Quick start to 2 blogs and an analysis site

My primary concern for the last 20 years was been the condition known as Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). I deduced some seven+ years ago that the simplest explanation of the multitude of symptoms and abnormalities reported was a stable microbiome dysfunction. This explanation can also be applied to many other conditions. My focus is still on ME/CFS but I wish to make the data and algorithms available to people with any conditions. My old home page is here (dry technical).

The basic model that is supported by studies is:

  • DNA Snps that results in increased risk
  • Environmental changes of DNA (epigenetics) that further increase risk
  • Microbiome function that acts as a catalyst to the risk.

The microbiome is the simplest to alter technically — but very complex to alter because there are thousands of bacteria that interact with each other in the human body. DNA can also encourage some bacteria and discourage others. Example: Typhoid Mary is an excellent example of some one whose DNA and a nasty bacterial infection co-existed nicely.

Does changing the microbiome work for ME/CFS?

Answer is yes:

Open-label pilot for treatment targeting gut dysbiosis in myalgic encephalomyelitis/chronic fatigue syndrome: neuropsychological symptoms and sex comparisons , 2018

Recommended Site For Testing

With ME/CFS, there is always a nasty cost factor for testing. My usual recommendation is for the cheapest, high quality provider that provides information for upload to my analysis site. Some sites provide a mountain more of information — but the benefit from that extra information is almost nothing (and it adds $$$$ and complexity).

  • uBiome.com is shutting down. This had been my personal usual site because using a variety of techniques, the cost was $25/sample. Don’t order from there.
  • BiomeSight.com (EU based but serves the world) – discount code “MICRO” has integrated with my analysis site with automatic data transfer. For most people it is likely the best deal.
  • Thryve (US Based) is what I have used. Their reports may be processed here for independent suggestions. I would also recommend

Who am I?

I am a citizen-scientist with reasonable scientist credentials: taught Chemistry and Physics at College Level; Master of Science, accepted for the PhD program, certified data scientist with R, one of the top mathematics and physics competition students in Canada during my university years, etc.

I am a closet academic — so I give links to my source of information everywhere and usually keep them to the highest quality sources (PubMed, professional journals). I have even had a letter of mine published in the Lancet.

The Sites

  • This site — over 1200 blog posts published over the last 5 years. This is where I publish most. You can subscribe to get new posts by email.
  • Microbiome Prescription site – started in 2018. This is a massive data store with a variety of artificial intelligence algorithms applied to it. Almost 800 people have uploaded their microbiome results to it and many annotated it with their symptoms.
  • Microbiome Prescription Word Press – started recently. This is intended as a reference to the above site. Just essential pages and a bunch of homemade videos taking you through some features.
  • Facebook Site: Where I usually post new blog entries and the occasional odd note that is not worth a blog post. Make sure that you like it so you get notices of new posts.

Findings to Date

The assumption that bacteria shifts connect to symptoms appears confirmed using the upload microbiomes.

  • We have found statistically significant patterns of some bacteria to symptoms, see this post
  • We appear to have a high probability of correctly predicting symptoms from a microbiome report. See this post.

These findings can be independently confirmed by using the public shared data at: http://lassesen.com/ubiome/

Tools to Help

The Microbiome Prescription site is a theoretical site, that is, it works from the logical application of data and is not based on actual human experience. It does have the ability to create suggestions of things to take and to avoid to try reducing abnormalities in your microbiome. It supports multiple models and algorithms because we do not know which actually works best.

The site states that the suggestions should be reviewed by a medical professional. The source of the information is provided by links (hundreds of articles are cited).

Evolving Story

As more data comes in, and more insight happens, there will be more posts and more features (some labelled experimental — because I am unsure of their accuracy) will be added. This is citizen science.

Video to kickstart using your microbiome use

Overview of this Blog and the Microbiome

My ideas on this blog have evolved, as more and more information becomes available. This post is an attempt to bring readers up to date with my current thinking. I am striving to be transparent in my logic — showing the evidence I am working from, and my thought processes.


