Suggest sequence and choice of Antibiotics if doing Jadin’s Protocol

A reader saw the new cross-validated suggestions for ME/CFS using his own microbiome. Cross validated means the item must meet two criteria:

  • They are computed by the expert system to correct bacteria shifts
  • They have been reported in studies to help people with ME/CFS (at least a study subset)

If interested, his cross validated suggestions are here.

He is exploring trying the Jadin Protocol (1 week of one antibiotic, 3 weeks off, then repeat for a different antibiotics). For more information see: Video Presentation of Dr. Jadin’s Current Protocol for ME/CFS, Q-Fever, Chronic Lyme and related conditions

He wanted to know which has the least risk — well, I have grown to trust Perplexity.Ai to give good answers (with the sources of information linked). The FULL ANSWER IS HERE (with References).

The preferences are with 1 being the lowest risk.

  1. Minocycline and 2. Doxycycline: These tetracyclines appear to have the lowest risk. The search results indicate that tetracyclines, particularly minocycline, have a low risk of adverse reactions. Minocycline had an adjusted odds ratio of 0.79 for community-acquired Clostridioides difficile infection (CA-CDI), while doxycycline had an adjusted odds ratio of 0.96, both lower than most other antibiotics.
  2. Neomycin: As an aminoglycoside, neomycin is likely to have a relatively low risk. The search results mention that aminoglycosides were classified among the safest antibiotics in terms of anaphylaxis risk.
  3. Metronidazole: While not specifically mentioned in the search results, metronidazole is generally considered to have a moderate risk profile.
  4. Azithromycin: This macrolide antibiotic had an adjusted odds ratio of 1.31 for CA-CDI, higher than tetracyclines but lower than other antibiotics on this list.
  5. Erythromycin: Another macrolide, erythromycin had a higher adjusted odds ratio of 1.53 for CA-CDI compared to azithromycin.
  6. Vancomycin: While not directly compared in the search results, vancomycin is known to have potential for significant adverse reactions, including nephrotoxicity and ototoxicity.
  7. Ampicillin: This penicillin antibiotic had one of the highest adjusted odds ratios for CA-CDI at 2.6, indicating a higher risk of adverse reactions.

As a FYI, a few decades ago, I persuaded my MD to give me Minocycline and Doxycycline by saying “Look you have no problem prescribing those to a teenager for acne — I have ME/CFS and on disability… are you saying that a teenager’s acne impacting their ability to get dates is more critical than ME/CFS? and being on disability?” I walked out with the prescriptions…..

New Suggestions Report in Progress

This uses the consensus model and does the following:

  • Identifies the bacteria shifts reported in the literature that are seen in your microbiome sample
  • Computes substances that should improve those shifts
  • FILTER these substances using the literature of what helps the condition.

So, you have a list of things to fix the microbiome that are also known to help the condition. Many studies find that only a portion of people are helped. Our hypothesis is that the microbiome is a key factor here.

Last we give the top other suggestions (in general, they have never been tested in a clinical study — and thus we are depending on the microbiome impact)

After this, we give a list of studies used to generate the report. This should buy creditability with MD for what is being done as well as educate them.

This new suggestions report also handles multiple conditions. The example below is for someone that has both Autism and ME/CFS. It gives a good illustration of the new report intent.

The list of items reported to help ME/CFS is here with the studies the items are cited in.


This report is for Private@Annon.comand uses their reported medical conditions, microbiome sample and a fuzzy logic expert system to compute recommendations

