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.
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.
I have been struggling with my medical symptoms. After over a year of persistent fatigue, I found your blog, and would like some additional help with determining the issues in my gut microbiome.
I had mono(Epstein–Barr virus – EBV ) in high school. I have had COVID once, in December of 2021.
In November of 2022, I started feeling a bloating-like symptom in my stomach. I saw multiple doctors, and had two endoscopies and a colonoscopy done. Nothing was found. I was diagnosed with IBS, and told to take a probiotic. I took it (GBI 30, Bacillus Coagulans).
The very next day, and ever since, I have been dealing with chronic fatigue, along with associated symptoms such as headaches and joint pain (mostly in the legs).
I’ve seen a variety of doctors including GPs, GIs, a rheumatologist, and a naturopath. None have been of very much help. One GP thought I may have undiagnosed lyme due to the inaccuracy of lyme tests, so I took a four week course of doxycycline, which did not make me feel any better or worse. I have tried gluten free, dairy free, and added sugar free diets, none of which helped either. Various supplements from my naturopath also did nothing.
This is an interesting scenario. Typically the ME/CFS associated event is an infection, a vaccination, or antibiotic use. A probiotic being a trigger does fit the model — but definitely an edge case.
Analysis
Looking at forecast symptoms, we see a lot of ME/CFS symptoms (DePaul University Fatigue Questionnaire was written for ME/CFS patients). A few is shown below.
I am going to assume the ME/CFS is indeed a diagnosis and thus go to the cross validated suggestions. I am going to restrict to only ME/CFS-Long COVID. First, we see a lot of bacteria shifts match that reported in the literature for ME/CFS
We also get a lot of suggestions for things suggested by the microbiome shifts and also reported in published studies to help ME/CFS.
My reading of this reader is that antibiotics or prescriptions items are unlikely to be available. I then proceeded to [Just give Me Suggestions] so we can get priorities for the above.
All of the top items are a mountain of antibiotics (From a priority of 908 down to 433 when the first probiotic shows up). If the following does not make progress, the reader may wish to revisit that option.
My usual advice is to keep to items in the top 50%. Ignoring antibiotics, our preferred range is 210 to 433. Items below that are more iffy…
Probiotics
Many of these are related (L. Casei, L Paracasei, Yakult). Dosages should be around 50 BCFU with weekly rotation (i.e. do one each week and then move on to the next one).
I then checked to see where Bacillus Coagulans ( renamed to Heyndrickxia coagulans) sit, and it is a definite avoid. B Coagulans triggering ME/CFS is very viable. Using KEGG, I hit the rare case of no probiotics being calculated.
We have a pretty rich list of foods. Rye and whole grain above go together strongest (Oats and Barley are weaker – WHEAT is a to be avoided). My suggestion for Rye is 100% Rye bread (NOT what is often labelled rye bread – a mixture of wheat and rye flour). Below is what I personally use (Amazon US) (Amazon UK equivalent)
Herbs and Spices
Again, a long list — often these have similar profiles to antibiotics, hence a lot of antibiotics suggestions often have a long list here. My own preference would to do:
1 Week of Neem, then
1 Week of Wormwood, then
1 Week of Tulsi, then
1 week of Oregano oil, then
etc
Wait, there’s more! Stuff to reduce or avoid
Lowest is -631, so items between 315 and 630 are definite avoids. All seaweeds related products
I favor Dr. Cecile Jadin approach of regular rotation and anything that inhibits or kill bacteria (antibiotics, herbs, spices and probiotic). This reduces the odds of the bacteria adapting around the mechanism that inhibits it. Always start with a low dosage and increase every second day — holding steady if die-off or other reactions appear. Once that has faded, resume the increase OR move on to the next item in the rotation.
Questions and Answers
Q: Although I do now notice that when I try to get the results again (I am using the simple UI), I see it is giving me different recommendations. Is this due to some sort of shift in the data used, some sort of difference between the Simple UI and the old UI, or am I misunderstanding?
The site is live data. There are several dimensions:
Adding new studies — recently I have been adding 20-30 per day. More studies should mean better suggestions
Associations of Bacteria to Symptoms are recomputed about once a week.
Thresholds for the reference range is computed about once a week.
The goal is to give the best suggestions at the time it is executed. I am aware that many people want absolute consistency from month to month; I am sorry but I prefer to give the best suggestions based on most current research.
