With this being the Thanksgiving Weekend, I had time to work on my backlog. One of the items was special studies. I have done the following changes:

• Executed the analysis for both uBiome and Thryve/Ombre samples. So more samples will have the option of using special studies.
• Implemented Consensus/Monte Carlo between the bacteria, casting the species (which are not reported consistently between labs) to their genus. These are shown on the [Key Bacteria] link below.

Last, I have added per  Peripheral neuropathy to the symptom list.

REMEMBER TO ANNOTATED YOU SAMPLES WITH YOUR SYMPTOMS

This is what Special Studies use.

Example: for Chronic Fatigue Syndrome

The page below shows a distinct pattern for ME/CFS with Bifidobacterium being the greatest significance. For this bacteria, my first suggestion is simple:  Human milk oligosaccharides (HMOs) and Bifidobacerium infantis probiotics.

• Human Milk Oligosaccharides: Health Benefits, Potential Applications in Infant Formulas, and Pharmacology [2020]
• “The results reflect the metabolic abilities of the respective bifidobacteria. B. bifidum used secretory glycosidases to degrade HMOs, whereas B. longum subsp. infantis assimilated all HMOs by incorporating them in their intact forms.” [2011]

It is interesting to note that Lactobacillus does not appear as significant.

Bottom Line

Special Studies are still a “work-in-progress”. Using them “as is” have not produced superior results to those from the standard triplet (Outside Lab Range, Box-Plot-Whiskers, Kaltoft-Møldrup) — see this post for an example. How do I determine which is better? For ME/CFS, we should have the top suggested items being cross validated with clinical studies. Feel free to explore the results.

I will continue working on getting superior results from special studies — stay tune!

Back Story

I go this email from someone who just moved to Spain from the U.S. She has being using Microbiome Prescription to try improving her ME/CFS. She had the testing done by Ombre Labs, and then transfer the data to BiomeSight. This allows her to keep consistent analysis on her journey of recovery.

I’m doing pretty well with bacillus coagulans and pretty bad with some other recommendations so I’m looking for some extra clarity. When I hit a great herbal antibiotic and a great probiotic life gets so much better, but oftentimes it’s harder than that. Sometimes I don’t get enough  herbal antibiotic recommendations. Some of the probiotics I may need, like e-coli or bifidus, cannot sustain me the way coagulans does -keeping my local infections at bay. So I try to combine them  or if it’s not clear if they are compatible, I tend to not take them, which is a shame. So I’m considering prescription medicine to see if I can get a bit more help.

I’m also figuring out where to buy supplements etc. Life is really an adventure!

Comparison Between Samples And Lab Interpretations

For those not familiar with the issue of Lab Interpretation of the identical data see The taxonomy nightmare before Christmas…[2019]. Ombre typically reports on 25-30% more bacteria types than BiomeSight. The quality improved, but the number of bacteria identified are very similar. I give observations below:

	Ombre	Lab	Results	BiomeSight	Lab	Results
Criteria	6-Jul	19-Aug	10-Oct	6-Jul	19-Aug	10-Oct
Lab Read Quality	2.1	5.4	7.1	2.1	5.4	7.1
Bacteria Reported By Lab	365	628	625	280	497	490
Bacteria Over 99%ile	5	6	0	2	7	1
Bacteria Over 95%ile	27	24	1	19	31	11
Bacteria Over 90%ile	49	51	1	37	58	24
Bacteria Under 10%ile	18	60	485	45	62	224
Bacteria Under 5%ile	10	28	411	28	30	175
Bacteria Under 1%ile	1	7	317	1	13	135
Lab: Thryve
Rarely Seen 1%	0	9	1	0	4	2
Rarely Seen 5%	8	40	27	4	18	17
Pathogens	19	28	25	15	26	16
Outside Range from Medivere	16	16	5	4	4	4
Outside Range from Metagenomics	7	7	19	17	17	16
Outside Range from MyBioma	14	14	8	7	7	7
Outside Range from Nirvana/CosmosId	23	23	8	9	9	7
Outside Range from XenoGene	33	33	25	22	22	19
Outside Lab Range (+/- 1.96SD)	10	14	42	28	28	22
Outside Box-Plot-Whiskers	64	61	12	6	13	7
Outside Kaltoft-Møldrup	112	182	31	70	84	64
Condition Est. Over 99%ile	0	0	542	70	113	175
Condition Est. Over 95%ile	0	0	0	0	1	0
Condition Est. Over 90%ile	2	2	10	0	4	0
Enzymes Over 99%ile	13	15	17	0	6	0
Enzymes Over 95%ile	69	82	0	0	10	0
Enzymes Over 90%ile	155	411	0	22	32	0
Enzymes Under 10%ile	55	138	2	45	51	21
Enzymes Under 5%ile	22	67	1593	308	219	212
Enzymes Under 1%ile	5	2	1320	187	132	146
Compounds Over 99%ile	104	126	641	12	47	67
Compounds Over 95%ile	385	397	4	30	7	19
Compounds Over 90%ile	533	548	60	112	76	138
Compounds Under 10%ile	183	248	103	342	313	323
Compounds Under 5%ile	109	127	359	180	125	224
Compounds Under 1%ile	16	17	303	37	64	73
Compounds Under 1%ile	17	21	224	17	21	40

The following are apparent, between the last two samples, the reader was trying to follow the suggestions.

• The number of high bacteria (> 90%ile, > 95%ile, > 99%ile) show significant decline
• Rarely Seen bacteria show significant decline
• The number of low bacteria (< 10%ile, < 5%ile, < 1%ile) show significant increases – suggesting more diversity
• The Outside Range is a little mixed, with either both labs showing a decline, OR one showing a decline and one an increase. None showed increase on both.
• High Enzymes show decline. Low Enzymes had inconsistent results.
• Compounds and Conditions had inconsistent results

Enzymes, Compounds and Conditions are best effort estimates (and experimental) and be taken with a grain of salt (50 mg). By conventional thinking, the microbiome has improved (less extreme high levels), less pathogenic bacteria types.

Going Forward

Consensus approach (also known as Monte Carlo Simulation) remains the safest choice. To simplify the analysis, I will use the standard triplet (Outside Lab Range, Box-Plot-Whiskers, Kaltoft-Møldrup) on both latest samples processed through Ombre and Biomesight data processing. Given the report that some did not work subjectively, I decided to proceed down the most restrictive approach. I used the new quick suggestions (best choice for someone with brain fog).

Probiotics

The #1 and #2 choices are lactobacillus paracasei and bacillus subtilis. Kegg choices are Escherichia coli, Bacillus subtilis (with Biomesight numbers being much less than Ombres).

