I started this post planning to look at diabetes and I had so many hits on microbiome and other autoimmune disease included that I thought that I would move to the full topic.
My word of warning is simple: once the microbiome (gut bacteria) gets shifted out of normal (like with CFS/FM/IBS etc), the odds are significant that the shift could continue to worsen (and depending on you DNA) results in additional and more severe autoimmune diseases.
- “in human male type 2 diabetes subjects as compared to non-diabetic healthy subjects, there were significantly fewer Firmicutes, including Clostridia.
There were positive correlations between plasma glucose levels and the ratios of Bacteroidetes to Firmicutes, and of the Bacteroides–Prevotella group
to C. coccoides–E. rectale group. Furthermore, Betaproteobacteria was more abundant in type 2 diabetes subjects than the controls….These results imply that lowered levels of butyrate-producing gut microbes in type 2 diabetes patients may lead to disease pathogenesis” 
- “Antibiotic-mediated gut microbiome perturbation accelerates development of type 1 diabetes in mice .
- The gut microbiota: a possible factor influencing systemic lupus erythematosus . “found a lower Firmicutes/Bacteroidetes ratio in SLE patients vs. controls, there were inconsistencies regarding significant differences in the abundance of specific genera or species. Studies of mouse disease models have shown some correlations between microbial compositions and disease states, also indicating differences between males and females.”
- Integration of microbiome and epigenome to decipher the pathogenesis of autoimmune diseases 
- Does the Gut Microbiota Influence Immunity and Inflammation in Multiple Sclerosis Pathophysiology?
- The Association of Specific Constituents of the Fecal Microbiota with Immune-Mediated Brain Disease in Dogs . “We found that Prevotellaceae were significantly less abundant”
- Correlation of Gut Microbiota Composition with Resistance to Experimental Autoimmune Encephalomyelitis in Rats .
- Altered gut microbiota in RA: implications for treatment . “Certain gut microbial strains have been shown to inhibit or attenuate immune responses in RA experimental models, suggesting that specific species among intestinal commensal bacteria may play either a pathogenic or a protective role in the development of RA.”
There are some 440+ articles on PubMed finding that some DNA SNPs are associated with diabetes (and other autoimmune conditions). The same appears to apply to almost all autoimmune diseases.
- Polymorphism E23K (rs5219) in the KCNJ11 gene in Euro-Brazilian subjects with type 1 and 2 diabetes .
- PTPN22 Single-Nucleotide Polymorphisms in Iranian Patients with Type 1 Diabetes Mellitus .
- Meta-analysis of STAT4 and IFIH1 polymorphisms in type 1 diabetes mellitus patients with autoimmune polyglandular syndrome type III .
Other diseases (sample)
- Vitamin D receptor gene polymorphisms are associated with multiple sclerosis in Mexican adults .
- CTLA-4 +49 G/A Polymorphism Confers Autoimmune Disease Risk: An Updated Meta-Analysis .
- Association of established hypothyroidism-associated genetic variants with Hashimoto’s thyroiditis.
- Polymorphisms of RAD51B are associated with rheumatoid arthritis and erosion in rheumatoid arthritis patients [2017[.
- Transethnic meta-analysis identifies GSDMA and PRDM1 as susceptibility genes to systemic sclerosis .
- The association between osteopontin gene polymorphisms, osteopontin expression and sarcoidosis .
- Single nucleotide polymorphisms of IL12B are associated with Takayasu arteritis in Chinese Han population .
- Association of KCNJ2 Genetic Variants with Susceptibility to Thyrotoxic Periodic Paralysis in Patients with Graves’ Disease .
- Association of a single nucleotide polymorphism upstream of ICOS with Japanese autoimmune hepatitis type 1 .
- A Variant in the BACH2 Gene Is Associated With Susceptibility to Autoimmune Addison’s Disease in Humans.
- Estrogen receptor alpha gene ( ESR1) polymorphism can contribute to clinical findings in systemic lupus erythematosus patients.
- Identification of susceptibility gene associated with female primary Sjögren’s syndrome in Han Chinese by genome-wide association study .
- IL-27 Gene Polymorphisms in Iranian Patients with Behcet’s Disease .
There are several points that I want to make:
- The hope of fixing your DNA is in the remote future at best; the ability to alter your microbiome — while still primitive — exists now.
- The number of DNA SNPs involved and the number of bacteria species and strains are so huge that there is no simple ‘cookbook recipe’. The recipe is to experiment with the “spices and the yogurts in the kitchen” until you find that perfect recipe!
Doing nothing risks moving onto worst autoimmune conditions. Not only worst in terms of symptoms — but also worst in terms of the difficulty to make the microbiome right!