Notes to Treating Physicians     Quick Self Start on treating CFS


Analysis of Microbiome/stool with recommendations

Site: has moved to http://microbiomeprescription.azurewebsites.net

The data is available in an online collaborative python workbook for analysis. See this post.


Microbiome Definition of CFS/FM/IBS

A coarse condition that results from:

  • Low or no Lactobacillus, AND/OR
  • Low or no Bifidobacteria , AND/OR
  • Low or no E.Coli , AND/OR
  • A marked increase in number of bacteria genus (as measured by uBiome) to the top range
    • Most of these genus are hostile to/suppress Lactobacillus, Bifidobacteria, E.Coli
    • Several are two or more times higher than normally seen
    • The number of bacteria genus goes very high (using uBiome results), but most of them are low amounts.
      (“Death by a thousand microbiome cuts” and not “Death by a single bacteria blow”)
  • The appearance of rarely seen bacteria genus in uBiome Samples.

A finer definition would be a condition with a significant number of abnormalities in the ‘Autoimmune profiles see this page for the current criteria (i.e. over 25%).

The specific genus and their interactions determine the symptoms seen — likely due to the over- or under-production of metabolites (chemicals). Other autoimmune conditions may share these core shifts. The specific high and low bacteria determine the symptoms if the person was the DNA/SNP associated with the symptoms.

Replace the metabolites produced by the missing bacteria

Replacing the metabolites should result in the reduction of symptoms associated with a deficiency of these metabolites.

See this post for the study references. These items should/could be done continuously.

Other Supplements Reported to Help

Bootstrapping Bifidobacterium and Lactobacillus

The items below were found in studies to increase bifidobacterium and lactobacillus:

Unless the bifidobacterium and lactobacillus (B&L) are human sourcedthere is almost zero chance of taking up residency. Taking probiotics will not allow B&L to get established. In fact, there are grounds to believe that most commercial probiotics actually reduce your  native B&L. You want to encourage your native B&L. See this post for citations.

Bootstrapping E.Coli

The E.Coli probiotics below are human sourced and known to take up residency in the human gut.

  • Core: D-Ribose a preferred food that it uses
  • Mutaflor probiotics — E.Coli Nissle 1917
  • Symbioflor 2 — multiple strains

Dealing with the other microbiome shifts

The other microbiome shifts appear to be in different clusters of microbiome shifts. This 2017 paper by Peterson, Klimas, Komaroff, Lipkin (and a stack of other CFS researchers) makes that clear in its title: “Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome”.

The best way at present to proceed is to order an analysis from uBiome. (Disclosure: I have no financial interest in this company.) When your get your results back, log in, click on the “Compare” tab, then go to “Genus,” and click on “ratio” twice, so the results are in descending order.

This is the “hit list” of what you are trying to reduce. DataPunk provides a nice summary of what we know about these. See, for example, Alistipes:

At this point, we run into a logistical challenge.  You want to avoid items that are “Enhanced By” (which is in common across all of the high items) and take the items that are “Inhibited By” (which are not on any of the “Enhanced By” lists).  You may also wish to reduce foods that are high in items listed in “Nutrients/Substrates.”  It becomes a jig-saw puzzle! I have done this exercise for many readers’ uBiome results:

I have discovered that DataPunk is not absolutely current, and have started creating posts based on its data, and then added studies from 2016 and 2017 to the page. Past pages are below, for current list MicrobiomePrescription site.

nihms-731256-f0001

Src: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4754147/

General Suggestions (no uBiome results)

Some of these items are contraindicated with a few uBiomes that I have reviewed. This likely is why person B reports no results while person A reports improvement. Example: Magnesium is usually very helpful — but there are a few cases where it encourages overgrowth of undesired  bacteria.

Probiotics

Most probiotics do not take up residency. They are “here today, gone tomorrow”. Their primary role in my model is producing natural antibiotics against other bacteria. For example:

Probiotics should be rotated: 2 weeks on a specific one, then several weeks off. As a general rule, you want about  6-12 B CFU taken three times a day (or 2-3 times the recommended dosage) — but work up slowly because you may get be a major herx! In general, do not take Lactobacillus with Bifidobacteria or with E.Coli etc. Keep to one family per cycle. You do not want them to kill off one another!

