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

Long Haul Covid – Welcome to the ME/CFS world!

Long haul COVID is sometime referred to as Post-Virus Syndrome. I prefer the more general, Post-Infection Syndrome. Most people with a CFS/ME diagnosis fall under that classification and causation. It appears to impact about 10% of people with a certain severity of COVID. The profile is very similar to ME/CFS: “were predominately white females, between the ages of 30 and 60, who lived in the United States. “[NIH]

Forget about Disability etc

A few people may get it, those with positive test results for something wrong, for example a SPECT scan of the brain. In general, long haul covid show no atypical results from standard medical tests. This has been the situation for ME/CFS for decades. Some people may get it granted for up to one year… and then will get turned down on renewal. The fact that they may not have been hospitalized or had a formal diagnosis may make a claim more difficult “More than half never sought hospital care. Only 8 percent said that they’d been admitted to the hospital for COVID-19.”[NIH] Insurance Company: “We need clinical evidence that you had COVID…”

How will the insurance company respond?

From ME/CFS experience, it will be suggested that it is either psychosomatic, or work-phobic , or someone using it as an excuse not to work, or psychologically crippled from COVID stress. There is nothing wrong with the patient according to medical tests. Hence, it is psychological or attitude. Benefit denied.

COVID cases grew exponentially, Long Haul Cases will decline with Exponential decline or decay. Unfortunately, insurance company will view it as linear decline…if 50% recover in 9 months, then anyone still with it at 18 months must be a faker.

Probable Cause … microbiome dysfunction

Microbiome dysfunction, even when shown, would be viewed as an experimental or research diagnosis and thus, not applicable for disability. This gets much worst because almost no physician knows now to effectively deal with a microbiome dysfunction apart from a Fecal Matter Transplant (which may require multiple attempts using different donors — they still have not figured out compatibility and compensation vectors for FMT). FMT in the US is restricted to a very small number of conditions, and long haul covid is unlikely to be included for decades.

Technically, sufficient information appears to be available on PubMed (National Library of Medicine). It is not consolidated into a cookbook formula but spread across over 3000 separate articles. Clinical MDs do not have time to consume this, and applying it would be contrary to existing standards of care. Their supervisors will veto it (been there, seen that!)

Bottom Line

The cure for Long Haul Covid is likely the same cure as ME/CFS. From existing studies, we know that a percentage will spontaneous recover every 6 months, with the percentage decreasing over time. Some will never recover. A few will, like ME/CFS. continue to get worse.

My hope is that some long haulers will get their 16s results (from one of these providers), upload it to Microbiome Prescription and in time, we’ll see the pattern and how to address it.

Microbiome Prescription customized for CFS/ME

Recently I have gotten several emails like that shown below.

 Hi Ken,I’m one of those CFS people who has such brain fog it’s very difficult  for me to use your microbiome prescription website even though you’ve done an excellent job with the  videos to get started. I’m dictating your email from my phone bc I’m too tired to type. 
Is it possible to have you look at my information that I’ve uploaded from Thrive and help me with which bacteria is important to replace.  I know I need Lactobacillus Casi.I don’t know how important it is to replace Faecalibacterum but my ave is 2.2% were The healthy ave is 12.89%. My Symptoms are severe fatigue, brain fog, tingling of extremities, moody.

From a reader on 26 Feb 2021

I have refactored a part of the site to address this (I have more UI changes pending from other feedback). In short, after you uploaded your sample, you will see a new choice in the first drop down:

When you click it, the suggestions page is less complex (all of the same information is there, just hidden on first load).

Very pleased with suggestions

I used this person’s sample for the video below. The suggestions matched those of some physicians that have had considerable success (and the suggestions are close to what I did too!)

The artificial intelligence on the site put these items in the top suggestions based solely on the microbiome. It is my belief that success or failure to treat depends on the microbiome (which is usually ignored!). There have been some recent studies finding that the microbiome was a key factor in the success or failure of some cancer treatments.