The reported condition(s) are

  1. Autism –
    Common Advice:
    1. Omega-3 Fatty Acids: Some studies have explored omega-3 supplements (particularly those containing EPA and DHA) due to their potential neuroprotective and anti-inflammatory properties. While research results have been mixed, some parents or caregivers of individuals with ASD might consider omega-3 supplements based on the belief that they could positively impact cognitive and behavioral functions.
    2. Probiotics: The gut-brain connection has sparked interest in the potential role of probiotics in influencing behavior and cognition. Some studies suggest that gut health might affect certain aspects of behavior in individuals with ASD. However, the use of probiotics for managing autism symptoms lacks robust scientific evidence, and their effectiveness remains unclear.
    3. Vitamin D: Low vitamin D levels have been observed in some individuals with ASD. While research is ongoing, maintaining adequate vitamin D levels is considered important for overall health. Some parents may opt for vitamin D supplements under the guidance of a healthcare professional.
    4. Multivitamins and Minerals: Individuals with ASD might have specific dietary habits that could lead to deficiencies in certain vitamins or minerals. Ensuring a balanced diet or supplementing with multivitamins and minerals under the guidance of a healthcare provider might be considered to address potential deficiencies.
  2. Chronic Fatigue Syndrome – CFS,ME,Myalgic encephalomyelitis
    Common Advice:
    1. Coenzyme Q10 (CoQ10): Some studies have suggested that CoQ10 supplementation might have potential benefits in reducing fatigue and improving energy levels in individuals with CFS. However, more research is needed to establish its effectiveness for CFS specifically.
    2. Omega-3 Fatty Acids: Omega-3 supplements containing EPA and DHA have anti-inflammatory properties and may support overall health. Some individuals with CFS might consider omega-3 supplementation for potential benefits, although evidence supporting their use specifically for CFS is limited.
    3. Probiotics: The role of probiotics in managing CFS symptoms is an area of ongoing research. Some studies suggest that probiotics might impact gut health and the immune system, which could potentially affect symptoms in some individuals with CFS. However, specific probiotic strains, dosages, and their efficacy for CFS require further investigation.
    4. Vitamins and Minerals: Nutritional deficiencies are common in individuals with CFS, possibly due to poor dietary intake or other factors. Some individuals might have deficiencies in vitamins (such as vitamin D, B vitamins) or minerals (like magnesium or iron). Supplements might be recommended to address identified deficiencies.

Significant Bacteria Shifts

Based on the existing literature on the US National Library of Medicine and this microbiome sample, we have the following matches of bacteria shifts. There is a growing body of literature finding that the effectiveness of interventions depends on the existing microbiome. We filter by suggested interventions and this person’s specific microbiome to produce this “double validated” list..


Acidobacteriota – phylum : High 13 15
Actinomycetota – phylum : Low 18
Akkermansia – genus : High 10 22 25
Akkermansia muciniphila – species : High 6
Alcaligenaceae – family : High 25
Bacteroides ovatus – species : High 17
Bacteroides uniformis – species : High 17
Citrobacter – genus : High 20
Coprococcus – genus : Low 10
Dorea – genus : Low 1 8 24 25
Eggerthella – genus : Low 5

Faecalibacterium – genus : High 9 21 25
Oscillospiraceae – family : High 23 25
Phascolarctobacterium – genus : Low 17 23 25
Phocaeicola vulgatus – species : Low 7 14 25
Pseudomonadaceae – family : Low 5
Pseudomonas – genus : Low 5
Ruminococcaceae – family : High 12
Staphylococcus – genus : Low 2
Sutterella – genus : High 3 8 11 19 21 25
Sutterellaceae – family : High 4 22
Veillonellaceae – family : Low 16

Cross Validated Suggestions

The following improves the bacteria identified above and also is reported in the literature of helping some people with this condition. Each is link to the source study.


(r)-propranolol hydrochloride,(prescription) 76
aripiprazole,(prescription) 55
Astragalus 71
azithromycin,(antibiotic)s[CFS] 70
bifidobacterium infantis,(probiotics) 61 62
bifidobacterium lactis bb12 (probiotics) 61 63
Cacao 33 104
Coenzyme Q10 33 56 72 87 89 98 105
colostrum 62
doxepin hydrochloride,(prescription) 76
doxycycline (antibiotic)s[CFS] 67
d-ribose 34 35 72
erythromycin (antibiotic)s[CFS] 68
Far infrared Sauna 82 83 84 85
folinic acid calcium salt,(prescription) 38 41 42
fructo-oligosaccharides (prebiotic) 61
glycyrrhizic acid (licorice) 101 102 103
guanfacine hydrochloride,(prescription) 76
inulin (prebiotic) 64
iron 72
ketotifen fumarate,(prescription) 72 74
lactobacillus paracasei (probiotics) 61
lactobacillus plantarum (probiotics) 36 37 58 59 60

