This is a thought experiment transformed into an implementation for people to experiment with.
In doing educational reviews of a variety of samples, I came across a person whose progressed had slowed. In trying to understand why [The ME/CFS Quest for Health], I looked at metabolites level between his current sample and previous sample. To my surprise, the highest ones (highest percentile) had barely budgeted.
I looked at the prior Dec 24 sample and compare the KEGG Compounds to the current sample starting with the highest percentile ones:
While the bacteria changed, the extreme metabolites remained high but with a few reducing. There is a potential to generate suggestions based on these KEGG compounds — a little messy and definitely pushing inference into new turf.
An Idea
I asked Perplexity.ai on how to reduce a few. A typical response is shown below
On MicrobiomePrescription.com, the suggestion algorithm works solely off the bacteria that is reported by the microbiome test. This is done by using facts harvested from US National Library of Medicine studies. There are no (or likely extremely few) studies dealing with diet and metabolites.
The key phrase is reported by. We know that reporting is not standardized and often using only 16s.
Idea!
Current logic on MicrobiomePrescription.com is bacteria => suggestion impact. What if we add another approach: metabolite => normalized bacteria distribution => suggestions. We want this to have less randomness than 16s. The folks at PrecisionBiome.Eu shared 1000 shotgun results from healthy individuals with me so I could construct a normalized bacteria distribution model. From this model, I computed metabolites using data from KEGG: Kyoto Encyclopedia of Genes and Genomes and ended up with a facts table consisting of:
Metabolite
Suggestion / Modifier
Estimated Impact
The metabolite is identified by KEGG ID.
Implementation
Since the microbiome and its metabolites are very interconnected and interact with each other. I decided that looking at the top and bottom 5-10%ile (i.e. those with a percentile ranking of 90-95%ile or higher, a percentile of 10-5%ile or lower) was a reasonable approach. There is a little trust that the central limit theorem will generate reasonable results and allow metagenomics to be directly used for getting suggestions.
On the [Research Features] tab, this panel has been added:
This produces a report listing the Metabolites targeted (High and/or Low) and then Suggestions
Observation
To me, what I found very interesting is that there are a few that are very high in impact with rapid drop off. This means there are only a few critical items to add to the general bacteria-based suggestions.
Hello, I’m sorry to message you privately, but I’m reaching out for help regarding my 15-year-old daughter, who has been homebound with ME/CFS for 2.5 years since contracting COVID in 2022. I came across your story on Facebook, and I felt truly inspired by how you managed to overcome ME/CFS by working with your microbiome. We are currently trying to follow a similar path.
We’ve recently done a Biomesight 16S test for her. As expected, it showed typical deficiencies, like a lack of Lactobacillus bacteria, along with an overgrowth of sulfate-reducing bacteria (possibly SIBO). Since we’re unsure how best to approach this dysbiosis, we sought the help of a microbiome specialist through Viola Sampson in the UK. She recommended lactulose, Lactobacillus reuteri, Lactobacillus rhamnosus, Lactobacillus plantarum, Bifidobacterium breve, along with Allicin and Goulds tincture from Australia. We’re just beginning this treatment, so it’s hard to say much about progress yet. We’ve started with Lactobacillus rhamnosus, plantarum, and breve, and she’s doing well with these so far.Honestly, I’m a bit concerned about these Lactobacillus bacteria because I read somewhere that all people with ME/CFS have some degree of lactic acidosis, so I’m worried that these probiotics might produce even more lactic acid. When I brought this up with my practitioner, she wasn’t aware of it.
I also uploaded a Biomesight test of my daughter to your Microbiome Prescription page, but I noticed that your site has somewhat opposite recommendations for her microbiome, such as advising against lactulose. To be honest, I’m struggling to navigate your page, and it’s a shame because I truly want to follow the recommendations accurately. I was hoping to identify which specific antibiotics or probiotics might be the best fit for my daughter’s case, but I’m not sure how to interpret that information from your site.
Currently, my daughter is mainly dealing with POTS (Postural Orthostatic Tachycardia), histamine intolerance, chronic fatigue, anxiety and panic attacks, and digestive issues. She’s become highly sensitive to various foods and medications, and it all points towards dysautonomia. Although she’s taking many supplements, she reacts to some, like iron supplements, which I suspect might be due to certain bacteria that feed on iron. She has many vitamin deficiencies, yet we can’t supplement effectively due to these reactions. It’s so difficult to manage.
I apologize for the long message, but I wanted to be as clear as possible about her situation. I’d be incredibly grateful if you could review her Microbiome Prescription and offer any insights on what stands out in her microbiome and where we might start. I’m also curious about any thoughts on the potential use of antibiotics or probiotics, as our microbiome practitioner is generally against antibiotics, though I know some people with ME/CFS have found success with a well-planned antibiotic approach.
