME/CFS siblings: Long Covid

COVID Comics: Decentering White Narratives in Graphic Medicine During the COVID-19 Pandemic

Neurological Complications and Sequelae of COVID-19

NIH-FDA COVID-19 SIG: NIH RECOVER Initiative: Early Findings and Other Emerging Long COVID Science

Contemporary Clinical Medicine: Great Teachers: The COVID-19 Pandemic: Looking Back and Looking Forward

lassesen 6:50 am on December 12, 2023
Tags: agriculture, antibiotic-resistance, bacteria ( 2 ), benefit, food-microbiology, food-science, health ( 9 )

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

lassesen 9:27 am on December 10, 2023
Tags: CFS ( 6 ), Chronic Fatigue Syndrome ( 4 ), chronic-fatigue ( 2 ), chronic-illness ( 4 ), fatigue, health ( 9 ), long-covid ( 2 )

Review of Recent ME/CFS Research, Dec 2023

The vast majority of papers were repeats of prior research (earlier research was in 1992 for some topics). The following were more interesting:

Understanding, diagnosing, and treating Myalgic encephalomyelitis/chronic fatigue syndrome – State of the art: Report of the 2nd international meeting at the Charité Fatigue Center [2023]
An Explainable Artificial Intelligence Model Proposed for the Prediction of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome and the Identification of Distinctive Metabolites [2023]
- “The metabolomics of C-glycosyltryptophan, oleoylcholine, cortisone, and 3-hydroxydecanoate were determined to be crucial for ME/CFS diagnosis.”
- The items identified are associated with other conditions too (see links). Prediction is not treatment.
DNA Methylation Changes in Blood Cells of Fibromyalgia and Chronic Fatigue Syndrome Patients [2023]
- “Methylomes of the blood cells of patients with FM and CFS in three independent studies have shown methylation changes that appear to be implicated in the pathogenesis of these syndromes.”
- Well known, see MEPedia, treatment based on this hypothesis has not been effective for most
Myalgic encephalomyelitis/chronic fatigue syndrome and fibromyalgia are indistinguishable by their cerebrospinal fluid proteomes [2023]
People with Long COVID and Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Exhibit Similarly Impaired Vascular Function [2023]
- ” both long COVID and ME/CFS patients exhibit similarly impaired endothelial function, indicating potential vascular involvement in the pathogenesis of these post-viral illnesses. The significant reduction in flow-mediated dilation values suggests an increased cardiovascular risk”
Increased gut permeability and bacterial translocation are associated with fibromyalgia and myalgic encephalomyelitis/chronic fatigue syndrome: implications for disease-related biomarker discovery [2023]
- “Biomarkers of intestinal barrier function and inflammation were associated with autonomic dysfunction assessed by COMPASS-31 scores in FM and ME/CFS respectively. Anti-β-LGB antibodies, ZO-1, LPS, and sCD14 may be putative predictors of intestinal barrier dysfunction in these cohorts.”
- Well known from prior studies, causality not explored.
Brain-regional characteristics and neuroinflammation in ME/CFS patients from neuroimaging: A systematic review and meta-analysis [2023]
- “Regional alterations were most frequently identified in the cerebral cortex, with a notable focus on the frontal cortex. However, our meta-analysis data revealed a significant hypoactivity in the insular and thalamic regions, contrary to observed frequencies. These abnormalities, occurring in pivotal network hubs bridging reason and emotion, disrupt connections with the limbic system, contributing to the hallmark symptoms of ME/CFS.”
- This is a repeat of prior research going back to 1992
Many studies with “Some patients …” with specific abnormalities
A Quick and Practical Approach to Secure a Chronic Fatigue Syndrome Diagnosis: The Novel Functional Limitation Index [2023]
- “The Functional Limitation Index (FLI) could provide an easy and accurate diagnosis of this condition in both genders in a one-day assessment.”
Effects of traditional Chinese mind-body exercises for patients with chronic fatigue syndrome: A systematic review and meta-analysis[2023]
