This is the son of a person with issues: Bad Diet and Antibiotics? ME/CFS like symptoms. As I have often cautioned, young people’s and children’s microbiomes are different than adults and we do not have appropriate reference ranges. We will do best efforts.

• Tired all the time
• Cannot gain weight (very skinny)
• Diagnosed with Marfan syndrome (a genetic disease he has since birth)
  [editor] About 1 in 5,000 people have Marfan syndrome
• Stomach pain
• Disgestion issues (yellow stool and fat in stool)
• Joint and Muscle pain
• Dark circles around the eyes

Analysis

There is no available literature on microbiome shifts with Marfan syndrome. Marfan syndrome (MFS) results from heterozygous mutations in the fibrillin-1 gene (FBN1; OMIM #134797), located on chromosome 15 at band q21. 1 (15q21. 1), which encodes for the glycoprotein fibrillin. [MedScape]. Coagulation plays a major role in Marfan syndrome. Both procoagulation and bleeding disorders participate in the disease. Platelet function abnormalities, compatible with von Willebrand syndrome or congenital thrombocytopathies, have been identified in 29% of patients. [2014].

 FBN1 is the causative gene for Marfan syndrome, an inherited disorder of connective tissue whose major features include tall stature and arachnodactyly, ectopia lentis, and thoracic aortic aneurysm and dissection. More than one thousand individual mutations in FBN1 are associated with Marfan syndrome, making genotype-phenotype correlations difficult. [2016]

At a high level we see potential issues. [NOTE: The Eubiosis value changed for many people after a defect was detected in how percentile was computed for some bacteria – often 100% dropped, which how agrees with people symptoms ].

However, there were no statistically significant matches (this page was just updated to use the latest algorithm). This algorithm is similar to the Eubiosis algorithm. We compute the expected number of matches to bacteria shifts associated with the symptoms. The expected number by randomness is 16%. A higher number indicate increased odds, a lower number decreased odds. This is based on the existing annotated samples uploaded data. It is not definitive and often there can be multiple subsets of bacteria associated with a symptom. The match is on too much or too few of a collection of bacteria associated to symptoms.

We will still check the matching symptoms. The top one is a match for symptoms but not a match for the typical bacteria seen for this symptom. We have to hope that there is sufficient matches to be worth while.

First, looking at all of the common, popular measuring sticks –

• General Health Predictors has a low number (just 8) with only one of possible concern: Veillonella atypica 
• All of the usual ratios are between 20%ile and 80%ile
• Anti inflammatory Bacteria Score is at 89%ile — very good
• No Potential Medical Conditions Detected detected
• Histamine issues are a potential health issue
• Bacteria deemed Unhealthy: Bacteroides fragilis and Parabacteroides merdae are the only one, both are potentially infectious bacteria.
• Dr. Jason Hawrelak Recommended Levels came in at 94%ile

So, everything looks like a reasonably healthy person.

Going Forward

With no clear issue associations, we are going to do two runs: One with symptoms and one without.. Using the standard ‘Just give me Suggestions’ The list below are for the items at a priority of 50% or more of the highest priority [506] [Symptoms: 440]. This limit has no rationale apart from reducing the volume of suggestions.

Suggestions

• polyphenols:
  • Hesperidin (polyphenol)
  • Arbutin (polyphenol)
  • diosmin,(polyphenol)
  • luteolin (flavonoid)
  • Guaiacol (polyphenol)
  • mannooligosaccharide (prebiotic) — Coffee is rich in them! as are chickpeas, lentils, and peas
• Herb and Spices – Nothing in range, highest was ginger
• Diet Style — last time nothing made it above the cut, that is no longer the case, two made it above the line
  • gluten-free diet
  • vegetable/fruit juice-based diets
• Amino Acid – nothing last time
  • l-glutamine made it above the cut
• Foods –
  • Caffeine (Coffee, Tea etc)
• Probiotics Nothing over 250
• Sugars – nothing in range, sucralose was highest
• Vitamins
  • The usual B vitamins B1,B3,B6,B7,B9,B12
  • WARNING: Make sure you are doing therapeutic dosages of these, See Supplement Dosages.
  • Vitamin B Mitigates Thoracic Aortic Dilation in Marfan Syndrome Mice by Restoring the Canonical TGF-β Pathway [2021]

Let us look at AVOIDS, given the general healthy state, just try reducing if taking,

• inulin (prebiotic), arabinogalactan (prebiotic), fructo-oligosaccharides (prebiotic), Human milk oligosaccharides (prebiotic, Holigos, Stachyose)
• fasting, ketogenic diet, fibre-rich macrobiotic ma-pi 2 diet (which agrees with item above and below)
• wheat bran and grains containing gluten, barley, whole grain,bran
• Pulses
• black raspberries, pomegranate, almonds/ almond skins
• Moringa Oleifera, Slippery Elm, berberine
• Pork
• Olive Oil — use Safflower Oil instead
• Conjugated Linoleic Acid (CLA)
• Most probiotics! See below!!

At this point, I attempted to do cross validation: Are there any literature of items suggested (or avoid) on improving Marfan syndrome. This is done to test the suggestions – for other conditions with lots of literature, we have usually seen 90-95% agreement. For ME/CFS, I know the literature well — for this condition, not. I found only symptom treatment (Mayo, NHS). Since this is a DNA condition and I know DNA can influence the microbiome (and the reverse), then trying to improve towards typical this youth’s microbiome is a reasonable (and low risk) approach.

Because of the platelet function abnormalities that could be present, as well as thick blood (procoagulation) — both areas that I am familiar with from ME/CFS. I checked suggestions for possible items that could be related to coagulation:

• Vitamin K — Nothing
• resveratrol (grape seed/polyphenols/red wine), grape polyphenols, grape seed extract, grapes — both negative
• Conjugated Linoleic Acid – negative

Questions and Answers

Q: Do you know why it suggest gluten Free diet? Could he have gluten intolerence/celiac maybe?

• The why is because of that type of diet impacts on bacteria that are off balance. We cannot detect  gluten intolerance/celiac. Only the impact of that type of diet on different bacteria. Some source papers to illustrate:

Bottom Line

The thing that strikes me most about the suggestions, the items to avoid are prebiotics and probiotics; the opposite of common advice for anyone with health issue, especially digestive issues. There are no studies on PubMed for probiotics and this condition which infers to me (given the popularity of trying probiotics) that there were studies with no effect or negative effect. In the sparse literature, we did have one of the take suggestions computing matching the literature.

