It All Starts With Your Gut: How Your Bacteria & Intestinal Inflammation Affect Your Mood, Health, Longevity & More!

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My guest on today's show, Dr. Patrick Hanaway, is one of the world's top authorities in the realm of functional medicine.

He is a board-certified family physician with a medical degree from Washington University and completed residency training at the University of New Mexico. He is a past President of the American Board of Integrative Holistic Medicine and co-founded Family to Family: Your Home for Whole Family Health with his wife in Asheville, NC. As an initiated Marakame (Shaman) by the Huichol people in the Sierra Madres of central Mexico, he incorporates these healing approaches in his clinical practice.

From 2002-2012, he was the chief medical officer at Genova Diagnostics, followed by the director of medical education for the Institute for Functional Medicine as well as the medical director at the Cleveland Clinic Center for Functional Medicine. He just last week published a keystone JAMA article on the improved outcomes of patient care with an integrative functional medicine approach, and in 2017, he won the Linus Pauling Award.

Teaching around the world on ‘Good Medicine,’ he brings his full presence to teaching clinicians about healing, with an emphasis on therapeutic relationships, connection, community, and wholeness.

During our discussion, you'll discover:

-Dr. Hanaway's background in functional medicine…6:40

  • Disillusioned with medical practice in the early 1980s
  • Books by Jeffrey Bland
  • Focus on root cause of disease and why disease occurs
  • Other ancestral means of treating disease (Ayurveda, Chinese, Tibetan, etc.)
  • Understand the synthesis between various methods of healing/treating disease; incorporate outside means as necessary
  • Understand the story, gather information on the patient; emotional shifts are key

-Why Dr. Hanaway is a shaman and how it synchronizes with his practice…11:30

  • Huichol people in the Sierra Madre region never indoctrinated with the practices of the church
  • Living tradition thousands of years old
  • Had series of dreams after connecting with Huichol; went to sacred spot to make offerings
  • Began working with Huichol people intermittently; initiated as a healer 8 years into the practice
  • “The way of listening” and perceiving emotional/spiritual issues is used for understanding the big picture of a patient's condition

-What makes functional medicine unique…14:45

  • Functional medicine is an “operating system”
  • Listen to the person's story: precursors, genetics, heritage, emotional triggers, etc.
  • Focus on diet and lifestyle
  • Initial visit is 2 hrs. to gather info
  • Insurance pays for quantity, not quality; not always conducive to functional medicine
  • JAMA Network Article on Functional Health

-Tools and resources Dr. Hanaway often uses in his practice…22:40

  • Understand a patient's nutrition: B vitamins, antioxidants
  • Gi Effects® 3-Day Stool Panel by Genova Diagnostics
  • Onegevity (Use discount code: BEN20 to receive $20 off your own test.)
  • Metagenomics

-Microbiome testing: which test is best to get the most accurate results…34:15

  • The jury is still out as to which is the best test
  • It's not possible to get comprehensive results with just one test.
  • Onegevity is the best on the market, according to Dr. Hanaway

-What a test result will reveal, and what steps to take from a functional medicine standpoint to address it…39:00

-Why Dr. Hanaway doesn't begin diagnosis with the brain…44:15

  • Relationship between permeability in the gut and brain permeability
  • TBI changes intestinal permeability – increased risk of infection
  • Address gut permeability first and foremost
  • Gut-blood barrier and blood-brain barrier can be addressed simultaneously
  • Look at prebiotics and foods rather than probiotics (which are tourists)
  • Diet changes the gut microbiome within only 1-2 days
  • Fecal microbial transplant is a powerful tool when used with caution

-Foods that Dr. Hanaway finds to be the most efficacious in his practice…51:30

-Tests other than Onegevity Dr. Hanaway finds particularly informative…57:15

-Hot topics currently being discussed in the functional medicine community…1:02:30

  • Autoimmune disease and cognitive impairment are hot button issues (Dale Bredesen)
  • Focus on the community of the microbiome, not the individual microbes in the gut

-And much more…

Click here for the full written transcript of this podcast episode.

Resources from this episode:

Click here to pre-order Ben Greenfield's new book “Boundless” now and to get in on the Boundless Sweepstakes!

The Jordan Harbinger Show

Click here to visit for the testing we discuss in this episode. Use discount code: BEN20 to receive $20 off your own test.

JAMA Network Article on Functional Health

How To Get 6 Gigabytes Of Data From Your Gut: The Fascinating Future Of Stool, Blood, Saliva & Urine Testing (From The Comfort Of Your Own Home).