lactobacillus rhamnosus (probiotics) 61
liothyronine,(prescription) 74
low fodmap diet 75
maprotiline hydrochloride,(prescription) 100
melatonin supplement 72 76
minocycline (antibiotic)s[CFS] 65 66
momordia charantia(bitter melon, karela, balsam pear, or bitter gourd) 90
N-Acetyl Cysteine (NAC), 57 72
naltrexone hydrochloride dihydrate,(prescription) LDN 72 74 77
omega-3 fatty acids 35 38 43 44 72
resveratrol (grape seed/polyphenols/red wine) 54
risperidone,(prescription) 55
SAM-e 31
selenium 72 87 88
ß-glucan 69
Sulforaphane (In broccoli sprouts,cauliflower, kale, cole crops, cabbage, collards, mustard, and cress) 38 39 49 50 51 52 53
trazodone hydrochloride,(prescription) 72 76
Tryptophan 72
Vitamin B1,thiamine hydrochloride 91 92 93
Vitamin B-12 38 47 48 72
Vitamin B9,folic acid 27 28 29 30 72 86
vitamin d 38 45 46 72 94
zinc 72

Suggestions Impact by Bacteria

Reviewing substances reported to help with this condition on the US National Library of Medicine, and which will correct the above bacteria shifts. the following are recommended. Some bacteria may lack literature because none of the studied substances for the condition(s) are known to modify the bacteria.

Additional Suggestions

There are many other interventions to correct the bacteria shifts seen with this person. The top 20 suggestions are listed below as the top 20 items to avoid.

Items to addItems to avoid
Human milk oligosaccharides (prebiotic, Holigos, Stachyose)bacillus subtilis (probiotics)lactuloselactobacillus sakei (probiotics)linseed(flaxseed)Shen Ling Bai Zhu Sanwheat brannavy beanraffinose(sugar beet)ketogenic dietchondrus crispus,red sea weedsesame cake/mealKimchialmonds/ almond skinsmediterranean dietnon-starch polysaccharidesbroccolivitamin awheylactobacillus plantarum,xylooligosaccharides,(prebiotic) (probiotics)oregano (origanum vulgare, oil) |barleyberberinethyme (thymol, thyme oil)Slippery Elmfastingquercetin,resveratrolcinnamon (oil. spice)vegetariansBofutsushosantriphalasyzygium aromaticum (clove)Curcumincranberry bean flourfoeniculum vulgare,fennelXanthohumolquercetinhigh-fat dietsstevialactobacillus rhamnosus gg (probiotics)