Why 3x per day? Because almost none of them are detected after 12-24 hrs. So to keep them — and the production of natural antibiotics — going, you need to keep taking them during the day. See this post for citations.

The following probiotics commonly seem to help people with CFS/Lyme/Fibro:

Some probiotics, however, may make your symptoms worse! And, unfortunately, most commercial probiotics contains some of these. At the moment Bifidobacterium animalis, Saccharomyces boulardii and Lactobacillus acidophilus are on my best to totally avoid list.

  • “. The findings show that the six species of Bifidobacterium differed in their ability to relieve constipation. B. longum, B. infantis and B. bifidum were the most effective in relieving constipation, B. adolescentis and B. breve were partially effective and B. animalis was not effective. Furthermore, edible Bifidobacterium treated constipation by increasing the abundance of Lactobacillus and decreasing the abundance of Alistipes, Odoribacter and Clostridium. .” [2017]

On my neutral list (no clear benefit) is Lactobacillus Plantarum.

Teas

Some teas can also be antibiotics (among other roles). There are two teas that seem to produce significant results quickly:

Again, rotate and, if practical, change brands too. Their antibiotic compounds are different from different sources.

Herbs and Spices

The best choice needs examination of your microbiome (i.e. uBiome results) and doing the work cited above.  Survey results found:

  1. Neem and Oregano with 80% improving
  2. Olive Leaf and Licorice with 56% improving
  3. Thyme with 50% improving
  4. Wormwood and Tulsi with 33% improving

Other things

If you do not know your microbiome, then see https://cfsremission.com/reader-surveys-of-probiotics-herbs-etc/  for suggestions. Your results will vary because your microbiome vary.

Thick blood is an issue also — but here things gets more complicated and not suitable for this recap.

Antibiotics can have a role — but getting prescriptions for the right ones can be a major challenge.

Metabolism Shifts

From volunteered data, we can identify some distinctive shifts, see Metabolism Explorer Summary

Bottom Line

Working with the microbiome and autoimmune is like working with fragments of the dead sea scrolls. For many bacteria we can identify it — what inhibits or encourages it is not known to modern medical science.  We have extremely thin slices of knowledge –Almonds enhances Bifidobacterium, Lactobacillus (B&L)  as do sesame seeds. What about sunflower seeds? Peanuts? Cashews? We find that Walnuts help the bacteria that inhibits B&L — so we cannot safely generalize to “all seeds/nuts are helpful”.

In many cases, we find that healthy diet or supplements demonstrated to work for normal people have the opposite effect on CFS and other altered microbiome conditions. This is made even worst because most of the studies were done on males and most people with CFS are females. We end up having to swim up-stream thru good and valid suggestions — that are just wrong for us.

My model is simple to understand and allows us to filter many suggestions and candidates. With the availability of uBiome testing (without needing a prescription!) we have entered the age of explicit treatment based on your unique microbiome. We do not know the role of many bacteria involved. We do not know what will inhibit or enhanced all of these bacteria. Frustrating little knowledge!

On the flip side, many readers have reported significant improvement, reduction of prescription medication, etc. so the model and suggestions have potential and thus hope of remission! Microbiome studies are exploding on PubMed, a lot of research is being done and we can often borrow their results.

This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of any medical condition. Always consult with your medical professional before doing any  changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.

Monitoring watch for CFS and other Conditions

This is a follow up from a previous thread to show what type of information is available.

The $45 watch

The store is BangGood and the price varies. Today it’s $44, I had gotten it on sale for $32 earlier this year

This is not “medical certificed”, but the numbers are good for on going monitoring. This watch can be set to record every 10 minutes of the day. Usually I need to recharge every 4 days with these constant readings

Example from the day that I got cellulitis

My watch was removed in the E.R. when I arrived at hospital, so only a half day was recorded. The charts illustrate the progression.

“White Coat Hypertension”

At my last checkup, the nurse reported high blood pressure… the BP chart agreed at the time she took my B.P. BUT it also showed that my BP is not high most of the time…..

A German CFS Patient Experience and Analysis

A reader had initial success from modifying the microbiome but it did not persist.