Psychobiotics and the Manipulation of Bacteria–Gut–Brain Signals

A Review of Traumatic Brain Injury and the Gut Microbiome: Insights into Novel Mechanisms of Secondary Brain Injury and Promising Targets for Neuroprotection

My article about Dr. William Davis's coconut yogurt recipe

Beneficial Effects of Pomegranate Peel Extract and Probiotics on Pre-adipocyte Differentiation

Urolithin A Is a Dietary Microbiota-Derived Human Aryl Hydrocarbon Receptor Antagonist

Nutreval Test

23andMe Genetic Testing

GiEffects 3 Day Stool Panel


MyHeritage DNA Panel

FoundMyFitness genetic tools

BiscuitHead Biscuits & Gravy In Asheville

Kettle & Fire Bone Broth

Thomas Cowan's Vegetable Powders

– Gutbio by Onegevity Health

Pomegranate peel extract

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Do you have questions, thoughts or feedback for Dr. Hanaway or me? Leave your comments below and one of us will reply!

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20 thoughts on “It All Starts With Your Gut: How Your Bacteria & Intestinal Inflammation Affect Your Mood, Health, Longevity & More!

  1. Lydia Rose says:


    This was the first interview of Ben I listened to. Great interviewer! I’m really interested in the gut-brain connection in relation to autism/Asperger. One very obvious topic of external influences that should be researched as a possible cause of the tsunami of auto-immune diseases and autism is vaccines. The Amish fi don’t vaccinate and their rate of autism among their children is significantly lower than average. Would that be a taboo topic?
    Thanks and greetings from Holland!

  2. blair says:

    Thank you for the stellar content. What I am wondering about is the biofilm product. In the show notes Dr. Hanaway referred to it as Biome Health. I could not find it via google, is it called something else perhaps?

    1. Patrick Hanaway says:

      Biohm Health

      1. blair says:

        Thank you!

  3. John Crosby says:

    Dr. Hanaway, I appreciate your expertise, experience, and the important information you shared. I’m curious, however, why no mention of GI-MAP as a lab option? I’m guessing you’re familiar with it. It’s CLIA certified, so unlike the majority of microbiome tests, it’s diagnostic. Summary:

    – qPCR/DNA-based molecular test;

    – One vial, one sample with fast turn around time;

    – Each target organism is independently validated;

    – Viruses, bacteria, fungi, occult blood, immune and pancreatic function, inflammation, parasites, anaerobes, virulence factors, and antibiotic-resistant drugs;

    – Results for both pathogenic and opportunistic infections, both quantitative and qualitative;

    – Screens for potential autoimmune triggers (Klebsiella, Citrobacter, Proteus, Yersinia), SIgA, anti-gliadin sIgA, H. pylori and its virulence factors and antibiotic resistant genes, inflammatory and pancreatic exocrine markers, worms, zonulin, and more.…

    Many thanks,


    1. Patrick Hanaway says:


      I’m familiar with the GI-MAP test.
      In my experience, the results have not been reproducible — especially Calprotectin.
      That is, I have reviewed split testing that did not meet a standard of reproducibility.

      I discussed the value of metagenomic testing versus the 16S rRNA sub-unit probes that are used by GI-MAP and others.
      This is the future of gut microbiome diagnostic testing.

      1. John Crosby says:

        Dr. Hanaway,

        I appreciate your response. I’m sure you know this but see Calprotectin considerations below. I have no affiliation so simply share this as info.

        Also, does shotgun sequencing provide quantitative data or just qualitative? My understanding is that this is what’s critical for diagnosing a pathogen. Otherwise, we might see patterns and relationships, but adjusting for differences in genomic DNA in stool and microbes with different DNA signatures in different regions are potentially missed. For example, some have lower amounts of DNA in their fecal specimen.

        Kind regards,


        1) Feedback regarding Calprotectin variation over time, even say four weeks:

        The time in between is the main reason for a difference in results. Calprotectin can rise and fall in a matter of hours. With really high results that clear in a week or so the likely cause would be a pathogen. Most pathogens of the GI are self-limiting, especially viruses. Other causes for significant high Calprotectin that resolves would be toxins. Mostly toxins from bacterial pathogens.

        In Europe most of the countries with government health care have all high Calprotectin results repeated 4-6 weeks later before sending to a Gastro, as most often it resolves. Calprotectin is only 45% predictive of IBD at levels of 500 or greater. That means 55% of the high readings resolve over time. At 250 it is even less predictive.

        2) Feedback regarding Calprotectin testing differences *between* labs:

        Labs like Quest use raw stool with a ‘device‘ that is supposed to measure out 50 mg of stool. The device is a plastic stick with ridges that you push into the stool, pull it out and place into a tube with a diluent. It does not work well across all forms of poop. This is what is used because it takes a long time to weigh out 50 mg of poo.

        Labs like DSL come in liquid and have been calculated based on weight also. They pipette the stool and that makes it uniform even if the sample started as a formed, as the liquid allows us to homogenize the sample before pipeting.

