The intent of this site to assist people with health issues that are, or could be, microbiome connected. There are MANY conditions known to have the severity being a function of the microbiome dysfunction, including Autism, Alzheimer’s, Anxiety and Depression. See this list of studies from the US National Library of Medicine. Individual symptoms like brain fog, anxiety and depression have strong statistical association to the microbiome. A few of them are listed here.
The base rule of the site is to avoid speculation, keep to facts from published studies and to facts from statistical analysis(with the source data available for those wish to replicate the results). Internet hearsay is avoid like the plague it is.
MCAS – Mast Cell Activation Syndrome as well as many other issues
EMF – Electromagnetic Fields– from sunlight to microwave to cellular radio wave
GRAS – Generally Recognized As Safe — an item deemed safe by authorities but may lack hard evidence. See GRAS History. It also include items that are “grandfathered” in and later shown to be unsafe:
Example: Smoking was healthy
PCB and Asbestos were safe
This is not intended to be JFK Jr like conspiracy theory — just raising questions and suggest testing approaches. If something is new and a potential profit maker, effective testing is never done.
EMF – Electromagnetic Fields
The chart below shows the scope of EMF
We know that values across this entire spectrum can cause disease, typically cancer.
“Too much ultraviolet (UV) radiation from the sun can damage DNA in your skin cells and cause skin cancer. ” [Src]
“Ionizing radiation, such as X-rays, has enough energy to remove tightly bound electrons from atoms. This process can lead to DNA strand breaks or alterations, potentially resulting in mutations that may cause cancer or other health issues.” [Src]
“Cancer in radar technicians exposed to radiofrequency/microwave radiation” [src]
In today’s world, we are adding more and more electromagnetic frequencies:
An analysis of data from five Northern European countries showed an increased risk of acoustic neuroma in those who had used a cell phone for 10 or more years [2600 studies on pubmed].
Microbiome shifts from radio waves
Several bacteria are known to be altered due to radio frequency (RF) exposure. Research has shown that RF radiation can affect bacterial growth, antibiotic sensitivity, and microbial composition.
Enterococcus faecalis:
Exposure to 900 MHz and 2.4 GHz RF radiation altered its antimicrobial sensitivity1.
After 6 hours of exposure, the bacteria showed decreased susceptibility to antibiotics.
Longer exposure (24 hours) increased the bacteria’s susceptibility to antibiotics1.
RF-exposed bacteria showed faster growth rates compared to non-exposed bacteria1.
Klebsiella pneumoniae:
Exposure to 900 MHz RF radiation for 12 hours significantly increased its sensitivity to various antibiotics2.
RF-exposed bacteria showed faster growth in the exponential phase compared to non-exposed bacteria2.
Gut microbiota:
Exposure to 4.9 GHz RF radiation altered the gut microbial composition in mice, reducing microbial diversity3.
The relative abundance of Firmicutes increased, while Muribaculaceae decreased after RF exposure3.
Other bacteria:
Studies have shown that RF exposure can affect the growth and antibiotic sensitivity of Escherichia coli, Enterococcus hirae, and Staphylococcus aureus1.
Hypothesis: Some conditions may be encouraged by RF Exposure
Whether this includes Mast Cell Activation Syndrome is to be determined. It is clear that other conditions are impacted.
What can you do:
Avoid carrying cell phone on your person, i.e. place on desk at home or car seat driving
Avoid Bluetooth headsets
Keep WiFi hubs as far away from your usual living space as practical
Experiment: Go camping in an area that is very low RF (turning off cellphones) My own favorite area is the drive between Hay River and Yellowknife in the Northwest Territories of Canada.
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 aspartamewere 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).
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.
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)
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.
I forwarded these on to a friend suffer from MCAS. She responded that she was mentally lost in the studies. She decided to ask Perplexity. to explain. She was delighted with the response and I thought that Perplexity should have a guest post!
This abstract describes how mast cells, which are key players in allergic reactions, release inflammatory substances through a process called degranulation. Here’s a simplified explanation:
Mast Cell Degranulation Process
Mast cells contain small packages (granules) filled with inflammatory chemicals.
When triggered, these granules fuse with the cell’s outer membrane to release their contents.
This fusion is controlled by a set of proteins called SNAREs, including Syntaxin4, SNAP23, and VAMP8.
Normal Degranulation Mechanism
A protein called IKKβ attaches to and modifies (phosphorylates) SNAP23.