The reason I ended up at your website doing research into the connection microbiome and ME/CFS was that firstly I tried Miyarisan and it turned out to be one of the best things I ever tried, MY headaches and brain fog were early completely gone and I had a lot more energy. Unfortunately this wonder only lasted about 6 weeks till I overdid it and crashed and with that crash Miyarisan lost it’s effect on me.

The other thing was Nystatin, which I was given for the candida found in my gut last year and right on from the first pills I took, it gave me more energy ( so I doubt it had anything to to with the candida, but rather must have changed something else in my gut for the better). This lasted about 10 weeks and then pooped out and was not reproducible. 

But these two times that I felt I got energy because of some changes in my gut, were very rare in the way the they just generally provided a relief in all symptoms, as I was just overall feeling better and had more energy, but without crashing. Most of the times I have trouble, because I am easily overstimulated and most things that give me energy give me instant fatigue rebound, so Miyarisan and Nystatin really were different and made me try to work on my gut. 

She attached her tests and summarized them as “As to my tests, I guess the most notable things are my low TH1(Interferon Gamma), my low glutathione, high TGF beta, my decreased SOD activity.”

Reminder that recovery is a journey

In an earlier youtube review of another ME/CFS patient, I used the graphic below

I used this model for my last flare and can be seen by the list of posts below on CFS Remission. Each report was associated with a new microbiome test and a change of supplements etc to address the changes that the prior changes caused.

  • Report #1
  • Report #2
  • Report #3
  • Report #4
  • Report #5
  • Report #6
  • Report #7
  • Report #8

I have been busy adding features that exposes more information about the microbiome. We shall see if these feature helps with the analysis.

Pro Formula Analysis

My usual starting point is to pick the low hanging fruit — identify outliers.

Bacteria Outliers

I quickly saw some massively high ones. I will focused on those. Note that  Firmicutes is massively overrepresented.

End Products

Only two items were suggested, none available as a supplement (a-Galactosidase , Phosphoamidase)

KEGG Bacteria Products Out of Range

A short list, as above none available as a supplement

KEGG Modules out of Range

Only one item (M00570) Isoleucine biosynthesis, threonine => 2-oxobutanoate => isoleucine

KEGG Enzymes Out of Range

A longer list — all being low. We hope over to KEGG Computed Probiotics and get the following list

Because this person is in Europe, they may be able to get lactobacillus kefiri which is described more in my post of 2017 and sold by online Italian sites. This is a researched probiotic. Also AOR, Probiotic 3 is a sweet one — all of the researched probiotic species in it, are on the above list. For the bifidobacterium, see Researched Probiotics list for recommended choices.

Predicted Symptoms – Citizen Science

At this point we get some very interesting results. First, the bacteria by themselves do not match any symptoms.

But when we go over to the KEGG components that the bacteria produces, we see the type of predictions that we would expect

Conclusion: She does not have the typical ME/CFS bacteria shifts but she has the typical jacked metabolites imbalance seen in people with ME/CFS. Same crime — different crime family!

Action Plan

At this point, we have identify major items of concern.

Hand Picked Suggestions

I am going to run it two ways — first with the extreme outliers shown above, then including Firmicutes (which I rarely do)

Without Firmicutes

Remember we need to set Precision to the kitchen sink to have Firmicutes included in the calculations for the suggestions

If you do not change — the suggestions will be the same as above.

What about the two strange strains?

These bacteria do not ring any bells with me, so over to pubmed.

Proposed Plan for next cycle

Rotate every 2-3 weeks:

  • Triphala (we usually buy organic and make our own capsules) – 2000+ mg/day (source)
Sponsored ad - GoodFarm Organic Triphala Powder 1kg - Organic Certified, Premium Quality |  Ayurveda |  Vegan |  Excellent ...
GoodFarm Organic Triphala Powder 1kg
  • Licorice (I prefer the Italian products — not teas or powders) . Dosage used in clinical studies are 24-32 grams/day
Amarelli - Spezzatina liquorice with its and unmistakable taste - 100 gr
Amarelli – Spezzatina liquorice with its and unmistakable taste – 100 gr from Amazon.De

If your physician is willing to prescribe “off-label” also do alternating every two weeks between a PPI and atorvastatin (prescription). PPI is over the counter in some places and includes:

  • omeprazole (Prilosec, Prilosec OTC, Zegerid)
  • lansoprazole (Prevacid)
  • pantoprazole (Protonix)
  • rabeprazole (Aciphex)
  • esomeprazole (Nexium)
  • dexlansoprazole (Dexilant)

For items from the suggestions above, I would suggest going with handpicked suggestion list without firmicutes.