Q: It’s interesting to see just how much of a shift has occurred- prescription antibiotics have gone from the number one recommendation, far outpacing everything else, to hardly on my top suggestions at all. That would make it easier for me to implement a plan, though, so I can hardly complain.
That shift is because of more studies being added to the database. One sweet study reported dozens of bacteria shifts for each antibiotic. The Algorithm counts the number of desirable or undesirable shifts for a modifier (i.e. antibiotic, probiotic, herb). Before the addition of more studies, the counts were very high for some antibiotics. Many of the probiotics went from 3 studies to 40 studies with the new additions, so the net weight of the probiotic or other modifiers went up and thus the antibiotics slipped down the list.
People can design algorithms in many manners — I tried many variations until I got one that had a strong cross-validation for ME/CFS (picked because I knew the literature well) and when I tested on a different condition, Nonalcoholic Fatty Liver Disease, I got 92% correct for substance to take and 83% correct for substances to avoid. In the machine learning/AI world those percentages are very, very respectable. Subsequent changes has been just increasing data volumes.
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’m writing because 8 months ago I got Covid and since then I have been very sick. My main symptoms are fatigue, exercise intolerance/pem, many histamine issues slash food intolerances, upset GI with alternating diarrhea and constipation, weight loss, headaches, anxiety and depression, panic attacks….the list goes on.
I know something is wrong with my gut but I’m having trouble fixing it because my diet is so limited and I have so many reactions to things. I know a limited diet is not good but I also feel so much worse when I eat certain foods especially carbs. I think I might have SIBO. I uploaded my profile to you site and would love any help. I’m giving permission to share.
Analysis
This person has added symptoms and we see a good match of bacteria shifts to reported symptoms
Further down, we have many more matches
Immune Manifestations: new food sensitivities ✅ – [86.7%]
We have 69 symptoms marked resulting in 44 bacteria flagged. This is common and shows that there is often bacteria overlap between symptoms. The other factor with symptoms is a person’s DNA.
The best suggestion is walnuts. Looking at the probiotics, I was not surprised at the top ones:
Why am I not surprised…. because my own post COVID symptoms cleared rapidly when I did high dosages of fresh Bifidobacterium (manufacture date was the month before). The top of the list is below.
On the avoid list are many items that appear related to carbs (fiber) — what this person reacts to
My take away for no known-risk probiotics are these items suggested
Various Bifidobacterium above were on the list too.
Foods
The “many histamine issues slash food intolerances” causes me to suggest looking at the foods suggested above, especially those that are not in a person’s typical diet. I.e. Walnuts, Acai, Burdock Root, Asparagus, Rye bread (100% – not wheat+rye mixture), Beets, papaya, etc.
But wait! Those are based on studies of those explicit foods. When we go to the associated food sites, we see 116 nutrients identified as to take or avoid
The top to take are:
And to avoid:
With a quick list of food to take:
And to Avoid
My Approach if this was me
I would see about getting a bottle of only Bifidobacterium species probiotic as soon as possible to try to kick start things (i.e. a local health food store, or online with quick delivery). There is a risk that there may be no living or barely living bacteria in this bottle (background). So fingers crossed. At the same time I would order bottles of the following (which may take 3-4 weeks to arrive). Direct links to Maple Life Science’s Ebay site are linked below.
Those prices include shipping, so $44.00 total (which may be close to the price of the local purchase bottle). They ship worldwide! Why this source? My experience has been very good with them. Manufacture date is usually within a few weeks of shipping. Everyone that I have tried has had “kick”, that is, I see changes of stools (shape, size, frequency) and changes of fart smells within days of starting. I would start with just one, one capsule only and then work up to 5/day. Once the first bottle is empty, start the next bottle with the same pattern.
Next, I will try to incorporate as many of the above things — especially items that are not usually in your diet. With that, check the to avoid and reduce as much as is practical.
After 2-3 months, do another sample with the same firm — things are expected to change significantly and a new set of suggestions should occur.
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.
Born premature 25 weeks ivf pregnancy on tons of hormones for myself. Vaccines for her. Can’t poop on her own. Gi maps test showed clostridia, strep, entero faec etc. Mycotox urine kit showed 2 most toxic molds citrinin ocratoxin a, fatty acid oxidation issues, methylation issues, mthfr, double slow comt gene, reactions to most foods (behaviors),restless sleep. Autism diagnosis. She is 6 years old now.
Analysis
I always approach under 15 y.o. with caution because they are very understudied, and the existing studies show major changes from adults.