Here, I am including the link to our microbiome analysis from Microbiome Prescription.
Analysis
First, disagreement between sites is well known and explained here: Why sites suggestions disagree on the same data. Microbiome Prescription tuned it’s advice by doing cross-validation for several conditions, for example: Cross Validation of AI Suggestions for Nonalcoholic Fatty Liver Disease. ME/CFS was the first explicit studies done. To the best of my knowledge, no other microbiome site has done cross-validations of their suggestions and been public in showing results.
Individual practitioners are hard to evaluate because they often find patterns that works for some people by trial and error. It is a rare practitioners that can provide documentation on their suggestions.
Quick boot strap
Long COVID is one condition that has a built in cross validation list of suggestions. This is on [Old Ui] / [Changing Microbiome]. POTS is not currently on the list because of insufficient studies.
This identified the following bacteria as being probable according to the published literature. The number of cross reference numbers after each item, indicate the number of studies For example Ruminococcus – genus : Low was reported in 4 studies.
The suggestions (based on microbiome shifts cross reference with substance that improved ME/CFS from studies are below. The number of cross reference numbers after each item, indicate the number of studies – as above. This leads to the best suggestions being the ones with the most cross reference. Thus:
Magnesium supplements – 6 studies
Vitamin B9 – 6 studies
Coenzyme Q10 – 6 studies
Far infrared Sauna – 4 studies — as a personal note, we purchased a small one at Costco and use it regularly as preventative.
Vitamin B1 – 3 studies
Omega-3 – 3 studies
Ribose – 3 studies
licorice – 3 studies — we usually use Spezzatina and just suck on them
carnitine Amino Acid – 3 studies
Melatonin – 3 studies
Selenium supplement – 3 studies
This is a significant list and I noticed that none of these were suggested by Viola Sampson despite published literature saying they help.
My suggestion would be to add one of these every three days, noting any changes that results. For dosages see Dosages for Supplements, start low and work up. The above will take a little over a month. All of these items can be taken continuously and together.
Probiotics
Probiotics are a popular “cure-all” which in some cases help and in other cases hurt. For example, lactobacillus probiotics often will increase brain fog.
Looking at probiotic with positive values, most are actually hard to obtain. For example Kefibios is only sold in Italy. Mutaflor in only a few countries. Of the choices, I would try Mutaflor after adding in the items above — but be warned, it may trigger severe die-off.
Top items
The list below are other things that likely have never been studied for ME/CFS but should have significant impact on the bacteria shifts.
On the other side, the following should be avoided:
Food Site
Going to https://food.microbiomeprescription.com/ and entering your login token will show the nutrients computed to help most. Iron supplements or food high in iron is at the top; for example thyme, basil, and my favorite Caterpillar, roasted ;-). Both herbs have positive recommendations.
The second one is found in cranberry (a suitable seasonal food) and raw Olive. The third one is found in maize, rye and Hard wheat, semolina. HOWEVER, none of these are recommended in the list of suggestions. I usually cross reference the two for safety.
Next Steps
I would continue with additional suggestions (1 and 2 studies) at the same pace. Two weeks after the last one was added, do another microbiome test (same firm of course) and get back to me for a follow up analysis if needed.
Postscript and Reminder
As a statistician with relevant degrees and professional memberships, I present data and statistical models for evaluation by medical professionals. I am not a licensed medical practitioner and must adhere to strict laws regarding the appearance of practicing medicine. My work focuses on academic models and scientific language, particularly statistics. I cannot provide direct medical advice or tell individuals what to take or avoid.My analyses aim to inform about items that statistically show better odds of improving the microbiome. All suggestions should be reviewed by a qualified medical professional before implementation. The information provided describes my logic and thinking and is not intended as personal medical advice. Always consult with your knowledgeable healthcare provider.
Implementation Strategies
Rotate bacteria inhibitors (antibiotics, herbs, probiotics) every 1-2 weeks
Some herbs/spices are compatible with probiotics (e.g., Wormwood with Bifidobacteria)
Verify dosages against reliable sources or research studies, not commercial product labels. This Dosages page may help.
Individual health conditions may make some suggestions inappropriate. Mind Mood Microbes outlines some of what her consultation service considers: A comprehensive medical assessment should consider:
Terrain-related data
Signs of low stomach acid, pancreatic function, bile production, etc.
