Month: October 2024

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]