The modified SNAP23 then joins with Syntaxin4 and VAMP8.
This three-protein complex drives the fusion of granules with the cell membrane, releasing the inflammatory substances.
Effect of E. coli on Degranulation
The researchers discovered that exposing mast cells to E. coli bacteria interferes with this process:
E. coli prevents IKKβ from interacting with and modifying SNAP23.
As a result, SNAP23 doesn’t join with Syntaxin4 and VAMP8 as effectively.
This disrupts the formation of the protein complex needed for granule fusion.
Consequently, the release of inflammatory substances from the granules is reduced.
In essence, the study shows that E. coli can suppress the allergic response of mast cells by interfering with the molecular machinery responsible for releasing inflammatory chemicals.
Similarly, I was ping by a reader who said “You can’t buy these in the US” — That is correct in that you will not find them in your local health food store. I live in the US and have no trouble getting them by internet order shipped to my door:
This is a preview of the next generation of analysis. I described a mathematical model in Microbiome Guilds, Metabolites and Enzymes. I mentioned a concept in it and over the weekend tried the concept out. It worked and is very sweet.
To explain it, look at the chart below. The blue line is for those that have a symptom and the orange line is what is expected. If you divide observed by expected for different percentiles, you get an odds ratio. Most people know odds ratio (OR) from things like:
For current male smokers consuming >30 cigarettes daily:
This pattern does not determine that you will absolutely get it. It means that your are more likely — odds. (My native environment as a statistican)
Biomesight Bacteria
The genus bacteria listed below, each have at least an odds ratio of 1.5 for general fatigue using Biomesight data if your percentile is below the amount show. I stopped listing at 10%ile items
Bifidobacterium <= 48.7
Collinsella <= 41
Coprococcus <= 39.3
Desulfosporosinus <= 38.7
Lachnobacterium <= 37.6
Oribacterium <= 35.8
Lactobacillus <= 30.5
Pseudobutyrivibrio <= 29.5
Legionella <= 28.9
Roseburia <= 28.3
Faecalibacterium <= 27.8
Lachnospira <= 27.3
Turicibacter <= 27.1
Mycoplasma <= 25.8
Peptococcus <= 24.3
Coraliomargarita <= 23.8
Sedimentibacter <= 23.7
Rhodothermus <= 23
Tindallia <= 22.4
Thiothrix <= 21.8
Eubacterium <= 21.7
Thermicanus <= 21.6
Sutterella <= 21.5
Alkaliphilus <= 21.5
Luteibacter <= 21.1
Sphingobacterium <= 21.1
Candidatus Phytoplasma <= 20.5
Anaerostipes <= 20.4
Haemophilus <= 19.9
Moorella <= 19.1
Catenibacterium <= 18.7
Olivibacter <= 18.5
Novispirillum <= 18.4
Butyricimonas <= 18.3
Natronincola <= 17.9
Macrococcus <= 17.3
Runella <= 16.6
Tepidanaerobacter <= 16.1
Caldicellulosiruptor <= 15.7
Enterococcus <= 15.4
Serratia <= 15.3
Salinicoccus <= 15.2
Gemella <= 14.9
Odoribacter <= 14.7
Thiohalorhabdus <= 14.6
Dorea <= 14.2
Escherichia <= 14.1
Chlorobaculum <= 14
Parabacteroides <= 14
Calothrix <= 13.8
Megasphaera <= 13.8
Selenomonas <= 13.6
Acetobacterium <= 13.6
Slackia <= 13.4
Pseudoclostridium <= 13.4
Peptoniphilus <= 12.4
Tetragenococcus <= 12.2
Johnsonella <= 12
Akkermansia <= 11.8
Veillonella <= 11.5
Holdemanella <= 11.5
Streptococcus <= 11.2
Pectinatus <= 11.2
Pedobacter <= 11.1
Klebsiella <= 11
Dysgonomonas <= 11
Erysipelothrix <= 10.9
Desulfurispora <= 10.7
Dolichospermum <= 10.5
Mogibacterium <= 10.4
Bilophila <= 10.2
Ruminiclostridium <= 10.2
Finegoldia <= 10.1
If you have 10 of them then 1.5 ^ 10 = 57x greater odds of having general fatigue. It is NOT one bacteria causing it, or even a specific group of bacteria, but different combinations of possible bacteria.
I should mention that these numbers only applies to Biomesight data. “results from one pipeline cannot be safely applied to another“. For background see: The taxonomy nightmare before Christmas.