	Thryve			Biomesight
Microbiome Modifier	Suggestions	Clinical Dosage	Est Confidence	Suggestions	Est Confidence
bacillus subtilis	Take	10 BCFU/day	340.4	Take	223.6
bacillus lichenformis	Take		279.1	Take	20.9
enterococcus faecium	Take	1 BCFU/day	13.2	Take	8
bifidobacterium longum	Take	10 BCFU/day	516.2	Take	182.5
lactobacillus paracasei	Take	40 BCFU/day	58.7	Take	397.5
pediococcus acidilactici	Take		157.7	Take	215.4

For other items, there were a surprisingly few in agreement.

Microbiome Modifier	Suggestions	Clinical Dosage	Est Confidence	Suggestions	Clinical Dosage	Est Confidence
galactooligosaccharides (GOS)	Take	10 gm/day	15	Take	10 gm/day	139.1
Calcium	Take	500 mg/day	129.2	Take	500 mg/day	36.2
Magnesium	Take	500 mg/day	189.7	Take	500 mg/day	119.2
D-Ribose	Take	10 gm/day	80.6	Take	10 gm/day	23.6
Glycine	Take	15 gm/day	409.2	Take	15 gm/day	258.5
Omega-3 fatty acids	Take	4 gm/day	166.8	Take	4 gm/day	289.4

Using the Consensus across Multiple Samples

This gives a lot more information, but at the cost of more complexities.

The approach is similar to the above, except for suggestions we change to Every thing. I have extracted the items > 100 that are 5 or 6 Take Count with 0 or 1 Avoid Count to the table below in decreasing order

• Cacao (426) — not an item on the quick suggestions
  • High cocoa polyphenol rich chocolate may reduce the burden of the symptoms in chronic fatigue syndrome [2010]
• bifidobacterium longum (probiotics)
• glycine
• high resistant starch
• palm kernel meal (300 and below)
• almonds/ almond skins
• bacillus subtilis (probiotics)
• bifidobacterium pseudocatenulatum,(probiotics) (Stain versus is negative)
• high fiber diet
• brown algae
• omega-3 fatty acids (200 and below)
• pediococcus acidilactic (probiotic)
• oligofructose (prebiotic)
• lactobacillus paracasei (probiotics)
• brown rice
• Mangosteen
• whole-grain wheat
• magnesium
• navy bean
• bacillus licheniformis,(probiotics)
• green tea
• lactulose
• lauric acid(fatty acid in coconut oil,in palm kernel oil,)

Prescription Drugs Analysis

The approach is similar to the above, except for suggestions we change to Every thing.

And then use the option on the Multiple Samples tab,

Remember to empty the old baskets.

The items that came up (as discussed above) are:

• minocycline (antibiotic)s
  • Oral Minocycline Therapy Improves Symptoms of Myalgic Encephalomyelitis, Especially in the Initial Disease Stage [2021]
  • Could Minocycline Be a “Magic Bullet” for the Treatment of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome? [2021]
  • Improvement of chronic nonspecific symptoms by long-term minocycline treatment in Japanese patients with Coxiella burnetii infection considered to have post-Q fever fatigue syndrome [2004]
• proton-pump inhibitors (prescription)
• ceftriaxone (antibiotic)s (often give with azithromycin – which has been used for ME/CFS)
  • “A study by Fallon et al found that some of the PTLDS patients in their trial experienced moderate short-term cognitive improvement from ceftriaxone treatment” [2008]
  • “Ceftriaxone has excellent penetration of the blood-brain barrier and is one of the most effective drugs for Lyme disease. Ceftriaxone is typically given once a day intravenously, typically in 45 minutes.” [Columbia-Lyme.Org]
  • “Ceftriaxone Compared with Doxycycline for the Treatment of Acute Disseminated Lyme Disease [1997]
• rifaximin (antibiotic)s – often used for IBS that is co-morbid with ME/CFS
  • See this 2015 post, Rifaximin and CFS , for CFS/ME that have used this

So every item at the top of the list (from over a possible choice of 3000 different prescription drugs), are cross-validated against the literature with the exception of proton-pump-inhibitor. This person can show their medical professional that the microbiome model suggests it and clinical studies confirm that they are reasonable.

I favor Dr. Cecile Jadin protocol of rotating antibiotics typically a course (7-10 days), then a break of 1-2 weeks, and then proceed to the next one.

Feedback from Reader

I love Dr. AI [Artificial Intelligence], which other doctor asks you to eat as much 100% chocolate I can??? And I tolerate it, luckily. And there are so many yummy brands in Spain, I don’t remember having that much choice when I left! 

Thanks for all the info, very helpful, very encouraging to see progress “on paper”, and to have clear things to share with my new doctor. I’m confident I’ll find a microbiome helper here in Barcelona.

The greatest challenge in treating ME/CFS is that there is no clear test to see if something is helping. Using repeated microbiome samples with systematic trials of suggestions, provides objective evidence — even when the subjective evidence is not pronounced. ME/CFS patients have a real challenge on doing subjective evaluation — they often cannot recall how they were two weeks ago!

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.

A reader asked to look at the data from an experiment she did.

I have provided two biomesight results from biomesight (BS) to microbiome prescription (MP). The sample consuming kefir daily was sent first (both to BS and MP). The second sample was after stopping kefir consumption between the two samples.

This was not the ideal sequence, getting a sample before doing Kefir and one after would be the typical approach. This approach should indicate what is lost by stopping. There was 3 weeks washout time before samples.

Analysis

The stopped Kefir sample is higher quality, so the expectation would be for the numbers to be higher. This is not the case. Stopping resulted in more extreme ranges for bacteria(1.5x more), less types of bacteria, dramatic drop in the count of bacteria out of range (93% decrease in Outside Lab Range). There was a significant in compounds being produced by the microbiome that were more extreme (8x increase) and enzymes also (3.6x increase).

