Month: October 2024

Chronic Fatigue Syndrome with Antibiotics

Request

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

AntibioticBS 2020Th 2020BS 2023BS 2024
amoxicillin [CFS]137181743746
ampicillin [CFS]266-19460581
azithromycin,[CFS]-33104260413
chloroquine diphosphate,(prescription)[CFS]-30-29156190
ciprofloxacin [CFS]617128663989
clarithromycin [CFS]-7041211327
clindamycin [CFS]180282654479
dapsone (antibiotic)[CFS]-12-1253105
doxycycline [CFS]-1105737894
erythromycin [CFS]-3075531381
lymecycline (antibiotic)[CFS]-14-19313537
metronidazole [CFS]192445582707
minocycline [CFS]65-30326377
neomycin [CFS]-1169144289
vancomycin (antibiotic)[CFS]4092547418

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).

Perplexity

Analysis

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.

Probiotics

The top ones are below:

From KEGG Analysis using deficient enzymes we have:

When there is a good agreement between the studies based (PubMed) and KEGG Enzyme based suggestions for probiotics, it makes them a priority.

Other Items

Using the new Simple UI

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.

Mexican oregano, dried x2
Chicory [Green], raw
Zinc
Olive, oil
Watercress,
Peanut,
Almond x 2
Fennel x 2
Common thyme, fresh
Globe artichoke, heads, raw
Common sage, fresh
Red huckleberry
Celery seed

And items to avoid by the food site:

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

  1. Rotate bacteria inhibitors (antibiotics, herbs, probiotics) every 1-2 weeks
  2. Some herbs/spices are compatible with probiotics (e.g., Wormwood with Bifidobacteria)
  3. Verify dosages against reliable sources or research studies, not commercial product labels. This Dosages page may help.
  4. There are 3 suppliers of probiotics that I prefer: Custom Probiotics , Maple Life Science™, Bulk Probiotics: see Probiotics post for why

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)
  • Potential underlying conditions (e.g., H-pylori, carbohydrate digestion issues)
  • Individual susceptibility to specific probiotics
  • Nature of symptoms (e.g., headache type – pressure, cluster, or migraine)
  • Possible histamine issues
  • Colon acidity levels
  • SCFA production and acidification needs

A knowledgeable medical professional can help tailor recommendations to your specific health needs and conditions.

From Southern India — Junk Food Crashed

Back Story

I am a 29-year-old male from Southern India.

  • 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.
  • Early Symptoms:
    • Weight loss of 20 kilos due to malabsorption
    • Lack of hunger due to no stomach acid
    • Constipation
    • Lack of focus and joint pain
  • Tests Conducted:
    • SIBO Breath Test: H2 and CH4 (+ve)
    • GI Maps: Dysbiosis
    • Biomesight: Sutterella, Proteobacteria, Escherichia
    • Gastroscopy: H. pylori (-ve)
    • Colonoscopy: No abnormalities
  • Protocols Followed:
    • Protocol 1 (Sep 2023 – Jan 2024):naturopath
      • Diet: High carb and high protein with all fruits and vegetables
      • Prebiotics: PHGG
      • Probiotics: S. boulardii
      • Herbs & Antibiotics: Rifaximin, Fluconazole, FC Cidal, Dysbiocide, Undecylenic Acid, Mastic Gum
      • Immunity: Vitamin D3 + K2, Magnesium, Fish Oil
      • Results: Weight loss persisted, constipation aggravated, and methane bacteria were not detected in Biomesight.
    • Protocol 2 (Jan 2024 – Present):Microbiome Group
      • Diet: Medium carb and protein with fruits and vegetables, recently switched to GAPS diet
      • Prebiotics: GOS by BIMUNO, PHGG, Sodium Butyrate, 2-FL HMO
      • Probiotics: Rhamnosus GG, S. boulardii, B. Longum bb536, L. plantarum 299, MegaSporeBiotic, Biogaia Protectis
      • Herbs: Oregano, Thyme, Clove Tincture, Neem, Turmeric, Ginger
      • Immunity: Vitamin B complex (B12, B6, Benfotiamine)
      • Additional Recommendations (Not Started Yet):
      • Prebiotics: GutGuardian, Prebiotic Repair, Tributyrin X, Lactulose, Inulin FOS
      • Probiotics: Visbiome Advanced GI Care, Paracasei Powder
      • Herbs: FC Cidal, ADP Oregano, Allicin, FLORASSIST PHage Technology
      • Fermented Foods: Fermented Vegetables, Kefir, Greek Yogurt
      • 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:

Potential Medical Conditions Detected has a lots of concerning ones, including:

  • NonCeliac Gluten Sensitivity (99%ile) or Celiac Disease (97%ile)
  • Mast Cell Issues / mastitis (97%ile)
  • Constipation (90%ile)
  • Weight Issues (83%ile)

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.

