Some readers have asked me to explain my view of what causes a wide range of conditions – from diabetes to autism, from myalgic encephalomyelitis to parkinson’s.
At a high level, there are three dominant factors:
- DNA – every autoimmune condition has SNP variations associated. This does not mean you will get the condition — just have greater odds of getting it. (1151 articles on PubMed)
- Epigenetic changes to DNA. This means that some environment influence has caused DNA functions to be turn off or on (or scale).
- Microbiome – every condition has microbiome shifts associated with it with more being reported every year
And genetics to microbiome:
- The effect of host genetics on the gut microbiome. 
- The effect of heritability and host genetics on the gut microbiota and metabolic syndrome. 
And last, is consequences of infection and even immunization which can alter the microbiome — often in a long lasting way. The best study example occurred in Bergen Norway. 60% of CFS suffers developed the condition after a flu (or ‘flu-like’) illness.
Each factor interacts with the other factors and if you are unlucky, you have a struggle ahead of you. Of the above factors, the microbiome is the simplest to adjust.
Modifying epigenetic changes is more challenging – with stress being likely the only exception. Stress induced epigenetic changes may be reduced or reversed with full removal of stress (speculation) — which is not a trivial path. We may need almost 100% removal of stress, not just reducing it. We know that diet can invoke epigenetic changes – just do not know how. Science is still working on just detecting epigenetic, modification may be decades away.
This perspective is highlighted in this article:
The genetics of human longevity: an intricacy of genes, environment, culture and microbiome .
At what microbiome level may we need to go down to?
Twins with identical DNA with one having a condition and another not, is the classic way of controlling for DNA variation.
” We collected fecal samples and clinical metadata from 20 monozygotic Korean twins … Finally, our unique study design allowed us to examine the strain similarity between twins, and we found that twins demonstrate strain-level differences in composition despite species-level similarities. “Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes. 2016]
The microbiome is the easiest factor to address. It is not an easy to do. Just the easiest of the available choices. It is made more comlex by different diets, life style (yes, exercising regularly alters the microbiome) and even age (diversity decreases with age).