Here is the process of how we help people with autoimmune diseases

  • Schedule a consult
  • Pursue diagnostic testing to evaluate the gut microbiome, immune system, and endocrine system
  • Start treatments focused on creating immunologic balance. We resolve the inflammation from the root cause- the human microbiome and immune regulation systems


Autoimmune diseases are conditions where the immune system attacks the body’s own tissues/organs. Such abnormal immune responses originate in changes to the gut bacteria, which can occur even at birth. The bacteria teach the immune system just as teachers teach students. If the bacterial ecosystem is off-balance compared to what has occurred in healthy humans for the past 200,000 years, then the immune system will not learn properly, and will confuse the body’s own tissues for potential threats.

Bacterial imbalances can occur from inadequate breast feeding as a baby, antibiotic exposure, and processed-food based diets.

The first step in understanding them is to understand the immune system, its ways, and how to balance it. There are two major categories of inflammation (pathways of immune system activation):

Th1 vs Th2 Inflammation

The “Th” refers to T-helper cells, which are regulatory cells that decide what kind of inflammation will be occurring. Autoimmune disease occurs when one of the two kinds are chronically activated.

Th1 Dominant:

  • Multiple Sclerosis (MS), rheumatoid arthritis, scleroderma, type 1 diabetes, psoriasis, late Sjögren’s syndrome, celiac disease, and Hashimoto’s autoimmune thyroiditis, osteoporosis
  • Purpose:
  • In healthy settings this inflammation is important to treat intracellular infections such as Mycoplasma, Chlamydia, EBV, viral infections, and Lyme disease as its promotes the eradication of infected cells via activated macrophages (white blood cells) and via complement fixation (immune complexes that bind up infected cells)
  • Mechanism:
  • Unhealthy changes to gut bacteria activate NF-kappa beta, which promotes Interferon-gamma to promote the autoimmune response featuring cytokines (IL-2, Interferon gamma, IL-12, IL-18) that activate macrophages and immune complexes to attack the human body in specific places (pancreas for diabetes, brain for MS, joints for RA, etc)
  • In the absence of interferon-gamma, IL-23 stimulates production of IL-17 producing T-cells (Th17 cells) can activate the Th1 response, and this is particularly harmful if occurring in the brain.
  • IL-23, IL-6, and TGF-beta all can promote central nervous system -based inflammation as is seen in MS, by activating the IL-17 pathway
  • IL-17 also promotes osteoporosis by activating osteoclasts and inducing bone resorption.
  • In women, unregulated estrogen can promote Candida (fungus) overgrowth in the gut microbiome, leading to enhanced IL-17 activity, which is why MS is more common in women
  • Our Enteroimmunology: Gut Microbiome Repair program decreases NFKB-based inflammation by balancing the gut bacteria and repairing the intestinal lining (leaky gut) that leads to the inflammatory response in the first place.
  • Importantly these illnesses improve during pregnancy as pregnancy switches the immune system to be more Th2, therefore safe pregnancy hormones such as progesterone or estriol are useful treatments for this class of diseases. Progesterone and testosterone both suppress Th1 mediated autoimmune inflammation. We use endocrine (hormone) treatments in our Endocrinology Program
  • Also delayed type hypersensitivity such as the kind of inflammation associated with contact dermatitis and chronic recurrent skin rashes is included in Th1 type inflammation.

Th2 Dominant:

  • Systemic Lupus (SLE), early Sjögren’s syndrome, allergic dermatitis, eczema, sinusitis, asthma and allergies, and ulcerative colitis
  • Purpose:
  • Rather than trying to kill infected cells, which is the main function of Th1, Th2 is focused on creating antibodies such as IgG subclass 1 through 4 and IgE, so allergies included in this kind of inflammation. Antibodies are proteins that bind up free antigens in the blood stream, liver, and spleen
  • Mechanism:
  • IL-4 is the main cytokine and when it binds its receptor this leads to phosphorylation of STAT-6 which binds to the IL-4 promoter and further induces more IL-4 production, essentially more of a positive feedback loop
    Cytokines: IL-4, IL-5, IL-10, IL-13, and IL-25 and these are involved with elimination of extracellular pathogens and parasites.
  • Fungus overgrowth in the gut microbiome can promote IL-4 based inflammation. Our CCIM Enteroimmunlogy & Endocrinology (EIE) Programs focused on gut microbiome repair and hormone balancing suppress IL-4 based inflammation