There are many reasons to manipulate the microbiome. Some simple reason may be to treat a condition like Psoriasis (see this post) where a reader wrote:
Ken – my head has stopped itching and I have only been taking the Align for 2 days!!!!!!!!!!!!!! I can’t believe it – but at the same time it makes sense – I had a severe gastrointestinal issue over a year ago for 6 months, and then I stopped eating yogurt because the soy yogurt maker went out of business…..and then the psoriasis started in last August…. Wow…. I will keep taking the Align and hopefully this will be permanent!! I am so grateful Ken! Thank you for writing the blog!!
For others, it is striving to optimise physical performance or mental performance.
Evidence for benefit manipulating
There are a large number of medical conditions that have microbiome shifts associated with it. I have created a chart of these relationship here. Many believe that these shifts either contribute to the conditions (or some of the symptoms) and in some cases may be the main cause.
The strongest evidence that microbiome shifts may be causing some of these medical conditions comes from dramatic results from Fecal
Microbiota Transplants. Some reports include:
- Fecal Microbiota Transplantation Induces Remission in Patients With Active Ulcerative Colitis 
- Fecal microbiota transplantation induces remission of infantile allergic colitis 
- “In Crohn’s disease, there has been no randomized,placebo-controlled trial evidence to date involving FMT. There are only observational data, which showed that approximately two-thirds of people went into remission with FMT.” 
- Fecal microbiota transplantation for managing irritable bowel syndrome 
- Fecal Microbiota Transplantation for Fibromyalgia: A Case Report and Review of the Literature 
- Fecal microbiota transplantation in metabolic syndrome: History, present and future 
- Dutch Clinical Trial Points to Fecal Transplant as Diabetes Treatment 
- “There are preliminary reports on the use of FMT therapy in a wide range of disorders including Parkinson’s disease, fibromyalgia, chronic fatigue syndrome, myoclonus dystonia, multiple sclerosis, obesity, insulin resistance, metabolic syndrome, and childhood regressive autism” 
FMT is the most extreme form of microbiome manipulation — and not something you can get at your local pharmacy — or even in many jurisdictions. For example, in the US — the FDA has taken a strong position (see this statement). Many people have done DYI FMT (with several reporting positive effects) — which have risks.
How to Manipulate
There are some major challenges when it comes to manipulation. These include:
- We do not what the right microbiome should be. Microbiome depends on both DNA and diet — and every one is different
- Any change may impact dozen of different types of bacteria in different ways
What are the tools of manipulation?
The most common ones for intentional manipulation are:
The most common ones for unintentional manipulation are:
- diet (including going vegan or gluten free)
- other prescription drugs
The chart  show that different types of protein have different effects.
Attempting to balance all reputable information
The site http://microbiomeprescription.azurewebsites.net/ attempts to take all of the known information about how hundreds of substances influence thousands of bacteria types using an Artificial Intelligence Engine.
No one knows which way is best, the choices available at this site are:
- You have a condition with common known shifts, what can I do to correct these shifts? No testing require.
- Just go to this page and click the condition.
- You suspect that some prescription drugs are responsible for symptoms and want to compensate for their impact.
- Just go this this page and click what you are taking
- You have a common (non-detail) stool report. You trust their standards.
- Just go to this page, select the lab and fill out the reports.
- You have done a uBiome, American Gut or Thryve detail analysis. You trust the ‘normals’ used by uBiome.
- Just go to this page and upload your data download.
- You have done a uBiome, American Gut or Thryve detail analysis and your family also. You do not trust the ‘normals’ used by anyone
- See this post on how to use family members to establish good norms..
Suggestions are not doctrine nor guaranteed
The suggestions are based often on a single study. In many cases, the study was not on humans. They are the best information that we have.
You can limit the scope of what you want to change on the suggestions page.
Yes, things are complex. Unfortunately, there is no simple “just take this pill” — actually, if it is the right FMT pill then that may be true.
Lacking this solution, it becomes changes of diet, supplements and probiotics — avoiding somethings and adding new things in.
Remember that many items will affect only some people (there is an average benefit — but you may not be in the average!). One small study found 50% are resistant to some probiotics.
My usual advice is to be systematic in trying things and keeping detailed notes.