Ombre Equivalent Bacteria
If you have Ombre’s microbiome results, these are the critical bacteria:
Collinsella <= 44.2
Erysipelatoclostridium <= 41.8
Bifidobacterium <= 41.1
Thomasclavelia <= 39.2
Lactobacillus <= 30.1
Dorea <= 27.4
Fusicatenibacter <= 24.1
Gemmiger <= 23
Terrisporobacter <= 17.9
Sutterella <= 16.1
Coprobacter <= 15
Coprococcus <= 13.7
Haemophilus <= 13.6
Flavonifractor <= 13
Casaltella <= 13
Ruminiclostridium <= 12.5
Faecalicatena <= 12.3
Mediterraneibacter <= 11.9
Slackia <= 11.8
Paraprevotella <= 11.5
Eubacterium <= 11.3
Subdoligranulum <= 11.2
Lachnospira <= 10.3
Phocaeicola <= 10.2
uBiome Equivalent Bacteria
This illustrates well the fact that ranges will differ a lot between tests.
Subdoligranulum <= 43
Faecalibacterium <= 38.9
Pseudobutyrivibrio <= 26.2
Veillonella <= 22.4
Dorea <= 21.4
Fusicatenibacter <= 21.1
Hespellia <= 19
Oscillibacter <= 18.6
Roseburia <= 18.2
Odoribacter <= 17.9
Collinsella <= 15.9
Intestinibacter <= 15.8
Bifidobacterium <= 15.1
Clostridioides <= 14.6
Papillibacter <= 14.5
Actinomyces <= 14.2
Sutterella <= 12.9
Blautia <= 12.8
Parabacteroides <= 11.9
Marvinbryantia <= 11.6
Anaerotruncus <= 10.8
Bottom Line
This transforms the ability to determine if a bacteria is too high or low. Given a symptom or condition, we can determine the bacteria likely involved and if the level is likely (odds) to contribute to the symptom.
We can thus focus on exactly the bacteria of concern and ifnore the noise elsewhere.
Stay tune, there is a lot of coding to do to implement this.
Trial of algorithm
I was helping someone transfer data from biomesight.com and decided to run their latest sample thru the odds ratio I had derived this weekend. She marked their symptoms, see below. The numbers are the odds ratio.
The evidence that hypersensitivity to noise is likely microbiome dysfunction based is sweet — since there is no conventional treatment for it.
Hello, I’m a 21-year-old with a moderate case of CFS. Currently, I’m having serious problems with concentration, reading, memory, and executive function to the extent of needing a caregiver. I react to any food with neurological symptoms and gas, and my energy production is so impaired that I get hungry just two hours after a large meal. I would like to hear your analysis of the sample, especially your opinion about the sky-high amounts of Bilophila wadsworthia.
At 13 years old, I started having hemiplegic migraines with aura, including paralysis, speech, vision, and orientation loss due to an ATP1A2 mutation. These were thought to be incurable until I randomly found an off-label local medicine, metamizole, which is prohibited in the US, Canada, and the EU but is available in my home country, Ukraine. This medication was effective in mitigating the aura. I started taking it every day for four years starting at age 16. Recently, I learned that it increases prostaglandins and has an immunosuppressant effect like NSAIDs in general. I suspect that my daily use of this medication may have contributed to developing CFS and hypersomnia through unchecked mucosal infections.
I was also diagnosed with 160,000 copies of HHV6 in my blood via PCR, which persisted for years (I stopped testing for it). I tried valganciclovir, artesunate and IFN-a, which did nothing but further worsened my baseline. A year and a half ago, I started Joshua Leisk’s Born Free protocol (https://bornfree.life/download/BF_Protocol.pdf), which improved my metabolic situation significantly. However, I coincidentally started living in an unhygienic, mold-infested environment, and subsequently had GI and Eustachian tube infections. After taking nifuroxazide, amoxicillin, and metronidazole a year ago, my condition worsened to a moderate level, and I haven’t recovered since.
I suspect that gut issues are the cornerstone of my problems, but I am quite lost lost regarding how to handle them. I am eager for any new information.
The model that I use for ME/CFS is some event (stress, food poisoning, virus, inoculation or dozen of other possible events) cause the microbiome to shift in response. The shifts can result in a feedback loop that keeps this “evil microbiome” shift going. A percentage recover naturally over time, and we have a longitudal study from Bergen Norway to illustrate this. The trigger was giardiasis for a large number of people. A medicine like metamizole on a continuous basis can easy cause this to happen.