Criteria	On Kefir	Stopped Kefir
Lab Read Quality	3.9	5.3
Bacteria Reported By Lab	470	404
Bacteria Over 99%ile	11	0
Bacteria Over 95%ile	30	5
Bacteria Over 90%ile	43	19
Bacteria Under 10%ile	10	74
Bacteria Under 5%ile	1	39
Bacteria Under 1%ile	0	7
Lab: BiomeSight
Rarely Seen 1%	2	2
Rarely Seen 5%	12	14
Pathogens	29	22
Outside Range from JasonH	4	4
Outside Range from Medivere	14	14
Outside Range from Metagenomics	7	7
Outside Range from MyBioma	5	5
Outside Range from Nirvana/CosmosId	19	19
Outside Range from XenoGene	21	21
Outside Lab Range (+/- 1.96SD)	18	1
Outside Box-Plot-Whiskers	73	29
Outside Kaltoft-Møldrup	81	74
Condition Est. Over 99%ile	0	0
Condition Est. Over 95%ile	0	0
Condition Est. Over 90%ile	1	1
Enzymes Over 99%ile	1	0
Enzymes Over 95%ile	3	2
Enzymes Over 90%ile	24	41
Enzymes Under 10%ile	79	240
Enzymes Under 5%ile	26	158
Enzymes Under 1%ile	1	47
Compounds Over 99%ile	0	2
Compounds Over 95%ile	4	113
Compounds Over 90%ile	29	453
Compounds Under 10%ile	44	163
Compounds Under 5%ile	18	61
Compounds Under 1%ile	2	8

As often happens, there is a Yin/Yang with some indicators improving and other worst. My general impression is that this microbiome does better on Kefir.

Bacteria Specifics

I then went to compare specific bacteria shifts that had special interest or large shifts

Bacteria	On Kefir Percentile (Percentage)	Stop Kefir Percentile (Percentage)
(genus) Bifidobacterium	35	72
(genus) Lactobacillus	none	43
(genus) Blautia	38 (6.5%)	46 (7.2%)
(genus) Faecalibacterium	34 (8.4%)	62 (14.6%)
(genus) Lachnospira	21 (0.6%)	70 (3.5%)
(genus) Bacteroides	66 (29.1%)	88 (40.5%)
(genus) Phocaeicola –	79 (15%)	93 (23%)

In terms of the literature, I could only find Bacteroides and Phocaeicola, which are both reported to increase (agrees). Different Kefirs will have different impact because each has different bacteria in it. “The kefir granules are a consortium of bacteria and yeasts embedded in a exopolysaccharide matrix. ” [2022]

See Milk kefir: composition, microbial cultures, biological activities, and related products [2015] for various lists of bacteria in different kefir tested.

List of Possible Bacteria in Kefir

The following list illustrates why I tend not to recommend Kefir — too many possible bacteria, some good and some bad. It’s probiotic roulette! If you buy commercial Kefir, have some fun — email the producer and ask which strains are in it, and the last full shotgun lab report verifying it.

1. Acetobacter acetic
2. Acetobacter fabarum
3. Acetobacter lovaniensis
4. Acetobacter orientalis
5. Acetobacter rancens
6. Acetobacter sp.
7. Acetobacter syzygii
8. Acinetobacter sp.
9. Bacillus sp.
10. Bacillus subtilis
11. Bifidobacterium bifidum
12. Bifidobacterium sp.
13. Brettanomyces sp.
14. Candida inconspicua
15. Candida krusei
16. Candida lambica
17. Candida maris
18. Candida sp.
19. Cryptococcus sp.
20. Dekkera anomala
21. Dysgonomonas sp.
22. Enterococcus durans
23. Enterococcus faecalis
24. Enterococcus sp.
25. Escherichia coli
26. Gluconobacter frateurii
27. Gluconobacter japonicus
28. Halococcus sp.
29. Kazachastania khefir
30. Kazachstania aerobia
31. Kazachstania exigua
32. Kazachstania unispora
33. Kluyveromyces lactis
34. Kluyveromyces marxianus
35. Kluyveromyces marxianus var. lactis
36. Lachancea meyersii
37. Lactobacillus acidophilus
38. Lactobacillus amylovorus
39. Lactobacillus brevis
40. Lactobacillus buchneri
41. Lactobacillus casei
42. Lactobacillus casei ssp. pseudoplantarum
43. Lactobacillus crispatus
44. Lactobacillus delbrueckii ssp. bulgaricus
45. Lactobacillus helveticus
46. Lactobacillus kefir
47. Lactobacillus kefiranofaciens
48. Lactobacillus kefiranofaciens ssp. kefiranofaciens
49. Lactobacillus kefiranofaciens ssp. kefirgranum
50. Lactobacillus kefiri
51. Lactobacillus lactis
52. Lactobacillus lactis ssp. lactis
53. Lactobacillus parabuchneri
54. Lactobacillus paracasei
55. Lactobacillus parakefir
56. Lactobacillus parakefiri
57. Lactobacillus plantarum
58. Lactobacillus satsumensis
59. Lactobacillus sp.
60. Lactobacillus uvarum
61. Lactococcus cremoris
62. Lactococcus lactis
63. Lactococcus lactis ssp. cremoris
64. Lactococcus lactis ssp. lactis
65. Lactococcus lactis ssp. lactis biovar diacetylactis
66. Lactococcus sp.
67. Leuconostoc lactis
68. Leuconostoc mesenteroides
69. Leuconostoc paramesenteroides
70. Leuconostoc pseudomesenteroides
71. Leuconostoc sp.
72. Naumovozyma sp.
73. Pelomonas sp.
74. Pichia guilliermondii
75. Pichia kudriavzevii
76. Pseudomonas sp.
77. Saccharomyces cerevisiae
78. Saccharomyces sp.
79. Saccharomyces turicensis
80. Saccharomyces unisporus
81. Saccharomycodes sp.
82. Shewanella sp.
83. Streptococcus durans
84. Streptococcus sp.
85. Streptococcus thermophilus
86. Weissella sp.
87. Zygosaccharomyces sp.

Comments from Social Media

There are two border walls that can be important to health, we will used these terms:

• increased intestinal permeability or IIP (often called Leaky Gut, but note: “Leaky gut syndrome is a hypothetical condition that’s not currently recognized as a medical diagnosis.”[src])
• blood–brain barrier permeability or BBBP

The first is an indicator of the availability of bacteria, fungi, chemicals, etc. to move from the intestines into the body/blood. The second is the ability of bacteria, fungi, chemicals, etc. to enter the brain. Both are important — the latter with neurological conditions (for example brain fog, autism, etc).

IIP – Increased Intestinal Permeability

This is usually associated with the Zonulin protein.

• Zonulin and Its Regulation of Intestinal Barrier Function: The Biological Door to Inflammation, Autoimmunity, and Cancer [2011]
• Zonulin, regulation of tight junctions, and autoimmune diseases [2012]

Zonulin is a protein modulator of intercellular tight junctions. It has been shown to induce a significant and reversible increase in gastroduodenal and small intestinal permeability and is involved in tolerance/immune response balance. The hybridization of wheat to dramatically increase gluten (gliadin) content and its overconsumption, multiple times a day, every day, in the typical diet, chronically disrupts this tolerance/immune response balance.