It will be just a “give me suggestions” plus some suggestions that are typical for autism. In general, I try to cross validate the suggestions with the current literature on Autism. Example: Go to https://pubmed.ncbi.nlm.nih.gov/, enter the item and autism and see if there is any literature.
In this case, one result was returned (a bit of a heavy and twisted read).
“luteolin and diosmin inhibited neuronal JAK2/STAT3 phosphorylation both in vitro and in vivo following IL-6 challenge as well as significantly diminishing behavioral deficits in social interaction. Importantly, our results showed that diosmin (10mg/kgday) was able to block the STAT3 signal pathway; significantly opposing MIA-induced abnormal behavior and neuropathological abnormalities in MIA/adult offspring.”
I have done a few, but the reader should check each one. Items that cross-validate should be choice #1, other items as a secondary choice.
Probiotics
bifidobacterium infantis,(probiotics) was high on the list, which is to be expected with autism. “participants on both treatments saw a reduction in the frequency of certain GI symptoms, as well as reduced occurrence of particular aberrant behaviors.” [2019]
lactobacillus reuteri (probiotics) – “However, L. reuteri combination yields significant improvements in social functioning [in autism] that generalized across different measure” [2023]
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.
Let us start with a more real world example: Dogs.
Take a vaccine against Rabies tested on dogs in a pound (Canis Lupis). It was successful. Inference means that there is a high probability that it would work for Welsh Pembroke Corgis — although there was none in the pound. This is a child inference.
There is a high probability that this vaccine would also work for the Genus Canis, which include wild dogs such as Jackals (Africa), Wolves, Coyote and Dingos (Australia). This is a parent inference.
There is a reasonable probability that this vaccine would also work for the Family Canidea which includes Foxes. This is a grandparent inference.
The key thing to remember is that each layer of the taxonomy hierarchy has significant DNA shared with those above and below. It is likely (not guaranteed) that the layer above or below will respond similarly.
In the last 20 years, different bacteria has been sequenced resulting in a more correct hierarchy based on DNA. For example, Lactocaseibacillus casei was originally Bacillus casei, then Lactobacillus casei. A short table of a few others is shown below.
Current name
New name
Lactobacillus casei
Lacticaseibacillus casei
Lactobacillus paracasei
Lacticaseibacillus paracasei
Lactobacillus rhamnosus
Lacticaseibacillus rhamnosus
Lactobacillus plantarum
Lactiplantibacillus plantarum
Lactobacillus brevis
Levilactobacillus brevis
Lactobacillus salivarius
Ligilactobacillus salivarius
Lactobacillus fermentum
Limosilactobacillus fermentum
Lactobacillus reuteri
Limosilactobacillus reuteri
We do not do sibling inference. Studies on Limosilactobacillus fermentum are not inferred to Limosilactobacillus reuteri, we do parent inference to Limosilactobacillus with no inference to Levilactobacillus, Lactiplantibacillus, Lactobacillus, nor Lacticaseibacillus (i.e. uncle inferences).
The recent reorganization of the bacteria hierarchy based on DNA makes inferences more probable.
Avoiding Inferences
It is technically possible to avoid inferences for some bacteria. For other bacteria, for example Propionibacterium freudenreichii subsp. shermanii, you may find just one study and that decreases only — when you want to increase it! Looking at Propionibacterium freudenreichii and inferences, you have over thirty studies. We do not know if these substances will work. There is a good probability that it may work
“Who you gonna Call? Call Sparse Data Busters!”
Using inference allows us to get suggestions with a reasonable chance of working. We give direct citations a high weight. We give inferences a diminished weight.
Microbiome Prescription works off probability estimators when using inference.
It’s your choice on Microbiome Prescription
Using inference is the user’s choice. You may agree or disagree on inference — if you disagree than please be consistent and only use the strains of probiotics cited in studies.
First things first — no vaccination, herb, supplement is absolutely safe for every person. To get approved for use, a vaccinated persons must have better outcomes (as a group) than an unvaccinated person. I am of the early vaccinated generation. A class mate got Polio as a child recovered, and then later in life developed Post-Polio syndrome. I got the Polio shots and was fine. A vaccine for whopping cough was not available when I was born, I got it and suffered some brain damage to my speech center. I once met someone my age that suffered major brain damage after whopping cough. Taking a shot for whopping cough has much less risk of life long adverse effects than getting it. I am pro-vaccination, being of the generation that saw disease after disease ripple through the population causing much harm. I do not want those times to return…..
