A Step-By-Step Guide To Testing Your Gut For Nasty Invaders.

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This morning, I drove through the snow and ice-covered roads of my hometown in Spokane, Washington to visit Dr. Toby Hallowitz – the same guy I introduced to you in the article “Natural Remedies for Travelers Diarrhea“.

The reason I drove to his office was to review the results of my most recent gut test.

See, I test my gut once a year. And a gut test is a really good idea if you want to know things like why you might have food cravings, insomnia, brain fog, constipation, gas, bloating, some kind of bacterial imbalance, a yeast or a fungus overgrowth, to know whether you should or should not take probiotics, or – God forbid – to know whether you have some kind of nasty invader in your gut, like a bad parasite.

Anyways, after my visit with Dr. Toby, I rushed home to make you the video below, in which I give you a step-by-step guide to testing your gut for nasty invaders, along with how to see if you have bacterial overgrowth, yeast or fungus issues, the right kind of bacteria in your colon, not enough fiber in your diet, fat malabsorption, pancreatic insufficiency and much more!



Resources mentioned in this video:

Bacterial Overgrowth-Genova KIT from DirectLabs (breath test)

GI Effects Gastrointestinal Function Comprehensive Profile-METAMETRIX KIT from DirectLabs (stool test)

Oil of Oregano (for yeast/fungal overgrowth)

Caprylic Acid (MCT Oil) (for yeast/fungal overgrowth)

Thorne Research Berberine (for yeast/fungal overgrowth)

Pancreatic Enzymes (for pancreatic insufficiency)

ProbioMax Plus DF (for Saccharomyces Boulardii and immunoglobulins)

Caprobiotics and Capracolostrum


Do you have questions, comments or feedback about how to test your gut, or about my results? Leave your thoughts below!

Ask Ben a Podcast Question

28 thoughts on “A Step-By-Step Guide To Testing Your Gut For Nasty Invaders.

  1. ming yau says:

    looks like this is an older you tube video. do you still recommend this test or are there more current and better ones?

    1. Dr. Arenas says:

      Same question…

  2. John says:

    Hey Ben,

    Which Stool analysis would you recommend from direct labs if you suspect you have a overgrowth or yeast or bacteria and have been on multiple really potent antibiotic cycles? Thanks

  3. Health Vibed says:

    Hey Ben,

    You said “When I had a parasite I took a high-grade oil of oregano four times per day and mastic gum twice per day.


    Were you able to overcome your blasto hominis infection with that? I am currently undergoing a protocol that cost me $400 + and I’m not really sure it’s working.

    I have crazy brain fog and feeling spaced out, my lab test 6 months ago said streptococcus overgrowth in my gut too. I don’t know if these things are causing the brain fog, but it’s really hard to deal with. I’ve tried antibiotics, but they didn’t seem to help, and it’s just destroying any good flora I have.

    Do you have any recommendations for supplements that can specifically really help to clear up brain fog? I also use bacopa, lion’s mane, some other adaptogens, ubiquinol 300mg a day and healthy omega 3 oils.

    I’m just at a loss here with this brain fog, it’s making my life extremely difficult. Any tips or pointers in the right direction would be appreciated!


    1. Yes, that was the combination I used it but if I could go back and do it again I would do four of this in the morning and for this in the evening with a large glass of water: https://greenfieldfitnesssystems.com/product/natu…. it is way more potent at a lower cost.

      1. Javier Panta says:

        hi Ben! i have blastocystis hominis parasites. the link you wrote in your previous reply take me to a magnesium supplement in your website. I guess that is bit what you recommend for b. hominis. or is it? thanks a lot for all the useful information you post! greetings from Peru

        1. Medical disclaimer: I am not a doctor and this is not to be taken, interpreted or construed as medical advice. Please talk with a licensed medical professional about this. These are just my own personal thoughts and not a prescription or a diagnosis or any form of health care whatsoever.

          This is exactly the type of question myself, my team of coaches and the community in my Inner Circle can help to answer for you.

          The Inner Circle is a collective of people who are pursuing the same goals you are – trying to live a healthy, happy, adventurous, fulfilling and limitless life in a modern world. In the Inner Circle, we all help each other with questions, ideas, motivation, suggestions and much more!

          Here is where you access that community: BenGreenfieldFitness.com/InnerCircle

          If you prefer a more direct, customized approach, I'd be happy to help you via a personal one-on-one consult. Just go to https://bengreenfieldfitness.com/coaching. and then choose a 20 or 60-minute consult, whichever you'd prefer. I can schedule ASAP after you get that. Additionally, if I'm "out of your price range" (yes, yes, I know I can be a spendy guy to access) I have a team of coaches I've personally trained who can help you here: https://greenfieldfitnesssystems.com/product-cate…

          I also urge to consider trying Nature Cleanse: https://greenfieldfitnesssystems.com/product/natu…

  4. Matti B says:

    Hi Ben,

    Thanks for sharing, this is really interesting.

    You certainly did a great job implementing the changes which you mention, and I am sure you retested.

    Were the results meaningful – I mean did they fit to your first test and did you see the expected results and changes?

    Or did it seem somewhat random?

    Please let me know,



    1. Stay tuned as I am currently going through a full gut retest and will release results soon!

  5. Ozzybeef says:

    I have had athletes foot for a long time, 15-20 years. Is that a sign that I may have fungal issues in the gut? What protocol would you recommend to fight it?