Analysis
We have two samples available, so let us look at the before and after antibiotics comparison. My impression is that the antibiotic made things worse. The latest sample has more items out of range despite having ~20% less bacteria reported
Since we are nominally dealing with ME/CFS, we can use the cross validated suggestions to get conservative suggestions of what may help
The result is a massive list!
We will backtrack to “Just Give Me Suggestion Including Symptoms” so we can rank order these suggestions.
The top items are antibiotics, with 60% being those used to treat ME/CFS (i.e. on the above cross validated list). I tend to follow Jadin’s approach so, do one of those marked [CFS] for a course (7-10 days) and the next month(3 weeks off), move to a different one. After the 3rd one, get a new microbiome test to see the next course adjustment.
Probiotics are dominated with Bifidobacterium species. I would tend to do 3 weeks on one strain between antibiotics, working up to a dosage of 50 BFU. At present, my favorite source is Maple Life Science™: they ship worldwide, typically the packages arrive with manufacture dates 4-6 weeks before (thus LIVING probiotics), and very reasonable cost. Yakult and Kefibios can be difficult to obtain in some countries.
Going over to KEGG suggested probiotics and although we are approaching it from a totally different path, we have consensus.
For prebiotics, just three stand out, take them with the above probiotics
For vitamins (can be taken continuously), I would suggest adding them one at a time (every 3-4 days) in case some create significant (good or bad) reactions.
For flavonoids, the list is very ME/CFS typical.
Second Pass – Cross Validated Suggestions
I picked these from the short list of options in the old UI.
The number of bacteria matches were relatively few.
The suggestions are shown below. Note that Lacticaseibacillus casei and Lacticaseibacillus paracasei shirota. Are on this list, just as they were above. Avoid other lactobacillus probiotics.
Questions and Answers
Some questions: — what are your thoughts on the sky-high levels of Bilophila (any specific advice on managing that?) and the very low overall species diversity. I did some troubleshooting with a CGM, and every time I eat some animal fat—and to a lesser extent, animal protein—after carbs, I experience a hyperglycemic spike. I attribute that and my brainfog to a Bilophila overgrowth (H2S & acetaldehyde). When I’m on a vegan diet, my blood sugar is generally perfect, except for one hypoglycemic event at night but it’s really problematic to sustain this diet long-term. — also, which advice here is aimed at increasing lactobacillus abundance as the recommended probiotics are mostly bifido?
Response
Here we hit a philosophy crossroad.
The road most travelled is focusing on the bacteria most heard about and trying to address them one by one.
The road that I take is to ignore this chatter, and aim to adjust everything in one pass using mathematical models.
Often I have read that something like Lactobacillus increases for a subset of people if other bacteria are present, (or absence).
I view this approach is most likely to cause desired changes and not chasing this bacteria or that bacteria.
Microbial Interdependence
Microbial interdependence occurs when different bacterial species rely on each other for growth or survival. This can happen through various mechanisms:
Metabolic cross-feeding: One species produces metabolites that another species uses for growth.
Signaling interactions: Chemical signals from one species trigger responses in another.
Modification of the environment: One species alters the local environment in ways that benefit another species.
Given that concentration is an issue, there is a high probability that high d-lactic acid is involved. This would cause me to suggest avoiding lactobacillus probiotics entirely. It is impossible to determine which retail brands produce d-lactic acid.
Bottom Line
Go slow, slowly increase dosages, keep track of your reactions on paper (or electronically). Some suggestions will have no effect, others may have dramatic effects.
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)
My journey to how I ended up where I am now is that I’ve always been one to catch illnesses like colds, flus, and stomach bugs easily. I was also frequently medicated with antibiotics for many years as a kid. Looking back, of course my microbiome is a mess.
To date, I have had COVID 6 times (that I know of/positive tests – there was probably more that didn’t “show up” or that I may have dismissed as a cold).
The first time I had Covid was January 2020, before it was “a thing”. It was later confirmed that it was indeed COVID, with an antibody test sometime in February-March 2020 when I donated blood. I was the sickest I’ve ever been in my life (26yo then, I’m 30 now). My main symptoms were feeling out of breath and lightheaded, as well as gastrointestinal (diarrhea and vomiting) – which at the time, no one was acknowledging that COVID could have any gastro symptoms, so I kept getting dismissed that it couldn’t have possibly been COVID. I was sick for a solid week and a half and it took me about 8 weeks to get back to feeling somewhat normal and not out of breath etc.