Michael T. Murray ND, John Nowicki ND, in Textbook of Natural Medicine (Fifth Edition), 2020

Zonulin is a member of the MASP (mannose‐binding lectin‐associated serine protease) family of proteins, and elevated serum zonulin levels have been reported in a number of neurological conditions such as multiple sclerosis ⁷ and Alzheimer’s disease. ⁸ 

Zonulin and blood-brain barrier permeability are dissociated in humans [2022]

There is a massive number of studies, speculations, and theories on addressing this issue, especially theories on fixing leaky gut. One example:

• Weight loss via a low-carbohydrate diet improved the intestinal permeability marker, zonulin, in prostate cancer patients. [2022]
• “Besides conventional treatments, several nutritional compounds including Colostrum bovinum (8), Apple-Derived Pectin (9), vitamins A and D (10) have been found to modulate the epithelial barrier by reducing serum levels of zonulin.” The Effects of Probiotic/Synbiotic on Serum Level of Zonulin as a Biomarker of Intestinal Permeability: A Systematic Review and Meta-Analysis [2020]

BBBP – blood–brain barrier permeability

First, we need to be aware that they are different: Zonulin and blood-brain barrier permeability are dissociated in humans [2022]. For a general discussion, see A blood–brain barrier overview on structure, function, impairment, and biomarkers of integrity [2020]

Some studies that are of special interest:

• Better together? Treating traumatic brain injury with minocycline plus N-acetylcysteine [2022] IMHO, for ME/CFS this is likely a very good combination.
• The molecular weight impacts the ability to cross the barrier ” An increase of the surface area of a drug from 52 A² (e.g., a drug with a MW of 200 Da) to 105 A² (e.g., a drug with a MW of 450 Da) dramatically decrease its BBB permeation [Blood-brain barrier permeation: molecular parameters governing passive diffusion].”

When dealing with neurological issues when there is a choice of several different substances, I have looked up the molecular weight and advocated for the lower molecular weight choice. For illustration,

• Acetylcysteine (N-acetylcysteine) has a weight of 163.19
• Minocycline has a weight of 457.5
• Azithromycin has a weight of 785
• Amoxicillin has a weight of 365.4
• Piracetam has a weight of 142 (this is a fast acting nootropic that clears brain fog in minutes for some people).
• Resveratrol 228, Quercetin 302, Curcumin 368, Aspirin 180

It is an easy way to do quick evaluation— for example, I would expect Resveratrol to have a greater effect on brain function than Curcumin, with Aspirin having a still greater potential effect.

Bottom Line

The purpose of this post is frame questions that may be relevant to you — and not provide general answers.

A reader reminded me of A short ME/CFS/MCS remission with microbiome samples [2019], which used uBiome. The toolset has changed a lot since those days, so I thought it would be a good learning activity to look at the samples with the new tools.

The person had a short remission from ME/CFS after:

• 19th-22nd Amoxicillin And Clavulanate
• 22-24th VSL#3

Analysis

The table below shows about the same number of bacteria identified but with an increase in the number of bacteria at extreme values. Condition Est. had a dramatic drop which would agree with the remission. We also see a dramatic drop in extreme Enzymes and Compounds.

In my humble opinion, it suggests that reducing extremes of enzymes and compounds is a desired objective goal.

Criteria	Current Sample	Old Sample
Lab Read Quality	9.1	8.1
Bacteria Reported By Lab	327	303
Bacteria Over 99%ile	8	5
Bacteria Over 95%ile	38	22
Bacteria Over 90%ile	70	56
Bacteria Under 10%ile	38	21
Bacteria Under 5%ile	24	11
Bacteria Under 1%ile	8	5
Lab: uBiome
Rarely Seen 1%	3	1
Rarely Seen 5%	26	4
Pathogens	26	24
Outside Range from JasonH	7	7
Outside Range from Medivere	16	16
Outside Range from Metagenomics	8	8
Outside Range from MyBioma	11	11
Outside Range from Nirvana/CosmosId	16	16
Outside Range from XenoGene	31	31
Outside Lab Range (+/- 1.96SD)	16	17
Outside Box-Plot-Whiskers	122	78
Outside Kaltoft-Møldrup	156	102
Condition Est. Over 99%ile	0	0
Condition Est. Over 95%ile	0	1
Condition Est. Over 90%ile	1	11
Enzymes Over 99%ile	0	0
Enzymes Over 95%ile	50	32
Enzymes Over 90%ile	148	94
Enzymes Under 10%ile	80	246
Enzymes Under 5%ile	45	50
Enzymes Under 1%ile	6	1
Compounds Over 99%ile	3	182
Compounds Over 95%ile	16	465
Compounds Over 90%ile	27	535
Compounds Under 10%ile	81	319
Compounds Under 5%ile	76	237
Compounds Under 1%ile	72	70

Spot Checking Specific Bacteria Shifts

The more extreme bacteria shifts are shown below. The drop of Faecalibacterium levels was likely due to the drop of lactic acid produced by Lactobacillus [Metabolic Response of Faecalibacterium prausnitzii to Cell-Free Supernatants from Lactic Acid Bacteria 2020]. Given that the person has a ME/CFS diagnosis, my thoughts point to the massive reduction of Lactobacillus caused by Amoxicillin and Clavulanate resulting in a drop of lactic acid (see Lactic Acidosis in ME/CFS). While the bacteria producing lactic acid may be killed, it takes time for the system to clear it. Some sources cite a half life of 18 hours in the body[src]. The VSL#3 may be incidental or may have contributed to the remission ending.

Bacteria	Newest Percentile(Percentage)	Older Percentile(Percentage)
(genus) Alistipes	31 (0.9%)	89 (5.7%)
(genus) Anaerococcus	97 (1.8%)	62 (0.08%)
(genus) Bifidobacterium	87 (3.6%)	96 (7.3%)
(genus) Erysipelatoclostridium	99 (3.9%)	69 (0.7%)
(genus) Faecalibacterium	19 (3.9%)	51 (12.1%)
(genus) Finegoldia	99 (3.5%)	68 (0.1%)
(genus) Intestinibacter	79 (0.4%)	97 (2.4%)
(genus) Klebsiella	91 (1.3%)	none
(genus) Kluyvera	89% (1.8%)	none
(genus) Lactobacillus	67 (0.01%)	97 (3.5%)
(genus) Megasphaera	96 (2.6%)	76 (0.01%)
(genus) Parabacteroides	95 (7.0%)	81 (3.5%)
(genus) Streptococcus	99 (7.3%)	13 (0.003%)

Bottom Line

Short term remission causes are often difficult to identify the cause. In this patient, the evidence appears to be for a model of Amoxicillin and Clavulanate being effective against existing lactic acid producing species (i.e. Lactobacillus). It takes time for the lactic acid to clear the body. On the flip side, the lactobacillus would start regrowing and producing lactic acid (thus ending the remission).