    1. We talked about athlete's foot in a podcast I did with Dr. Roby Mitchell and the factors he mentioned were low testosterone, low iodine, hypothyroid issues, and low vitamin D. Check it out here https://bengreenfieldfitness.com/2010/07/episo…

  6. katelynfaison says:

    Thanks so much for this overview, I love your content. I am currently doing a parasite cleanse for cryptosporidium. I am also on a protocol for Stage 3 adrenal exhaustion from the Kalesh Institute, my cortisol levels were extremely low 13.4nmol/L. I was just wondering what your advise is for adapting training and what effects you notice during a parasite cleanse. How one should feel, ect. I am 5-6 weeks in of an 8 week test. I will be doing another test to make sure I have gotten rid of it;)

    1. You can expect a dip in energy levels, rapid fluctuations in bowel movement quality and quantity, and a bit of a "blah" feeling sometimes when doing a cleanse. My best advice to you for adapting training is to use the Overtraining and Adrenal Fatigue Recovery plan at http://home.trainingpeaks.com/products/trainingpl…

  7. John says:


    Great write-up and video. I’m having some trouble locating the exact combination of testing kits that you showed in your video on the direct labs website. It appears the 2200 kit (GI Effects Gastrointestinal Function Comprehensive Profile-METAMETRIX KIT) is available, but after reviewing their sample test for this $466 dollar kit, it appears that the 2155 GI Effects Fungi Sensitivity Profile – Stool test is not a part of that package. I’ve looked at the rest of the test options on their website and none of them are labeled quite the same as your final results pages showing sensitivities/resistance. Can you provide any direction? Also, is there any chance that direct labs might offer some kind of discount for your subscribers? Not all of us have insurance or insurance that will cover these types of tests. Thanks again for the material you are putting out and keep up the great work!

    1. Yes, GIEffects has been changing a bunch of stuff up – so closest you’re going to get is:

      A) “Comprehensive Stool Analysis w/Parasitology”.

      B) Do the GI Effects Gastrointestinal Function Comprehensive Profile-METAMETRIX KIT but then add in the GI Effects Microbial Ecology Profile-METAMETRIX KIT

      DirectLabs is already HEAVILY discounted! Stay tuned to Monday’s blog post for more insurance tips…

      1. GutCurious says:

        Thanks for the quick reply, Ben. Looking forward to Monday's post. I checked direct labs per your new recommendation and when reading the metametrix microbial ecology profile details, it begins by saying that this test is already included in the metametrix GI function comprehensive profile. After more searching, it looked to me like the micobiology profile DD kit seems similar to the last test in your video, albeit with some visual differences (when comparing sample test to your results). Anyway, I'm not trying to nit pick, just want to make sure I understand how to properly navigate this process. Thanks.

        1. Yes that test is similar too but from a different company!

  8. Karen says:

    Thank you for sharing your results with us. I recently found out that I also have blasto, along with thyroid malfunction, and it is affecting me a lot :(

    What are your thoughts regarding diet and parasites?

    1. When I had a parasite I took a high-grade oil of oregano four times per day and mastic gum twice per day. I talk about parasites in this chapter of book https://bengreenfieldfitness.com/2013/07/how-t… It’s a good place to start.

  9. alice says:

    Do you have a list of drs. in this area(McKinney, TX) who would have this conversation with their patients? What kind of dr. does one look for? Thx, Alice

    1. Jack Kruse has good advice about this at JackKruse.com.

      If you need to find a good doctor in your area to support your journey to optimal, here are a couple of tricks:

      Talk to your local compounding pharmacist. They likely are familiar with doctors who treat their patients using bioidentical hormone replacement therapy [BHRT] and other holistic treatments.

      Contact Genova and ask them who in your area orders their labs. This is a “tell all” of sorts, as the practitioners that order Genova labs are more likely to be aligned with holistic, paleo-oriented healthcare. You can then research those practitioners and hopefully find one or more that accept your insurance or who your insurance company would view as qualified for some type of reimbursement.

      Additionally, here are a few directories that may help you find a good functional medicine or naturopathic practitioner in your area:

      The Institute for Functional Medicine

  10. Martin says:

    Great breakdown of the results Ben. I am just wondering whether your high level of exercise effects the gut flora, you did not say anything about that.


    1. Yes from http://chriskresser.com/how-stress-wreaks-havoc-o… – "The gut is especially vulnerable to the presence of chronic (and even acute) stress, demonstrating stress-induced changes in gastric secretion, gut motility, mucosal permeability and barrier function, visceral sensitivity and mucosal blood flow. There has also been evidence to suggest that gut microbiota may respond directly to stress-related host signals."

  11. Karen McGuire says:

    Other than oregano, do you use any other essential oils for health?

    1. Yes, I use oils from http://www.mountainroseherbs.com/index.php?AID=12…

      Particularly echinacea oil for immune system, lavender for sleep, and lemon oil (for my son's plantar warts)

  12. carmine says:

    Hey Ben, thanks as always for the amazing info! I may be mistaken but I dont think there is a link for your gut test video here.

    1. The video is embedded in the post right above the "Resources" section. If you don't see it, you can watch it on Youtube at https://www.youtube.com/watch?v=2MdZikakRQM

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