I’ve missed so much work because of this illness and I just keep catching it – the most recent time being just a month ago.
I developed the skin condition Rosacea around late 2022-early 2023 which I believe is microbiome related – I’ve tried many topical prescriptions that don’t do a dang thing, and it has since spread to my eyes and I now have Ocular Rosacea as well.
I’ve always had chronic constipation but it is worse since 2020. I have fatigue and am always tired, no matter how much I sleep. At one point I had high iron, so I was told to donate blood to lower it, but then my iron and ferritin fell so low that I was told to stop and instead take iron supplements to get my iron and ferritin back up – which I cannot tolerate, because it causes stomach issues for me.
I’d love to figure out how to really improve my microbiome and finally heal from all of this. I’m constantly living in fear that I’ll catch COVID again and lose any progress I’ve made.
Analysis
Rosacea is a chronic inflammatory skin condition that can have systemic effects and comorbidities. While not directly linked to ME/CFS or long COVID, it shares some characteristics of chronic inflammatory conditions. I have encountered several ME/CFS with it
Constipation is commonly associated with ME/CFS (Myalgic Encephalomyelitis/Chronic Fatigue Syndrome).
Both are suspected to be cause by imbalance of gut flora (microbiome).
We see a lot of pattern matching to other people with the same symptoms.
But since we are dealing with a situation with some cross-validation data being available (i.e. lists of things with studies that helps with the symptom/diagnosis), I like to start there. On [Changing microbiome tab].
Updated Analysis
The original draft was done before the Simple UI was released. There was 6 forecast matches over 70%, so I went with symptoms, Despite having 11 symptoms, only 9 bacteria was selected.
The suggestions are shown below
Probiotics
These are the top items, some can be hard to get. Some of my usual sources are:
The above are based on how they are known to alter other bacteria from published studies. Next I swing over to KEGG to see which probiotics can provide metabolites and enzymes that the person is low in. This is a complimentary approach that does not depend on a study being done, rather working from the DNA of the microbiome. I have annotated the above with their [Metabolite/Enzymes] scores above. The highest lactobacillus was 4, Bifidobacterium [7]. One bacillus ranked high, but is not easily available as a probiotic: Bacillus thuringiensis -[15/9]. My preferred sequence would be to start with B.Subtilis and then B. Coagulans.
Foods
The food menu suggests that Turkey and Chicken are the best meats. Kiwis and Soy are next. To avoid: carrots, beans, sweet potatoes,
Vitamins are the usual for ME/CFS
One word of warning — do not use B-Complex. They contain some B-vitamins that are to be avoided. Get the specific B-vitamins shown.
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)
ME/CFS has many causes, a very common cause are virus (in the case of Long COVID, the COVID virus).
Back Story
A quick summary of my story: I got ME/CFS after two viruses about a month apart in late 2016, when I was 27 – one upper gastrointestinal and one upper respiratory. After struggling to work for a couple of months after my body eventually gave up and I had to be signed off sick, and then eventually let go. I haven’t returned to any work since. I would say I am at the moderate end of the spectrum – able to socialise outside of the house on occasion as long as transport isn’t too strenuous, but not well enough to do things on a consistent basis, with obviously lots of rest all the time. Since then I’ve been on a journey seeing various doctors mostly to no avail, although not for a few years now.
My main symptoms now:
Fatigue
Muscle weakness
POTS
Unrefreshing sleep
Various mild / moderate pain
Very prone to overheating / sweating
I take 40mg Duloxetine once a day, ostensibly for nerve pain although it has helped significantly with my overall energy levels and wellbeing, moving me from severe to moderate from when I started taking it a few years ago.
It’s worth pointing out that over the course of my illness I have tried several probiotics and things suggested with the gut. These are as follows (if I remember correctly):
Optibac
BioKult
Generic acidophilus probiotic
GI Synergy antimicrobials
Yakult (more on that in a minute)
Every single one of these has caused these symptoms of varying severity:
Increased blood pooling
Sore throat
Flushing
Fatigue
Disorientation
General malaise
So in general I have stayed away from things to do with the gut because of these bad experiences. Yakult is actually something I stopped only recently – I read your blog post about d-lactate and given it’s so cheap and easy to get hold of decided to give it a go. I would say that while the other probiotics caused those symptoms almost on the first or second dose, with Yakult it took a lot longer to set in. I took it for 3 weeks before I finally realised that I was at the same place symptom-wise as the others, it just took me much longer to get there. A shame as it i was a low-cost and easy thing to try. They’re obviously all doing something! Just not what I’d like, haha.