A compounding factor is “Antibiotic Resistance of LACTOBACILLUS Strains [2019]”

For the subset of people with ME/CFS that improves on antibiotics and then regress; it is likely because the antibiotic suppress (but does not eliminate) lactic acid bacteria which then regrows…

Question:

Quick question—I noticed, for my BiomeSight-via-Ombre sample, that I’m not getting Vitamins, Minerals and similar suggestions. I used to get them on this sample. This only happens when I set the “Everything” option.

Anything I might be doing wrong? I’m generating the suggestions with the KM, Box Plot whisper, and Standard Lab Ranges. Avoiding Special Studies per your recent advice.

Answer: No Reproduction

I did a video to show what I did and the results.

Hi I’m a 15 year CFS sufferer with severe GI / neuro problems.  I got my second Thryve results recently.  They look really quite normal to me and it says I have significant diversity.  Is there any help / analysis you could provide to help me narrow down if there’s something actionable?  I’m not sure how much capacity you have for that, but it doesn’t hurt to ask.

  And unfortunately have been sick for longer.  Got sick at age 25 with an infection (low grade fever for months), lost 30 pounds, had vision problems, headaches, fatigue and so on.  I was able to work four years in this state but eventually I had much worsening neuro and vision symptoms and was unable to work.  I developed POTS a couple years later and at times was using a walker to get to the bathroom and was bedbound.  I’ve had some episodes of vision loss that are very strokelike in that they debilitated me cognitively and visually for long afterwards (the vision loss itself resolves after some minutes or hours).

I want to emphasize the visual and cognitive impairment are totally debilitating.  I can barely read anything or reliably focus my eyes on anything, and I went from a previously extremely high functioning person to feeling drugged, barely here 24/7.  I have severe eye pain all the time.

So I’ve been sick for really my whole adult life, to varying degrees.  Primary debilitation is visual and cognitive but I have severe physical fatigue, POTS, am 30 pounds underweight, have been diagnosed with gastroparesis years back I just can’t keep the pounds on.  Also it is notable food makes me feel TERRIBLE. Right away I can feel stupid and drugged from it, but also 2-5 hours later is when I ache everywhere and get tired and non-functional.  The 2-5 hours I’m presuming is from some dysbiosis but right away is a little more puzzling.

I clearly have such bad digestion that it is not hard to imagine it is perpetuating my brain / eye / POTS symptoms.  I’ve tried everything under the sun, mainstream and holistic and nothing that is supposed to help the gut helps.  I think fasting gives me some relief but is not practical for someone so underweight.

My first thryve was on January 13, 2020.

My most recent thryve (now ombre) was October 2, 2022.

In between the two times I’ve cycled through several gut protocols, such as taking s boulardii, soil probiotics, bifidobacteria, sourkraut, and polyphenols.  Other times I tried a more killing oriented protocol with oregano oil, berberine, and once based on a stool test a prescription antifungal (sporonox).  I eat a very restricted diet and seem to react to pretty much every food, but I have cycled through different foods in the last couple years.  I’ve tried prebiotics like PHGG and lactulose recently and are finding at least in the short term I am losing weight and have worse neuro symptoms.

My digestion and overall symptoms have not really changed between the two times.  ombre says I have a quite high microbial diversity score which is surprising because I have a massive history of antibiotics.

The request

First Look at the sample

Comparing the samples, I see a much lower quality report (2.5) in 2020. It was interesting to see

• Bacteria Over numbers drop despite more bacteria is latest sample
• Bacteria Under numbers grew — which may be due to a better quality of sample (more bacteria)
• Two of my usual measures showed improvement (despite more bacteria) — Outside Lab Range, Outside Box-Plot-Whiskers while the last one showed an increase which was a smaller percentage than the increase of bacteria reported.
  • My impression is that objectively he appears better than in 2020.

Criteria	Jan-20	Sep-22
Lab Read Quality	2.5	8.5
Bacteria Reported By Lab	442	656
Bacteria Over 99%ile	10	2
Bacteria Over 95%ile	45	10
Bacteria Over 90%ile	88	23
Bacteria Under 10%ile	54	154
Bacteria Under 5%ile	21	94
Bacteria Under 1%ile	6	19
Lab: Thryve
Rarely Seen 1%	5	7
Rarely Seen 5%	28	37
Pathogens	32	32
Outside Range from JasonH	6	6
Outside Range from Medivere	16	16
Outside Range from Metagenomics	10	10
Outside Range from MyBioma	13	13
Outside Range from Nirvana/CosmosId	18	18
Outside Range from XenoGene	9	9
Outside Lab Range (+/- 1.96SD)	27	5
Outside Box-Plot-Whiskers	124	51
Outside Kaltoft-Møldrup	183	239
Condition Est. Over 99%ile	0	0
Condition Est. Over 95%ile	1	0
Condition Est. Over 90%ile	4	0
Enzymes Over 99%ile	12	190
Enzymes Over 95%ile	208	516
Enzymes Over 90%ile	457	585
Enzymes Under 10%ile	59	265
Enzymes Under 5%ile	20	154
Enzymes Under 1%ile	2	20
Compounds Over 99%ile	73	24
Compounds Over 95%ile	264	101
Compounds Over 90%ile	368	172
Compounds Under 10%ile	297	265
Compounds Under 5%ile	225	223
Compounds Under 1%ile	62	165

In terms of bacteria distribution (not “diversity”). we see an abundance of domineering bacteria (90-99) in the earlier sample which flipped to proliferation of weak bacteria (0-9). Have tons of small amounts of bacteria at low levels should result in a good diversity. The over-representation of these nominal bacteria is a concern to me.

His attempts to change was successful. Ideally we can help more change in the desired direction.

Approach

Using PubMed data, nothing stands out and we have a very short list. This simply means that there is not a good match to the conditions reported there. In terms of Dr. Jason Hawrelak Recommendations we are at 89%ile, so generally good. The main items missing the goals by his criteria are: Faecalibacterium prausnitzii, Lactobacillus, Bifidobacerium and Akkermansia.