I would suggest an initial retest at 4 weeks or so, a full cycle of a PPI and atorvastatin, at the same time a cycle of alternating licorice and triphala. We want to see if this has caused a downward movement of the two species of concern.

I am a strong advocate on doing alternative pulses. It is what C. Jadin does for antibiotics (changing them every month) and I also have read several modelling studies that found rotation had better success than continuous. The english explanation is simple: for anything you may take — 90% of the bacteria may be killed and 10% survive (resistant). If you keep up with the same, then that 10% slowly regrows as resistant to whatever you are using. Changing between two things that are 90% effective (and different), then it becomes 99% killed and 1% survive.

As you have witnessed, 6 weeks with one item and then the resistors recovered your dysfunction, for another substance it lasted 10 weeks. We want to keep to 2 weeks on and then rotate.

I checked the parent taxa on these two, and I see  Carthamus tinctorius L (Safflower) inhibits one of them – so using safflower oil may help. There is no simple parent for the other.

As always, consult with your medical professional before implementing.

Spouse of 35 year CFS Patient

This is a two goal post. First, to see if literature indicating that healthy partners of microbiome dysfunction reflect their partner’s microbiome. Second, just a look at his microbiome and any possible concerns.

There is a very significant difference between the two in terms of diet:

  • Patient has been eating gluten free for years, supplements. etc
  • Husband eats gluten and dairy and some junk food. Minimal supplements.  High lipids, possibly genetic.

Similarity between CFS and Spouse

Picking the two closest samples by date

End Products Outlier – CFS 11 x Husband 0

KEGG Enzymes Outliers: Wife 639 – Husband: 30 Common: 1 (but opposite extremes)

Scanning Bacteria

Items that are common

Items with stark differences:

Goal #1 Bottom Line

Contrary to some studies, there appear to be little similarity between these people microbiomes. The reason is likely that the shifts due to diet are so very significant. It does raise the issue of using uncorrected ranges for diet types (junk food, organic, gluten free, vegetarian, pork eater, chicken eater [Yes, studies have shown difference between people that eat pork mainly instead of chicken!], etc.). Similarly age is a factor How the microbiome ages [2019]

Goal #2 Husband Health

As I know first hand, a wife usually cares more about a husband eating habits than he does himself. The risk of a kiss on the spouse cascading microbiome changes is a technical possibility.

First I went to Expert consensus

On the resulting screen, I checked all of the genus and species that were out of range and create a hand-picked selection and then got suggestions for them, shown below. Given that they are in the sixties, I note with interest that the first suggestion is the type of sugars found in mother’s milk, it almost seems to be a collection of restoring a younger microbiome suggestions.


Next I checked the Nat.Library of Medicine Explorer. To my delight, there were only two items above 50.

The items are:

  • hypertension (High Blood Pressure) — at 60%ile — still fine and not unexpected since hypertension is age related (likely connected to aging of the microbiome) see Hypertension – What we know [2019]
  • NonCeliac Gluten Sensitivity – This may be a false positive. Let me explained, since the wife is Gluten free, the husband will likely eat more gluten free food than most people. It you starve the gluten consuming bacteria… the shift may look like gluten sensitivity.

Going over to citizen science, there were no matches for symptoms. Again, compared to most people that have uploaded samples — no concerns.

Standard Kaltoft-Moldrup Suggestions

The suggestions are similar to those above. Many of the items are not unexpected for someone in the 60’s — Vitamin D. There is one significant change from above — resistant starch is a to Add, above, a common source of resistant starch (broad beans, black beans, etc) were on the to avoid list. Personally, I would go for eating the beans and other sources of resistant starch (see  Resistant Starch Content in Foods Commonly Consumed in the United States: A Narrative Review [2020]).