I did the simple suggestions option since the number of symptom matches to symptoms prediction was low. We found 43 bacteria out of range. None of the following probiotics were on the recommended list: Optibac, BioKult, Generic acidophilus probiotic, GI Synergy antimicrobials, Yakult
Going over to KEGG Computed Probiotics Report, we have these being the top one
Limosilactobacillus reuteri – On main suggestion list
Since economics is cited, I would suggest ordering one bottle of each from Maple Life Science. They are direct from factory to retail customers; ships world wide; no shipping costs. Cost per bottle is around $9
Limosilactobacillus reuteri
Lactiplantibacillus plantarum
Lacticaseibacillus rhamnosus
Bacillus Subtilis
For the other ones, see how you react to these first. My usual suggestion is one capsule for ONE of these on the first day, increase according to your reaction. If adverse reaction, move on to the next one. Once the bottle is empty, go to the next one.
Personally, my own ME/CFS experience favors Mutaflor — but it created a massive herx for 2 weeks; so I tend to suggest moving it to the very end.
Other issues
I have no information on Duloxetine impact on the microbiome. Other suggestions have many familiar in treating ME/CFS over the last 30 years. The include:
Unusually, B-vitamins are not high on the list. If you take them, keep to Vitamin B1,B2 and B12.
Going over to the Food Site we have these nutrients at the top
The first one, Resveratrol, is found in fresh grapes in the supplement form is not desired. The second one is mainly in raw Chicory . The third one is found in Black elderberry (and a small amount in Pomegranate). The fourth item, (-)-Epigallocatechin, is found in Green/Oolong Tea and Broad Beans. The next one, Cyanidin 3-O-xyloside, is mainly in Black chokeberry (and a small amount in Blackberries). Hesperetin is found in Lime and Oranges (not orange juice). Resistant starch is in Broad Beans, Lentils and Peas. Syringaresinol is found in Rye (i.e. whole 100% rye bread) and the Swedish Cloudberry (likely out of season now). Diosmin is found in Hyssop (I tend to buy it as a supplement).
As a FYI, my regular “ME/CFS preventative” diet is usually heavy in grapes or Resveratrol (depending on season and price); 100% Rye Bread; Broad Beans and Lentils; Hesperetin and Diosmin.
Questions And Answers
Q: The herx / die off stuff do you have any guidance on that? What I meant was: given my adverse reactions to any probiotic I have tried – whether that’s on the same day after initially taking, or eventually building up after several doses – how can I tell the difference between a reaction that’s bad and should cease taking it, or supposed “die off” symptoms, if you see what I’m saying. Basically how to tell the difference between stopping needing to stop taking a probiotic due to the symptoms its producing, or pushing on, and seeing if it tails off. Does that make sense?
Your question makes a lot of sense. I have done a few posts on that:
The issue is more complex for probiotics because often extra ingredients are included which some people react to.
A short version for probiotics is this:
If the adverse effect is ongoing 18 hours later, it is likely an adverse reaction or feeding bad bacteria. Many studies find that some probiotics are not detectable after 24 hours (not true for all of them).
The duration of the reaction should be decreasing each day. You should feel a little better after the effect ebbed each day. Often, there can be a quick ending of the reaction. If it increased or do not change, it is likely an adverse reaction or feeding bad bacteria.
I have improved the Lookup Modifier Page to flag what a probiotic is impacting. You need to break a mixture apart and examine it parts. Most of his probiotics were mixtures containing L. Acidophilus. Note that Sutterella is in common with both
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.
As I’ve been suspected to have Lyme disease, I have taken antibiotics for several months which have damaged my microbiome. Now I am taking antibacterial herbs. * As my brain fog severely increased, I need your help to adjust my strategy. In addition, there are some specific questions: I am contacting you as I have done a new microbiome analysis with BiomeSight. I haven’t been doing well in addition to my previous health issues. As I’ve been suspected to have Lyme disease, I have taken antibiotics for several months which have damaged my microbiome. Now I am taking antibacterial herbs. As my brain fog severely increased, I need your help to adjust my strategy. In addition, there are some specific questions: ❔mutaflor isn’t among the suggestions done. Would it be a good thing to add it ? ❔how long should I wait between probiotics and antibacterial herbs ?