If this was my own child, I would likely follow the items in suggestions above. There is low risk in following them and one suggestion does cross-validate with the available literature (which has almost nothing published in this area).

I work off the axiom that a disease or conditions modifies the microbiome to be favorable to the condition. Undoing those shifts have a reasonable change of slowing, and in some cases, reversing the condition. I have had antidotal reports of this approach speeding cancer treatment.

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 result 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 anyone. Always review with your knowledgeable medical professional.

This is part of a continuing series of analysis for ME/CFS or/and Long COVID.

Background

I am contacting you as you may provide a microbiome analysis for you has cfs – long Covid 19.
I have been struggling for years with cfs-me. I also have Covid 3 times (the last one was in December 2023). When I did the test, I just had few days before a food poisoning that led me to ER.
I did a GI map last year because I wanted to have more information after failing to cure a methane SIBO with herbs. I have a very bad infection (enterohemorrhagic e choli).
I was suggested by the functional doctor whom I ordered the test some thyme and probiotics but obviously it had no impact. I redid a stool test (biomesight) but I am really overwhelmed by the results.

Would you mind give me some insight on those tests ?

• joint pain, neck pain, TMJ, migraines
• hypothyroidy, insulin resistance, low cortisol,
• possibly Lyme (low nk57 but negative test)
• possibly mold intoxication 
• heavy metal intoxication 
• brain fog
• Attention-Deficit/Hyperactivity Disorder (ADHD)
• skin issues on the face and eczema on my hand 

Analysis

We have some dysbiosis (i.e. Eubiosis is not 100).

Looking at reported symptoms, we see a number of matches to reported symptoms over 16%ile, with one of the unchecked,  inability to focus eye/vision , being a potential missed item. There are 67 symptoms entered with 58 of them above 16% (the threshold)

Explaining the new Algorithm

This algorithm is similar to the Eubiosis algorithm. We compute the expected number of matches to bacteria shifts associated with the symptoms. The expected number by randomness is 16%. A higher number indicate increased odds, a lower number decreased odds. This is based on the existing annotated samples uploaded. It is not definitive and often there can be multiple subsets of bacteria associated with a symptom. The match is on too much or too few of a collection of bacteria

Looking at Health Indicators

• General Health Predictors: 11 items, with Veillonella atypica being the greatest concern
• Potential Medical Conditions Detected: None. I double checked, and there were no significant matches.
• Dr. Jason Hawrelak Recommendations: 94%ile

Going Forward

Doing just give me suggestion with symptoms gives the following suggestions for items to add (50% of 516 or hgh

• Supplements
  • melatonin supplement
  • Hesperidin (polyphenol)
  • Arbutin (polyphenol)
  • diosmin,(polyphenol)
  • luteolin (flavonoid)
• Foods
  • Caffeine
  • Two items were border-line: whole-grain barley and gluten-free diet. These are not exact contradictions, the gluten in barley is different than the gluten in common gluten foods
• Probiotics
  • bifidobacterium lactis,streptococcus thermophilus probiotic
  • lactobacillus kefiri (NOT KEFIR) – available in Italy
• Sugars
  • sucralose (an artificial sweetener)
  • chitosan,(sugar)
• Vitamins
  • Vitamin C, B1,B3,B6,B7,B9,B12 – typical for ME/CFS ones:
    • Vitamin B Mitigates Thoracic Aortic Dilation in Marfan Syndrome Mice by Restoring the Canonical TGF-β Pathway [2021]
  • Make sure you are doing adequate dosages, see this page for dosages used in studies.

The Avoid List

The lowest value was -550, so items below -275 should be the highest priority.

• Foods
  • Apple
  • Wheat bran
  • Fasting
  • Pulses
• Herb and Spices
  • Slippery Elm
  • grape seed extract
• Prebiotics
  • inulin (prebiotic)
  • arabinogalactan (prebiotic)
  • Human milk oligosaccharides (prebiotic, Holigos, Stachyose)
  • partially hydrolysed guar gum,fructo-oligosaccharides (prebiotic)
  • galacto-oligosaccharides (prebiotic)
• Sugars (the following suggests reduced dairy consumption)
  • lactulose
  • non-starch polysaccharides
  • galactose (milk sugar)
• Misc:
  • acetaminophen,(prescription) Paracetamol in UK

Comparing to Suggestions from GIMAP

The data transcribed is below. Our consensus report above picked 67 bacteria of concern

As expected (See this post) there was agreement and disagreements between these reports on what is high or low, and some agreements. For example,  Faecalibacterium prausnitzii was at the 81%ile on Biomesight data and very low above.

Suggestions will always be different because of the much smaller set of bacteria being used. We do note the following agreement in suggestions:

• lactulose – avoid
• Hesperidin (polyphenol) – Take
• Caffeine – take
• Chitosan,(sugar) – take
• Apple – avoid
• wheat bran – avoid
• Disagreement
  • inulin (prebiotic) –
  • fasting

Many suggestions are not found at all in the GIMap suggestions because there is no literature for those substances and the bacteria reported.

Questions and Answers

Q: Would you have any specific recommendations about enterohemorrhagic e coli (ehec) ?

• There are three approaches to consider
  • Have them pushed out by a beneficial E.Coli probiotic (Mutaflor, E.Coli Nissle 1917) [2020]
  • Use supplements that are researched:
    • Lactobacillus casei [2024]
    • L-glutamine [2023]
    • carvacrol, oregano extract [2021]
    • L. johnsonii, L. plantarum, and L. rhamnosus [2021]
  • Looking at the lists on Microbiome Prescription (with number of studies)
    • thyme (thymol, thyme oil) – 6
    • cinnamon (oil. spice) – 5
    • oregano (origanum vulgare, oil) – 5
    • triphala -3 (My personal preference)
    • Human milk oligosaccharides (prebiotic, Holigos, Stachyose) – 2
    • lactobacillus plantarum (probiotics) – 5
    • mutaflor escherichia coli nissle 1917 (probiotics) – 4
    • bacillus subtilis (probiotics) -3
    • lactobacillus casei (probiotics) – 3
    • lactobacillus paracasei (probiotics) -3
    • clostridium butyricum (probiotics),Miya,Miyarisan – 3
    • Zinc – 4
    • Vitamin B-12, B9, Vitamin C — 2 each

Q: Another question about the antibiotics protocol for me/cfs (in case I succeed to convince my GP). Dr Jardin suggests : 1 week on with one antibiotics then 3 weeks off, then another cycle with another antibiotics. Is it right ? 

