Learning about Autoimmune and Chronic Infections


On Saturday, I drove down to Philadelphia with my mom to attend a day-long conference about autoimmune and “stealth” infectious disease, and how nutrition and supplementation can be used to manage these conditions. It amazes me how many diseases may have some level of autoimmune etiology, and it’s even more amazing to me that conventional rheumatology does not use nutrition as a therapeutic tool. I feel like one day the allopathic medical community will catch up to the osteopathic/naturopathic one, but until then, it’s up to savvy patients to seek out alternative information about their chronic, sometimes debilitating conditions.

Though I do not have an autoimmune disease, I did (do?) have Lyme disease – a fact that I have not previously shared on this blog but one that makes me more interested in using nutrition to treat mysterious diseases that most doctors are unable to deal with. Perhaps one day I’ll share my experience with Lyme, since I’ve been treated twice for it and am currently unsure if I even still have an active infection. It’s my belief that the only reason I didn’t get majorly sick from Lyme is because I have a pretty good handle on the nutrition and lifestyle factors. I learned a lot about Lyme from Dr. Todd LePine at this conference, and about autoimmune disease from Dr. David Brady. I definitely want to “specialize” in these conditions in the future, even though there is no educational program for RDs to learn how to use nutrition therapy to manage these conditions. Who knows, maybe I’ll get another degree to help boost my clinical skills in integrative healthcare!

Here are some of the most interesting facts I learned this weekend:

  • There has been a 3-4 fold increase in autoimmune diseases since 1950
  • Women are generally more susceptible to autoimmune disease than men
  • 75% of the immune cells of the body are in the GI tract
  • Certain strains of gut bacteria can either cause or prevent certain autoimmune (AI) diseases
  • Research supports the theory that gut changes happen first, and then AI disease occurs
  • Oral infections are correlated with AI disease like rheumatoid arthritis – aka “leaky mouth”
  • Several major classes of bacteria may induce AI like MS and thyroiditis due to their structural similarity to body protein, a theory known as molecular mimicry
  • Patients with SIBO should not be taking probiotics or eating probiotic foods until their SIBO is treated
  • Probiotics should be taken with food to protect them from degradation
  • The variety of strains in a probiotic is more important than the absolute number of organisms
  • Some probiotics can directly treat leaky gut
  • Saccharomyces boulardii, a probiotic yeast, should be taken by anyone with diarrhea, c. diff infection, or being treated with antibiotics
  • Celiac patients have ~10 times the rate of autoimmune thyroid diseases like Hashimoto’s and Graves disease compared to non-celiac patients
  • The American diet is more than 50% wheat, corn, and dairy
  • One of the major environmental triggers for Type 1 diabetes may be cow’s milk proteins
  • Children who grow up on traditional farms and drink “farm milk” (aka raw milk) are protected from asthma, hay fever, and allergies
  • In Europe, there is a medication called Ovamed that is used to treat IBD and Crohn’s – it is literally a whipworm parasite (helminth)
  • N-Acetyl Glucosamine may be useful in treating autoimmune disease as it attaches to antigens and blocks T cell activation
  • Zinc Carnosine supplementation may help tighten leaky gut junctions
  • Melatonin might be a therapeutic agent in GERD treatment
  • Other supplements helpful in treating IBD by reducing gut inflammation include resveratrol, EGCG, curcumin, and boswellia
  • There is such a thing as too much omega-3, which can cause an unhealthy drop in inflammatory response and immune suppression
  • Vitamin D deficiency may be another etiologic factor in AI disease
  • Vitamin A is a crucial nutrient for supporting immune regulation, as it boosts the production of T-regulatory cells, which prevent too low and too high immune activity. T-regulatory cells are also upregulated by active vitamin D hormone and pregnancy
  • Mercury fillings may stimulate the production of antinuclear antibodies, increasing AI disease risk, and N-Acetyl Cysteine may help increase mercury excretion by binding to it
  • Specific autoantibodies that predict AI disease can be found from 10-25 years before a clinical diagnosis
  • H. Pylori may actually be protective against certain conditions like asthma, so simply testing positive for H. pylori doesn’t necessarily warrant treatment
  • Biofilm disruption is important for treatment of dysbiosis, since pathogens are protected by this biofilm
  • There is a theory that all chronic disease, including aging and cancer, is related to infection
  • Lyme disease is commonly associated with co-infections such as Borellia B., Babesia, Bartonella, and Erlichia
  • The Iceman was found to have Lyme disease
  • The Lyme spirochete avoids immune attacks through downregulation of outer-surface proteins (Osp’s), by hiding in the extracellular matrix, and by suppressing the immune system
  • There are three forms of the Lyme bacteria: atypical, cystic, and granular. Each of these have different life cycles, and may be found in intracellular or extracellular space
  • Each of these three forms is sensitive to different antibiotics, so a combination of antibiotic therapy must be used
  • There is an association between Lyme disease and Autism Spectrum Disorders (ASD) and Alzheimer disease
  • Chronic illness blocks the vitamin D receptor (VDR), causing 1,25-Vitamin D (the active form) to increase dramatically, while 25-vitamin D (an inactive precursor and the form usually tested for) goes down, giving the appearance of vitamin D deficiency in conventional testing
  • Ingested vitamin D suppresses the immune system, which is good for autoimmunity but bad for chronic infection
  • Chronic infections like Lyme, tuberculosis, Epstein Barr virus, and HIV are associated with an increase in AI disease
  • Ferritin levels typically decrease in chronic infection, leading to fatigue
  • Organic acids testing can tell you if you have nutrient deficiencies, metabolic issues, or certain infections
  • Yeast overgrowth can be detected by testing the urine for D-Arabinitol and other metabolites
  • Stool tests show what’s going on in the lower GI tract (large intestine), while urine testing shows what happening in the upper GI tract (small intestine)
  • A good test to determine leaky gut is the Lactulose to Mannitol ratio
  • Mercury or lead poisoning can cause a decrease in porphyrin synthesis, which is essential for hemoglobin synthesis and can cause anemia
  • A genetic polymorphism in the apoE gene (specifically apoE4) negatively affects ones’ immune response to mercury and Lyme disease
  • Testing for inflammatory cytokines using the iSpot Lyme Test can show if you have an active Lyme infection
  • Post Lyme Disease Syndrome is a possible condition where the Lyme bacteria is gone but the immune response to the antigens continues, causing constant inflammation

