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

HHV, Mycoplasma and Microbiome

A reader asked about what we know. They were looking for food for a child that may inhibit these by inhibiting the bacteria that provides them with the metabolites to flourish. These two have a high prevalence with ME/CFS.

We need to be aware that there may be a ‘mafia family’ in operation, for example: “HIV also acts synergistically with multiple other viruses, such as HPV, EBV, varicella zoster virus (VZV), and HHV-8. ” [2019]

Unfortunately available literature on PubMed contains few human studies.

  • Lower  Prevotella,Mycoplasma pneumoniae, Staphylococcus epidermidis, and Staphylococcus aureus  [2019]
An integrated respiratory microbial gene catalogue to better understand the microbial aetiology of Mycoplasma pneumoniae pneumonia [2019]

The reader had uploaded a microbiome from Thryve and I wanted to see how severe mycoplasma was:

The sample of concern placed them at the 8th percentile (very low). So mycoplasma is unlikely to the cause. 70% of Thryve reports had this group.

My intent was to see if there were any statistically significant association with other bacteria (friend or foe analysis).

Drilling down to the species level, we find that he numbers were not abnormal (below average but at median)

Concerning HHV virus — that is outside of the scope of my analysis site. There is no published literature to work from. I do have a personal belief that HHV and other virus reactivation is a side effect of microbiome dysfunction. Yes, some antivirals help — but those same antivirals also alter the microbiome leaving these antiviral mechanism of action unclear.

Returning to the person

  • The reader child “he still have learning disabilities”. I looked at Naive Predicted Symptoms with their microbiome and with a score of 1.0 (highest), we have these predicted that match this description (25 possible of 5200 pairs possible). HHV6 and Mycoplasma were included in the symptom list! (this does not mean the child has them — rather that people who were told or believed they had them; self reporting and not a lab test)
What is identified

I proceeded to pick the bacteria (clicking the checkboxes above) that matched these symptoms and built a custom profile. The result was that many bacteria recurred in different combinations, so we ended up with just 9.

Running it through the suggestions machine learning we got:

As often happens — some probiotics are good and other bad. A “good probiotic mixture” is often the wrong thing to take.
The recommended probiotics,,,

Bottom Line

The above are suggestions from a machine learning algorithm. They should be reviewed and discussed with your medical professional before starting.

The goal was to modify diet to help with the symptoms. We were not able to find anything based on the presumed cause in conventional medical literature. We were able to identify some specific bacteria shifts that corresponded to reported symptoms and get diet suggestions from those.

Wifi and Cell Signal impact on immune system

This is an area that people will often block out — they are not willing to give up wifi or cell phones — regardless of health risks. There are people that associate(blame) the use of cell phones on increasing autism, irritable bowel syndrome and many other conditions. It is actually impossible to do solid valid studies that would confirm or debunk these theories. Why? because you cannot find a matched control group!

We do know somethings — that it does impact the microbiome.

Cell phones and electronic appliances and devices are inseparable from most people in modern society and the electromagnetic field (EMF) from the devices is a potential health threat. Although the direct health effect of a cell phone and its radiofrequency (RF) EMF to human is still elusive, the effect to unicellular organisms is rather apparent. Human microbiota, including skin microbiota, has been linked to a very significant role in the health of a host human body…. These findings led us to hypothesize that cell phone level RF-EMF disrupts human skin microbiota.

The Response of Human Bacteria to Static Magnetic Field and Radiofrequency Electromagnetic Field [2017]

” For instance, the issue of so-called non-thermal effects and potential long-term effects of low-dose exposure were scarcely investigated prior to the introduction of these technologies. Common electromagnetic field or EMF sources: Radio-frequency radiation (RF) (3 MHz to 300 GHz) is emitted from radio and TV broadcast antennas, Wi-Fi access points, routers, and clients (e.g. smartphones, tablets), cordless and mobile phones including their base stations, and Bluetooth devices. Extremely low frequency electric (ELF EF) and magnetic fields (ELF MF) (3 Hz to 3 kHz) are emitted from electrical wiring, lamps, and appliances. Very low frequency electric (VLF EF) and magnetic fields (VLF MF) (3 kHz to 3 MHz) are emitted, due to harmonic voltage and current distortions, from electrical wiring, lamps (e.g. compact fluorescent lamps), and electronic devices. On the one hand, there is strong evidence that long-term exposure to certain EMFs is a risk factor for diseases such as certain cancers, Alzheimer’s disease, and male infertility. On the other hand, the emerging electromagnetic hypersensitivity (EHS) is more and more recognized by health authorities, disability administrators and case workers, politicians, as well as courts of law.”