• Correct for Jadin.  One week on and 3 weeks off… and then change antibiotics.  This comes from old clinical experience at the Pasteur Institute.  I have read studies dealing with sewage plants that found this pattern works better.

Q: On your blog, it also says to pick one of the 4 suggestions of supplements and switch every week during 8 weeks and retest. Does it mean I must choose 4 supplements, take 1 supplement during 1 week then switch to another 8 times and so on. Am I right ? (I am not English fluent so I struggle a little to understand everything)

• 4 SETS of supplements…. so each week you change sets.  This again is suggested to prevent dysbiosis adapting. I have too often heard “It works for 3 months and then stopped working” . As an analogy, think of cops setting up cameras to stop people speeding, their existence improves traffic — but once people learn that they are always at the same place … bad behavior returns.

Q: Last question : could symbioflor1 help for my enterrococcus faecalis overgrowth? Or is it the opposite?

• There is nothing that I could find for  symbioflor1 impact on enterrococcus faecalis overgrowth in the 13 studies I have processed. So we are again into the “fuzzy knowledge area”, in general (especially the EU), probiotics are not troubles strains and thus can be used to shift related bacteria.
• From https://link.springer.com/article/10.1007/s11259-024-10324-0, we see that it is hard to treat. BUT Curcumin is better than 2 antibiotics tested.

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.

We have a varied history with some storms blowing us off courses. Here’s a list of the tests and prior blog posts:

• 2018: Irritable Bowel Syndrome (IBS) diagnosis
• 2021-11-18 – IBS + BioNTech COVID Vaccine -> ME/CFS? [Jan 6,2022]
• 2022-05-20 – Follow up Analysis for ME/CFS (After COVID) [Jun 16,2022]
• 2023-06-22 – Repeat IBS + Vaccine + COVID [Jul 22,2022]
• 2023-09-04 – Biomesight #4 Sample: IBS and COVID

This is one of two set of ongoing samples from readers that “have appeared to almost stalled”. The other reader sent me this note at the same time (and another sample) “I have to say, symptoms are pretty dead on accurate to what I’m experiencing like all but one box. PEM is my highest ,”

This implies strongly that the association between symptoms and bacteria shifts are strong. The microbiome is just stubborn.

Feedback

He has 49 different symptoms checked and unusually, have a friendly MD in terms of antibiotics.

I would say some small subjective improvements since last time, but no major changes. Also I increased squats from 14 to 15 and push-ups from 9 to 10 at the time of the sample. (I also increased walking distance a little, but only after the sample was taken. I probably could have increased them by more, but I wanted to start really slowly with increasing those things.)

Between the last test and this sample, Amoxicillin was the only antibiotic I did. I also did some of the top herbs and probiotics (B. infantis, Mutaflor and L. Kefiri).

Also anxiety is a bit of a problem, but only sometimes, not every day. I’m not really sure what the cause is. I think it might be connected with winter, cold, rarely seeing the sun, maybe piracetame, people around me coming to me with suggestions on what I should do, maybe noise. (Noise has been a problem for me since the beginning of CFS. I really can’t endure noise well.) But those all don’t have to be the cause, they can also just be triggers or be connected to it. (Eating might also be connected to it. It seems to me that on the days I eat bacon for breakfast and a large portion of potatoes and beef for lunch (like once a week), it is better. On the days I eat sth. made from corn flour for breakfast (like every four days), it is worse. But I cannot eat the same things multiple days in a row because I quickly develop food intolerances if I do that, so I have to eat alternating things that I tolerate.) I am just wondering whether something can be done to help with that (anxiety).

Analysis

The eubiosis index is a recent addition and I am curious on how it behaves compared to other measures. Having a magic number to indicate health is an ideological goal, my gut feeling is that there is no such magic — rather many aspects need to be examined.

Sample	Eubiosis (balanced) gut.	Unhealthy Bacteria
2021-11-18	99.6	8
2022-05-20	48.5	12
2023-06-22	38.5	12
2023-09-04	100	12
2023-11-23	100	12

The traditional analysis

Criteria	11/23/2023	9/4/2023	6/22/2023	5/20/2022	11/18/2021
Lab Read Quality	5.4	4.7	7.2	8.1	5.5
Outside Range from GanzImmun Diagostics	12	11	11	15	15
Outside Ran ge from JasonH	7	9	9	6	6
Outside Range from Lab Teletest	25	22	22	20	20
Outside Range from Medivere	11	15	15	16	16
Outside Range from Metagenomics	8	7	7	9	9
Outside Range from Microba Co-Biome	3	3	3	1	1
Outside Range from MyBioma	6	6	6	5	5
Outside Range from Nirvana/CosmosId	22	23	23	20	20
Outside Range from Thorne (20/80%ile)	235	241	241	231	231
Outside Range from XenoGene	33	35	35	29	29
Outside Lab Range (+/- 1.96SD)	2 🙂	21	7	8	6
Outside Box-Plot-Whiskers	31 🙂	58	42	37	69
Outside Kaltoft-Moldrup	47 🙂	51	92	94	48
Bacteria Reported By Lab	508	568	582	674	527
Bacteria Over 90%ile	17 🙂	41	24	38	52
Bacteria Under 10%ile	83	50	147	177	36
Shannon Diversity Index	1.59	1.272	1.556	1.853	1.826
Simpson Diversity Index	0.047	0.087	0.09	0.056	0.038
Chao1 Index	6986	10061	9016	14744	7390
Shannon Diversity Percentile	43.8	12.7	40	81.8	78.2
Simpson Diversity Percentile	45.3	77.5	78.6	54.8	33.6
Chao1 Percentile	25	48.9	41.4	79.4	27.8
Pathogens	22	23	29	32	20
Condition Est. Over 90%ile	5	0	9	3	4

At first look, there seem to be little change. Looking at specific items, there is improvement (highlighted in red above), namely less bacteria with extremes levels. For all of the reference ranges from 3rd party labs, there is no effective change.

Going Forward

Since symptoms were also entered, we proceeded with [Just give me Suggestions Include Symptoms]. The results surprised me a little; the top items were CFS antibiotics and whole-grain barley (likely a proxy for beta glucan — see this post: Beta-Glucan: The Microbiome Fixer; ß-glucan is on the to take list). The following was sorted by Take Count descending (which means that all five sets agreed)

Personally, given the slow progress, I would be inclined to try talking a medical professional into prescribing one of these.

