At present suggestions on http://microbiomeprescription.azurewebsites.net work by naming specific strains. This can often be a challenge to obtain for many readers. On the flip side, people will have a mixture and ask if they should take it.
The solution is to support mixtures:
By allowing registered users to add probiotic mixtures
By having the suggestions review the mixtures and identify
good ones (some on the to take list, none on the to avoid list),
neutral ones (none on the to take or to avoid list) and
possibly risky ones (1 or more on the avoid list).
This post describes the first step.
There are several new pages added today. First is a listing of probiotic mixtures
Clicking it will shown the probiotics mixture that are in the database:
Adding A Probiotic Mixture
Once you login, you will see an additional menu item:
Clicking this will take you to a screen to select (in case of errors) an existing one, or add a new one.
Below, I am adding a new one, just fill in the input box and click [Add]
The next screen lists probiotics by their genus and then species. A few special strains ones are explicitly added.
Just check the ones that are in the mixture and click Update.
You can confirm the correct entry by returning to the prior page.
Some 6 years ago, I documented in a blog post a hypothesis that I had been using and felt sufficiently confidence about to commit to paper. I referenced an even earlier more speculative post from 2012.
” My best hypothesis on CFS is currently a stable dysfunctional microbiota (gut flora) that was triggered by an illness, poor diet, vaccination or chemical exposure. It is good to put this hypothesis to the test against prior successful treatments that resulted in some remissions. I have already looked at this in an earlier post, but thought a revisit on certain aspects would be good. “
Infection or even a single Phage changes the microbiome
Phages are specific hunters: each type kills just one type of bacteria. So when the scientists introduced a phage to the mice, they would see a decline in that type of bacteria. However, the impact on other bacteria was more surprising…. They found that when they introduced a phage to the mice and the bacterial composition changed, there were also changes in the levels of certain biologically active chemicals. If phages make sweeping changes to a mouse microbiome, they are likely to make changes in the human microbiome, too. The changes might be different, but the principle remains.
The effectiveness of any ME/CFS treatment depends on the microbiome
Some drugs work well for one person but are ineffective for another; some also produce adverse events for certain individuals but not others. A study, using human gut bacteria and a mouse model, investigates whether our gut bacteria might help explain why.
‘Using those data, they developed a mathematical model that successfully predicted the role of gut bacteria in metabolizing a second antiviral drug and clonazepam, an anti-seizure and anti-anxiety drug. The study found that the gut microbes were responsible for producing 20 to 80 percent of the circulating toxic metabolites derived from the three drugs.” The gut microbiome may be to blame for the toxic side effects some people experience from drugs that help many others, according to new research.11 Feb 2019
My earlier Eureka Post — found strong statistical relationships between many symptoms and bacteria.
Where Science is at and where I have leapt ahead
Science is just starting to accept the wide effect that bacteria has with the latest studies. In traditional scientific caution, it may take another decade before it is well accepted (look at the 30 years that it too for H. Pylori to be accepted as the cause of stomach ulcers).
Over the last six years, I have seen study after study come supporting my seven year old hypothesis. As more information came in, I moved on to accepting it and the logical consequence: we need to have approaches to modify / correct the gut bacteria. Unlike the usual bad bacteria infection, there is often no good or bad bacteria — rather too much of one and too little of another. Add to this that all of the bacteria interacts with each other.
If you go to DataPunk, and look at Dorea genus, you will see a long list of interactions with other bacteria… a very long list. Any change may have worst cascading effects!
Add to this already complex situation, the absence of research on what various drugs do — I recently try researching what the impact was of three different common histamines. I was lucky to find some material on one of them, the other two has unknown impact.
A reader recently shared this post from my long time friend, Cort Johnson
With my hypothesis, such a drug is likely to impact gut bacteria significantly. It turns out that there was a study on it’s impact and I had add it to my microbiome prescription site. Over 30 impacts. Whether it worked or did not work for a ME/CFS suffer would likely depend on their microbiome!
Suggestions are cutting edge science
I have looked at many sites giving diet advice, even those connected with microbiome testing such as Thryve. The quality of the advice is effectively at general dietitian level, or naive using the microbiome (i.e. used a few studies only). The microbiome prescription site uses a database containing the following information:
The relationships are constantly being updated from new studies.
There was an interesting comment on my facebook page, something like “Correcting the microbiome have never been proven to cure any condition!” – absolutely correct, technically. BUT ALSO:
“There have never been a study published that showed that you can correct the microbiome” – In other words, the above comment was polemics.
My own experience (especially with the ongoing flare) is that you can correct the microbiome to some degree (totally normalize is a different question) and as you correct it, symptoms should reduce (as it has for me).
I know of no other resource, free or paid, that provides suggestions based on as many studies, considering as many factors as being produced by the microbiome prescription site. It may not be perfect, but it is probably more effective than the advice most MDs would hand out — which is often “Take a good quality probiotic” — whatever that means!
After 7 years, trying a hypothesis, I am still using it and applying it. It holds water. It appears to work — but more importantly, it explains things. Using it and addressing some ‘black holes’ like histamines and mast cell issues are ongoing challenges. We are making progress.
“Hypotheses grow out of explaining empirical data.That is basic science.” Empirical data for me was the published reports of responses to various treatments for ME/CFS, as well as studies on the symptoms reported. All on PubMed or in conference reports. Most of the significant ones were published in 1998-2001.
The event that triggered my paying notice to the microbiome was during the 2010’s relapse — I could control all of the other symptoms with things like heparin, etc, herbs etc… but I never had GI issues before. As a result, I had filtered out all of the GI information looking at the literature. This event caused me to re-inspect the literature and lead to this hypothesis (after trying multiple others). It was far better at explaining all of the information and data then any other proposed at that time.
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.
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.
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.
When you go to Advance Suggestions and click see Bacteria Selection Choices
You will find at the bottom of the page, a new section: the Lactic acid/Lactate producing bacteria reported in your sample where you have more than the median amount.
Back on the custom suggestion pages, I select this filter option, as shown below.
Then filter the modifiers and click for suggestions:
This is all theoretical and focuses solely on reducing bacteria associated with lactic acid and lactate production. The suggestions should be reviewed by a medical professional before starting. It may potentially make other issues worst, so use caution and make sure you are being monitored.
A reader email indicating that he believe that some of my suggestions also produced lactic acid. At present that is no option for filtering, but I am working on that. This appears to be a subset of ME/CFS patients. A 2015 Guest Blog post on Health Rising provided a summary of early studies. The latest study is below.
This is associated with neurlogical issues (brain fog etc).
I have lactate acid producer estimates on the microbiomeprescription site for uploaded 16s samples (typically ubiome). My own numbers appear to follow the research. With onset it kept increasing, and with the last ubiome started to decrease.
I did not have significant neurological issues BUT these values are all low according to the uploaded samples. Which suggests that while the amount increased, it did not reach impairing levels for neurological issues
The list below are what is in the database as producing the two items above. If you know of additional items, please forward the information (with a link to the study of course!).