Reference

The following is a partial list of the critical citations used above.1New evidences on the altered gut microbiota in autism spectrum disorders.
2The valproic acid rat model of autism presents with gut bacterial dysbiosis similar to that in human autism.
3Analysis of gut microbiota profiles and microbe-disease associations in children with autism spectrum disorders in China.
4Fecal microbiota and metabolome of children with autism and pervasive developmental disorder not otherwise specified.
5Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome.
6Ketogenic diet modifies the gut microbiota in a murine model of autism spectrum disorder.
7Can we reduce autism-related gastrointestinal and behavior problems by gut microbiota based dietary modulation? A review.
8The Role of Gut Microbiota in Gastrointestinal Symptoms of Children with ASD.
9Association Between Gut Microbiota and Autism Spectrum Disorder: A Systematic Review and Meta-Analysis.
10Analysis of gut microbiome, nutrition and immune status in autism spectrum disorder: a case-control study in Ecuador.
11Increased abundance of Sutterella spp. and Ruminococcus torques in feces of children with autism spectrum disorder.
12Autism spectrum disorder is associated with gut microbiota disorder in children.
13[Correlation between gut microbiota and behavior symptoms in children with autism spectrum disorder].
14Changes in the Gut Microbiota of Children with Autism Spectrum Disorder.
15Altered gut microbiota and short chain fatty acids in Chinese children with autism spectrum disorder.
16Gut Microbial Dysbiosis in Indian Children with Autism Spectrum Disorders.
17Potential role of microbiome in Chronic Fatigue Syndrome/Myalgic Encephalomyelits (CFS/ME).
18Altered Gut Microbiota in Korean Children with Autism Spectrum Disorders.
19Are Fecal Metabolome and Microbiota Profiles Correlated with Autism Severity? A Cross-Sectional Study on ASD Preschoolers.
20Serum Oxytocin Level Correlates With Gut Microbiome Dysbiosis in Children With Autism Spectrum Disorder.
21Mucosa-associated specific bacterial species disrupt the intestinal epithelial barrier in the autism phenome.
22Autism Spectrum Disorders and the Gut Microbiota.
23Altered Gut Microbiota and Short-chain Fatty Acids in Chinese Children with Constipated Autism Spectrum Disorder.
24Machine Learning Algorithms Applied to Predict Autism Spectrum Disorder Based on Gut Microbiome Composition.
25The Role of Short-Chain Fatty Acids and Altered Microbiota Composition in Autism Spectrum Disorder: A Comprehensive Literature Review.
26Open Trial of Vitamin B12 Nasal Drops in Adults With Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: Comparison of Responders and Non-Responders.
27Response to vitamin B12 and folic acid in myalgic encephalomyelitis and fibromyalgia.
28[Vitamin B12 and chronic fatigue].
29[Vitamin B12, chronic fatigue and injection treatment].
30Liver extract-folic acid-cyanocobalamin vs placebo for chronic fatigue syndrome.
31Alternative medical interventions used in the treatment and management of myalgic encephalomyelitis/chronic fatigue syndrome and fibromyalgia.
32Cognitive behaviour therapy for the chronic fatigue syndrome. Evening primrose oil and magnesium have been shown to be effective.
33Dietary and nutrition interventions for the therapeutic treatment of chronic fatigue syndrome/myalgic encephalomyelitis: a systematic review.
34The use of D-ribose in chronic fatigue syndrome and fibromyalgia: a pilot study.
35Role of dietary modification in alleviating chronic fatigue syndrome symptoms: a systematic review.
36Effects of Lactobacillus plantarum PS128 on Children with Autism Spectrum Disorder in Taiwan: A Randomized, Double-Blind, Placebo-Controlled Trial.
37Lactobacillus plantarum PS128 and Other Probiotics in Children and Adolescents with Autism Spectrum Disorder: A Real-World Experience.
38Dietary Supplement for Core Symptoms of Autism Spectrum Disorder: Where Are We Now and Where Should We Go?
39Effect of camel milk on thymus and activation-regulated chemokine in autistic children: double-blind study.
40Camel Milk as a Potential Therapy as an Antioxidant in Autism Spectrum Disorder (ASD).
41Blocking and Binding Folate Receptor Alpha Autoantibodies Identify Novel Autism Spectrum Disorder Subgroups.
42Folinic acid improves verbal communication in children with autism and language impairment: a randomized double-blind placebo-controlled trial.
43Effects of large doses of arachidonic acid added to docosahexaenoic acid on social impairment in individuals with autism spectrum disorders: a double-blind, placebo-controlled, randomized trial.
44Internet-based, randomized, controlled trial of omega-3 fatty acids for hyperactivity in autism.
45Retraction: Randomized controlled trial of vitamin D supplementation in children with autism spectrum disorder.
46Vitamin D status in autism spectrum disorders and the efficacy of vitamin D supplementation in autistic children.
47Pilot study of the effect of methyl B12 treatment on behavioral and biomarker measures in children with autism.
48Randomized, Placebo-Controlled Trial of Methyl B12 for Children with Autism.
49Sulforaphane treatment for autism spectrum disorder: A systematic review.
50Dietary Intake of Sulforaphane-Rich Broccoli Sprout Extracts during Juvenile and Adolescence Can Prevent Phencyclidine-Induced Cognitive Deficits at Adulthood.
51Sulforaphane treatment of autism spectrum disorder (ASD).
52Sulforaphane treatment of autism spectrum disorder (ASD).
53Sulforaphane as an adjunctive treatment for irritability in children with autism spectrum disorder: A randomized, double-blind, placebo-controlled clinical trial.
54Resveratrol as adjunctive therapy in treatment of irritability in children with autism: A double-blind and placebo-controlled randomized trial.
55Aripiprazole for the treatment of irritability associated with autism.
56Coenzyme Q(10) supplementation reduces oxidative stress and decreases antioxidant enzyme activity in children with autism spectrum disorders.
57N-acetylcysteine as an adjunctive therapy to risperidone for treatment of irritability in autism: a randomized, double-blind, placebo-controlled clinical trial of efficacy and safety.
58Enhancing social behavior in an autism spectrum disorder mouse model: investigating the underlying mechanisms of Lactiplantibacillus plantarum intervention.
59Lactiplantibacillus plantarum N-1 improves autism-like behavior and gut microbiota in mouse.