        “We did a small study on raw samples and our sample. What we found is that our method has a much lower CV (coefficient of variation) than the raw stool. And as the Calprotectin increases the raw stool CV also increases. We saw 40% variation on samples over 500. However, our method with the sample in liquid for transport had CV’s less than 13% at 500+.

        We then looked at studies done recently in peer-reviewed literature. One large study in Europe showed CV’s of up to 58% on samples over 600. This means the result could have been plus or minus 300. That means it could have been 300-900+.

        Add to this that patients on NSAIDs can have results over 125 just from the NSAID and you understand why Quest and Lab Corp increases their normal ranges from 50 to over 150. This is very unusual in the lab industry to more than triple the reference range…….”

        1. Patrick Hanaway says:


          The comments you have forwarded appear to be sent by the lab.
          1. Please site the reference for this claim, as it is different than the papers I have read . . . and my clinical experience.
          2. The test I am referring to is the FDA approved kit. In the instructions, there are dilutions that must occur to refine the answer if the values are >500.

          I am unclear what point you are trying to make with your comments.

          To help our readers, I want to make clear my understanding of this biomarker:
          1. I was the Chief Medical Officer @ Genova Diagnostics and helped bring this biomarker to market in the USA
          2. I authored the documentation which lead to FDA approval of the assay.
          3. I authored the documentation and testified before the AMA CPT coding committee to secure the CPT code for Calprotectin.
          4. I have authored papers and supported additional studies on Calprotectin

          1. John Crosby says:

            Dr. Hanaway,

            Sorry for the delay, but it took me some time to confirm source. First, my intention was only to comment that Calprotectin variations can occur both between tests/testing and between labs and to share some of the causes of those variations–everything from pathogens or NSAIDS, to lab methodologies. I was never questioning your expertise, experience, and part in authoring guidelines, biomarkers, documentation, etc.

            The source of the information came from a doctor that works with (not for) the lab. I was not trying to be misleading, but simply shared in an attempt to explain potential variations and was curious if you experienced those in your own clinical work. (No need to reply.)

            Kind regards and Happy Thanksgiving,


  4. John Crosby says:

    Will a transcript of this episode be available? Thanks.

    1. It's up now. It usually takes a few days.

  5. Jeremiah Johnson says:

    Ben, you do a great interview as usual. While I’m seeking a no-BS functional MD/DO or unique guru, something seemed off about this guy Hanaway. Sure enough, go to his website and particularly his wife tosses out a laundry list of foreign jargon and name-dropping, and a history of lurching from one “calling” to another; ending with preposterous costumes to signal “shamanism” and BS status cues (the best guides look no different from you and me). Referring to yourself as “courageous” for taking off work to have a child is also a tell for self-absorbed nonsense. The lack of case studies and actual A-to-Z diagnosis and even one treatment example for a person with IDIOPATHIC/GENETIC autoimmunity (NOT “stress-based”) is telling. You tried to press him in the interview, but in the end the answer was “we do lots of stuff – laundry list to follow”. Okay, how about a single example of someone with arthritis, say HLA-B27 (GENETIC) Spondylitis, whose condition they treated better than traditional medicine? “You don’t know me, but trust me – no examples needed” no longer works for me after hundreds of “cash only” BS vendors.

    I sense the next great leap could be in peptides as you have illuminated – not a “healer” in a ridiculous hat – and ask that you dig ever deeper and get very specific about peptide EVIDENCE for healing intractable autoimmunity, such as the various arthritises, Hashimoto’s, and hormonal dysbiosis/mal-signaling. ASSUME people are controlling what they can after listening to hundreds of your podcasts: A great whole foods diet, good sleep, stress limited, already does sauna, cold bath and exercise, but is still suffering terribly from autoimmunities per above. We all know what to do to optimize, 80/20. What about the unlucky ones, for whom traditional medicine is failing? And “alternative” hucksters pushing “Ayurveda” etc. are also failing? We are ready for a revolution, maybe you can lead this next leg. Thanks for all the quality supplements, now how about the next level seen through, not just introduced.

    1. Patrick Hanaway says:

      Thank you, Jeremiah . . . there is a lot of commentary to discuss here.
      I work with people who are focusing on many layers of health, which often end up revealing themselves a little bit at a time. While my learning has deepened through numerous teachers and methodologies, the deepest learning comes through the school of life — listening to my patients, connecting to my own vulnerability, and evaluating the 30+ years of experience with what works and what doesn’t work. My recent use of these tools to reverse Stage IV laryngeal cancer has also taught me a great deal.

      I am doing my best not to be defensive. Please note that I am a practicing functional medicine physician publishing the first peer-reviewed paper on Functional Medicine. Many people write books with claims . . .research requires rigor, data integrity and peer review. I am involved in applying these tools in numerous other studies on Diabetes, Asthma, AutoImmune Disease, Prostate Cancer and Inflammatory Bowel Disease.

