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-Moldrup	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-Moldrup 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-Moldrup 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.