60Lactiplantibacillus plantarum ST-III-fermented milk improves autistic-like behaviors in valproic acid-induced autism spectrum disorder mice by altering gut microbiota.
61Probiotics and fructo-oligosaccharide intervention modulate the microbiota-gut brain axis to improve autism spectrum reducing also the hyper-serotonergic state and the dopamine metabolism disorder.
62Pilot study of probiotic/colostrum supplementation on gut function in children with autism and gastrointestinal symptoms.
63Bifidobacterium animalis subsp. lactis Probio-M8 alleviates abnormal behavior and regulates gut microbiota in a mouse model suffering from autism.
64A synbiotic formulation of Lactobacillus reuteri and inulin alleviates ASD-like behaviors in a mouse model: the mediating role of the gut-brain axis.
65Oral Minocycline Therapy Improves Symptoms of Myalgic Encephalomyelitis, Especially in the Initial Disease Stage.
66Could Minocycline Be a “Magic Bullet” for the Treatment of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome?
67Long-term effect of cognitive behavioural therapy and doxycycline treatment for patients with Q fever fatigue syndrome: One-year follow-up of the Qure study.
68Open-label pilot for treatment targeting gut dysbiosis in myalgic encephalomyelitis/chronic fatigue syndrome: neuropsychological symptoms and sex comparisons.
69Yeast Beta-Glucan Supplementation with Multivitamins Attenuates Cognitive Impairments in Individuals with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: A Randomized, Double-Blind, Placebo-Controlled Trial.
70Azithromycin in chronic fatigue syndrome (CFS), an analysis of clinical data.
71Chronic fatigue syndrome post-COVID-19: triple-blind randomised clinical trial of Astragalus root extract.
72[Post-COVID syndrome with fatigue and exercise intolerance: myalgic encephalomyelitis/chronic fatigue syndrome].
73Neurovascular Dysregulation and Acute Exercise Intolerance in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: A Randomized, Placebo-Controlled Trial of Pyridostigmine.
74Advancing Research and Treatment: An Overview of Clinical Trials in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) and Future Perspectives.
75Review of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: an evidence-based approach to diagnosis and management by clinicians.
76Diagnosis and Management of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome.
77Low-dose naltrexone for post-COVID fatigue syndrome: a study protocol for a double-blind, randomised trial in British Columbia.
78Effects of Hyperbaric Oxygen Therapy on Long COVID: A Systematic Review.
79Reversible widespread brain (18)F-FDG PET hypometabolism in chronic fatigue syndrome treated by hyperbaric oxygen therapy.
80[Fibromyalgia and myalgic encephalomyelitis: The oxygen clue].
81The efficacy of hyperbaric oxygen therapy in the management of chronic fatigue syndrome.
82Effects of Waon therapy on chronic fatigue syndrome: a pilot study.
83Targeting mitochondrial dysfunction in the treatment of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) – a clinical audit.
84[A new treatment: thermal therapy for chronic fatigue syndrome].
85The effects of repeated thermal therapy for two patients with chronic fatigue syndrome.
86Clinical activity of folinic acid in patients with chronic fatigue syndrome.
87Does Coenzyme Q10 Plus Selenium Supplementation Ameliorate Clinical Outcomes by Modulating Oxidative Stress and Inflammation in Individuals with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome?
88Therapeutic Effect and Metabolic Mechanism of A Selenium-Polysaccharide from Ziyang Green Tea on Chronic Fatigue Syndrome.
89Coenzyme Q10 + alpha lipoic acid for chronic COVID syndrome.
90News and views in myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS): The role of co-morbidity and novel treatments.
91Effects of Qiye Shen`an Pian Combined with Glutamate and Vitamin B1 on Fatigue State, Immune Function and Quality of Life in Patients with Chronic Fatigue Syndrome.
92B-vitamins, related vitamers, and metabolites in patients with quiescent inflammatory bowel disease and chronic fatigue treated with high dose oral thiamine.
93Randomised clinical trial: high-dose oral thiamine versus placebo for chronic fatigue in patients with quiescent inflammatory bowel disease.
95Complementary and alternative medicine for patients with chronic fatigue syndrome: a systematic review.
96[A case of chronic fatigue syndrome who showed a beneficial effect by intravenous administration of magnesium sulphate].
97Intravenous magnesium loading in chronic fatigue syndrome.
98Prospective observational study of treatments for unexplained chronic fatigue.
99[Therapy of chronic fatigue syndrome].
100Psychotropic treatment of chronic fatigue syndrome and related disorders.
101Chronic fatigue syndrome and liquorice.
102Chronic fatigue syndrome and liquorice.
103Liquorice and chronic fatigue syndrome.
104High cocoa polyphenol rich chocolate may reduce the burden of the symptoms in chronic fatigue syndrome.
105Effect of Dietary Coenzyme Q10 Plus NADH Supplementation on Fatigue Perception and Health-Related Quality of Life in Individuals with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: A Prospective, Randomized, Double-Blind, Placebo-Controlled Trial.
106Assessment of Bioautography and Spot Screening of TLC of Green Tea (Camellia) Plant Extracts as Antibacterial and Antioxidant Agents
107GUT MICROBIOTA DYSBIOSIS IS LINKED TO HYPERTENSION
108Modulation of the gut microbiota composition by rifaximin in non-constipated irritable bowel syndrome patients: a molecular approach
109The Influence of Nonsteroidal Anti-Inflammatory Drugs on the Gut Microbiome
110Impact of probiotic supplements on microbiome diversity following antibiotic treatment of mice
111Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men
112Sodium butyrate attenuates high-fat diet-induced steatohepatitis in mice by improving gut microbiota and gastrointestinal barrier
113Antibiotic use in childhood alters the gut microbiota and predisposes to overweight
114Low-dose penicillin in early life induces long-term changes in murine gut microbiota, brain cytokines and behavior
115Energy-dense diet triggers changes in gut microbiota, reorganization of gut-brain vagal communication and increases body fat accumulation
116Health benefit of vegetable/fruit juice-based diet: Role of microbiome

