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.
I’ve had ME/CFS 14 years (symptoms came on stronger after breast augmentation 2008) but the last 9 yrs I’ve been mostly housebound & bed bound 21 hours per day. I’d say I’m moderate/severe. (I live in the Uk)
- Brekkie :- muesli (take raisins out) with coconut milk or almond milk Or poached egg on 1 seeded brown bread Or scrambled egg with cumin, coconut milk, salt & black pepper on 1 seeded brown bread Or porridge with coconut milk, frozen blueberries or dried goji berries
- Lunch:-A banana, nuts (walnuts, pecans, almonds) & mixed seeds
- Dinner:-Salad (bistro salad leaves with a little shredded beetroot) cucumber, celery, grated carrot, with jacket potato (or sweet potato) & vegan cheese on top.. I’ve just started to add a sprinkle of organic olive oil & black pepper (tasty) Or Steamed veg – carrots, green beans, broccoli, stringless beans & sugar snap peas (or mangetout) with sweet potato & usually something out the freezer I pop in oven… which I know I need to stop as it’s processed. I will begin to change that for chicken or salmon (it’s just been easier)
More information on diet and supplements was also sent.
Looking at Bacteria Deemed Unhealthy, the sole item that stands out was moderately high Streptococcus oralis. Dr. Jason Hawrelak Recommendations came out to 90%ile — so better than most people.
For this person, we have a shift towards rarer bacteria with those seen in only 30-50% of samples being over represented.
|0 – 9||2||2|
|10 – 19||8||5|
|20 – 29||11||9|
|30 – 39||10||20|
|40 – 49||11||19|
|50 – 59||9||13|
|60 – 69||9||9|
|70 – 79||5||9|
|80 – 89||4||6|
|90 – 99||5||6|
Since ME/CFS is the condition, I checked the list of antibiotics often prescribed with the following being the top of the list. It is interesting to note that the literature finds that they do improve some ME/CFS patients
- gentamicine sulfate (antibiotic) (1) [See 2021] 
- rifaximin (antibiotic)s (0.949) [Health Rising]  and many more
- amikacin hydrate (antibiotic) (0.845) – no significant literature
- gentamicin (antibiotic)s (0.745) 
- metronidazole (antibiotic)s (0.727) “Metronidazole/Flagyl is reported to have 75% of CFS patients improving ” [Src] also [BMJ]
On the avoid list are some antibiotics that are also prescribed for ME/CFS
- rifampicin (antibiotic)s ( – 0.423 )
- tetracycline (antibiotic)s ( – 0.291 )
- azithromycin,(antibiotic)s ( – 0.289 )
- rifampicin (antibiotic) ( – 0.289 )
- doxycycline (antibiotic)s ( – 0.191 )
She provided some of the items that she is taking so I looked at the estimated impact on her microbiome
- sertraline,(prescription) which she is reducing. This is likely a good course of action
- Take Estimate: 20.4, Avoid Estimate: 24.7
- dopamine (prescription) – this is a bit of a concern to me because it is likely to contribute to microbiome dysfunction
- Take Estimate: 13.2, Avoid Estimate: 23.1
- Vitamin C, — keep taking
- Take Estimate: 22.3, Avoid Estimate: 13.9
- Take Estimate: 20.4, void Estimate: 29.1
Note: the above are estimates on whether they will improve or contribute to the microbiome dysfunction. Medical concerns should always dominate.
Doing my usual pick the bacteria to change using different criteria we have:
- Use JasonH (15 Criteria) – 8
- Standard Lab Ranges (+/- 2 Std Dev) – 3
- Box Plot Whisker – 19
- Kaltoft-Moltrup Normal Ranges – 34
- Percentile in top or bottom % – 27
The number of bacteria selected for each of the above was lower than I often seen.
Going to the Consensus
The following suggestions stand out:
- whole-grain barley (she does report porridge, she may wish to make sure that it includes barley)
- Vitamins: Note ME/CFS usually benefit for B-Vitamins  
- Conjugated Linoleic Acid
- melatonin supplement
- N-Acetyl Cysteine (NAC),
- lauric acid(fatty acid in coconut oil,in palm kernel oil,) – She does use coconut milk, this is good. She may wish to increase.