Let us do the usual breakdown by types, most are below 1/2 of the highest value.

• Vitamins: B1, B2, B3,B6, B7, B9, B12 are all positive; with Vitamin A being top vitamin.
  • REMEMBER to insure your dosages are at least at the level used in clinical studies.
• Supplements:
  • All are variations of grape products
    • red wine polyphenols
    • grape polyphenols
    • resveratrol (grape seed/polyphenols/red wine)
    • grape fiber
  • and the common trinity of: Hesperidin (polyphenol), diosmin,(polyphenol), Arbutin (polyphenol)
• Foods: The frequently seen mixture of whole-grain barley and walnuts which I usually translate to Barley Porridge with Walnuts every day.
• Probiotics
  • bifidobacterium animalis lactis (probiotics)
  • bifidobacterium longum bb536 (probiotics)
  • bifidobacterium breve (probiotic)
  • and one that is only available in Italy: lactobacillus kefiri (NOT KEFIR)
• For sugars: sucralose(a.k.a. Splenda) and aspartame (sweetner), all natural sugars are negative.
  

Further analysis

I did a second run, but excluded symptoms, there was no significant shifts. The top items were the same but other antibiotics shifted position.

From the early draft, this reader responded with more information:

• He has started nicotine patches which has a significant positive score of 113

I used the ability to do a double sort (Descending Take Count, Descending Priority) to get a double conservative list.

Tudca is Tauroursodeoxycholic Acid and available as a supplement. Based on this clinical study: Safety, Efficacy and Pharmacokinetics of Doxycycline Plus Tauroursodeoxycholic Acid in Transthyretin Amyloidosis, I would suggest that it be taken concurrently with the metronidazole. There are 34 clinical studies using it. It is interesting that metformin (a diabetes drug) is suggested at the same time we see avoid all natural sugars in our suggestions – there is an interesting symmetry here. Teicoplanin is also interesting and very suitable (literature here). Literature for Ceforanide is here.

My prescription model to be discussed with the MD would be:

• Week 1:A course of metronidazole with Tudca
• Week 2-4: metformin (possibly with Tudca)
• Week 5: Teicoplanin with Tudca
• Week 6-8: metformin (possibly with Tudca)
• At end of week 8 do another sample
• Week 9: Ceforanide with Tudca
• Week 10- new report: metformin (possibly with Tudca)

Barley porridge and similar alternating with beta-glucan supplements (since food sensitivities appear to develop quickly). Perhaps consider a diabetes-like diet (to keep the natural sugars low).

For Tudca, we read about some possible adverse effects in this paper Pharmacokinetics, Safety, and Tolerability of Orally Administered Ursodeoxycholic Acid in Patients With Parkinson’s Disease—A Pilot Study [2021] namely ” gastrointestinal discomfort, rated by subjects as mild to moderate“. It has a half-life of 2.1 ± 0.71 hr, so taking 4 staggered 500mg dosages per day should be considered.

Speculation: monitoring blood glucose levels (like what diabetics do) may be a waste or time OR may provide insight. I have a smart watch that monitors blood glucose ($30 from Banggoods to Temu). There are also more professional monitors.

Question:  I ate cornflour for breakfast, which I wrote about in my first mail. On those days anxiety is worse

• This is often cited on influencer’s health pages, we have some potential researched supporting it:
• TRPM2 may be involved in high fructose corn syrup-induced anxiety-like behavior in adult male rats [2023]
• High Fructose Corn Syrup-Moderate Fat Diet Potentiates Anxio-Depressive Behavior and Alters Ventral Striatal Neuronal Signaling.[2021]
• However, blue maize may reverse it:
• Effect of consumption of blue maize tortilla on anxiety-like behaviour, learning, memory and hippocampal BDNF expression in a chronic stress model in rats. [2023] “The consumption of anthocyanin extract or tortilla made with blue corn decreased anxiety-like behaviours”

I tried out a new medical Large Language Model (LLM) API, https://www.drgupta.ai/ to see what it would suggest for a simple microbiome shift compared to what the Expert System(ES) (NOT LLM) AI system does on microbiome prescription. The first significant one Expert System for Medicine was called MYCIN and was written by Stanford University in 1972.

The main business differences between LLM and ES are costs. LLM run heavy computer costs, ES runs heavy human costs. An ES often require article by article review with suitably skilled reader (or example, a grad student). LLM are easy targets for getting venture capital funds — often based on pie-in-the-sky beliefs of how easy it would be to do that is sold to venture capitalists. Earlier I had several sessions with folks at the The Allen Institute for Artificial Intelligence exploring machine analysis of the literature. Their conclusion was that existing AI is still incapable of good analysis of medical and clinical studies.

LLM Report

I tossed a simple, three taxa problem at the API. Reality is that typically we are seeing 40-80 taxa of interest.

Expert System Response

Compared to:

We do not have vague “probiotics” but provide their specific names and dosages. We also include probiotics to avoid.

With information on suggested dosage for probiotics with links to sources.

As well as the names and links to studies used to make these suggestions.

Nothing in the LLM indicates that Pectobacteriaceae was considered. The Expert system does consider it:

And provide background

Bottom Line

This post intent was to contrast the difference between LLM and ES systems. Both can have data entry/text interpretation issues. With a suitable ES system, the suggestions can be audited and issues addressed. With LLM, this does not seem to be available with common code bases.

The table below from PubMedQA shows that accuracy is barely over 80% for the best models out there. Expert systems can exceed 95%. Is 80% “good enough” for treating patients especially if the ability to audit the logic is missing? By Audit, I mean provide links to all source studies).

This is a follow up on the prior post below. The reader’s comments are “I am feeling much better but still very fatigued and lately been quite achey.  The recommendations have changed significantly except for whole grain barley.”

• 24 Years of ME/CFS with Mouth Microbiome

For more analysis see: Analysis Posts on Long COVID and ME/CFS

Comparison of Samples

Let us first do the simple numbers. A lot of values are the same (typical) but many of them show improvement. 😃 indicate significant reduction is out of range values See Technical Note: Lab Quality Versus Bacteria Reported We would expect a 15% drop from lower lab quality, the drops shown are well below that).