Gender based Microbiome Shifts for ME/CFS

A question was ask – are there significant gender differences with ME/CFS. A partial answer is possible from our citizen science data (Available here). The number of bacteria identify as statistical drops because we are reducing sample sizes. The table below shows the shifts that are seen in common with P < 0.01.

For Symptom of ME/CFS

SourceTax_nametax_rankMaleFemaleMale_Chi2FeMale_Chi2
thryveThermodesulfobacteriaphylumincreasesincreases234.0375138.4544
biomesightVerrucomicrobiaceaefamilyincreasesincreases8.3333337.262051
biomesightRhodothermaeotaphylumincreasesincreases179.2217.3071
biomesightAkkermansiaceaefamilyincreasesincreases8.7183789.965634
biomesightErysipelothrix murisspeciesincreasesincreases9.53388910.08333
biomesightAkkermansiagenusincreasesincreases8.7183789.965634
biomesightRhodothermalesorderincreasesincreases179.2217.3071
biomesightAkkermansia muciniphilaspeciesincreasesincreases8.7183789.965634
biomesightErysipelothrixgenusincreasesincreases9.6632899.663289
biomesightRhodothermiaclassincreasesincreases179.2217.3071
biomesightThermodesulfobacteriaphylumincreasesincreases281.1738299.9112

ME/CFS With IBS

We find differences here.

