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-Moldrup	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-Moldrup) 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.