Criteria	Current Sample	Old Sample
Eubiosis Index	62.8%😃	59%
Lab Read Quality	4.3	8.4
Outside Range from JasonH	8	8
Outside Range from Medivere	20	20
Outside Range from Metagenomics	10	10
Outside Range from MyBioma	8	8
Outside Range from Nirvana/CosmosId	18	18
Outside Range from XenoGene	42	42
Outside Lab Range (+/- 1.96SD)	9😃	16
Outside Box-Plot-Whiskers	38😃	98
Outside Kaltoft-Moldrup	56😃	139
Bacteria Reported By Lab	494	752
Bacteria Over 90%ile	20😃	82
Bacteria Under 10%ile	66😃	232
Shannon Diversity Index	1.465	1.701
Simpson Diversity Index	0.035	0.028
Chao1 Index	7474	17093
Shannon Diversity Percentile	28.5	61.4
Simpson Diversity Percentile	30.2	21.5
Chao1 Percentile	28.9	87.7
Lab: BiomeSight
Pathogens	18😃	39
Condition Est. Over 90%ile	4	4
Kegg Compounds Low	969😃	1242
Kegg Compounds High	5😃	23
Kegg Enzymes Low	272	284
Kegg Enzymes High	17😃	75
P or P Chi2	.9999245	.999999999

Health Analysis Comparisons

I have not created an automatic compare yet (on to do list). Many values were similar, some interesting ones with improvements are below. Jason Hawrelak Criteria got worse, but I have deep reservations on using his criteria on Biomesight tests (he based them on a very different test method).

	Recent	Prior
General Health Predictors: Flagged Bacteria	8😃	10
Anti inflammatory Bacteria Score	14.4%ile😃	13.3 %ile
Lactate (controls many bad bacteria) 📚	33.1 %ile😃	20 %ile
L-Lactic Acid (controls many bad bacteria) 📚	47.1 %ile😃	25.2 %ile
NADH (Typically low with ME/CFS) 📚📚	26.5 %ile😃	13.7 %ile
Hydrogen peroxide (controls many bad bacteria) 📚	17.3 %ile😃	5.8 %ile
D-Lactic Acid (Associated with brain fog) 📚	6.5 %ile😃	7.9 %ile
Potential Medical Conditions Detected	2😃	7
Bacteria deemed Unhealthy	7😃	22
Jason Hawrelak Criteria	56.4 %ile	75.8 %ile

Going Forward

A review of the Health Analysis was done above, with the two items: Mood Disorders and COVID-19 (a proxy for ME/CFS IMHO). A secondary review of all the items on [Changing Microbiome]/[US National Library of Medicine Studies] for high items not flagged. Nothing added.

Doing what is becoming a regular pattern: “Just give me suggestions” and then using given symptoms under Special Studies using these items:

Note: items like age and gender are omitted as well as any other symptoms that we do not have sufficient data.

First the filtered PDF suggestions. The list is much longer than usual:

And the to avoid list is more typical.

Let us go over to viewing the consensus to get some priorities

The highest value was 485 (so 240 for cutoff), lowest value was -574 ( so-287 for cutoff)

• Foods
  1. whole-grain barley
  2. lauric acid(fatty acid in coconut oil,in palm kernel oil,)
  3. Vegemite (with apologies — it’s an acquired taste)
• Diet Style
  • Only gluten-free was in positive range
  • Avoids: animal-based diet, high beef diet, ketogenic diet
• Herb or Spice
  1. momordia charantia(bitter melon, karela, balsam pear, or bitter gourd)
  2. garlic (allium sativum)
  3. eugenol (from clove oil, nutmeg, cinnamon, basil,bay leaf.)
• Prebiotics and similar
  • Nothing in take
  • Avoid: inulin (prebiotic),xylan (prebiotic),Psyllium (Plantago Ovata Husk) etc
• Probiotics
  1. lactobacillus kefiri (NOT KEFIR) — only available in Italy
  2. lactobacillus casei (probiotics)
  3. bifidobacterium breve (probiotic)
  4. bifidobacterium longum bb536 (probiotics)
  5. AVOIDS: lactobacillus plantarum (probiotics), lactobacillus rhamnosus (probiotics), bacillus licheniformis,(probiotics)
• Sugar and similar- Effectively LOW SUGAR DIET
  1. sucralose
  2. chitosan,(sugar)
  3. Avoid: stevia, saccharin, galactose (milk sugar), sugar, polydextrose
• Vitamins, Minerals and similar
  • The typical ME/CFS ones: Vitamin B1, B3, B6, B7, B9, B12 and Vitamin C
• Amino Acid and similar
  1. melatonin supplement (it helps with sleep but also alters the microbiome)
  2. Taxifolin
  3. Avoid most of the other ones
• Antibiotics (limited to those used for ME/CFS)
  1. metronidazole (antibiotic)s[CFS]
     • “Metronidazole/Flagyl is reported to have 75% of CFS patients improving according to some surveys.” 📚
  2. amoxicillin (antibiotic)s[CFS]
  3. dapsone (antibiotic)[CFS]
  4. lymecycline (antibiotic)[CFS]
  5. azithromycin,(antibiotic)s[CFS]

So in summary, shift a diet to low sugar, gluten free with moderation in meat (no guidance on chicken or fish). If your MD is willing, I would suggest reviewing Cecile Jadin📚 approach with antibiotics and rotate with those suggested above. IMHO Continuous on a single antibiotic is more likely to complicate the microbiome.

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.

A reader asked me to evaluate their offerings. Remember, I do NOT sell testing, I offer a free citizen science analysis on over 3 dozen different microbiome tests using Artificial Intelligence. One of the first thing that strikes me is false and misleading statements on some sites. The following is from Jonas Health for illustration purposes. A few are below, taken from their site in November 2023.

This is incorrect. They cannot identify ALL organisms, they can only identify the items in their reference library. For example, there are 30 new fungi species being added every year in 2004 ( Biodiversity of Fungi, 2004) and I would expect that rate to be increasing. NCBI currently lists over 2.5 million taxa. In 2012 it was just 235,000. That’s a 10 fold increase in 10 years.

It is unlikely to be “all”

Looking at their sample report we see numbers given with no scale.

As for research, we see two papers, neither titles suggests that lactose was the focus of the study. One seems focuses on Rice and oats. The article is here – the word lactose is never mentioned in the article. As this is a demo report, I would expect correctness. Also, the journal was Front Immunol. 2021; 12: 787797. and NOT Nature.

Next we see what may be correct per the sample, but no guidance on how to:

• Increase Faecalibacterium Prausnitzii WHILE CONCURRENLTY Decreasing Faecalibacterium .