Detailed health history
Specific symptom characteristics (e.g., type and location of bloating)
A reader messaged me about some issues she was having
Hi, could I just have a quick question? I read in the Gut Health group on Facebook that you wrote that if there is too much, for example, lactobacillus, it can cause neurological problems. I suffer from anxiety and depression and was recommended a transplant of intestinal microflora, which made the condition 100 times worse and since then I can’t get out of it and the doctors don’t know what to do with it. I’m still trying to treat dysbiosis, but now I don’t know if the problem is one of the good bacteria? Thank you very much.
yes, I have a biomesight and a GI map, there is an overgrowth of Prevotela, Streptococus, Enterobacter and Citrobacter and a little bifido and lacto. I have yellow stools after the transplant, if I don’t take probiotics. But it seems that nothing works, diet, antimicrobials, probiotics, enemas with probiotics, prebiotics, nothing helps
Initial Comments
This person is not in the US. She lives in a place where Fecal Matter Transplants is allowed for many conditions than the US (where it is only authorized for Clostridioides difficile –after everything else has failed). I view FMT as Russian roulette hoping that a silver ballet will happen to end up in the cylinder. IMHO, before a FMT is done we need at least two shotgun microbiome tests done. One for each candidate donor and one for the recipient. These need to be carefully reviewed by a third party who is very well informed on the microbiome. Only the best donor will be used. After the FMT, monthly shotgun reports of the recipient microbiome should be done for at least 6 months.
Analysis
The first step is to look at predicted symptoms, most are neurological, with the two reported symptoms sitting high up the list.
Comorbid: High Anxiety – [66.6%]
General: Depression – [64.1%]
I marked all of the items with depression and anxiety and then asked for suggestions. The top items are shown below,
The failure to understand that all probiotics are not created equal is a common problem. Often I have heard “I tried probiotics and it did not work”. That is not surprising because often they are sold with dozen of species in one bottle — “because the more species you have, the better your sales will be” from manufacturers and influencers.
You need to get specific species and ideally recently manufactured. A bottle of probiotics stored in an unrefrigerated warehouse for 12 months may have very few viable bacteria left. When they get to a retail store, they may be put into a refrigerator — but that is too late.
Where do I get the probiotics?
I prefer single species — and where I get mine?
Single species with (almost) no fillers. There are precisely three sources that I use:
Maple Life Science™: No strains yet, but shipments usually have manufactured date within 4 weeks of arrival (i.e. FRESH). Contains FOS
Bulk Probiotics: US based Newbie — but has some species not available at the other two sites. No other ingredients just the bacteria. Specifically, Lactobacillus Jensenii that has great potential for Crohn’s disease.
NOTE: none of these sell though retail outlets. This keeps their costs down and their product fresh.
Another Alternative to get Suggestions
On the old UI we have this section and we have enough studies for Depression show up.
With this sample, we have the following bacteria matches against published studies (with links to the studies).
This results in the suggestions below. Each suggestion has also been reported in studies to help depression. This means that the odds of them working is pretty good.
Treatment Suggestions for
This report is for Reader using this sample BiomeSight:2022-10-25 Self 🛑 . It uses their reported medical conditions, microbiome sample, US National Library of Medicine, and a fuzzy logic expert system to compute recommendations balancing study reliability and contraindications. These suggestions should always be reviewed by a medical professional before starting.
NOTA BENE: This is working solely from published studies. Other suggestions algorithms are available on Microbiome Prescription. The URL above may be sent to your MD if you wish to share it.
The reported condition(s) are
This person has a significant amount of bacteria known to form biofilms
Substances with a 🦠 are reported to reduce biofilms. See for studies.
Depression – Depressive Disorder
Omega-3 Fatty Acids: Some studies suggest that omega-3 supplements, particularly those rich in EPA (eicosapentaenoic acid) and DHA (docosahexaenoic acid), might have modest benefits as adjuncts to traditional treatments for depression. Omega-3s are essential for brain health, and they may have some mood-stabilizing properties.
Vitamin D: Low levels of vitamin D have been associated with depression. While the exact relationship is complex and not fully understood, maintaining adequate vitamin D levels through supplements or exposure to sunlight may support overall mental health.
B Vitamins: Some B vitamins, such as B6, B9 (folate), and B12, are involved in neurotransmitter synthesis and may have a role in mood regulation. Folate deficiency, in particular, has been linked to depressive symptoms.
Probiotics: The gut-brain connection has led to studies exploring the potential impact of probiotics on mental health. Research suggests that gut health may influence mood, and some studies propose that certain probiotics might have a modest effect on reducing depressive symptoms. However, more research is needed to determine specific strains, dosages, and their impact on depression.
Significant Bacteria Shifts
Based on the existing literature on the US National Library of Medicine and this microbiome sample, we have the following matches for bacteria shifts. There is a growing body of literature finding that the effectiveness of interventions depends on the existing microbiome. We filter by documented interventions that helps some with this condition and suggestions based on this person’s specific microbiome to produce this “double validated” list.
Bacteroidaceae – family : Low 516 Bacteroides – genus : Low 13162022 Bifidobacterium longum – species : Low 710 Collinsella – genus : Low 9 Collinsella aerofaciens – species : Low 9 Escherichia – genus : Low 2512
Lactobacillus – genus : Low 5814151718192123 Parabacteroides – genus : Low 1120 Porphyromonas – genus : High 1 Prevotella – genus : High 3424 Sphingobacterium – genus : Low 13 Streptococcus – genus : Low 6
Cross Validated Suggestions
The following improves the bacteria identified above and also is reported in the literature of helping some people with this condition. Each is link to the source study.