High lipids – any known microbiome component?

I do not have lipids in the database yet, so the reader should review the following studies.

Bottom Line

The husband seems fine and has no apparent health issues associated with the microbiome. There are suggestions above which may help prevent microbiome issues developing.

A CFS Patient after 35 years

A reader asked me to review their microbiome and test results, for items to discuss with their medical professional. As always this is not advising what to do; suggestions should always be reviewed by your medical before implementing.

The Person

This woman developed CFS around Lake Tahoe in 1987. Lyme and Mold issues.

  • Adverse effects from:
  • Resulting in MD prescribed Iron supplements, resulting in
    • 23 lb gain (heaviest ever!) (fat gain)
    • High cortisol,
    • Insulin resistance,
    • Bloating
  • Antifungals and antibacterial herbs for the past 3 years for mold and Lyme. history of off and on antibiotics for Lyme and coinfections for decades etc.
  • Cytomegalovirus and Epstein Barr (common with ME/CFS)
  • Tried resistant starch(oatmeal and green banana) and my bad microbes tripled (unclear which ones were deemed bad)
  • Gluten-free for years
  • Food poisoning 5 years ago
  • Feels hypoxic (low oxygen to brain) – likely caused by Protein S deficiency that is part of the coagulation change (according to tests)
  • Genetic issues processing phenylene, leucine and lysine. And also oxalate issues

Markov Cascade Model

This chart shows how overtime the microbiome can recover or continue to cascade (evolve). It is not a one step change, it’s a series of changes over time caused by diet, treatment attempts, age etc. This is essential to understand why things change and that it is not a one-step recovery.

Over time, the stable dysfunction microbiome develops a unique evolution
Path to recovery can be many steps

The Samples

We have five samples from Dec 2020 until May 2021. Multiple samples is a short period of time allows the daily variation to be minimize. Due to age, we do not have to be concerned with time in cycle impacting her microbiome (a key factor for females doing comparison samples)

Initial Notes

Going to comparing multiple samples, I walked thru each of the outliers and jolt down concerns

There are a few more, but we should call out that one species of a genus(Blautia) is very high and another is very low.

  • Medical Condition (PubMed)
    • No matches – this may indicate that the person has moved outside of the typical ranges

Building Suggestions

The numbers for the recommendations are among the highest that I have seen!!! This implies taht a lot of enzymes are not being produced. I would suggest the three easiest to obtain for a start, single Species with research (as shown below with the Books emoji)

For dosages, start low and slowly increase to the common therapeutic dosages

KEGG supplement list is long, even when reduced to just 3%ile

  • Amylase (Enzyme)
  • beta-alanine
  • D-Ribose
  • Glycine
  • L-Cysteine
  • L-glutamine
  • L-Histidine
  • L-Lysine
  • L-methionine
  • L-Serine
  • NADH
  • Selenocysteine

Prior to suggesting any of this list, i want to look at advance suggestions. The options that I picked

First, out of curiosity, given the experience with antibiotics, I looked at only antibiotics. Only a few of several hundred in the database made it on the possible list and at low confidence. The top 3 are often suggested with ME/CFS patients. the avoid list is massive. My impression is no antibiotics, but we need to confirm other paths are more probable to help.

I played with the other prescription options and the results were similar. So returning to the default suggestions we end up with an interesting list of do and don’ts

What makes it interesting is that a lot of to avoid are common suggestions from MDs treating ME/CFS with one-recipe fits all for ME/CFS. For example

  • Avoid all B-vitamins
  • No vitamin C
  • No Melatonin
  • No quercetin
  • Avoid Lactobacillus probiotics and likely bifidibacterium

The top item to avoid is luteolin. The foods that contain it are listed here and include celery seed, thyme, parsley, peppermint, rosemary and olives.

On the plus side I see my favorite ‘antibiotics herb’ being listed,   triphala. Changing the diet to resistant starches and away from high gluten food. Care must be taken to make sure you do not destroy the resistant starch as shown below:

Using Resistant Starch Content in Foods Commonly Consumed in the United States: A Narrative Review [2020], we see that Lima (butter) beans and Kidney beans should become part of your regular diet.