Given no strong pattern to match against, I will build a consensus from Lab Range, Box-Plot-Whiskers, Kaltoft-Møldrup and Dr. Jason Hawrelak Recommendations

Cross validation to the literature on the above (i.e. seeing if any has been documented to help ME/CFS). Since neurological issues were called out (and I had just done another sample with this recommendation, a few more for Hesperidin)

• Assessment of N-Acetylcysteine as Therapy for Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (NAC ME/CFS)
• Hesperidin
  • 8-Week Supplementation of 2S-Hesperidin Modulates Antioxidant and Inflammatory Status after Exercise until Exhaustion in Amateur Cyclists [2021]
  • Hesperidin as a Neuroprotective Agent: A Review of Animal and Clinical Evidence [2019]
  • The Anti-Depressive Effects of Hesperidin and the Relative Mechanisms Based on the NLRP3 Inflammatory Signaling Pathway [2020]
• Response to vitamin B12 and folic acid in myalgic encephalomyelitis and fibromyalgia. [2015]
• “Promising results are obtained by treatment with Momordica charantia extract, ” News and views in myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS): The role of co-morbidity and novel treatments [2019]
• Open Trial of Vitamin B12 Nasal Drops in Adults With Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: Comparison of Responders and Non-Responders [2019]
• Randomised clinical trial: high-dose oral thiamine[b1] versus placebo for chronic fatigue in patients with quiescent inflammatory bowel disease. [2021]
• The value of the dehydroepiandrosterone-annexed vitamin C infusion treatment in the clinical control of chronic fatigue syndrome (CFS). I. A Pilot study of the new vitamin C infusion treatment with a volunteer CFS patient [1996]
• Response to vitamin B12 and folic acid[B9] in myalgic encephalomyelitis and fibromyalgia [2015]

So all of the top suggestions appear to have documented benefits for various subsets of ME/CFS. I use the term subsets because, while similar in some symptoms, there may be a lot of differences.

We also have the simplified suggestions (with dosages). This list is intended for the brain fog person.

Looking at this list, we see that he should consider using some of the probiotics he cited in his history: bacillus subtilis, bacillus clausii, bifidobacterium (animalis)lactis, bifidobacterium breve bifidobacterium infantis. We also have 3 lactobacillus which seems to often appear with ME/CFS samples: lactobacillus casei, lactobacillus gasseri and lactobacillus salivarius.

In terms of prebiotics, only chitosan was a positive. Selenium shows up as a strong recommended supplement. See the above download for more details.

Very atypically, KEGG probiotics reports very low recommendation values with E.Coli NOT being on the top of the list. I would keep to the above probiotics and ignore the KEGG list because of the low values.

Going over to the last, experimental, modelled food suggestions, Barley was the sole take. In terms of the consensus report, it’s a toss up with different variation being good to take or to avoid. Checking oats by itself, it’s a significant negative so I would exclude the last item below and suggests barley be considered.

Bottom Line

The top suggestions can all be verified in medical literature as helping ME/CFS and the suggestions are based on this individual’s microbiome — hence patient (and not study group) specific. Hopefully he will try them and in 3-4 months do another sample so we can evaluate the change (for better or worse — I want to learn, not be right).

Because of the weight issue, I would suggest trying Pendulum, the akkermansia probiotic. I noticed that it resulted in weight loss for me and recall that is also reported in the literature.

• Akkermansia muciniphila: A Next-Generation Beneficial Gut Microbe and Its Role in Obesity and Diabetes [2022]
• Akkermansia muciniphila Suppresses High-Fat Diet-Induced Obesity and Related Metabolic Disorders in Beagles [2022]
• Akkermansia muciniphila and Gut Immune System: A Good Friendship That Attenuates Inflammatory Bowel Disease, Obesity, and Diabetes [2022]

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 appears to 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.

I use modelling and various mathematical technique to estimate forecasts when there is no hard data available.

The information below comes from Integrated analysis of gut microbiome and host immune responses in COVID-19 [2022]. While the data comes from COVID patients, there is a good chance that it may apply to other conditions. The items below are for the strongest p-values (most likely). My intent is to add all items with a value with a p Value of 0.05 or less as an experimental page, before creating the page I hope people will find similar studies that can be combined with this data. Please add as comments.

Gut_microbes	Blood_clinical_features	Correlation	Pvalue
Coprococcus_comes	CD8_counts	0.73173549	1.95E-06
Coprococcus_comes	CD3_counts	0.714258257	4.41E-06
Coprococcus_comes	Lymphocytes_counts	0.649787455	5.71E-05
Coprococcus_comes	CD45_counts	0.647009338	6.29E-05
Roseburia_intestinalis	CD8_counts	0.63669604	8.94E-05
Roseburia_intestinalis	CD3_counts	0.619860729	0.00015457
Roseburia_intestinalis	CD45_counts	0.611747625	0.000199038
Streptococcus_oralis	Eosinophil_counts	0.603056198	0.000258997

Gut_microbes	Organ_damage_related_factors	Correlation	Pvalue
Akkermansia_muciniphila	Creatine_kinase_isoenzymes	0.889522704	1.00E-11
Bacteroides_cellulosilyticus	Creatine_kinase_isoenzymes	0.88177523	2.63E-11
Streptococcus_oralis	Gamma_glutamyltransferase	0.788443186	8.39E-08
Akkermansia_muciniphila	Aspartate_Transaminase	0.784368908	1.08E-07
Bacteroides_cellulosilyticus	Aspartate_Transaminase	0.766075518	3.22E-07

Gut_microbes	Cytokines	Correlation	Pvalue
Ruminococcus_gnavus	IL17	0.513431966	0.002652723
Klebsiella_pneumoniae	IFNG	0.484801301	0.004922183
Klebsiella_pneumoniae	IL10	0.431582818	0.01364772
Lachnospira_eligens	IL2	0.393008018	0.026072229

Gut_microbes	Coagulation_factors	Correlation	Pvalue
Enterococcus_durans	APTT	0.358216937	0.044101648
Enterococcus_faecium	APTT	0.357152676	0.044780215

I started Microbiome Prescription site using data uploads from ubiome, a firm that was founded by a crowdfunding campaign, went to venture capitalists, and went unethical due to pressure from venture capitalists and died. I received over 800 samples processed by ubiome.

Readers started to request the microbiome reports to be processed on the Microbiome Prescription site and I started adding them according to constraints of the reports available. BiomeSight.com, a UK firm, has been the most cooperative. We worked together to allow automatic transfers directly from their web site to the Microbiome Prescription site by using a API.

Xenogene | Metagenómica y Biología Molecular Reports were shared to me. I found that I could do an accurate extract from one of the reports they made available to users. The result was that they became the most comprehensive report as see by the statistics below

There were few uploads because of their higher costs. The report that I used is shown below.