Your Microbiome determines how effective the Vaccine is
“the abundance of Prevotella copri and two Megamonas species were enriched in individuals with fewer adverse events” [2021]
“Bifidobacterium adolescentis was enriched in high-responders while Bacteroides vulgatus, Bacteroides thetaiotaomicron and Ruminococcus gnavus were more abundant in low-responders ” [2021]
“At 1 month after second dose of vaccination, seven species including B. adolescentis, A. equolifaciens and A. celatus were more abundant whereas B. vulgatus remained less abundant in high responders” [2021]
Lactobacillaceae, Rumen family, and Clostridium bacteria were associated with vaccine efficacy [2021]
The abundance of Clostridium and Lactonemae was positively correlated with vaccine efficacy [2020]
“Of the species altered following vaccination, 79.4% and 42.0% in the CoronaVac and BNT162b2 groups, respectively, recovered at 6 months.” [2023]
“Bilophila abundance was associated with better serological response, while Streptococcus was associated with poorer response.'[2023]
“vaccination can also change the composition of the gut microbiome. We found that 1 month after a second vaccine dose, the relative abundances of Bacteroides caccae increased significantly” [2023]
“This study demonstrated a statistically significant reduction in alpha diversity and a shift in gut microbiota composition following vaccination, characterised by reductions in Actinobacteriota, Blautia, Dorea, Adlercreutzia, Asacchaobacter, Coprococcus, Streptococcus, Collinsella and Ruminococcus spp and an increase in Bacteroides cacaae and Alistipes shahii. ” [2022]
“Bifidobacterium and Faecalibacterium appeared to be microbial markers of individuals with higher spike IgG titers, while Cloacibacillus was associated with low spike IgG titers. ” [2023]
“vaccine responders were associated with an increased abundance of Streptococcus Bovis and decreased abundance of Bacteroides phylum;’ [2017]
“Responders were associated with increased Streptococcus Bovis abundance and decreased Bacteroides phylum abundance” [2018]
“Proteus and Egella abundance were positively correlated with vaccine efficacy, and Fusobacterium and Enterobacteriaceae were negatively correlated with vaccine efficacy” [2020]
“The abundance of Bifidobacterium longum subspecies was positively correlated ; Clostridium, Enterobacteriaceae, and Pseudomonas abundance were inversely correlated with vaccine efficacy [2019]
The Specific Vaccine and Your Microbiome
It is possible that the microbiome alteration caused by a vaccination will interact with an existing microbiome dysbiosis and cause adverse effects. The adverse effect could move the microbiome into a stable and more severe dysbiosis — the claims of a child developing autism after a vaccination is viable. The vaccination may be just a contributing cause to an existing disposition. The literature below suggests that there is no statistically significant evidence supporting some people beliefs.
A 2024 study found “Rates of early childhood vaccine receipt did not differ between autistic and non-autistic cohorts.” as well as “Notice of Retraction: Measles, Mumps, Rubella Vaccination and Autism” indicating early studies claiming association was questionable, if not outright ideological. “At the same time, other environmental factors, such as vaccination, maternal smoking, or alcohol consumption, are not linked to the risk of ASD. ” [2024]
I have severe /very severe ME/CFS and have noticed partially dramatic changes (although short lived) when taking a probiotic, especially Myorisan [Clostridium butyricum].
Analysis
Sample Comparison
My general impression is that this person has lost some ground in terms of reference ranges(more found at extremes), but has gained ground with Kegg Compounds and Enzymes (less ones at extremes).
To get better insights, I added a Pattern Matching Comparison. Only symptoms marked in either samples are compared. We see some improvement happened.
Going Forward
My updated starting point with the new UI when the person has one or more conditions picked to [Beginner-Symptoms: Select bacteria connected with symptoms]. As shown below, we have a large number of symptoms matching the patterns from our data analysis. This suggests that we are likely to pick the right bacteria to focus on (based on statistical evidence – which any skilled person can reproduce using data on https://citizenscience.microbiomeprescription.com/).
The top suggestions are below
As well as the top avoids
Probiotics
The top probiotics using published studies on PubMed were:
With the new UI, we also have probiotics computed from RNA/DNA of your microbiome and probiotics. Usually I select only low compounds (i.e. some bacteria will be inhibited from starvation).
As is typical with ME/CFS, the top ones are E.Coli probiotics.