SourceTax_nametax_rankTaxonMaleFemaleMale_Chi2FeMale_Chi2
biomesightSutterellagenus40544decreaseincreases8.33333311.25018
biomesightRhodothermalesorder1853224increasesincreases139.9274114.5716
biomesightDoreagenus189330increasesdecrease18.7516.17875
biomesightRhodothermiaclass1853222increasesincreases139.9274114.5716
biomesightThermodesulfobacteriaphylum200940increasesincreases280.3333187.9779
biomesightSutterellaceaefamily995019decreaseincreases8.33333311.25018
biomesightAlcaligenaceaefamily506decreaseincreases8.3333339.120714
biomesightRhodothermaeotaphylum1853220increasesincreases139.9274114.5716

ME/CFS Without IBS

We found no differences yet (given the sample size)

SourceTax_nametax_rankTaxonMaleFemaleMale_Chi2FeMale_Chi2
biomesightBacteroides fluxusspecies626930increasesincreases7.3551617.910588
biomesightThermodesulfobacteriaphylum200940increasesincreases124.4571170.4624

Irritable Bowel Syndrome

Following up from above and noting that there is a gender bias in incidence, we find some differences

thryveThermodesulfobacteriaphylum200940increasesincreases252.823295.10095
biomesightRhodothermalesorder1853224increasesincreases125.1467110.6182
biomesightRhodothermiaclass1853222increasesincreases125.1467110.6182
biomesightThermodesulfobacteriaphylum200940increasesincreases314.4971174.6182
biomesightRhodothermaeotaphylum1853220increasesincreases125.1467110.6182
biomesightSharpea azabuensisspecies322505increasesincreases16.185266.80625
biomesightSharpeagenus519427increasesincreases16.185266.80625
thryveMycoplasmagenus2093increasesdecrease12.8152420.3229
thryveMycoplasmataceaefamily2092increasesdecrease14.8858120.3229
thryvePhocaeicola vulgatusspecies821increasesdecrease7.89349217.06273
thryveMycoplasmatalesorder2085increasesdecrease14.8858126.01485

Depression

Another condition with a gender association

SourceTax_nametax_rankTaxonMaleFemaleMale_Chi2FeMale_Chi2
thryveThermodesulfobacteriaphylum200940increasesincreases227.7557148.4336
thryveParabacteroides distasonisspecies823decreaseincreases9.11835613.46941
thryveEubacterium oxidoreducensspecies1732decreaseincreases12.995076.76
biomesightRhodothermalesorder1853224increasesincreases121.200291.125
biomesightRhodothermiaclass1853222increasesincreases121.200291.125
biomesightThermodesulfobacteriaphylum200940increasesincreases223.4402189.2431
biomesightRhodothermaeotaphylum1853220increasesincreases121.200291.125
thryveLactobacillus rogosaespecies706562decreasedecrease23.8836812.12781

Symptom: Problems remembering things

This is one of the characteristics of ME/CFS, Long Covid, etc

SourceTax_nametax_rankTaxonMaleFemaleMale_Chi2FeMale_Chi2
thryveThermodesulfobacteriaphylum200940increasesincreases316.4446120.0944
biomesightRhodothermalesorder1853224increasesincreases171.7445133.3333
biomesightRhodothermiaclass1853222increasesincreases171.7445133.3333
biomesightThermodesulfobacteriaphylum200940increasesincreases369.0078289.0992
biomesightOdoribacteraceaefamily1853231increasesincreases12.793117.962632
biomesightRhodothermaeotaphylum1853220increasesincreases171.7445133.3333
biomesightAcetivibriogenus35829decreaseincreases9.18086517.49208
biomesightOdoribactergenus283168increasesincreases9.33494912
biomesightAcetivibrio alkalicellulosispecies320502decreaseincreases9.18086519.95636
biomesightHathewaya histolyticaspecies1498decreaseincreases9.1808657.262051
biomesightHathewayagenus1769729decreaseincreases9.1808657.262051
biomesight[Clostridium] thermoalcaliphilumspecies29349increasesincreases7.356.880909
thryveIntestinimonasgenus1392389decreaseincreases168.552727
thryveIntestinimonas butyriciproducensspecies1297617decreaseincreases16.486469.992258
ubiomeBacteroides sp. EBA5-17species447029increasesdecrease9.0555777.314286

Symptom: Worsening of symptoms with stress.

