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.
  • Thryve is what I am starting to use. 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

The ALA Herb: Shiso

A reader continues going thru traditional folk medicine looking for items off the beaten path that may be of interest and sending candidates to me.

The latest request for me to research is a gem. Mast cell inhibitor, anti-allergy, reduces gut inflammation, likely help with SIBO, etc

EidolonGreen [China Medicinal Herb] Perilla Frutescens (Perillae Folium/Zisuye/紫苏叶/자소엽) Dried Loose Leaves 3 Oz (88 g)

Perilla frutescens var. crispa, or shiso containing 58-65% alpha-linolenic acid [2006] [2008], It is sometimes referred to as purple mint

Microbiome Impact

Bottom Line

For additional information, see https://content.selfdecode.com/perilla-oil/

Needless to say, it will be added to the database at http://microbiomeprescription.azurewebsites.net/ and increased the number of direct citations.


Technical Study on Autism Microbiome

Over this weekend, we finally reached the threshold for citizen science to look at Autism (20+ symptom annotated uploads). This coming weekend I am attending a conference on Autism in Vancouver, British Columbia, Canada where Jason Hawrelak from Tasmania will be speaking (schedule below).

In preparation for this I decided to do a technical study comparing published studies on Autism and the results of citizen science. Is there agreement? What are the factors that come up with different results?

No photo description available.
Tickets are still available

Source Data

Data comes from two sources (both are subject to change with time):

We had agreement on several items, namely:

We had disagreement on only one item:

  • Veillonella was high on citizen science and low on published studies

Age is a significant factor for both Bifidobacterium and Lactobacillus. Studies on autism under 6, 6-12 and older will have significantly different amounts. This may account for disagreement between published studies.

Critique of Published Studies

Reproducibility of studies is important. There are 17 Pub Med studies on the autism microbiome. If you look at Publish Studies, the same bacteria is only reported 7 times at most. Many bacteria are only reported once. Whether a bacteria is evaluated depends on the equipment being used, for example – Bilophila is reported as significant in 2 studies but Thryve 16s results do not report it.

The usual criteria is to detect statistical significance of averages between the target group and the control group. This requires some major, likely false, assumptions:

  • Representative samples in each group
  • Normal distribution of the bacteria in each group

A single outlier in a group can cause statistical significance to appear while a more sensitive (but require more effort) test like Pearson’s chi-squared test would find nothing to publish about. It is important to note that Pearson’s usually results in sample sizes of at least 20; many published studies do not have that number.

If I exclude non-matches with at least 2 studies with consistent results (a single study in 17 studies is likely unreliable), then we have the following not detected yet with Citizen Science (which have barely enough studies to do any analysis).


On the flip side, Citizen Science reports on some bacteria not reported in published studies over 10 with high significance.

Bottom Line

Large representative samples and in depth skilled statistical analysis is needed to reliably identify the bacteria associated with a symptom, medical condition or characteristic.

From Publish Studies and Citizen Science, we have apparent agreement on 5 taxa, disagreement on 1, and silence in terms of repeatability on some 20 additional ones. I hope/ believe that as the number of samples in Citizen Science data set grows we will find more agreement with some of the published studies.

Below is a spreadsheet for interested parties.

For people not aware of the Microbiome Prescription site, this gives an overview.


Hello, a few months ago I saw a comment at the ME-Research Forum in which a sick commented that a doctor in Spain is prescribing hidroaltesona to the sick as palliative treatment for the ME.
I have tried to investigate about it since I have been taking 10 mg of hidroaltesona daily for a year having improved my intestinal problems (swelling and diarrhea, about 6 times a day in the last 15 years) passing to a Normal frequency.
My doctor put me the treatment for hipocortisolismo but the intestinal improvement was immediate.
Do you know studies or testimonies of people who have maintained this long-term treatment? 

From a reader

Hidroaltesona [C21H29Na2O8P] is related to Cortisol [
] (chemically different) containing two sodium atoms. Searching PubMed did not find any studies — I have never seen this happen before! I checked Hydrocortisone [C21H30O5] and found studies but the absence of sodium and phosphate atoms left me with a feeling that it was only vaguely similar.

Image result for hidroaltesona
Available only in Spain

From Manufacturer Site

All indications of oral corticotherapy, except in states that involve life-threatening and require intravenous route. The most important ones are:

  • Replacement therapy in primary or secondary adrenocortical insufficiency.
  • Congenital adrenal hyperplasia.

Other indications are:

  • Rheumatic and collagen diseases: treatment of exacerbations and / or maintenance therapy of rheumatoid arthritis, juvenile arthritis, ankylosing spondylitis and psoriatic arthritis when conservative treatments have been shown ineffective; Polymyalgia rheumatica; acute rheumatic fever; systemic lupus erythematosus; severe dermatomyositis; noia periarteritis; cranial arteritis and Wegener’s granulomatosis; scleroderma and dermatomyositis.
  • Dermatological diseases: allergic eczema, bullous pemphigoid pemphigus, generalized exfoliative dermatitis, severe erythema multiforme, erythema nodosum and severe psoriasis.
  • Serious allergic diseases: allergic rhinitis, contact dermatitis and bronchial asthma refractory to conventional therapy.
  • Lung diseases: sarcoidosis with pulmonary disease, extrinsic allergic alveolitis (organic dust pneumoconiosis), desquamative interstitial pneumonia (idiopathic pulmonary fibrosis).
  • Eye pathology: keratitis, choroiditis, chorioretinitis, iritis and iridocyclitis.
  • Hematological diseases: idiopathic thrombocytopenia, hemolytic anemias and palliative treatment of leukemia and lymphomas.
  • Gastrointestinal and hepatic pathology: ulcerative colitis, Crohn’s disease and hepatitis.