I checked each of the PubMed suggestion to see their relative impact and put in [ ] below.
Food avoid list is high in food containing fiber (in agreement with diet style)
Bottom Line
The user report of improvement with miyarisan and the suggestions are a nice agreement to see. The issue of being short termed is not atypical to see when there is no rotation of probiotics and antibiotics.
IMHO, probiotics should be viewed as natural antibiotics. As with all antibiotics, antibiotic resistance (probiotic resistance) may developed from continuous use. For Lactobacillus reuteri we have Reuterin; for Clostridium butyricum we have: CBP22, Butyricin 7423, Butyricum M588, Perfringocin 1105. (see Effects of Clostridium butyricum as an Antibiotic Alternative [2023]).
The same applies to herbs and spices with antibiotic characteristics… resistance will often develop from continuous use.
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.
My preferred provider for herbs etc is Maple Life Science™ – they are all organic, fresh, without fillers, and very reasonably priced.
Professional Medical Review Recommended
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)
Started feeling slightly tired in 2014, but I didn’t pay much attention to it. Around 2016 I am told the fatigue I am suffering from is likely caused by depression and so I take various SSRIS for 4 years. They made me anhedonic[inability to feel pleasure] and actually caused fatigue to somewhat worsen.
In 2022 after recovering from covid, I take aj immune boosting supplement to try and finally break free from the fatigue I was suffering. It actually worked and brought me back to life, which is when I decided ro come off my SSRI.
This was a mistake. It made me even more anhedonic and caused me to crash. I have not recovered since.
Lately, I have been dealing with actinic acid build up which is very weird for me as I was a professional athlete.
Analysis
This has been sitting in my backlog (waiting for feedback from reader). I just discovered that he has since done a second sample, so this is a revision and update.
Comparisons
I do not know how many of the suggestions made in the earlier draft was done. Note that we went from 760 bacteria down to 447 (just 58%). So for most of the numbers below, we need to see at least a 50% drop in bacteria for something to be an improvement. Most of these measures failed to make this criteria.
We have added a new comparison table of changes of fit to reported symptoms. This also show a general loss of ground.
With the new UI appearance, I am also trying to keep the analysis simple by not obfuscating with too many measures.
Going Forward
I am going to do [Beginner-Symptoms: Select bacteria connected with symptoms] and then [Probiotic computed from Kyoto Encyclopedia of Genes and Genomes compounds].
We ended up with 8 bacteria being selected. The top suggestions are shown below
I decided to also try [Novice: Just tell me what to take or avoid] which increased the selected bacteria to 23. There are some similarities and differences (to be expected from the targeted bacteria increasing from 8 to 23)
The probiotics suggested were the same.
Going to KEGG Probiotics
We have a very different list. One jumps out: E.Coli probiotics. The number is the number of low compounds that it increases.
Why did I go with two from KEGG? The reason is simple — this is computed across the entire microbiome and does not depend on someone doing studies. The two other ones are based on published studies.
All of the above are typically deficient in samples (or assumed by some medical practitioners to be the cause of issues). This is not the case, and suggestions reflect this.
Items to Take
I would work off the two lists above – there is a reasonable amount of agreement. I note that fiber and high fiber foods are common on both of to-avoid list as is wheat, gluten (and bifidobacterium probiotics).
General Guidance
For items to take, remember that goal is to disrupt the dysbiosis. This means subjecting it to constantly changing “shocks” so it is unable to adapt. This has been shown to be effective when dealing with antibiotics (i.e. rotating between different antibiotics with breaks is more effective than taking the same antibiotic continuously). It likely applies to probiotics and herbs.
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.
Some supplements that I have been taking since the last test:
Tetracycline
Clove
Holy basil (Neem)
Augmentin + Bromelain
Grapefruit seed extract
Monolaurin
Apple peel powder
Thyme
My symptoms:
Still get the red nose (some form of rosacea).
Still feel fatigued (both physically and mentally). But it is better than before.
Feeling stressed. But it is better than before.
Brain fog.
Bloated.
Lots of gas – I fart and burps a lot.
