What You Should Know About Gut Microbiome with Dr. Jill Carnahan

In this episode of The Functional Medicine Radio Show, Dr. Carri’s special guest Dr. Jill Carnahan talks about what you should know about your gut microbiome.

Dr. Jill received her medical degree from Loyola University School of Medicine in Chicago and her Bachelor of Science degree in Bio-Engineering at the University of Illinois. She is board-certified in Family Medicine and Integrative Holistic Medicine. In 2006 Dr. Jill was voted by faculty to receive the Resident Teacher of the Year award and elected to Central Illinois 40 Leaders Under 40. In 2010, she founded Flatiron Functional Medicine in Boulder, Colorado where she practices functional medicine.

Dr. Jill is also a 10-year survivor of breast cancer and Crohn’s disease and passionate about teaching patients how to “live well” and thrive in the midst of complex and chronic illness. She is also committed to teaching other doctors how to address the underlying cause of illness rather than just treating symptoms through the principles of functional medicine.

Main Questions Asked:

  • How did you get involved in Functional Medicine?
  • How does autoimmune disease relate to our intestinal health?
  • How do the bacteria that live in us and on us influence our health?
  • What is leaky gut? What causes leaky gut?
  • How do I know if I have SIBO?
  • How do I get tested for SIBO?
  • How do I get tested for yeast overgrowth?
  • How do I get tested for leaky gut?
  • How do we heal a leaky gut?
  • How do we maintain healthy intestinal bacteria?

Key Points made by Dr. Jill:

  • It was through her personal health journey with breast cancer and Crohn’s disease that Dr. Jill got involved with Functional Medicine.
  • Autoimmune basically means your body starts to think of itself as dangerous and starts attacking itself.
  • Crohn’s disease is when the body attacks the lining of the digestive tract, basically causing ulcers though the entire digestive tract.
  • Autoimmune disease always starts along the gut lining. This is because 80% of our immune system is here.
  • The bacteria in our gut, whether they’re healthy or not, will determine our health.
  • There are always three pieces to any and all autoimmune diseases: 1. Genetic predisposition; 2. Environmental triggers (like toxins, stress, gluten, infections, etc); and 3. Leaky gut (aka: intestinal permeability).
  • Everyone with an autoimmune disease should stop eating gluten and whatever other foods they have food sensitivities to.
  • The most common food sensitivities are dairy, sugar, corn, soy, alcohol, and yeast.
  • Zonulin is a little trap door between every cell that lines the intestines, and if this trap door stays open then the microbes in the intestines and the food in the intestines leaks into the bloodstream directly. This is what ‘leaky gut’ is.
  • Zonulin is directly triggered by gluten – whether you have gluten sensitivity or not.
  • Bacteria wear a coating called LPS which is a big trigger for autoimmunity and inflammation.
  • A big part of healing autoimmune disease is to assess and heal the gut first.
  • Gas, bloating, and constipation and/or diarrhea are not normal, and are common signs of SIBO – Small Intestinal Bacterial Overgrowth.
  • The majority of bacteria should live in the colon – not the small intestine.
  • The toxins that are created from SIBO can cause fatigue, brain fog,
  • Yeast overgrowth is another common cause of leaky gut.
  • Common symptoms of yeast overgrowth include rashes, psoriasis, craving sweets, bloating, diarrhea, and for women these symptoms are worse around their period.
  • An Organic Acids urine test can show markers of bacterial and yeast overgrowth in the intestines.
  • Stool testing can also be helpful to determine bacterial and yeast infections, as well as parasite infections.
  • The ‘poor man’s test’ for SIBO would be to try FODMAPs foods – for 24 hours eat the foods highest in FODMAPs and if you feel worse and have terrible abdominal symptoms there’s a pretty good likelihood you have SIBO and/or yeast overgrowth.
  • Other signs of leaky gut include: rosacea; chronic unexplained iron deficiency; B12 deficiency; multiple food allergies; worsening environmental allergies; weak peeling cracking fingernails; eczema; and psoriasis.
  • Healing a leaky gut first begins with identifying what the problems are – not just throwing probiotics at it.
  • The first place to start is with diet – Paleo Diet is the best place to begin.
  • Herbs and medications can be used to kill off microbial overgrowth.
  • Probiotics are definitely necessary – the right kind of probiotics for the right patient.
  • Inflammation often needs to be addressed with L-Glutamine, DGL, and even organic ghee.
  • Diet is the most important factor to maintaining healthy intestinal bacteria.
  • If you have an autoimmune disease you have to stick to your healthy diet 100% for life.

Resources Mentioned:


Dr. Jill’s website

Dr. Jill’s facebook page

Book – Reclaim Your Energy and Feel Normal Again

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