From Email
Analysis Of Data
I have a pretty fixed attitude to Lyme
It’s Lyme only with a very clear laboratory result (i.e. tests for actual Borrelia species and strains and conforms to the rest of CDC criteria).
“Chronic Lyme” is likely post-infection syndrome and the use of “Lyme antibiotics” can often do more harm than good. “Suspected Lyme” is a red flag that the medical practitioner is outside of their depth.
We have three samples available. There was some apparent improvements from earlier samples (
Comparing current sample to the first sample is shown below. The number of bacteria reported is almost half of the prior test, making comparison difficult, but my impression is that there was some improvement.
Looking at the new symptom matching comparison , we see some significant drops.
Going Forward
Since symptoms have been entered, we will go with [Beginner-Symptoms: Select bacteria connected with symptoms]. This results in 29 bacteria being identified (about 8% of the bacteria – my preferred range is 4- 12% being flagged to be of concern).
The top suggestions are below which are heavy in fiber and beta-glucan. A common pattern with post-infection syndrome.
The numbers in the [ ] are the number of compound that are low that the probiotic produces. Enzymes shortage usually leads me towards probiotics because they are producers of many enzymes. Most of these enzymes are not available as supplements. When there are shortages, bacteria misbehaves… “when the manager is empty, horses bite”
My suggestion for rotations (1 probiotic for 1-2 weeks and then move on to the next)
At this point, we branch into two additional paths — one by using Kyoto Encyclopedia of Genes and Genomes (KEGG) data on compound being produce and consumed by your microbiome. With KEGG we look for probiotics that can provide enzymes etc that you are deficient in. Why these alternative paths? Simple, there is not enough data available so we use inference.
The second path is going to the food site to identify foods rich in suggested nutrients. The foods may not have been used in studies, but the dominant nutrients in the foods may have been studied.
KEGG
The top suggestions are below. #1 item is common for ME/CFS, Mutaflor is available in some countries in Europe, I warn people that it may cause a major die-off / herx reaction. Symbioflor 2 is the same probiotic species but at ~ 1/100 of the BCFU and unlikely to cause die off. These are reasonable “2nd rank” probiotics to try. The evidence is by inference and not direct study.
Food
Going to the food site, we find walnuts, almonds,cocao/dark chocolate, and beef at the top of the list. The following food groups should be added to the menu also:
Questions
❔ Brain fog
Usually this is due to d-lactic acid which is produced by some Lactobacillus species but not by Bifidobacterium and others. You may wish to skip those in the above list. Thick blood is another common cause for brain fog. Other things to try (assuming d-lactic is the cause):
Sodium Bicarbonate (baking soda)
Thiamine (Vitamin B1) – Low on Avoid list
Calcium Supplements – Low on suggestions list
❔mutaflor isn’t among the suggestions done. Would it be a good thing to add it ?
Mutaflor is at present on the avoid list but top of the KEGG list. It is worth doing a short trial to resolve if it is good or bad for you. I put it at the bottom of the list, in the hope that the other probiotics would cause changes that it can use.
❔how long should I wait between probiotics and antibacterial herbs ?
Typically I suggest 2-3 weeks of probiotics and then a switch. Above we have a variety of nuts (remember peanuts are not nuts) and other foods that are not deemed antibacterial. My general impression of the suggestions is that encouraging good bacteria (instead of killing bad bacteria) is the desired direction.
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)
This person has ME/CFS and is familiar with Cecile’s Protocol (see her 2023 presentation here). So my focus will be atypically on antibiotics.
I have just uploaded a new sample and I wanted to ask you if “just give me suggestions” is enough in order to get suggestions regarding a new antiobiotic therapy? Or is there anything else you would recommend me to check on your site?
From Email
Antibiotics Analysis
First, we have multiple samples available. Given that the microbiome is always changing. A first sample in the morning and last sample in the evening will rarely agree, I will actually review the suggestions from all 4 samples.
The table below contain only antibiotics that have been tried (with some degree of success) for ME/CFS
My impression is that a round of metronidazole, followed by amoxicillin, followed by a short round of ciprofloxacin appears to be consistent with the pattern of suggestions. From perplexity, I got:
Amoxicillin showed a moderate risk with an adjusted odds ratio of 2.29 (95% CI, 2.02, 2.60). However, it’s important to note that amoxicillin/clavulanate had a much higher risk than amoxicillin alone
Ciprofloxacin, a fluoroquinolone, had a risk level closer to later-generation cephalosporins with an odds ratio of 6.83 (95% CI, 6.56–7.10).