They Changed Their Report

Recently I have had two people trying to upload their reports. The report was different than the above. I asked them to contact Xenogene to get the above; they were not successful. I examined their reports (they were several years apart), and found two different formats, as shown below:

While both give the same information, the structure of the page was different. The report do not give the hierarchy, for example, Eubacteriaceae was found in neither report. I looked for Blautia and could find species and strains — but no total, so you cannot apply Dr Jason Hawrelak criteria.

Summing up all of the species and strains under Blautia does not give a correct total, in some cases the Blautia total will be 2x higher. Why, because many strains and species has not received names and / or “fingerprints”.

Bottom line: I no longer recommend this lab

Despite these issues, I have updated the import to support both of the above PDF formats and synthesize all of the missing layers of the bacteria hierarchy. The new import should be on line by November 13th.

WARNING: the genus level and above may often be low because of the total synthesis.

I did extract their recommended ranges and added it as an option:

Citizen Science Action

I would suggest emailing them and asking them if they make a CSV file available of the results (including the bacteria NCBI taxon number), if so, can you get a sample. If you do not get a positive results, do a return email asking you to be informed if they change and indicating that you are going to use Ombre or Biomesight instead…… The risk of loosing customers can often change business practice.

Microbiome Activism Please!!

This applies not only to Xenogene but

• Bioscreen (cfu/gm)
• Biovis Microbiome Plus (cfu/g)
• DayTwo
• Diagnostic Solution GI-Map (cfu/gm)
• GanzImmun Diagnostic A6 (cfu/gm)
• GanzImmun Diagnostics AG Befundbericht
• Genova Gi Effects (cfu/g)
• Genova Parasitology (cfu/g)
• GI EcologiX (Invivo)
• GI360 Stool (UK)
• Gut Zoomer (vibrant-wellness)
• InVitaLab (cfu/gm)
• Kyber Kompakt (cfu/g)
• Medivere: Darm Mikrobiom Stuhltest (16s limited)
• Medivere: Darn Magen Diagnostik (16s Limited)
• Medivere: Gesundsheitscheck Darm (16s Limited)
• Metagenomics Stool (De Meirleir) (16s Limited)
• Smart Gut (ubiome 16s – Limited Taxonomy)
• Verisana (cfu/ml) aka (kbe/ml)
• Viome (No objective measures)

and also these lacking NCBI taxon numbers

• Medivere – Germany
• Microba – Australia

Backstory

I emailed about six months ago with questions. Since then I’ve attempted an evaluation of my microbiome’s needs through a thorough look at your site’s AI suggestions. I attempted to implement some of those, with my primary care’s approval. I didn’t have much luck and I was looking to have another go at it, with a fresh Ombre analysis. I’m formally requesting a review for an educational post. Before I jump back into trying the AI’s suggestions again, I thought it would be foolish if I didn’t seek out the assistance of the one who designed it. I understand there are others in line and you may decline the request, but I appreciate that you are offering this to people. Hope is such a necessary lifeline with CFS. 

It feels a little odd to be giving such detailed information about myself without having a firm “go ahead” from you. From what I understand though, you want all the info before you’ll consider the request. I’ll attempt to make it brief. I have also uploaded my symptoms to the website. I consent to your use of my information.

• Symptoms
  • Fatigue
  • Exaggerated loss of muscle strength with exertion
  • Brain fog
  • Trouble reading and comprehending
  • Post exertional malaise
  • Constipation
  • Panic Attacks

-Intolerance to any probiotics, *DAIRY*, caffeine, alcohol, refined sugars, and a growing list of fruits and vegetables.

-Whatever herbs I try there is almost always an initial benefit, but then things go back to the way they were. (Possible bacterial adaptation?)

• Diagnosed
  • “Chronic Lyme”
  • ME/CFS
  • IBS-C
  • Panic Attacks
  • Depression

~ Backstory ~

Dec 2012 – I had been working multiple full time jobs while eating very poorly. Essentially fasting, and what I did eat was high carb, low nutrient foods. No fruits, vegetables, or other nutrient rich items. I felt something snap in me in an instant. I felt panicky and went and ate a large meal immediately. From that moment on I’ve suffered from CFS. The most prominent features being fatigue, exaggerated loss of muscle strength with exertion, brain fog, trouble reading and comprehending, post exertional malaise, and constipation. My symptoms were the most exaggerated at that time, although recently they have started to get back to that point in time. Examples: I would eat a carb rich food like pasta and 30 minutes later I would literally be on the floor in a quasi lucid state; Two and a half weeks without a BM. My primary care at the time put me on antidepressants and thyroid medications, which did nothing for me.

March 2016 – I started to see an integrative medicine MD who thought that I had reactivated Lyme. He reasoned that it was dormant in my system from when I had it as a 5-6 year old, and that the stress allowed it to manifest itself again. I was on an absurd amount of supplements and various antibiotics. I found initial improvement that I felt stopped my decline and helped with some symptoms, but didn’t solve the CFS. The one drug that I felt the best on was Tinidazole. I stopped seeing him in 2017.

July 2017 – I stopped working as my symptoms had continued to get worse over the years. I started taking care of my sister who was diagnosed with terminal brain cancer. She died in 2019.

July 2018 – Started to see a new primary care. He confirmed the CFS diagnosis but refuses to help in any way. He encourages me to seek solutions on my own however.

Dec 2018 – Started to see another Lyme specialist who told me about the herbalist Stephen Buhner. I bought his book and attempted a slew of his proscribed herbs over the course of a year or two, with little benefit. He also put me back on doxycycline for 6-12 months. It did help but just by taking the edge off of my symptoms.

Fall 2019 – I started to develop panic attacks. It was clear to me that stress made them worse but that it was primarily an issue stemming from a physical problem, rather than an emotional one. This was evinced by the fact that certain foods could manifest them. I felt that whatever my problems were, they were physical and were slowing progressing.

Summer 2021 – I started looking into gut health as a cause of CFS. I started the Wahl’s diet and found some improvement through that. It afforded me enough strength to go back to work for six months. I never entered fully onto the diet as it was prohibitively expensive, but I did keep some of the foods that helped.

2021 – I started to see a gastrointestinal dr. who was absolutely no help. He diagnosed me with IBS-C but didn’t have any answers or solutions. He did proscribe Amoxicillin, which I declined to take as I was not sure if it would help or hurt my gut bacteria.

April 2022 – I found your website, uploaded an Ombre test, and attempted some of the suggested herbs. I found initial benefits from cinnamon but any long-term attempt at any of the herbs is really a trial (and I’m not one to back down from a fight or a stranger to discomfort). I continued on some of them until I thought there might actually be a chance of dying from it. I just couldn’t tell if it was herxing or hurting.