Bottom Line

Based on this sample report, I see ugly problems. Thorne Gut Testing is 40% of the cost and much more useful, especially if used with Microbiome Prescription. I attach a copy of their sample report below.

A reader asked me to assemble information from studies on Low Dosage Naltrexone. For conditions like Fibromyalgia, we have 49 studies with good or no effects.  I speculate that the effectiveness is dependent upon the microbiome prior to starting.

A lot of the published literature are case-reports (i.e. on individuals). My general impression from larger studies is that it is a 50-50 toss of the coin if improvement will happen. There is an absence of literature on its impact on different bacteria in the microbiome.

• Efficacy and Safety of Low Dose Naltrexone for Chronic Pain [2024]
  • “Seven (23%) reported side effects. LDN was associated with a statistically significant reduction in PEG in adult chronic pain patients, however the clinical significance is unclear as over 75% of patients discontinued LDN due to lack of benefit.”
• Low-Dose Naltrexone Improves post-COVID-19 condition Symptoms [2024]
  • “The relative hazard of improvement for those taking low-dose naltrexone was 5.04 (95% CI, 1.22-20.77; P = 0.02) compared with physical therapy alone. Both fatigue and pain were improved in patients taking low-dose naltrexone”
• Low-dose naltrexone use for the management of post-acute sequelae of COVID-19 [2023]
  • “The use of LDN was associated with a fewer number of symptoms, improved clinical symptoms (fatigue, post-exertional malaise, unrefreshing sleep, and abnormal sleep pattern), and a better functional status.”
• A systematic literature review on the clinical efficacy of low dose naltrexone and its effect on putative pathophysiological mechanisms among patients diagnosed with fibromyalgia [2023]
  • “One study reported baseline erythrocyte sedimentation rate (ESR) predicted LDN response (≥30% reduction in fibromyalgia symptoms) and a second study showed plasma concentrations of inflammatory biomarkers were lower after LDN treatment.”
• Complex Presentations, Identification and Treatment of Mast Cell Activation Syndrome and Associated Conditions: A Case Report [2023]
  • “The patient was ultimately deemed to have other associated conditions including a mast cell-mediated disorder as well as joint hypermobility due to her response to antihistamine and mast cell stabilizing agents. Final outcomes include immense improvement upon mast cell stabilization with ketotifen, and remission of SIBO with low-dose naltrexone (LDN).”
• Low-dose naltrexone as a treatment for chronic fatigue syndrome [2020] – Three(3) Case Reports
  • “it was clear she was stable and well, and could walk, and more recently, cycle, without problems. Prior to starting LDN, her intellectual and cognitive functioning was very limited. “
  • “She no longer requires acupuncture for symptomatic pain relief. However, her functional level did not improve with LDN. also continues with other symptoms of myalgic encephalomyelitis including postexertional neuroimmune exhaustion, periodic muscle weakness, orthostatic intolerance, symptomatic sinus tachycardia, urticarial rashes and susceptibility to bacterial infections”
  • “His functional level improved from being mild–moderately limited on a daily basis (60%–70% on a functional activity scale) to mild limitations (80%–90% on a functional activity scale). “
• Repurposing low-dose naltrexone for the prevention and treatment of immunothrombosis in COVID-19 [2022] “we hypothesize that the immune-modulating and known pharmacologic properties of LDN could be leveraged as a novel therapeutic strategy in COVID-19.”
• Low-dose Naltrexone Therapy for Psoriasis [2020]
  • Three adverse events included insomnia, diarrhea, and self-limited headache. Marked improvement was seen by 53% of the 15 patients. Low-dose naltrexone regulates lymphocyte responses, reduces cytokine production, and likely reduces mast cell activity.
• Low Dose Naltrexone in Dermatology [2019]
• Pharmacology Update: Low-Dose Naltrexone as a Possible Nonopioid Modality for Some Chronic, Nonmalignant Pain Syndromes [2019]
  • “When used in doses of 1 to 5 mg it acts as a glial modulator with a neuroprotective effect via inhibition of microglial activation. It binds to Toll-like receptor 4 and acts as an antagonist, therefore inhibiting the downstream cellular signaling pathways that ultimately lead to pro-inflammatory cytokines, therefore reducing inflammatory response. Low-dose naltrexone (LDN) may also have utility in improving mood disorders and the potential to enhance the quality of life”
• The Safety and Efficacy of Low-Dose Naltrexone in the Management of Chronic Pain and Inflammation in Multiple Sclerosis, Fibromyalgia, Crohn’s Disease, and Other Chronic Pain Disorders [2018]
  • “Currently, evidence supports the safety and tolerability of low-dose naltrexone in multiple sclerosis, fibromyalgia, and Crohn’s disease. Fewer studies support the efficacy of low-dose naltrexone, with most of these focusing on subjective measures such as quality of life or self-reported pain. These studies do demonstrate that low-dose naltrexone has subjective benefits over placebo, but evidence for more objective measures is limited.”
• Low dose naltrexone for induction of remission in Crohn’s disease [2018]
  • “The results of the study in adult patients suggest that low dose naltrexone may provide a benefit in terms of clinical response (i.e. an improvement in disease symptoms) and endoscopic response (i.e. a reduction in inflammation of the gut as shown by examining the gut with a scope)”
• Successful treatment of postural orthostatic tachycardia and mast cell activation syndromes using naltrexone, immunoglobulin and antibiotic treatment [2018]
• The Effect of Low-Dose Naltrexone on Medication in Inflammatory Bowel Disease: A Quasi Experimental Before-and-After Prescription Database Study [2018]

A reader that does microbiome analysis of her ME/CFS daughter’s microbiome using Microbiome Prescription expert system sent me this note with some literature. The daughter has Celiac Disease and ME/CFS.

Your wonderful system recommended beta-glucans [also written β-Glucan] for my daughter,  and when I looked further, I found this. I’m trying her on them for a month-, after testing her for reactions for three days- the first week has been hopeful. Will keep you posted if you wish.

Reader

β-Glucan is a nonstarch polysaccharide having documented health benefits and industrial applications. It can be extracted from various sources, including cereals, bacteria, molds, and fungi. The chemical nature of extracted β-glucan from these sources differs slightly. This variation in chemistry defines its industrial uses and health benefits.

Biopolymers for Food Design, 2018

Literature

There is not much literature available for ME/CFS.