There is no definitive right way to determine how to correct a dysbiosis. We just do not have enough studies. Above, you have two main approach (with some overlap of suggestions)
Working off the microbiome that are too high or too low.
We cross check probiotics suggestions using KEGG data
Working off the microbiome using only peer reviewed studies for one condition: depression.
This report should have high creditability with most medical types — because all of the evidence used to make the report is cited.
I have not been feeling so well lately (since the last 6 months). I would say that my symptoms has become worse. Earlier it has always felt as I have done some progress but the last 6 months it has been the opposite.
At the end of January I had my appendix removed. Since then I have felt even worse. Received some antibiotics while I was hospitalized. Earlier I got rid of my muscle and joint pain but it has come back and I have much bigger issues with my red nose and my body feels very stressed. Also feel very bloated.
A summary of my biggest issues:
Get the red nose (some form of rosacea).
Feel fatigued (both physically and mentally).
Feeling stressed.
Brain fog.
Bloated.
Lots of gas – I fart and burps a lot.
Issues with allergies
Muscle and joint pain
For the last 3 years I’ve been eating large amounts of rye and oats.
Around 150-200 gram of rye bread every day.
Around 70 gram of oats every day.
Been eating low fat, low protein and high carb (specially from rye, oats, apple juice and potatoes) because this diet seem to reduce my symptoms.
As soon as I start to eat high meat and high fat my symptoms get worse.
Quick Overview
I will continue with a table showing recent changes (see above for earlier values)
Criteria
3/30 2025
12/3 2024
9/2 2024
1/22 2024
2/22 2024
Lab Read Quality
7.6
9.8
9.1
7.9
9.7
GanzImmun
10
14
16
16
15
Outside Range from Lab Teletest
21
17
23
20
24
Outside Lab Range (+/- 1.96SD)
10
7
12
5
10
Outside Box-Plot-Whiskers
59
47
48
54
42
Outside Kaltoft-Moldrup
111
85
113
123
139
Bacteria Reported By Lab
718
689
600
511
666
The most striking change was the 4% increased number of bacteria. Looking at Symptom Pattern Matching, we see significant improvement with 15% with significant improvement.
Current Takes Evaluation
I have put together a video trying to describe the complexities of shifting the microbiome. My own experience during a flare was “suggestion whiplash”, the suggestions from one test became avoid on the next and became suggestions on the next test. This is not what I was expecting and caused me to question the process — until I dug deeper and did some modelling. My understanding is in this video.
What he reports taking is below. I look at the suggestions and added the weight after each.
amoxicillin: +490.3
Noni -206.1
Propolis {Bee glue} +19.5
Dandelion + 155.3
allium sativum {garlic} -214.4
Parsley + 145.3
Grapefruit seed extract +168.8
mutaflor -78.8
Takes flipping to avoids is not unexpected. It does emphasis the need to do regular tests, especially when progress slows or reverses.
Building Suggestions
Since we have symptoms we use Beginner-Symptoms since it will focus on bacteria associated with symptoms present.
Looking at the Consensus report we see the top 3 antibiotics are all ones associated with CFS
The other items is interesting and would suggest Whole Milk (high Fat) (Yogurt) from A2 cows, I do not know if that is easily available in his country. I happen (as a recovered ME/CFS person) to have some to my daily morning porridge.
The suggestions above do not fit typical patterns that I have seen. I went back and did “just give me suggestions” in case the bacteria filtering by symptoms caused some odd twist. Results were similar as shown below.
One More Analysis
I looked at the prior Dec 24 sample and compare the KEGG Compounds to the current sample starting with the highest percentile ones:
While the bacteria changed, the extreme metabolites remained high but with a few reducing. There is a potential to generate suggestions based on these KEGG compounds — a little messy and definitely pushing inference into new turf.
I have decided to build an adjacent Suggestions Agent using metabolites ONLY. The microbiome is a very complex system and there is a possibility that the metabolites approach may work better. Stay tune!
Reconciliation of Recent Diet and Suggestions
During my own recovery, I had “whip-lash” between suggestions from one test until the next test. One test results had to take, the next result was the same items on the avoid list. This “pendulum” swinging back and forth may be happening here. My own response was to be “less religious” in keeping to the suggestions (i.e. “moderate compliance”) and retest after 6 weeks doing suggestions. The pendulum swing dampened down and lead to a full remission (with patience).
The 300 grams of fiber (Rye, Oats) should be reduced. If you can get a willing MD, then you may wish to rotate to a different antibiotic because of the risk of antibiotic resistance occurring.
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