For other analysis for ME/CFS see this list.

Prior Posts:

• A review of a ME/CFS Microbiome Jan 2021
• Evidence of ME/CFS improving using Microbiome Data May 2022
• Comparing 4 ME/CFS Samples with New Tool Jul 2022
• A Microbiome Trek Continues thru the land of ME/CFS. Feb 2023
• Biomesight vs Thorne Tests – Differences Mar 2023
• Post Exertional Malaise (PEM) with diminished ME/CFS Nov 2023

Analysis

This person had been doing duel interpretation of their FastQ files (Thyrve and BiomeSight). The results are mixed. A common problem comparing results is not there, the Lab Quality is similar for most of the samples,

Criteria	2/2/2024	3/23/2023	10/29/2022	8/22/2022	7/21/2022	4/30/2022
Lab Read Quality	4.9	8.7	5.1	5	4.9	4.8
Eubiosis	100% 🙂	36%	50%	66%	87%	74%
Outside Range from GanzImmun Diagostics	13	13	18	18	16	16
Outside Range from JasonH	6	6	6	6	7	7
Outside Range from Lab Teletest	26	26	27	27	29	29
Outside Range from Medivere	17	17	17	17	17	17
Outside Range from Metagenomics	9	9	8	8	9	9
Outside Range from Microba Co-Biome	9	9	9	9	11	11
Outside Range from MyBioma	8	8	8	8	9	9
Outside Range from Nirvana/CosmosId	19 🙂	19	22	22	24	24
Outside Range from Thorne (20/80%ile)	217 🙂	217	300	300	216	216
Outside Range from XenoGene	48	48	53	53	45	45
Outside Lab Range (+/- 1.96SD)	26	4	6	16	8	4
Outside Box-Plot-Whiskers	104	34	36	120	73	44
Outside Kaltoft-Moldrup	126	161	85	125	102	70
Bacteria Reported By Lab	694	632	604	843	752	575
Bacteria Over 90%ile	65 🙁	28	30	87	47	37
Bacteria Under 10%ile	76	140	28	61	51	25
Shannon Diversity Index	3.107	3.028	2.987	3.227	3.126	3.121
Simpson Diversity Index	0.044	0.085	0.076	0.045	0.088	0.075
Chao1 Index	16886	13972	13231	27357	20690	9772
Pathogens	29	30	25	34	35	28
Forecasted	4	3	n/a	n/a	4	4

We have a few matches with the latest symptom forecast. Remember this is pattern matching over symptoms that likely have dozen of subsets.

Going Forward

We are going to do the [Just give me suggestions include Symptoms] . This gives us 5 packages of suggestions.

Looking only at what is suggested by all 5 sets of suggestions

• whey
• aloe vera
• Tributyrin
• Shen Ling Bai Zhu San

• Avoids
  • non-starch polysaccharides
  • proton-pump inhibitors (prescription)
  • lactobacillus plantarum (probiotics)
  • blueberry
  • Limosilactobacillus fermentum (probiotic)
  • alcoholic beverages

Highest value was 280, thus a threshold of 140, lowest value was -220, thus a threshold of -110. What was VERY DIFFERENT then most samples, there were not a swarm of prescription items hogging the top. Also the range of priorities was much less than most samples examined. This implies less severe dysbiosis (or less that we can do, i.e. suggestions).

Takes

• Amino Acids and Supplements
  • epicatechin
• Foods and Herbs
  • aloe vera
  • Shen Ling Bai Zhu San
  • eggs
• Probiotics and Prebiotics – nothing
• Antibiotics: The top two are all common with ME/CFS
  • clarithromycin (antibiotic)s[CFS]
  • metronidazole (antibiotic)s[CFS]

Avoids

• alcoholic beverages
• blueberry
• pea (fiber, protein)
• dairy
• Slippery Elm
• Rhubarb Peony Decoction
• Limosilactobacillus fermentum (probiotic)
• non-starch polysaccharides
• proton-pump inhibitors (prescription)
• Slippery Elm
• Bile Acid Sequestrant
• glycerol monolaurate (Monolaurin)

Antibiotics as FYI

The top 3 antibiotics that had all 5 agreement on were also often used for ME/CFS:

• clarithromycin (antibiotic)s[CFS]
• metronidazole (antibiotic)s[CFS]
• azithromycin,(antibiotic)s[CFS]

Shot in the Dark for PEM

PEM is an ongoing issue for this person. With the new symptoms algorithms, I decided to run both with only PEM selected. The top results are

• Take
  • inulin (prebiotic)
  • Human milk oligosaccharides (prebiotic, Holigos, Stachyose)
  • arabinogalactan (prebiotic)
  • pectin
  • clostridium butyricum (probiotics),Miya,Miyarisan
  • barley,oat
  • l-proline
  • soy
• Avoid
  • Hesperidin (polyphenol)
  • gluten-free diet
  • Curcumin
  • Vitamin C (ascorbic acid)
  • thyme (thymol, thyme oil)
  • Vitamin B1,thiamine hydrochloride (and most B-vitamins)
  • low fodmap diet
  • Arbutin (polyphenol)
  • diosmin,(polyphenol)

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.