More Information

I found some experience from MDs with it at https://www.doctoralia.es/medicamentos/hidroaltesona/preguntas

That may be the best source to get solid information.

  • “long-term corticosteroid treatments, and depending on the dose, can induce changes and side effects in practically the entire economy of the organism, affecting almost any “
  • What is the relationship between hydroaltesona and prednisone? Both active ingredients are corticosteroids, with different potency and are used in many processes and diseases. “
  • ” In principle, in adrenal insufficiency, the doses range between 25 and 40 mg per day. ” – so this patient is on a low dosage.

PubMed on Hydrocortisone and ME/CFS

  • ” Cortisol levels, before or after dex, did not differ between CFS and Healthy Controls (HCs). Cortisol levels were more variable in CFS than HCs. ” [2018]
  • ” we found an inverse relationship between cortisol reactivity and symptom severity. There was no relationship between cortisol reactivity and illness duration. ” [2016]
  • Low-dose Hydrocortisone in Chronic Fatigue Syndrome: A Randomised Crossover Trial [1999] ” Interpretation: In some patients with chronic fatigue syndrome, low-dose hydrocortisone reduces fatigue levels in the short term. Treatment for a longer time and follow-up studies are needed to find out whether this effect could be clinically useful. “
  • ” The anti-inflammatory effect of cortisone at an adequate dose has, to my knowledge, not been investigated so far. I am left with the impression that the potential effect of cortisone on myalgic encephalopathy / chronic fatigue syndrome has been rejected on the basis of three studies that have investigated only low-dose hydrocortisone therapy of an hypocortisolism presumed and which are believed to have too little potency to conclude. with something. ” [2016]

Bottom Line

This drug is prescribed for ulcerative colitis, Crohn’s disease and is known to impact the entire body. We know that it inhibits many bacteria (list here).

Checking predictions on this page, it is predictive to help ME/CFS without IBS, but worsen ME/CFS with IBS and basic CFS. On the flip side, it is predictive to help IBS. The predictions are based on a naive estimate of it’s impact on the many reported shifts with these conditions.

Are the custom probiotics from your 16s Provider right?

I have often been asked that question. The general answer is “it depends”. This post gives you a science based answer.

Enter the probiotic Mixture

Once you are logged in, a new item appears on the menus as shown below

On the next screen enter a name (including the provider), for example

Or do Thryve/ L. Reu,Rha, being an abbreviated list

Now go back and get your suggestions.. What you just entered will be shown,

Their recommendations is a NEGATIVE in the mixed results, In the Humble Opinion of the Artificial Intelligence behind this page, a poor choice.

Bottom Line

A simple process. If you have your thryve (or other providers) custom probiotic mixtures handy, run them thru add add the results as a comment on this page.

Antibiotic Treatment of ME/CFS

A reader asked me to compile a list of of published studies and articles on the use of antibiotics with ME/CFS. Note that with gut dysbiosis as the model, the choice of antibiotics may depend on the details of the dysbiosis (this a 16s or shotgun GI report is suggested. Xenogene.es offers excellent reports).

At the Whittemore Peterson Institute (WPI) is a non-profit medical research institute dedicated to the support of those with a spectrum of neuro-immune diseases (NIDs) including: myalgic encephalomyelitis, (ME), fibromyalgia, and similar complex chronic diseases of the immune system and the brain. Dr. De Meirleir earned his medical degree from the Vrije Universiteit Brussel in 1977, and completed an internal medicine residency in the Department of Internal Medicine, University Hospital of Vrije Universiteit Brussel. His current research focuses on a subgroup of ME patients who show evidence of chronic bacterial infection and gut dysbiosis. These patients are responding to specific antibiotic/ probiotic therapy.


A treatment plan (Cecile Jadin’s is similar)

Treatment with antibiotics is difficult because drugs have to penetrate the host cell wall as well as the intracellular organisms. Treatment needs to be prolonged and pulsed, because of continual replication of the intracellular forms. Until adequate diagnostic facilities are readily available treatment needs to be in two stages: the first stage, which is diagnostic, involves the use of two long-term bacteriostatic antibiotics for 6 weeks, and the second, meant to be curative, involves the introduction of a third bactericidal antibiotic.

One possible choice of antibiotics for the first stage is a combination of Doxycycline and Azithromycin. Initially, the Doxycyline needs to be given alone in low dosage for two weeks, because of the risk of a Herxheimer reaction resulting from the release of toxins by damaged bacteria. Such reactions are usually mild and short-lived. If stable after two weeks, Azithromycin in low dosage is added for 4 weeks. Roxithromycin can be used in place of Azithromycin. . Improvement of symptoms, or the occurrence of a Herxheimer reaction, confirms the diagnosis.

Chronic fatigue syndrome or myalgic encephalomyelitis (2007) in British Medical Journal

From Published Books

Chronic Fatigue Syndrome: A Treatment Guide, Second Edition
By Erica Verrillo 2002
In this summary by two of the leading researchers

Bottom Line

There is a high success rate reported with antibiotics. Recent research suggests that the failures may be selection of inappropriate antibiotics for the person’s specific gut dysbiosis. IMHO, a 16s or shotgun (Xenogene) microbiome report should be done and carefully analyzed prior to selecting the various antibiotics needed.

The microbiomePrescription site supports evaluation of antibiotics against a microbiome, as well as other prescription drugs.

Unfortunately, there has been only one comprehensive study done, so relative ranking may not apply for many samples (i.e. do a show all and scan for the ones that are most acceptable)

With hand-picking against ME/CFS profiles, results can get quite good. All of the antibiotics involved with prior successful treatment were listed.