Using New Simple UI

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:

  • Inulin: Chicory, Burdock
  •  Luteolin: THyme, Sage, Oregano, artichoke
  • Chrysoeriol 7-O-(6”-malonyl-apiosyl-glucoside): Celery seed (leaves provide some, 10% of the seed)
  • Folic acid — go supplement
  • 4-Hydroxybenzaldehyde: Tian Ma
  • Coumarin: Tonka Bean
  • Resveratrol: grapes
  • 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.

Long COVID with EBV and COVID

Back Story

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.

Other Items

There are just two items in range

Foods

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

See the full list and for anything that is negative and a regular part of your life, consider reducing or eliminating.

Food Site Menu

Since the first draft of this post, I have reconnected the food site. I have used the Novice suggestions nutrients below.

Grape
Chicory 
Black elderberry
Broad bean x 2
Green / Oolong Tea
Pecan nut
Black chokeberry
Blackberry, raw
Abalone
Lime
Orange (not juice)
Lentil
Pea
Chickpea
Lima / Kidney Bean
Rye, whole grain flour (i.e. 100% Rye bread)		Pomegranate,
Chicory
Burdock
Vinegar x 2
Peanut
Oil, linseed or flaxseed
Oil, sunflower, linoleic, (approx. 65%)
Oil, grapeseed
Caterpillar, roasted,
Iron fortified foods
Oat, whole grain flour
Tahini, sesame seed pulp
Rhubarb, stalk, raw
Spinach,
Wine [Red]

Cross Validated Suggestions for this Sample

Bottom Line

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

  1. Rotate bacteria inhibitors (antibiotics, herbs, probiotics) every 1-2 weeks
  2. Some herbs/spices are compatible with probiotics (e.g., Wormwood with Bifidobacteria)
  3. Verify dosages against reliable sources or research studies, not commercial product labels. This Dosages page may help.
  4. There are 3 suppliers of probiotics that I prefer: Custom Probiotics , Maple Life Science™, Bulk Probiotics: see Probiotics post for why

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)
  • Potential underlying conditions (e.g., H-pylori, carbohydrate digestion issues)
  • Individual susceptibility to specific probiotics
  • Nature of symptoms (e.g., headache type – pressure, cluster, or migraine)
  • Possible histamine issues
  • Colon acidity levels
  • SCFA production and acidification needs

A knowledgeable medical professional can help tailor recommendations to your specific health needs and conditions.

Long COVID at 8 months

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%]
  • Neuroendocrine Manifestations: marked weight change ✅ – [84.6%]
  • Post-exertional malaise: Post-exertional malaise ✅ – [84%]
  • DePaul University Fatigue Questionnaire : Does physical activity make you feel worse ✅ – [82.7%]

When there are many reported symptoms to predicted symptoms, then I usually run with two methods. The second gives probiotics only:

Because of the food issues, I will be explicitly going to the food menu feature.

Histamine Bacteria

Looking at the Microbiome Tree, we see why histamine may be an issue

Results

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

Clicking on the Food Menu Planner Button

KEGG Probiotics

The results very typical for ME/CFS and Long Covid

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.

Premature Autisic Child

Back Story

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.

Key Bacteria identifies two species:

I then checked some literature: Commercial microbiota test revealed differences in the composition of intestinal microorganisms between children with autism spectrum disorders and neurotypical peers [2021]

  • “Other microbes observed in large quantities in the feces of ASD compared to neurotypical children include such species as Akkermansia muciniphila “
  • For Bacteroides uniformis, there was no clear literature associated.

I then went over to look at typical items from the literature.

Going Forward

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.”

Flavonoids, a prenatal prophylaxis via targeting JAK2/STAT3 signaling to oppose IL-6/MIA associated autism [2009]

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.

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.

Taxonomy Inference with the Microbiome

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.

A Common Inference Seen with Medical Consultants

A consultant may read an article like “Whole genome sequencing of Lacticaseibacillus casei KACC92338 strain with strong antioxidant activity…” and based on this study recommend Lactobacillus Casei probiotic for a patient. This is a parent inference. We do not know definitely if this general species would have any of the desired behavior. There is a reasonable probability. If you reject inference then you can only recommend this explicit strain, no substitutions allowed. If you are using herbs, Greek Oregano (Origanum vulgare L. ssp. hirtum) may be cited in the study (Origanum vulgare ssp. hirtum (Lamiaceae) Essential Oil Prevents Behavioral and Oxidative Stress Changes… so Oregano Oil cannot be assumed to do similar — that is an inference.

The Microbiome has stricter overlaps than mammals

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 nameNew name
Lactobacillus caseiLacticaseibacillus casei
Lactobacillus paracaseiLacticaseibacillus paracasei
Lactobacillus rhamnosusLacticaseibacillus rhamnosus
Lactobacillus plantarumLactiplantibacillus plantarum
Lactobacillus brevisLevilactobacillus brevis
Lactobacillus salivariusLigilactobacillus salivarius
Lactobacillus fermentumLimosilactobacillus fermentum
Lactobacillus reuteriLimosilactobacillus 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.

Vaccinations and the Microbiome

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

  • Antibiotics-driven gut microbiome perturbation alters immunity to vaccines in humans [2019]
  • “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]