Foreword – 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 a knowledgeable medical professional before starting.
Patient Notes
My son has headache, lethargy and reduced sleep. He’s in the spectrum so there are a lot more symptoms associated with it. But these are things I am trying to figure out, help him at least have a life without pain.
Analysis
As a result on my involvement with Long Covid Study – VERY early data, I built some private tools (computational intense, with good statistical understanding requires) .
The number of bacteria flagged for the closest match to the symptoms (with good sample sizes) are shown below. Each set of suggests had a lot of similarity to each hour, especially with red wine near the top of most lists. Red wine to children was historically done (especially French and Italian kids), but . . .
| Symptom Obs | No Symptom Obs | Symptom Name | Bacteria Flagged |
|---|---|---|---|
| 83 | 901 | General: Headaches | 32 |
| 41 | 943 | Post-exertional malaise: General | 22 |
| 70 | 914 | Neurological-Sleep: Chaotic diurnal sleep rhythms (Erratic Sleep) | 72 |
| 77 | 907 | Autism: Official Diagnosis | 26 |
At this point, I decided not to grind thru the standard set of suggestions, instead look at the consensus data (which is attached as a download below). The list was less than usual, 180 items.
I also went over to the KEGG determined probiotics and saw some items had consensus between them for probiotics, the top agreements are below
- Prescript-Assist®/SBO Probiotic ( Equilibrium Probiotics are likely an alternatives)
- PIANETA FARMA/KefiBios
In terms of supplements:
- Biotin (Vitamin B-7), B-12, B-1
- Calcium
Check the diet for food that may be high in choline (aka choline deficiency) and reduce them. See NIH page for a list.
Pro Forma Analysis
I went on to do the usual analysis:
- Use JasonH (15 Criteria) – 7 bacteria picked
- Standard Lab Ranges (+/- 2 Std Dev) – 19 bacteria picked
- Box Plot Whisker – 62 bacteria picked
- Kaltoft-Moltrup Normal Ranges – 148 bacteria picked
- Percentile in top or bottom 10% -324 bacteria picked (out of 696 available, 46%!!)
The consensus report is attached, the suggestions appear similar but with shifting up and down on the list and a lot more items (567 vs 180 above). This video shows the process
Bottom Line
I did a VLookUp in Excel between the two lists to see the similarities and differences. There were a few difference. My usual advice is “if we don’t know the right answer, omit unless there is a strong reason to include”
| Custom | Pro Forma | Modifier2 |
| 317.5 | 262.4 | choline deficiency |
| 309.3 | 382.7 | rice bran |
| 205.2 | 79.2 | Prescript Assist (2018 Formula) |
| 193.6 | 208.6 | vitamin b7 biotin (supplement) (vitamin B7) |
| 164.9 | 80.4 | high red meat |
| 153 | -13.2 | saccharomyces boulardii (probiotics) |
| 152.3 | 63.6 | low fodmap diet |
| 152.3 | 159.4 | low protein diet |
| 138.8 | -21.6 | low-fat diets |
| 130.8 | 62.8 | calcium |
| 124.2 | -24.4 | fructo-oligosaccharides (prebiotic) |
| 118.5 | -32.7 | vsl#3 (probiotics) |
| 108.5 | 72.3 | saccharin |
| 105.4 | -15.6 | red wine |
| 105.4 | 2.4 | schisandra chinensis(magnolia berry or five-flavor-fruit) |
| 105.4 | 44.2 | stevia |
| 105.4 | 22.8 | l-citrulline |
| 98.4 | 74.7 | Prescript Assist (Original Formula) |
Questions and Answers
One of the fundamental challenges of the microbiome is a lack of information on many interactions because studies have not been done. The site attempts to use whatever fragments of information that is available as well as the genes of the bacteria (when the data is available).
- Question #1 PIANETA FARMA/KefiBios – I saw his Akkermansia is at a good level. Do you still recommend this probiotics?