• “The findings showed that the beta-glucan supplementation significantly improved cognitive fatigue (assessed with FIS-40 scores) after the 36-week treatment compared to the baseline (p = 0.0338). Taken together, this study presents the novel finding that yeast-derived beta-glucan may alleviate cognitive fatigue symptoms in ME/CFS.” [2023]
• β-Glucan Improves Conditions of Chronic Fatigue in Mice by Stimulation of Immunity [2020] Reduces TNF-α (which is connected to mast cell issues)
• Effects of β-(1,3–1,6)-d-glucan on irritable bowel syndrome-related colonic hypersensitivity [2012]
  “β-Glucan did not affect the pain response in general but specifically affects the visceral pain response.”
• Serum concentrations of 2′,5′-oligoadenylate synthetase, neopterin, and beta-glucan in patients with chronic fatigue syndrome and in patients with major depression. [1994]
• “ the dosage of supplementation ranged from 2.5 to 1000 mg daily [of beta-glucan] for up to 6.5 months … The primary physiological outcome of the majority of the interventions was immunomodulation, which resulted in (a) strengthened immune defense that reduces the incidence and symptoms of cold, flu and other respiratory infections and (b) improvement of allergic symptoms.” [2021]
• β-glucan attenuates cognitive impairment via the gut-brain axis in diet-induced obese mice [2020]

Some literature for Autism

• Improvement of sleep and melatonin in children with autism spectrum disorder after β-1,3/1,6-glucan consumption: An open-label prospective pilot clinical study [2022]
• Study: Beta glucan improves behaviour in autistic children [2022]
• Benefits of Gut Microbiota Reconstitution by Beta 1,3-1,6 Glucans in Subjects with Autism Spectrum Disorder and Other Neurodegenerative Diseases [2023]
• Improvement of behavioural pattern and alpha-synuclein levels in autism spectrum disorder after consumption of a beta–glucan food supplement in a randomised, parallel-group pilot clinical study. [2022]

Many Sources of Beta Glucan

Often the expert system on Microbiome Prescription comes up with Barley as a strong recommendation for ME/CFS people. Barley is an excellent source. Personally, I have oats or barley porridge a couple of times every week. The impact of the β-Glucan in the Barley may be the mechanism — we just do not have as many studies as we do for Barley.

• “The primary sources of food β-glucan for humans are cereals (especially oats and barley), fungi, algae, and yeast ” [2023] A table from this article is below

• “β-glucans bind to specific receptors on immune cells and initiate immune responses…. In vitro study found that the fermentation of barley and oat β-glucan by human fecal samples show variations in SCFAs production and the bacterial populations of Clostridium histolyticum and the ratio of Bacteroides–Prevotella species. Absorption of these SCFAs by the gut epithelial cells helps in regulating cell differentiation, proliferation, apoptosis, and gene expression (210). Butyrate increases the protein expression of tight junctions such as ZO-1 and claudin-1, resulting in enhanced intestinal barrier function.”
  “β-glucan is an essential food ingredient in controlling metabolic dysregulations linked to metabolic syndrome. β-glucans have a very minimal probability of having any unfavorable side effects and are reasonably inexpensive.” [2023]

Bottom Line

Real simple: Barley or Oats porridge for breakfast each day! Since there are some chemical differences between the β-glucans in these two grains– rotate between these (and different brands) at least monthly.

Using the generic suggestions for me/cfs we see both barley and B-glucan are positive (but oats are slightly negative). The more detailed citizen science suggestions are still be worked on, but I expect similar.

Reviewing Clinical Trials, my impression is 1 gram/day of β-glucans which translates to 20 grams of Barley or 40 grams of Oats per day.

“30g uncooked oats or barley will make a fairly small bowl of porridge whilst 70-80g will provide a particularly large serving for one person. Traditional porridge recipes tend to use oatmeal with approximately 200ml of water per 50g oats, and a pinch of salt.”

University of Aberdeen

Some people will advocate just eat mushroom. While correct that it contains beta-glucans, we need to be careful not to slip into homeopathic dosages!

Among those, mushrooms feature a particularly high level, so it’s no exaggeration when we say “for beta glucans, look to mushrooms!” The amounts of beta glucans found per 100 g of raw mushroom include 2.3 g (maitake), 2.0 g (bunapi), 1.9 g (eryngii), 1.8 g (bunashimeji) and 1.5 g (shimofuri hiratake) (Hokuto data).

https://www.hokto-kinoko.co.jp/lang/en/kouka/jiten/jiten06/

When we go to typical US mushrooms (i.e. Button), we drop to .75 g/100 grams [FDA]. So we are talking about 5-6 oz of mushrooms per day. That 3/4 of the typical mushroom package per day per person.

Celiac and Gluten Sensitive Issue

Most beta glucan supplements are produced from Saccharomyces cerevisiae (thus gluten free). For example the item below is about US$17.00 and gives 100 days at 1 gram per day.

I should note that there are different forms of beta glucan, for example above it is the 1,3/1,6 forms. Another product has 1,3/1,4 and is derived from Oats (you will have to write the company to see if it is gluten free or low gluten).

The cost per gram is much lower as bulk powders than with pre-filled “premium” capsules – the same volume of beta glucan can be as high as $250 (12x more) with some products.

Backstory:

I got COVID in Feb 2022. Over the next few months I developed long COVID symptoms. Within 6 months I was severe (bedbound), and within a year I was very severe (24/7 dark silent zero stimulation bed rest). About six months ago I progressed back to being severe and have stayed there. I’ve been officially diagnosed as having ME/CFS as well as long COVID.

I have basically all the symptoms but the worst are light and sound sensitivity, post exertional malaise, brain fog, fatigue, and cognitive and sensory processing issues.

I have severe episodes of d lactic acidosis when I eat dairy. D lactic acidosis was actually my very first long COVID symptom.

If it’s relevant – all “mitochondria boosters” make me significantly worse. Ubiquinol/CoQ10 is what pushed me into being very severe. [Editor note: We have limited information on Coenzyme Q10  and cannot propose reasons for this response – it was not listed in the suggestions]

A few months ago my GI symptoms (diarrhea, bloating, stomach pain, etc.) got more severe, I think as a result of taking Pepcid[Famotidine] daily for MCAS. I tested positive for H Pylori and was off the charts for methane and hydrogen SIBO. [Famotidine is a weak positive, but positive]

I did a GI Map before starting treatment, which is uploaded to my profile. I then did 2 weeks of metronidazole + doxycycline + pepto bismal to try to tackle the H Pylori. My histamine intolerance and d lactic acidosis got MUCH worse during treatment. I did my BiomeSight test a week after finishing antibiotics.