Beware of pentadecapeptide BPC 157

Today I got hit with a bunch of ads on Facebook for the above. I see that some of the ads are targeted for irritable bowel syndrome (IBS). My first impression is what is it? Has it been demonstrated to help anything (besides the pocket book of promoters)? What is the probable monthly cost of an effective dosage? This post attempts to answer these questions. Similar posts from the back:

The aim of this paper is therefore to critically review the current literature surrounding the use of BPC 157, as a feasible therapy for healing and functional restoration of soft tissue damage, with a focus on tendon, ligament and skeletal muscle healing. Currently, all studies investigating BPC 157 have demonstrated consistently positive and prompt healing effects for various injury types, both traumatic and systemic and for a plethora of soft tissues. However, to date, the majority of studies have been performed on small rodent models and the efficacy of BPC 157 is yet to be confirmed in humans.

Gastric pentadecapeptide body protection compound BPC 157 and its role in accelerating musculoskeletal soft tissue healing [2019]

The first question is simple, should be expect it to be confirmed in humans? The longer it has been since discovery, the higher the probability. IMHO 5-7 years is a reasonable expectation. Turning to PubMed, we see it has been written about for thirty years.

What is it?

Pentadecapeptide BPC 157, composed of 15 amino acids, is a partial sequence of body protection compound (BPC) that is discovered in and isolated from human gastric juice. Experimentally it has been demonstrated to accelerate the healing of many different wounds, including transected rat Achilles tendon.

The promoting effect of pentadecapeptide BPC 157 on tendon healing involves tendon outgrowth, cell survival, and cell migration [2010]

The version being sold is patented, older versions do not survive stomach acid etc. The patent gives the sequence of these amino acids is given in the patent, “pentadecapeptide (abbr. BPC-157 or bepecin) having an amino acid sequence: Gly Glu Pro Pro Pro Gly Lys Pro Ala Asp Asp Ala Gly Leu Val “

The FDA has issued warnings about it. From unsafe manufacturing [2018], as well as other agencies

While the peptide BPC-157 is not presently included on the World Anti-Doping Agency (WADA) Prohibited List, it is important for athletes to be aware that this substance is not approved for human clinical use by any global regulatory authority, it may lead to negative health effects, and it could be added to the Prohibited List at any time based on new research. A

BPC-157: Experimental Peptide Creates Risk for Athletes

Who is selling it?

LIQUID STABLE BPC from BioPure Supplements. 100 mg (total) is $60.00. or $600 per gram

There is a clinical study from 2015 that I found PCO-02 – Safety and Pharmacokinetics Trial The high dosage was 8-24 mg/day. Thus the above bottle is enough for 4 days, so about $450/month. There has been no update of this trial for 7 years. Usually, no update means no positive results (99% of the time)….

Bottom Line

There is no trustworthy evidence that it helps, it has a high cost (when purchased from the promoters) and lack FDA approval (it is being sold as an unregulated supplement). The price being asked is CRAZY! Some sources are selling it in bulk for as low as $3/kilogram! So BEWARE and save your money!

Why you MD knows almost nothing about the Microbiome

I view Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) — and many other conditions– as being either a pure microbiome dysfunction, or a microbiome dysfunction that contributes significantly to many of the symptoms. If you walk into your typical medical office and ask questions about this you will likely be met with a variety of responses (depending on their psychology) that are not helpful.

A reader asked “Why is this?” The easiest way to understand the issue is to look at the number of studies on pubmed about the microbiome


What does this translate to? Unless your MD finished his studies in the last 5 years, there is very little chance that there was any significant coverage of the microbiome in courses. Yes, they took microbiology — the study of bacteria; but the microbiome is different. How so?

Microbiology can be compared to understanding how a person‘s psychology changes as they ages from a child, to an adult, to an elderly. The microbiome is understand sociology of people in a society. The microbiome is the understanding of interactions and interplays. It is more complex. Far more complex.

This is why MDs and naturopaths tend to look for the single bacteria or virus responsible. That is precisely what they had training in, the comfort principle of medicine.

A second factor is simple, specialization. “Ah, the microbiome belongs to the human gastrointestinal system, so the patient should be referred to a gastroenterologist!” Wait! they treat very specific diseases only and not items like a diabetic’s microbiome. Tossing patients to specialists is a common practise — the problem is that there are rarely specialists in this area. It’s my least favorite game: PPP – “Patient Ping Pong”.

