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:
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.
- 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).
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.