Dropping down to the avoid list, we see
- nuts (including walnuts, almonds/ almond skins ) – she currently use these as snacks. banana and plantain bananas are fine to use as snacks
- peppermint (spice, oil) – she may wish to change to use ginger and especially Echinacea tea instead
The full list is attached.
Trying out an Experimental feature
I have used this feature of the several recent blogs on autism (Bacteria to Hand-Pick for Autism with Ombre/Thryve samples, Bacteria to Hand-Pick for Autism with Biomesight samples). I have posted the bacteria identified here. Unfortunately sample size are small (1/3 of the Long COVID samples)
Using the 61 samples annotated with CFS and processed thru the same lab (Biomesight.com). We found 11 bacteria identified as statistically associated with CFS. Three were too high and 8 were too low.
The results from this custom picked set are shown below.
|Modifier – Suggestion to take||Confidence|
|Human milk oligosaccharides (prebiotic, Holigos, Stachyose)||1 📏|
|whole grain diet||0.576|
|vitamin k2||0.4 📏|
|bacillus subtilis,lactobacillus acidophilus (probiotics)||0.38|
|lactobacillus fermentum (probiotics)||0.38 📏|
|lactobacillus gasseri (probiotics)||0.38 📏|
|lactobacillus reuteri (probiotics)||0.38 📏|
|arabinoxylan oligosaccharides (prebiotic)||0.328|
|chondrus crispus (red sea weed)||0.328|
|Modifier to avoid||Confidence|
|glycyrrhizic acid (licorice)||0.382|
|refined wheat breads||0.214|
|Probiotics that are best to take Name||Impact|
|Bromatech (IT) / Rotanelle plus||7.9|
|probiotic pur (de) / realdose nutrition||6.18|
|Jetson (US) / Immunity Probiotics||6.09|
|douglas laboratories / multi probiotic 40 billion||6.09|
|Thryve L.PCasei Th1, L.PCasei Th2,L.Ferm IBF1, L.acidoph||6.09|
We have some contradictions between these suggestions and the ones above. Why? The data we are using is very very incomplete. It is the best that is available. In keeping with my principle of less risk, when suggestions are in disagreement (for example Nuts and almonds – recommended here but to avoid above), then omit them. There are a lot of possible items, keeping to positive items where there are no disagreement is the best path.
Because this person suffers from brain fog, they may wish to sit down with a nutritionist to go thru the download list above to craft a diet plan. The suggestions are in no way a balanced nor complete diet. For example increase food rich in magnesium on the take suggestions, or using supplements.
As always, this information is computed from the best available data and is not based on clinical experience. Always review with your medical professional for appropriateness of suggestions before starting.
I check with this person and the breast augmentation has not been undone. In other words, there is a reasonable chance that it is a significant contributor to the ongoing symptoms. I expect some progress from microbiome manipulation, but I suspect the side effects from augmentation will limit it. The literature seems to confirm it.
- “Subclinical bacterial infections (biofilms) are strongly implicated in breast augmentation” 
- “The most common cause of surgical readmission after breast implant surgery remains infection. Six causative organisms are principally involved: Staphylococcus epidermidis and S. aureus, Escherichia, Pseudomonas, Propionibacterium, and Corynebacterium.” 
- “The researchers found that the women with silicone gel-filled breast implants were significantly more likely to be diagnosed with autoimmune or rheumatic disorders, such as Sjögren syndrome, systemic sclerosis, and sarcoidosis, compared with women without breast implants of a similar age and socioeconomic status.” 
- “Silicone breast implants(SBI) are associated in a proportion of patients with complaints such as fatigue, cognitive impairment, arthralgias, myalgias, pyrexia, dry eyes and dry mouth. Silicones can migrate from the implant through the body and can induce a chronic inflammatory process. Explantation[Removal] of SBI results in the majority of patients in an amelioration of the symptoms.”