Spring 2022 – Developed food sensitivities, primarily to dairy. Dairy gives me intense psychological issues. The best I can describe them is that they are like racing thoughts accompanied by the feeling that my head will explode and there is no way to escape. Food that once helped, like carrots and berries, now make my intestines feel like overinflated balloons: a lot of pain. 

August-October 2022 – I started to care for my mother who was diagnosed with terminal stomach cancer. She died and the stress of it has amplified my already mounting symptoms to a fevered pitch. It almost feels like when things started back in 2012.

This story is unfortunately very typical for many people. My wish is that Microbiome Prescription will be able to help. I do not have “the cure”; what is generated are suggestions (many — so pick and choose what works for you), items modelled to have better than random impact on the microbiome.

First Look at the sample

We have two Ombre samples on the account:

• May 2,2022
• Oct 18,2022

With two samples from the same lab, my first step is typically to compare them. I omitted the KEGG data which was not illustrative of changes.

Criteria	Old Sample	New Sample
Lab Read Quality	4.2	5.6
Bacteria Reported By Lab	561	677
Bacteria Over 99%ile	2	7
Bacteria Over 95%ile	18	21
Bacteria Over 90%ile	38	43
Bacteria Under 10%ile	92	121
Bacteria Under 5%ile	37	62
Bacteria Under 1%ile	3	11
Lab: Thryve
Rarely Seen 1%	5	8
Rarely Seen 5%	23	54
Pathogens	40	30
Outside Range from JasonH	3	3
Outside Range from Medivere	14	14
Outside Range from Metagenomics	9	9
Outside Range from MyBioma	12	12
Outside Range from Nirvana/CosmosId	21	21
Outside Range from XenoGene	8	8
Outside Lab Range (+/- 1.96SD)	9	40
Outside Box-Plot-Whiskers	67	128
Outside Kaltoft-Møldrup	136	244
Condition Est. Over 99%ile	0	0
Condition Est. Over 95%ile	0	0
Condition Est. Over 90%ile	0	1

My read is that between the samples, the person has gotten worse. Why?

• Outside Lab Range (+/- 1.96SD), Outside Box-Plot-Whiskers, Outside Kaltoft-Møldrup all have very significant increases,
  • This is also reflected in Bacteria Over ??%ile and Under
• Not having any strong matches to (PubMed Studies) Conditions is unusual. It suggests that the compounding of issues results in the microbiome not falling into any established “box”.

We see that also with the distributions, a massive surge of under-represented bacteria (0-9)

While he attempted suggestions after the first sample, we see a mountain of microbiome changing events also occurred (especially stress which, for me, has been very significant cause of my own historic dysbiosis). Whether the suggestions helped or hurt cannot be determined.

Approach

Building a consensus from Lab Range, Box-Plot-Whiskers and Kaltoft-Møldrup seems the best approach.

Early Sample

From the consensus we see a list which agrees with what is often reported as helping ME/CFS from the earlier sample.

Some illustrations from the literature of the suggestions

• A Botanical Product Containing Cistanche and Ginkgo Extracts Potentially Improves Chronic Fatigue Syndrome Symptoms in Adults: A Randomized, Double-Blind, and Placebo-Controlled Study. [2021]
• Nigella sativa seed extract attenuates the fatigue induced by exhaustive swimming in rats [2017]
• Randomised clinical trial: high-dose oral thiamine versus placebo for chronic fatigue in patients with quiescent inflammatory bowel disease. [2021]
• Response to vitamin B12 and folic acid in myalgic encephalomyelitis and fibromyalgia. [2015]
• Assessment of N-Acetylcysteine as Therapy for Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (NAC ME/CFS)

The person cited issues with dairy. In the consensus it was listed as an avoid. Also listed was also: galactose (milk sugar), high saturated milk fat diet, milk-derived saturated,fat.

For #1 suggestion: Hesperidin (polyphenol) [available as a supplement] we see the following studies:

• 8-Week Supplementation of 2S-Hesperidin Modulates Antioxidant and Inflammatory Status after Exercise until Exhaustion in Amateur Cyclists [2021]
• Hesperidin as a Neuroprotective Agent: A Review of Animal and Clinical Evidence [2019]
• The Anti-Depressive Effects of Hesperidin and the Relative Mechanisms Based on the NLRP3 Inflammatory Signaling Pathway [2020]

What I did above is called, cross-validation. This means checking if the suggestions generated by the model agrees with clinical experience. It does. This implies that items not seen in studies (like a grapefruit for breakfast) seems likely to have positive effects.

Cross validation is always a good step after getting suggestions. The suggestions using this trio of methods to select will mostly be good — but odd cases may produce poor results.

Latest Sample

Given the stress etc. I know that the microbiome will shift and may not be so easy to cross-validate. We see many of the same things, they have just rearrange themselves.

As a FYI, Dairy was 10x more negative in this sample, and other dairy items similarly MORE stronger to avoid: Whole Milk, high saturated milk fat diet, milk-derived saturated,fat. In agreement with dairy issues.

Two Other versions of Suggestions

We have the simplified suggestions (shown above) with the to-take probiotics being:

• bifidobacterium (animalis) lactis
• lactobacillus gasseri
• bacillus coagulans (with bacillus subtilis being a very strong avoid).
• KEGG suggested Escherichia coli Probiotics — which is to be expected from ME/CFS. A low level of Escherichia coli has been reported in the 1999 Australian Conference papers.

My suggestion would be ONLY bifidobacterium (animalis) lactis (Custom Probiotics has it available as a single species without additives) and E.Coli (i.e. Symbioflor-2 )

The last version of suggestions is a food list derived from flavonoids etc in food. It is an experimental exploration (so a grain of caution is suggested).

The only thing that was positive was Barley which is on the avoid list. So nothing (safe) useful from this experimental method.

As a FYI, I checked for items that are adaptogens (helps with stress) and the following were on the to-take list.

• ashwagandha (withania somnifera)
• chamomile (chamaemelum nobile)
• hypericin(St. John’s Wort)

Note on the numbers on various lists

The suggestions often have numbers beside them. The numbers are relative numbers for things in the same list. In simpler words:

• One in Metric, – meters
• One is Imperial/American, miles
• One is Roman, league
• One is nautical, knots
• One is astronautical – parsec

They cannot be compared to each other. The goal of each list is find the best given the approach.

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 appears to 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.

I use modelling and various mathematical technique to estimate forecasts when there is no hard data available.