Antibiotics for Fusobacterium

The reader is interested in antibiotics for fusobacterium. I usually try to discourage single-bacteria focus because side-effects on other bacteria may make the person worse. Often this approach leads to frustrations because things “did not work“.

We start by looking at the antibiotics (this link) where we find 103 different antibiotics that reduces it. Just below this section of the page we also see the bacteria that encourages or discourage; for her latest sample, none of these appear to be in play.

Looking at the suggestions for antibiotics only, and turning all the 🔬 Show links to studies used for suggestions and setting the number of suggestions high, we see all antibiotics with probable positive impact, we end up with this list only.

We then click each  link to see what each suggestion actually modifies, on #2, we encounter success. It reduces this bacteria AND increases a different bacteria in the wrong direction (Pediococus is TOO high). This illustrates the challenge of being focused on one bacteria.

Remember that we balance good and bad impact — so remember to check each items

There is no option to model what will probably happen. My goal is to increase the probability of a suggestion being helpful. This is a decision that the medical professional needs to make (ideally after being made aware of side-effects).

Bottom Line

This person is not the usual pattern with pretty extreme shifts in the microbiome. My suggestion for a course of action to discuss with your medical professional would be

  • reduce/eliminate any supplements/drugs not listed above for a month
  • shift over to the diet style above, with the few probiotics suggested
  • start at a low dosage of Triphala (we buy it organic bulk and make our own capsules) and increase it slowly to at least 2 grams/day, ideally 8 grams/day [basis of dosages]

To me the key thing is to simplify the influences on the gut and allow it to stabilize and then proceed from there with changes followed by re-test and a new set of changes.

Piracetam – A Recap

I have often recommended Piracetam for cognitive issues. I have personally observed dramatic improvement within minutes in others, and observed it with myself. Unfortunately in the US it is not directly available because of FDA rulings (the same situation as for Mutaflor — E.Coli Nissle 1917 probiotic). Mutaflor is well documented (citations) with over 240 studies, and safely used in Europe for over a century — and works far better than any probiotic approved by the FDA.

Today, when I mentioned it, a facebook user wrote “Piracetam seems to come with warnings:” and linked to a JAMA article from 2019.

Our findings demonstrate that even after the FDA rejected an application to market piracetam as a new supplement ingredient,3 the drug was nevertheless introduced into the marketplace. Despite FDA warning letters,6 the products remain on the market. Until the law governing supplements is reformed such that products adulterated with drugs can be effectively removed from the market, clinicians should advise patients that supplements marketed as cognitive enhancers may contain prohibited drugs at supratherapeutic doses.

This was not a warning of the dangers of this substance — but a warning of the sale of a substance direct to retail as a supplement ignoring FDA rulings in some products (which seems like a very American attitude 🙂 )

Originally marketed by UCB Pharma in 1971, piracetam was the first nootropic drug to modulate cognitive function without causing sedation or stimulation 1. It is not approved for any medical or dietary use by the FDA. In the UK, piracetam is prescribed mainly for myoclonus, but is used off-label for other conditions such as learning difficulties in children, memory loss or other cognitive defects in the elderly, and sickle-cell vaso-occlusive crises 4. Evidence to support its use for many conditions is unclear.

Piracetam, DrugBank

What is known from studies

Checking PubMed, I found over 3700 studies on it! You do not get that volume of studies from something that does nothing. A few randome studies:

The JAMA was concerned about supratherapeutic doses, i.e. above 1500 mg. Going over to DrugBank Pharmacology resource we read


The cases of overdose with piracetam is rare. The highest reported overdose with piracetam was oral intake of 75g which was associated with diarrhea and abdominal pain; the signs were most likely related to the extreme high dose of sorbitol contained in the used formulation

Piracetam, DrugBank

Bottom Line

I suspect that the FDA ruling for piracetam is similar to that for Mutaflor. The decision was influenced by established american industries with a vested interest in selling their existing (ineffective often) products.