Since we have two samples over time from the same labs, I usually like doing a high level compare. First, the classic comparison which shows the two samples do not have major shifts. An increase of low enzymes usually points me to probiotics via KEGG computations.
Looking at the new Symptom Pattern Matching, we see a definite improvement (defined as having less bacteria matching symptom patterns). The amount was not huge, but it shows positive change.
A quick check of symptoms entered versus forecasted had a low match ratio and identified just 7 bacteria, all low: Streptococcus, Rhodospirillaceae, Oribacterium, Natronincola, Lactobacillales, Blautia and Bacilli.
The suggestions to correct these 7 are below. Because all of these are LOW, antibacterial herbs are usually on the avoid list.
Going to the default Novice choice, we get 38 bacteria with both highs and lows. As expected, we have some things changed from avoid to take – for example Neem. The bacteria selected makes a major impact on the suggestions (and why I keep working on better ways of selecting bacteria).
The Food Site is now working again so we can see the suggested best nutrients. The purpose of the Food Site is to transform scientific chemical names (nutrients) into foods.
All of these are based on the nutrients in these foods and the good/harmful nutrients calculated.
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)
I have had a long history of consuming high sugar and high carb junk foods. Recently, in October 2022, I noticed significant weight loss and developed chronic constipation.
Other Ideas: Considering FMT using my 1.5-year-old breastfed son’s stool for microbial diversity after screening his poop using biomesight16s testing.
Current Symptoms:
Constipation
Weight loss and unable to gain weight.
No stomach acid
As an amusement, we have the microbiome suggesting some patterns that are in agreement. (India is very very eastern Europe!)
Looking at the new revised Simple UI we see a number of matches at the top of the list.
Analysis
Eubiosis is a shocking 0.3%ile with the following chart, note that there are a large number of very high %ile bacteria.
Looking at Health Analysis we see Overall Volume Percentile 17.3%ile | By different Taxa 92.6%ile – higher values indicates more leak. That is, the mouth may be really over-seeding the gut bacteria. This hints that a FMT may not last because the mouth bacteria will just move back in! The dominate leaked bacteria at the family levels OVER 90%ile are:
Scanning other factors, I see Rickettsia at the 100%ile and Morganella at 95%ile
In short, so many issues to chase!
Going Forward!
Since the person is in India where prescriptions are not needed for most antibiotics, I will include those. I am going with “Just Give Me Suggestions” — mainly because there are too many issues involved. KISS.
Top Antibiotics
Keeping with Cecile Jadin model, I would suggest trying one of these for 1 week each month. Rotating each month starting with Ciprofloxacin and then Piperacillin-tazobactam. You should discuss with your MD before starting.
Ciprofloxacin (a fluoroquinolone) is effective against Rickettsia [src]. Piperacillin-tazobactam (and most fluoroquinolone) is considered an effective first-line treatment option for Morganella infections [src]. Rifaximin (Protocol 1) is on the list but at 30% of the above weights. Fluconazole is at 10%
Other Substances
In the above protocols, there was a huge number of items tried — i.e. the herbal kitchen sink was tossed at you– probably without clear reasons for the choices. The effectiveness of the prior protocols may have been inhibited by the Rickettsia and Morganella.
S. boulardii is on the list (Protocol 1) but well down on the list.
I would suggest dissolving the powders in a glass of warm water (away from food),swish in mouth, gargling before drinking. This is directed at the Oral Bacteria.
The above was done with original UI (still there). Using just the 3 symptoms above, we have 21 bacteria identified that are associated to those symptoms. In terms of antibiotics, the top ones are all typically used with ME/CFS. The suggestions are changed from above because we are focused on only the bacteria associated with these 3 symptoms.
In terms of Probiotics, we have the following that are available from Maple Life Sciences (located in India, with a website too)
My current suggestion is to order one bottle of each (average cost $8-9) and start with one probiotic at one capsule, increasing slowly the dosage. When a bottle is empty, go on to the next bottle.
Top Herbs are:
I jumped over to the food planner (which has been reactivated) and see these items:
Riboflavin — go supplements and/or Oats and Barley
1-Sinapoyl-2,2′-diferuloylgentiobiose: Raw Broccoli
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.
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