Old techniques versus Best techniques

Often old techniques could be rephrased as ‘current accepted best practises’. In my Uni days, I has several professors tell me “Do not go into Engineering or Medicine, you are brilliant — but you are also creative and innovative, that will end your career in those areas”. I have an additional characteristics, I am a high functioning ASD person. Why is that important? It means that I tend to ignore social pressure and conformity; instead, I march to my own drum beat along whatever path looks interesting (and have little anxiety about stepping off existing paths). Back to the topic….

What is the best technique for dealing with the microbiome? It is simple, use various types of artificial intelligence and machine learning. The problem with this for MDs is that machines are giving them advice that they are incapable of understanding the why. It is not that the MD is dumb, it is because the problem is very very complex.

One type of machine learning is called “Random Forest“. I have used them professionally when I worked for Amazon. Microbiome studies started using this in 2010 and the number of studies are exploding yearly — why, because it works!


The problem is that this is a new discipline called data science, an specialized application of advanced statistics. Yes, MDs and medical researchers often did a basic statistics class at Uni. The problem is that they have simplified what they were taught and incorrectly applied it.

A typical mistake that I have seen is reporting something like “the control group average as 30 and the treated group average was 50 with a less than 5% chance of being random”. Klaxon sounding!!!!

  • They looked at 100 different bacteria in their study, there is a good chance that 5 of them will have a 5% chance of being significant at random!
  • Often they will report on averages and appear to assume that the data is a well behaved normal or gaussian distribution.
    • On occasion, I have looked up the distribution of some of these “discovery” bacteria. The average was not at the 50%ile or median (expected with every normal curve) but at the 87%ile. The mode (most common value) was at the 10%ile.

In short, they are deficient in appropriate skills in handling numbers that arise with the microbiome.

Bottom Line

We need someone to fund serious state-of-the-art research into the microbiome and then evangelize the results into the medical community. This is a hot topic with many many microbiome testing firms being launched by venture capitalists. They see that this has the potential of being financially rewarding.

My own contribution is making a free site that uses data science and artificial intelligence on 16s samples. https://microbiomeprescription.com/ I have seen a few 16s firms, adapt/borrow, features from my site to their clients — I am very fine with that. We are just at the start of the microbiome journey – unfortunately, many still wish that this was just a walk in the park, instead of having to cross the Alps!

Best ME/CFS Posts

I have written almost 1400 blog posts on ME/CFS on this site over the last 9 years (first post was in 2012). One of the first ones was Symptom Mitigation. In recent years, I have focused on the microbiome aspect of ME/CFS – a technical area not suitable for the brain fogged. In this post, I will deal with traditional treatment without using the microbiome, trying to keep things simple for the brain fogged..

Best Feed Back from Readers

Neem has constantly had users surprised, this morning I go this comment on facebook

My post from 2016, Neem – Azadirachta indica gives a summary of the literature at that time. A more recent article is quoted below. There have been no clinical studies on using it with ME/CFS.

Different parts of the plant including flowers, leaves, seeds and bark have been used to treat both acute and chronic human diseases; and used as insecticide; antimicrobial, larvicidal, antimalarial, antibacterial, antiviral, and spermicidal….Over 1000 research articles published on neem has uncovered over 300 structurally diverse constituents, one third of which are limonoids including nimbolide, azadarachtin, and gedunin. These agents manifest their effects by modulating multiple cell signaling pathways.

Neem (Azadirachta indica): An indian traditional panacea with modern molecular basis [2017]

There are two other Indian Ayurvedic Plants that are well worth trying (one at a time, working from a low dosage up)

  • Triphala
  • Tulsi or Holy Basil

My earlier post on Triphala is from 2017, Triphala – an ancient medicine, a more recent post is relevant if your ME/CFS is associated with IBS or leaky gut.