Issues with allergies (itching eyes, stuffed nose and itchy skin)
Video
Analysis
We will start with the high-level comparison. Note that some numbers will change with time. There are no major changes. Since the latest sample reports 20% more bacteria, many counts are expected to be 20% higher – for example: Thorne Ranges: old: 230 + 20% = 276, with the seen count being 253 (so an apparent improvement although the number went up)
Criteria
9/2/2024
1/22/2024
9/12/2023
2/22/2023
8/11/2022
3/25/2022
12/3/2021
8/31/2021
Lab Read Quality
9.1
7.9
3.5
9.7
5.5
6.2
3.6
7.8
Outside Range from GanzImmun Diagostics
16
16
16
15
15
17
17
20
Outside Range from Lab Teletest
23
20
20
24
24
22
22
25
Outside Range from Medivere
14
16
16
15
15
15
15
19
Outside Range from Metagenomics
6
7
7
9
9
7
7
8
Outside Range from Microba Co-Biome
3
2
2
7
7
1
1
1
Outside Range from MyBioma
6
5
5
7
7
7
7
8
Outside Range from Nirvana/CosmosId
21
20
20
23
23
18
18
21
Outside Range from Thorne (20/80%ile)
253
230
198
223
223
217
217
246
Outside Range from XenoGene
32
32
24
32
32
36
36
39
Outside Lab Range (+/- 1.96SD)
12
5
15
10
11
9
9
14
Outside Box-Plot-Whiskers
48
52
56
42
36
42
59
42
Outside Kaltoft-Moldrup
113
123
70
139
56
78
59
140
Bacteria Reported By Lab
600
508
399
666
478
613
456
572
Bacteria Over 85%ile
48
52
Bacteria Under 15%ile
118
157
Pathogens
23
26
25
30
23
39
24
30
Condition Est. Over 85%ile
2
5
There is a new comparison table added that compares sets of symptoms bacteria for symptoms reported in either sample. This is a thought experiment on a different way of evaluating the microbiome, i.e. are symptom bacteria reducing. Remembering that we have 20% more bacteria reported, the improvement may be slightly under-reported.
Going Forward
My current preference is to use symptom associations suggestions with KEGG suggested suggestions. This assumes that the person has added their symptoms.
Using Entered symptoms
Since this person has access to antibiotics, I opted to include all classes of modifiers. We have 38 bacteria selected — a reasonable number
The suggests were a nice mixture for ME/CFS. Typically, I see the top being just antibiotics, in this case we have several probiotics there.
And suggested retail probiotics are:
Using Diagnosis and PubMed
Using a diagnosis provides less precise filtering compounded by different labs (with different identification of bacteria). If the person is using a lab that lacks a large number of annotated samples from that lab, then it is the best path.
The suggested path is to go down the list and pick the ones that has the highest value(s) that agrees with one or more of the diagnoses that you have.
In this case we have only 4 bacteria in the selection, so the suggestions will be likely more generic than specific.
There are no antibiotics in this list
The probiotic list is below. It has some similarities to the above list.
Using KEGG Derived Probiotics
This is an experimental approach that attempts to do a metagnòmia approach from the available data. We estimate which compounds are too high or too low. Then we match them to probiotics which produce or consumes them. Postbiotics can be used for items that are too low. There is no filtering of any type; we look at the entire microbiome.
The results are different — as to be expected. Why expected? The prior ways depended on studies being done what each probiotics bacterium does. Often there are no studies. This way uses the DNA/RNA sequences of everything and thus we do not need studies.
I usually focus on too low, with the assumption that a surplus will just be ignored or has less impact (i.e. starvation versus obesity) We can see where there is agreement between the lists.
This can be made more complex by using consensus / Monte Carlo Model
Reader Plan
Microbiome Prescription produces suggestions, the weights/priorities are the odds of causing a change and not the amount of change (there is simply no objective data to compute the amount). This reader did their own evaluation of what they felt comfortable with (excellent idea).
I have also bought 2 more tests so I will do them with max 3 months apart as you said in the video.
I came up with this protocol by using the “Beginner-Symptoms: Select bacteria connected with symptoms”:
Week 1-2: Gum arabic
Week 3-4: Monolarin (lauric acid)
Week 5-6: Psyllium
Week 7-8: Rosemary
Week 9-10: Parsley
Week 11-12: SymbioFlor-2
I found that I get best results from herbs, prebiotics and antibiotics. The only probiotic I’ve got good results from is Symbioflor 2 (an E.Coli probiotic) [Editor: E.Coli probiotics also worked best for me]
A lot of probiotics that I’ve tested I’ve got bad results from.
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.
My preferred provider for herbs etc is Maple Life Science™ – they are all organic, fresh, without fillers, and very reasonably priced.
Professional Medical Review Recommended
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)
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