      As I evaluate difficult conditions like ‘intractable autoimmunity’ I find that there is no one-size-fits-all answer. Rather, I have to listen to the person and put together an approach that addresses the imbalances for that person. Indeed, as noted in most other healing traditions, the gut as the principle interface with the environment needs to be worked with first. That is why I discussed new metagenomic approaches to evaluating the gut microbiome. Understanding the key role of the gut microbiome with other gut functions (digestion, absorption, metabolism, barrier/ discernment, immunologic, and nervous system) leads to an initial focus on the diet, stress and exercise. Many of my patients have worked hard on this arena, but don’t have the components optimized. My approach emphasizes correcting these elements first, then (sometimes concomitantly) evaluating the exposome (toxins, infections, antigens). Nutritional and herbal supplementation is often necessary to support the person as the healing process unfolds. Once the person is moving in the right direction, then we can begin to decrease the (potentially) toxic pharmaceuticals. Our current investigations (soon to be published) show us that this also decreases health care costs.

      Ultimately I do look to the training i’ve received by indigenous elders, that connections to ourselves (our feelings, our behaviors, our attitudes), to each other (the importance of friends, family, community), and connection to the natural world (gratitude, respect, laughter, play, awe, joy, and the sacred) are essential for healing. That feels like the true revolution to me.

      Sadly, I also find that there are many hucksters selling a story and a product, usually marketed with some emotional charged anecdotes. I also hope that peptide therapy is helpful, but my clinical experience with ‘the next great thing’ leads me to believe it will be adjunctive support, rather than a fundamental shift. I prefer to go with an evidence-based approach, which includes the peer-reviewed literature, clinical experience, and the patient’s own wishes. Maybe this is why my practice is filled with people who have been referred by previous patients who are now doing better. Hopefully Ben will invite me back and we can discuss more specifics!

      1. Jeremiah Johnson says:

        Dr. Hanaway,
        Very measured and high-emotional-intelligence response to my challenging statements. Thank you. (You are a proper physician, unlike most hucksters who appropriate the “Dr.” moniker).
        I’m sure my frustration is evident.
        I would like to hear anonymous case studies of your patients with real and severe arthritis, and specifics of diagnosis and treatment, like they used to publish in the old days.
        Good on you for the response in any case, and for summoning the better angel of my nature. I hope many people do find value in your treatments, notwithstanding the faux chapeaux or animism.
        More to the point I was left wondering why you left Cleveland Clinic after a short time and the prior corporate job – and why you did those things in the first place.
        Final question: Can psilocybin treat autoimmunity?

        1. Patrick Hanaway says:


          Thank you for your kind and thoughtful reply.
          I have had patients with lupus, Sjogren’s, relapsing polychondritis, polymyositis, and rheumatoid arthritis who have benefited from the Functional Medicine approach. The underlying issues have ranged from food issues, to mold, to Babesia/ Lyme, to heavy metals (Mercury. Lead, and Cadmium). I can write you about case specifics. I have not published any specific case studies (yet), but I am involved with a research group that has worked specifically with self-insured employers and has demonstrated significant cost reductions in auto-immune patients receiving Functional Medicine care. Additionally, we are preparing to publish a retrospective analysis of patients with Rheumatoid Arthritis being seen @ Cleveland Clinic who have also received Functional Medicine.
          On a personal level, I left Genova to pursue work with the Institute for Functional Medicine, a non-profit educational institute. They asked me to help support the development of the Center for Functional Medicine as its first Medical Director, which I did — it turned out successfully, but I never planned to move to Cleveland full-time. I terminated my work there when I was diagnosed with cancer at the end of last year.

          As for the fascinating work with psylocibin, MDMA, ketamine and other neuro-active agents, I am not an expert in that domain. My sense is that there is a sub-set of patients with auto-immunity who have past traumas that may be healed by these agents. Interestingly, it is a similar sub-set of people who can benefit from ‘shamanic’ healing (though that term is filled with ambiguity and further hucksterism!)

          If you want to discuss further, please include your eMail in a followUp reply.

  6. Dianne McIntosh says:

    Ben, what do think about Castor oil and the different Omegas? Dr Marisol has a lot of information about the benefits of castor oil.

  7. Denis Hopking says:

    Ben what is a good keto recovery snack and/or meal after playing a competitive game of tennis? Before keto I used to do the carb meal…

  8. Django Freeman says:

    Not related to this podcast but can you tell me which transdermal nitroglycerin cream you use to fight the droopy dick affect of ketamine/oxytocin combo?! My wife thanks you in advance :)

  9. Mj says:

    Hey guys. Any idea if you can use your viome testing data to determine if you are likely to have SIBO?

    1. Nick says:

      Mj, as far as I know, you cannot. Viome data is a representation of the transient microbiome of your colon/large intestine. SIBO lives in the small intestine.

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