EUROPAEM EMF Guideline 2016 for the Prevention, Diagnosis and Treatment of EMF-related Health Problems and Illnesses [2016]

Bottom Line

We try to have most internet connections to be wired. For example, Smart TV and Roku are all using wired. Unfortunately, tablets do not have that as an option — so we tend to turn wifi on and off when needed. We turn off cell-data when we are at home. Using Wifi sniffers, we typically see only our own devices (we have a good distance from neighbors) compare to 50 or more devices seen in town/city.

We know the EMF impacts bacteria/microbiome. The consequences of this impact is unknown. A wise approach may be simple:

  • Turn off devices when not in use/really needed
  • Use wired connection over wireless
  • If possible, move to lower population density (ideally, rural)
  • Be aware of location of cell towers when you move. You want to maximize the distance
  • Maximize distance from all screens….

Vasodilation – Supplements

Vasodilation means opening up or dilatation of blood vessels, which will often decreases blood pressure. I put together a list of supplements (with links to PubMed studies) that reduces blood pressure in a September 2019 post. An item that reduces blood pressure does not always mean that it does vasodilation. Some migraines and headaches are improved by vasodilation

In this post I will review these and other supplements that dilation of blood pressures.

And so on, almost every item that reduces blood pressure also induces vasodilation (not really much of a surprise).

Complex Interactions

  • Calcium “The influx of calcium into vascular smooth muscle initiates contraction by binding to” [1983]

Pycnogenol and Allergies/Mast Cells

A reader asked about this, which I have no covered yet. Increased allergies and mast cell issues often occur with microbiome dysfunction and chronic fatigue syndrome.

Bottom Line

The research to date suggests that it may take 2 or more months before significant benefits may be seen in some cases.

Symbioflor-1 A sinus probiotic

“The probiotic Symbioflor 1 is a historical concoction of 10 isolates of Enterococcus faecalis. Pulsed-field gel electrophoresis revealed two groups: one comprising eight identical clones (DSM16430, DSM16432, DSM16433, DSM16435 to DSM16439) and a further two isolates (DSM16431, DSM16434) with marginally different profile” [2016]

“A double-blind, placebo-controlled multicenter study in 157 patients with chronic recurrent sinusitis investigated the occurrence of acute relapses during treatment of patients with a bacterial immunostimulant (3 x 30 drops/day), comprised of cells and autolysate of human Enterococcus faecalis bacteria (Symbioflor 1, n = 78) in comparison to placebo (n = 79)…. the occurrence of relapses (50 incidents) was about half (56%) the number observed under placebo (90 incidents)” [2002]

“the time span until occurrence of the first relapse was clearly longer under verum[Symbioflor-1] (699 days) than under placebo (334 days) and after the end of the observation period 91% of patients under verum experienced only one relapse compared to 62% in the placebo group (p = 0.01). ” [2001]

From PubMed

  • “Compared with the controls, probiotic intervention significantly upregulated the level of IL-10 and TGF-β, downregulated levels of IFN-γ, and increased progesterone level that reversed the trend of being Th1 predominance state ” [2020]
  • 1. E. faecalis stimulates the liberation of interleukin 1 (IL-1 beta) and interleukin-6 (IL-6) in a dose-dependent manner; the E. faecalis induced liberation of IL-1 beta and IL-6 is inhibited by dexamethasone (Dm) but not by cyclosporin A (CsA).”
    2. E. faecalis stimulates the liberation of gamma-interferon (IFN-gamma) in a dose-dependent manner, which is inhibited by both Dm and CsA.”
    3. Phytohemagglutinin (PHA)-induced liberation of gamma-IFN and interleukin-2 (IL-2) is inhibited by E. faecalis in a dose-dependent manner. ” [1994]
  • “For instance, Escherichia coli Nissle 1917 was a poor inducer of iNOS gene expression compared to the other E. coli strains, while Enterococcus faecalis Symbioflor-1 was more potent in this respect compared to all the eleven Gram-positive strains tested. ” [2014]
Symbioflor 1

Personal Experience

I have used this for sinus issues in the past and it has been effective in clearing them.

Source: https://www.paulsmarteurope.com/symbioflor-1-tropfen-drops-50ml/