- “In patients with CFS, TCME probably reduces post-intervention fatigue, depression, and anxiety and may improve sleep quality and mental function compared with passive control, but has limited long-term effects. “
Frontiers in chronic fatigue syndrome research: An analysis of the top 100 most influential articles in the field [2023]
- “The prospective research directions in this field include the search for biological markers, with a particular focus on immunology; the advancement of diagnostic techniques; the screening of risk genes associated with CFS; and the conduct of epidemiological investigations.”
- So treatment does not seem to be an active dimension.
Onset Factors:
- Increased risk of chronic fatigue syndrome following infection: a 17-year population-based cohort study [2023]
  - “infection with common pathogens, including bacteria, viruses, is associated with an increased risk of developing CFS.”
  - This matches my model that ME/CFS is a post-infection persistent microbiome dysfunction.
- Genetic risk factors for severe and fatigue dominant long COVID and commonalities with ME/CFS identified by combinatorial analysis [2023]
  - Genetics have long been identified as a factor
- Typing myalgic encephalomyelitis by infection at onset: A DecodeME study [2023]
- There is an overlap between long covid and ME/CFS.[2023]
Is there a role for traditional and complementary medicines in managing chronic fatigue? a systematic review of randomized controlled trials [2023]
- “recommendations of T&CMs in treating CFS remain inconclusive. To develop better quality evidence about T&CMs for CFS, future studies should employ more objective diagnosis standards and outcome measurements, larger sample size, and better bias control, and ensure the compliance with the corresponding reporting guidelines”
- I have seen this constantly in studies: too small sample size, poor statistical analysis, spinning results to “find something”.
Treatment:
- Successful treatment of myalgic encephalomyelitis/chronic fatigue syndrome using hydrogen gas: four case reports [2023]
  - “In conclusion, since this was a case study based on self-assessments by a small number of patients and not a clinical study”
  - Hydrogen is a gas used by bacteria (illustrated by SIBO testing for Hydrogen), this approach is likely to influence the microbiome. Looking at the data on Microbiome Prescription, we found that ME/CFS patients microbiome has a significantly higher consumption of Hydrogen — thus the extra hydrogen may alter the microbiome.
- B-vitamins, related vitamers, and metabolites in patients with quiescent inflammatory bowel disease and chronic fatigue treated with high dose oral thiamine [2023]
  - Glucan (or foods containing it: Barley etc) is a very frequent suggestion from Microbiome Prescription when a ME/CFS microbiome was processed through microbiome prescription.
- Repetitive transcranial magnetic stimulation ameliorates symptoms in patients with myalgic encephalomyelitis (chronic fatigue syndrome) [2023]
  - Some symptoms improved: “orthostatic intolerance with the inability to complete the 10-min standing test was resolved in 10 (83%) out of 12 patients, and disequilibrium was resolved in 15 (88%) out of 17 patients. “
- Yeast Beta-Glucan Supplementation with Multivitamins Attenuates Cognitive Impairments in Individuals with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: A Randomized, Double-Blind, Placebo-Controlled Trial [2023]
  - Beta-Glucan (or foods containing it: Barley etc) is a very frequent suggestion from Microbiome Prescription when a ME/CFS microbiome was processed through microbiome prescription.
  - “significantly improved cognitive fatigue (assessed with FIS-40 scores) after the 36-week treatment

CFS Remission

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

Recent Updates Page 2

Tool for getting suggestions for your specific ME/CFS Symptoms

The Steps

Post-Script

Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Conference Videos

Patient Movies

Chronic Fatigue Syndrome Advisory Committee

NIH Long COVID 19 Videos

List of Bacteria significant for ME/CFS

Review of Recent ME/CFS Research, Dec 2023

The Steps

Post-Script

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Patient Movies

Chronic Fatigue Syndrome Advisory Committee

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