Prior Posts
Dealing with ME/CFS and many microbiome dysfunction is rarely a short journey
- ME/CFS Continues Improvement + Lab Read Quality Issues [Feb 2024]
- Update on ME/CFS Person [Sep 2023]
- Follow up Microbiome Analysis from a prior post [Apr 2022]
- Rosacea, Circulation and mild CFS [Dec 2021]
Comparisons
I have done a trimmed version below excluding ranges from most various labs. Remember lab ranges are suspect because of The taxonomy nightmare before Christmas… For the measures based on other samples from the same lab, we see improvement from the prior test although we have 15% more bacteria reported.
| Criteria | 12/3 2024 | 9/2 2024 | 1/22 2024 | 9/12 2023 | 2/22 2024 | 8/11 2022 | 3/25 2022 | 12/3 2021 | 8/31 2021 |
| Lab Read Quality | 9.8 | 9.1 | 7.9 | 3.5 | 9.7 | 5.5 | 6.2 | 3.6 | 7.8 |
| GanzImmun | 14 | 16 | 16 | 16 | 15 | 15 | 17 | 17 | 20 |
| Outside Range from Lab Teletest | 17 | 23 | 20 | 20 | 24 | 24 | 22 | 22 | 25 |
| Outside Lab Range (+/- 1.96SD) | 7 | 12 | 5 | 15 | 10 | 11 | 9 | 9 | 14 |
| Outside Box-Plot-Whiskers | 47 | 48 | 54 | 56 | 42 | 36 | 42 | 59 | 42 |
| Outside Kaltoft-Moldrup | 85 | 113 | 123 | 70 | 139 | 56 | 78 | 59 | 140 |
| Bacteria Reported By Lab | 689 | 600 | 511 | 399 | 666 | 478 | 613 | 456 | 572 |
Looking at Symptom Matching Patterns, we see significant improvement. 10 have improved and 1 has become worse. Remember that with 15% more bacteria, the odds matching should increase if there was no change.
Remember, Microbiome Prescription does not claim to cure or fix issues; it’s aim is produce suggestions that are more likely to help than picking random items. Let us look ahead for the next leg of the journey for better health.
Going Forward
Since we have Symptoms entered, we will get 3 sets of suggestions, two will produce probiotics only. The Using PubMed Studies to filter is ignored since we have a good collection of symptoms. I view this choice to be inferior because the reported shifts are suspect due to The taxonomy nightmare before Christmas…
From the 51 symptoms indicated, we ended up with 49 bacteria deemed to high or low. That is about 7% of the reported bacteria. I usually expect 5-10% of the bacteria being flagged using symptoms. If the percentage is over 10%, I advocate removing milder symptoms — why? to reduce “noise” in targeting bacteria.
In terms of results, there was an unexpected result, walnuts and aspartame were near the very top suggestion(. This was followed by a bunch of antibiotics with 50% being reported by specialist to help CFS. These include (in order).
The top probiotics were:
- Lacticaseibacillus casei {L. casei}
- Limosilactobacillus reuteri {L. Reuteri}
- Bifidobacterium longum subsp. longum BB536 {BB536}
- Saccharomyces cerevisiae var boulardii {S. boulardii}
- Lactobacillus gasseri {L.gasseri}
Only one vitamin makes it above by arbitrary 50% of highest priority: Vitamin A. My personal approach taking Vitamin A is 5-7 days of 50,000 IU per day. This dosage is deemed safe, especially for a short period [2004]. This approach came from the Complete German Commission E Monographs. View this as an antibiotic to include in the rotation.
Amino Acids were: {glycine}, {Theanine} and {Glutamine}. Common supplements: Tauroursodeoxycholic acid a.k.a. Tudca. Diet type: Low FODMAP. Herbs or spices: Morinda citrifolia {Noni}. {Baicalin }, {garlic}, {Eugenic acid} – usually found in clove, cinnamon, nutmeg, basil, and bay leaf.
Foods of special interest:
- walnuts
- Propolis {Bee glue}
- {Almonds}
- Taraxacum officinale {Dandelion} i.e. tea
- Secale cereale {Rye}
- Whole Cow milk {Whole Milk}
- blueberry
- {Acai}
I will leave it to the reader to review the avoids (the top ones include: {slippery elm}, {Stevia}, Heyndrickxia coagulans {B. coagulans}, High Fat and High Sugar diets).
The probiotic list are only those with no adverse effects and positive effect. This boils down to two: Lacticaseibacillus casei (as above) and Lactobacillus Helveticus
KEGG Probiotics
Based on Compound, we have:
And for Enzymes
Why E.Coli probiotics are not in the first list.
The first list is based on published studies. Most published studies use 16s (cheap) processing and that technology is very weak for detecting E.Coli so shifts go unseen and unreported. See ME/CFS: The Evils of Lactobacillus Probiotics? for more information. The table below show that Shotgun detects E.Coli 90-100% of the time, while 16s detects it 0.1% to 50% of the time. If the research cannot see it, they cannot report what shifts it.
The KEGG approach is not dependent on someone doing a study with (expensive) shotgun testing; it uses the genetics of the bacteria alone.
Notes on Changing Symptoms
My first draft of this post used his symptom list before he trimmed it of items that are now mild. The core suggestions did not change much — but there was some reordering happening.
Trying out the new Over and Under Represented Algorithm
The question is how do you deal with over or under represented? I mentally stepped away from this individual sample and realized that for a population of similar people, you will try to increase the under represented and decrease the over represented. Using this as my initial algorithm, I went to the Old UI where you can individually select it (if you have symptoms entered).
The top items were the same antibiotics as above
And the commercial probiotics had the top one being one of those listed above.
This suggests that there is significant convergence in suggestions although a very different path was taken. Adding this to the above consensus, I noticed a few significant shifts:
- Walnuts dropped down the list (but at #6 for foods)
- Bifidobacterium longum moved to the top for probiotics
- {Dandelion} moved back to the top for foods
I extracted a “everyone agrees” food list that is shown below
- Taraxacum officinale {Dandelion}
- Petroselinum crispum {Parsley}
- (2E,4E)-5-(1,3-Benzodioxol-5-yl)-1-(1-piperidinyl)-2,4-pentadien-1-one {Piperine}
- Citricidal {Grapefruit seed extract}
- Hibiscus {Rose mallow}
- Euterpe oleracea {Acai}
- Myristica fragrans {Nutmeg}
- Apium graveolens {Celery}
- Carum carvi {Caraway}
- Armoracia rusticana {Horseradish}
- Dysphania ambrosioides {Epazote}
- Coriandrum sativum {Coriander}
- Sinapis alba {yellow mustard}
- Cuminum cyminum {Cumin}
- Tea tree
- Garcinia mangostana {Mangosteen}
Bottom Line
Assuming antibiotics are available, I would do the following sequence with 7-10 days of each.
- metronidazole [CFS]
- Bifidobacterium longum subsp. longum
- Vitamin A (Increases B.Longum and E.Coli)
- Symbioflor-2
- amoxicillin [CFS]
- Limosilactobacillus reuteri {L. Reuteri} (No studies found that it is decreased by amoxicillin)
- ciprofloxacin [CFS]
- Bifidobacterium longum subsp. longum (ciprofloxain increases it)
- Mutaflor
While not listed at all in the consensus, I would suggest doing d-ribose concurrently because it increases both E.Coli and Bifidobacterium. It does show up in the under/over representation as a negative with no impact on the other 6 suggestions list — so I would ignore this negative.
As always, no one knows how to precisely fix the microbiome, the above is computed (thus no human bias) to most likely help.