Well there you have it – that’s most of what I learned this weekend. Lots of interesting facts that I didn’t know before and that I hope will help me with my treatment of patients in the future.

Is there anything I listed in this post that you didn’t know before, or that shocked you? Let me know in the comments below!

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  1. What tests do you recommend for SIBO? before the ingestion of probiotics? why?
    How does the Ovamed work on IBD?
    thanks. what a blast to attend the conference.
    I have BS in Biology, a newly graduated NTP. empty nester. love this stuff.

  2. My teen daughter was recently diagnosed with SIBO (hydrogen breath test). Gastro gave her Metronidazole. I’m so concerned about this that I was about to start her on a Probiotic… until I read this post!!! There is so much mixed information about how to treat SIBO. Can you please tell me your best sources for information on treatment of SIBO?


    1. Raw honey daily is great for sibo also try garlic oregano oil and olive leaf extract if honey doesnt help but it should if you keep using it daily

  3. Wow, great list of facts! I think it’s so important to learn these instead of applying overarching ideas, especially for probiotics, omega 3s, and vitamin D. They may be appropriate for one person but not another. Thanks for sharing!

  4. I read all of this but wondered what is a person to do about all of this?..Who do we get to treat such things that can be understood..I live In Delaware and would welcome a doctor that understands what you wrote as well as treat all of this..It would be great to find someone in surrounding states -Pennsylvania, Maryland, New Jersey .? Thanks so much

  5. Thank you for posting all of this. I’m outside Philadelphia & would be interested in attending such a conference. Would you please tell me or post which one it was?

    Many thanks,

  6. If not already feeling lost with my number of gut related symptoms, I feel even more so now as I’m currently taking omega-3, Vitamin D, magnesium.

    Had several tests with GP but no sign of a diagnosis yet! 🙁

    Although it’s very interesting I’m sure if and when I get a diagnosis the above will be very helpful.

    1. Usually start with Paleo then move to Autoimmune Paleo if that doesn’t help. After that, it depends on the individual.