The only known impact is on Akkermansia but that was not the basis of the suggestion. The suggestion came by looking at the amount of various compounds that he appears to be low in (using Kyoto Encyclopedia of Genes and Genomes on the bacteria he has, and the bacteria in various probiotics). Most of these compounds are not available as supplements.
| Compound Name | OtherName | Formula |
| D-Alanine | D-2-Aminopropionic acid D-Ala | C3H7NO2 |
| L-Homocysteine | L-2-Amino-4-mercaptobutyric acid Homocysteine | C4H9NO2S |
| Aromatic aldehyde | C7H6O | |
| CDP-diacylglycerol | CDP-1,2-diacylglycerol 1,2-Diacyl-sn-glycero-3-cytidine-5′-diphosphate | C14H19N3O15P2R2 |
| Thioredoxin | Reduced thioredoxin | C10H14N4O4S2R4 |
| N-(L-Arginino)succinate | 2-(Nomega-L-Arginino)succinate L-Argininosuccinate L-Argininosuccinic acid L-Arginosuccinic acid | C10H18N4O6 |
| 2-Dehydro-3-deoxy-6-phospho-D-gluconate | 6-Phospho-2-dehydro-3-deoxy-D-gluconate 2-Keto-3-deoxy-6-phosphogluconate 2-Dehydro-3-deoxy-D-gluconate 6-phosphate | C6H11O9P |
| 4-O-[(2R)-1-Glycerophospho]-N-acetyl-beta-D-mannosaminyl-(1->4)-N-acetyl-alpha-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol | C74H125N2O22P3 |
- Question #2: Prescript-Assist®/SBO Probiotic – I saw the list on your website. Sorry, I want to understand a little more detail about it. I know its soil based probiotics. I wanted to understand if it will help improve bifido .. I saw this has bacillus.
- Answer: There is no known direct impact on bifido. If Bifidobacterium is your primary concern, excluding every other bacteria involved, then see this page. Suggestions are based on a holistic analysis, not a blinkered view.
- Question #3: Also do you have any recommendations to help reduce the histamine level?
- Answer: Diamine oxidase (DAO) is the supplement commonly used to reduce the impact of histamine [study]. “Histamine is a monoamine synthesized from the amino acid histidine through a reaction catalyzed by the enzyme histidine decarboxylase (HDC)”[2018] Trying to find the bacteria involved is a bit more speculative.
Searching for histidine involved enzymes, we see that he has very high levels of two:
The three greatest producers are: Erysipelatoclostridium ramosum, [Clostridium] innocuum, Turicibacter sanguinis and Streptococcus iniae. For Erysipelatoclostridium ramosum, most items increases it ( dairy, resveratrol (grape seed/polyphenols/red wine)) but two items decreases it: xylooligosaccharide (prebiotic), bifidobacterium bifidum (probiotics). You could try hand assembling suggestions for these 4 bacteria.
The other way, using Diamine oxidase, is to go over to KEGG, it is Enzyme 1.4.3.22, none of the bacteria he has appear to produce it, nor do any of the bacteria reported from 16s samples.
- Question #4: Choline Deficiency – Does it mean we have to give him a PC?. You had mentioned there might be Choline in his diet. So is it more or is it deficient?, I think choline and Ammonia might be impacted because of the Antifungal regimen he is in?.
- Answer: Choline occurs naturally in food, Background: https://www.hsph.harvard.edu/nutritionsource/choline/ A study on choline deficiencies found that the bacteria we targeted were shifted in the desired direction. There is a lot of literature on choline ( https://pubmed.ncbi.nlm.nih.gov/?term=choline+deficient+diet ) and digesting that is a job for your medical professional. My usual takeaway is check what is normally eaten for choline content and consider reducing it a bit by changing foods (after consulting with your medical professional). No need to go to extreme measures… it is just one possible factor.
- Question #5: Also the modifier 2 means he needs all those based on his microbiome, Is it right?
- Answer: I do NOT know what he needs, the suggestions are strictly things that have been calculated from available data that has improved odds on shifting the microbiome towards the typical microbiome. Everything is probability and odds — nothing is definitive. In the absence of definitive knowledge, I believe that modelled data gives better suggestions than “let us try A,B,C”. For dealing with ME/CFS, the suggestions of what should help matches the literature on what helps – which increases my confidence in the model.