Another common symptom of ME/CFS

SourceTax_nametax_rankTaxonMaleFemaleMale_Chi2FeMale_Chi2
thryveThermodesulfobacteriaphylum200940increasesincreases282.4023185.22
biomesightThermoanaerobacterales Family III. Incertae Sedisfamily543371decreaseincreases22.004548.491649
biomesightSharpeagenus519427increasesincreases17.5562512.38345
biomesightHathewayagenus1769729decreaseincreases16.9861211.70814
biomesightRhodothermalesorder1853224increasesincreases142.9353188.8704
biomesightHathewaya histolyticaspecies1498decreaseincreases16.9861211.70814
biomesightSharpea azabuensisspecies322505increasesincreases17.5562512.97965
biomesightRhodothermiaclass1853222increasesincreases142.9353188.8704
biomesightThermodesulfobacteriaphylum200940increasesincreases352.2616362.7038
biomesightAcetivibrio alkalicellulosispecies320502decreaseincreases12.658188.491649
biomesightRhodothermaeotaphylum1853220increasesincreases142.9353188.8704
biomesightAcetivibriogenus35829decreaseincreases12.658188.491649

Other Symptoms with Significant Gender Differences in patterns

  • Immune Manifestations: Abdominal Pain
  • Sleep: Unrefreshed sleep
  • Comorbid: High Anxiety
  • General: Fatigue
  • Neurological-Audio: hypersensitivity to noise
  • DePaul University Fatigue Questionnaire : Unrefreshing Sleep, that is waking up feeling tired
  • DePaul University Fatigue Questionnaire : Fatigue
  • Neurocognitive: Brain Fog
  • Neurocognitive: Problems remembering things
  • DePaul University Fatigue Questionnaire : Anxiety/tension
  • General: Myalgia (pain)
  • Immune Manifestations: Constipation
  • Post-exertional malaise: Rapid muscular fatigability,
  • Neuroendocrine Manifestations: Poor gut motility
  • Comorbid: Restless Leg
  • Comorbid: Small intestinal bacterial overgrowth (SIBO)
  • DePaul University Fatigue Questionnaire : Difficulty finding the right word
  • DePaul University Fatigue Questionnaire : Mood swings
  • DePaul University Fatigue Questionnaire : Pain in Multiple Joints without Swelling or Redness
  • Sleep: Problems falling asleep
  • Sleep: Problems staying asleep

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.

Also we had significant interaction with

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:

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:

Other books can be found here:

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.

Suggested Questionnaire for Evaluating a MD

What testing would you like to do?

Are you going to just provide symptom relief or are you going to search for the underlying cause to eliminate it?

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.”

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).

CriteriaCurrent SampleOld Sample
Eubiosis Index62.8% 🙂59%
Lab Read Quality4.38.4
Outside Range from JasonH88
Outside Range from Medivere2020
Outside Range from Metagenomics1010
Outside Range from MyBioma88
Outside Range from Nirvana/CosmosId1818
Outside Range from XenoGene4242
Outside Lab Range (+/- 1.96SD)9 🙂16
Outside Box-Plot-Whiskers38 🙂98
Outside Kaltoft-Moldrup56 🙂139
Bacteria Reported By Lab494752
Bacteria Over 90%ile20 🙂82
Bacteria Under 10%ile66 🙂232
Shannon Diversity Index1.4651.701
Simpson Diversity Index0.0350.028
Chao1 Index747417093
Shannon Diversity Percentile28.561.4
Simpson Diversity Percentile30.221.5
Chao1 Percentile28.987.7
Lab: BiomeSight
Pathogens18 🙂39
Condition Est. Over 90%ile44
Kegg Compounds Low969 :-)1242
Kegg Compounds High5 🙂23
Kegg Enzymes Low272284
Kegg Enzymes High17 🙂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).

CurrentPrior
General Health Predictors: Flagged Bacteria8 🙂10
Anti inflammatory Bacteria Score14.4%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 Detected2 🙂7
Bacteria deemed Unhealthy7 🙂22
Jason Hawrelak Criteria56.4 %ile75.8 %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)

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.