The components of TLP are believed to cause restoration of the epithelium lining of the digestive tract, and by exhibiting mild laxative properties facilitate passage of stool in the colon. TLP is rich in polyphenols, vitamin C and flavonoids, which provide antioxidant and anti-inflammatory effects. It also contains various types of acids, such as gallic, chebulagic and chebulinic, which additionally possess cytoprotective and antifungal properties…Currently, there are no clinical trials assessing the effects of herbal formulations of TLP on clinical course of IBS …

Contrary to pharmaceutical laxatives, which tend to stimulate the bowel, TLP has a regulating effect and can be used long-term. The large intestine is permanently exposed to various toxins, parasites, etc. therefore, it is important to provide adequate bowel cleansing. Literature data indicate that TLP acts as a colon cleanser, which helps to clean the waste matter from the lower GI tract and improve its proper functioning [1288]. To sum up, TLP can be particularly helpful if constipation is a symptom, but it can also be useful in some cases of alternating constipation.

Triphala: current applications and new perspectives on the treatment of functional gastrointestinal disorders [2018]

My earlier post on Tulsi is from 2016, Tulsi – Holy Basil – Ocimum sanctum, and it is adaptogenic (more on this word later).

A total of 24 studies were identified that reported therapeutic effects on metabolic disorders, cardiovascular disease, immunity, and neurocognition. All studies reported favourable clinical outcomes with no studies reporting any significant adverse events. The reviewed studies reinforce traditional uses and suggest tulsi is an effective treatment for lifestyle-related chronic diseases including diabetes, metabolic syndrome, and psychological stress. 

The Clinical Efficacy and Safety of Tulsi in Humans: A Systematic Review of the Literature [2017]

Stress is a Contributor Usually… and we can do something about it

Stress is reported to be a factor in 30-70% of ME/CFS cases. Getting ME/CFS becomes a major source of stress, thus establishing a feedback loop that keeps it going. Stress alter many things in the body. A class of substances classed as adaptogenic, have been found to reduce the alterations in the body. One of these is Tulsi above. There are several others:

For Rhodiola Rosea, see my post from 2014: Review: Rhodiola Rosea Root (Rosavin). 600 mg/day is suggested

  • “Preparations of Rhodiola rosea root are widely used in traditional medicine. They can increase life span in worms and flies, and have various effects related to nervous system function in different animal species and humans. ” [2020]
  • “Rhodiola rosea extract is widely used to alleviate stress and improve cognition and mental resources. A total of 50 adult participants were treated with 2 × 200 mg R. rosea extract (Rosalin®, WS® 1,375)…how an improvement of mental speed and moreover, suggest improved mental resources. ” [2020]
  •  “the Rhodiola capsule shows anti-depressive potency in patients with depression disorder when administered in dosages of either 0.3 or 0.6 g/day over a 12-week period.Rhodiola capsule can improve the quality of life and clinical symptoms.The high doses of Rhodiola capsule are better than the lower doses.” [2020]

Some other adaptogenic herbs that I have reviewed: Jujube Fruit, Magnolia Bark (also helps sleep), and some probiotics, see Psychoactive Probiotics!

Go Organic! Make your own capsules!

Most of the above herbs can usually be obtained in bulk as organic powder or as a tea(for example, https://www.starwest-botanicals.com/ ). This means no fillers to react with, nor pesticide residues. Both of these issues have been reported with commercial prepared capsules. It is also cheaper.

The Dilemma of getting a ME/CFS diagnosis

<SOAPBOX> At one time, the official diagnosis criteria was having 4 out of 18 symptoms for no cause being found. Often a diagnosis of IBS or other comorbid diagnosis will be given instead of ME/CFS. Analysis on MicrobiomePrescription.com has found very strong statistical significance of certain symptoms with specific groups of bacteria in the microbiome across many diagnosis. This implies that the symptoms are a reflection of a stable microbiome dysfunction and it’s consequences – imbalances with over 1500 known enzymes, etc. In other words, a complex metabolic disorder.

Readers have often reported that the symptoms disappear when the associated bacteria is normalized. Approaching this issue with a focus on the microbiome is where this blog evolved to.

To translate it from geek speak: what we call ME/CFS is likely several hundred technically different conditions that because of a lack of fine resolution (or any resolution) tests, gets dropped into a large “circular filing cabinet” by most physicians entitle ME/CFS. Unfortunately, because it has a name — it is slotted as a single condition in most medical minds (“It’s a forest with a name” and thus all plants in it are assumed to be the same, thus an Oak and a cloudberry bush are viewed the same). </SOAPBOX>