Then I did 2 weeks of Xifaxan + Nitazoxanide + PHGG for the SIBO. I just finished this. My bloating is a little better but my histamine intolerance and d lactic acidosis worsened even further and now my cognitive function is the worst it’s been in months.

I’ve just started Mutaflor and have also obtained Symbioflor-2, Miyarisan, and Equilibrium, and am planning on cycling through those (in addition to whatever recommendations pop up from my BiomeSight test).

Analysis

The Eubiosis index and percentages of percentiles show quite dramatic (and a typical) results. We have a large number of bacteria which I am inclined to described as “pedal to the metal”. These are all at extreme levels. Chao Index and Shannon Index are at 0%ile and Simpson Index at 83%ile.

Some of these extremes bacteria ( > 90%ile) with known health impacts are:

• Fusobacterium / Fusobacterium nucleatum 
• Klebsiella / Klebsiella pneumoniae 
• Veillonella atypica 
• Actinomyces
• Bacillus
• Clostridium perfringens
• Eikenella / Eikenella corrodens
• Enterobacter / Enterobacter ludwigii
• Legionella
• Morganella
• Proteus
• Providencia
• Salmonella / Salmonella enterica
• Streptococcus anginosus
• Vibrio

Morganella is a known extreme histamine producer (Histamine and biogenic amine production by Morganella morganii isolated from temperature-abused albacore [2000]) which accounts for the histamine issues. The KEGG estimate of histamine producers is up at 84%ile. Most of KEGG estimators are at extreme – for example Oxalate is at 100%ile and Oxalate degrading is at 0%ile [which indicates a risk of kidney stones developing over time]

The Bacteria deemed unhealthy is an impressive list.

Going Forward

The joy of using an expert system is that despite a very complex microbiome, the system will grind thru all of the data and produce a better results than a human doing so. A human will typically pick one or two bacteria to address “and see what happens”.

The person has marked their symptoms so we have five sets of suggestions going into our consensus.

The top suggestions have a few antibiotics but a lot of items are intermixed between them. In such a scenario I favor not doing antibiotics.

One item in the avoids really stand out, proton-pump inhibitors (prescription) at -637.

The following are items picked above 400 or below 300. The reason to do 50% of the extreme button is not to overwhelm the brain with too many suggestions. Check the site for dosages[Click here].

• Supplements
  • vitamin d
  • Alpha-Ketoglutarate – likely hard to get
  • Ursolic acid – likely hard to get
  • inulin (prebiotic)
  • Human milk oligosaccharides (prebiotic, Holigos, Stachyose)
  • arabinogalactan (prebiotic)
• Probiotics
  • lactobacillus rhamnosus gg (probiotics) — see how you react, may not be the best choice.
  • lactobacillus reuteri (probiotics) – Use ONLY BioGai. It is known not to produce histamine or d-lactic acid
  • clostridium butyricum (probiotics),Miya,Miyarisan
  • enterococcus faecium (probiotic)
  • bifidobacterium longum (probiotics)
  • bacillus subtilis (probiotics)
• Herb and Spices
  • syzygium aromaticum (clove)
  • foeniculum vulgare,fennel
  • laser trilobum l.,kefe cumin
  • nigella sativa seed (black cumin)
  • Curcumin
  • neem
  • thyme (thymol, thyme oil)
  • triphala
  • and many more!
• Foods and Diet
  • ketogenic diet
  • methionine-choline-deficient (MCD) diet
  • soy
  • papaya
  • banana
  • barley — a regular suggestion for ME/CFS
  • xylaria hypoxylon (fungi)
  • laminaria digitata,oarweed – seaweed and laminaria hyperborea( tangle/cuvie – seaweed)
  • apple

So, for breakfast every day: Barley porridge with soy milk with slices of bananas/apples?

One at a Time and Rotate

We want to identify items that help or hurts you specifically. Tossing everything in at once denies us this knowledge. My general guidance would be:

• Spices and Herbs with meals
• Probiotics at bed time

Break the suggestions into 4 groups and take them for a week at a time. After 8 -12 weeks (2-3 cycles) get a new microbiome test to see changes. Keep up this pattern until you have new test results.

Remember our goal is to destabilize a stable dysbiosis. We effectively want to do a guerilla war against it — constantly hitting it from different places.

Questions

• Q: Question about herbs/spices. Is the recommendation to take them at the same time as probiotics? Or do a week of herbs, then a week of probiotics, and keep trading off? You’ve posted before about how some of the herbs can nullify the probiotics so I’m not sure how to stack correctly. 
  • Answer: If you click on one the herbs and spices you will be taken to a detail page where the first section is on the impact on probiotics. For the first item, we find that clove and clostridium butyricum have no interactions — so taking both on the same day is fine.

Similarly, for fennel we find that it actually enhances lactobacillus reuteri

So there is a manual process to identify what is neutral or helpful. If a herb or spice impacts every suggested probiotic, then either just do the herb, or keep 8-12 hours between them.

A recent study identifies which bacteria are involved: Defining Small Intestinal Bacterial Overgrowth by Culture and High Throughput Sequencing [2023].

At a high level, Small Intestinal Bacterial Overgrowth (SIBO) appears to have low levels of Streptococcus and Rothia.

SIBO is accounted for primarily by 2 E coli strains and 2 Klebsiella species. This remarkably specific group of microbes account for 40.24% of duodenal bacteria in SIBO subjects, compared with 5.6% in non-SIBO subjects.

Using Microbiome Prescription expert system with these 4 pieces of information, we can get some suggestions on how to shift the bacteria.

Including antibiotics into the scope, we have this list

My own preference for non-antibiotic treatment would be:

• triphala
• clostridium butyricum (probiotics),Miya,Miyarisan – using Miyarisan pressed tablets and letting them slowly dissolve in the mouth.
• oregano (origanum vulgare, oil)
• thyme (thymol, thyme oil)

Of special note is mutaflor escherichia coli nissle 1917 (probiotics) which to some may appear to be a contradiction to the results. It is not, this is a beneficial probiotic that is aggressive in pushing out bad E.Coli strains.

I would do only one at time for one week each — because a “herx” type reaction (temporary worsening of symptoms) may happen.

NOTE: Probiotics in capsules should not be used. The capsules may not dissolve until after the targeted area. Custom Probiotics sells powders of many of these probiotics with instruction to dissolve in a glass of water and then consumed. That process is likely to produce the best results.

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 can compute items to take, those computations do not provide information on rotations etc.

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.