NOTICE: This blog is no longer being updated, so medical information may no longer be accurate.

Hello Flora, How You Doin’?

In case you missed my first installment from our trip to HealthNOW Medical Center, on Adrenal Fatigue, you can read about that here.

In today’s testing profile, I’m going to give you an up-close and personal view of our microbiota, a.k.a the intestinal flora, probiotics, or, the “good bugs” as I tell my kiddos.

I’ve long been aware of some the health benefits of probiotics, but truthfully, it was a rather narrow understanding.  I mostly took probiotic supplements to usurp the repeat yeast infections I would get each and every time I took an antibiotic (and I took antibiotics several times a year for decades to treat the symptoms of my chronic sinusitis), but I always made sure to have my daily plain Greek yogurt and a glass of plain Kefir blended with some fresh fruit.  I made sure to never miss my daily servings of “good bugs.”

Everything changed a few months ago when I made the decision to go dairy/casein-free after my kids were discovered to have a casein intolerance, and all of a sudden I was without my favorite yogurt. Not to mention the fact that most probiotic supplements contain dairy, so it took some time to find dairy-free versions.  Even then, while I was diligent in giving them to my kids, I was never consistent about taking them myself.

True blogger confession: I’m horrible when it comes to taking supplements on a regular basis, it’s no wonder I don’t reap the benefits! 🙄

Truthfully though, I had NO IDEA just how crucially vital healthy bacteria are to your overall health and wellbeing.  And I do mean vital.

To give you a better understanding, I highly recommend watching the following 7 minute video from Dr. Mark Hyman:

To further drive home the points that Dr. Hyman made in the video, I would like to share the link to a comprehensive article written by Alessio Fasano, M.D., Director, Center for Celiac Research at The University of Maryland.

I urge you to download this article, read it, print it, and give a copy to your healthcare provider (as recently as this past November (2010), I discovered that my former board-certified gastroenterologist had never heard of zonulin, which was a rather clear indication to me that he does not read his gastroenterology journals and hence the reason (among others) that he is my *former* GI).

So what is zonulin? The following is taken directly from The Center for Celiac Research Website:

“Zonulin regulates the permeability of the intestines by controlling the opening and closing of specialized structures that act like gates between cells. When the body produces too much zonulin, these gates get stuck open for too long and allow undigested foodstuff, toxins and other bacterial and viral particles access to the immune system.”

Zonulin and Its Regulation of Intestinal Barrier Function: The Biological Door to Inflammation, Autoimmunity and Cancer Physiological Reviews, January 2011

I would like to point out the following statement from Dr. Fasano on page 157 of the above linked article (bold emphasis added):

“Among the several potential intestinal luminal stimuli that can trigger zonulin release, we identified small intestinal exposure to bacteria and gluten as the two more powerful triggers.  Enteric infections have been implicated in the pathogenesis of several pathological conditions, including allergic, autoimmune and inflammatory diseases, by causing impairment of the intestinal barrier.  We have generated evidence that small intestines exposed to enteric bacteria secreted zonulin.”

*For more information on zonulin, see Gliadin, zonulin and gut permeability: Effects on celiac and non-celiac intestinal mucosa and intestinal cell lines, Scandinavian Journal of Gastroenterology, April 2006

To check the health of our intestinal microbiota, we took a test by Metametrix Clinical Laboratories called the GI Effects Profile.

From the Metametrix website:

Gastrointestinal function is important for general health. The intestinal tract contains significant amounts of bacteria; some beneficial, some neutral, and some harmful. Balancing beneficial microbial flora in the gut is key to proper digestion, efficient nutrient usage, and ridding the body of waste and pathogens. Poor digestion and malabsorption can lead to immune dysfunction, nutritional insufficiencies, mental/emotional disorders, and autoimmune diseases.

Metametrix offers the Complete GI Effects profile for the most thorough look at the gut microbiome.

This is an amazingly informative test and I personally think it should be part of everyone’s annual checkup!

Since I am not someone who inherently understands how to interpret these tests, I will be sharing direct quotes taken from the Metametrix GI Effects Stool Profile Patient Interpretation Guide.  The first thing you will need to understand is what Predominant Bacteria are:

Predominant Bacteria:

Microorganisms in the GI tract perform a host of useful functions, such as fermenting unused energy substances, communicating with the immune system, preventing growth of harmful species, regulating the development of the gut, providing vitamins for the host (such as biotin and vitamin K) and producing hormones to direct the host to store fats.

Intestinal flora are also thought to have many beneficial local and systemic roles such as improving lactose intolerance, supplying short chain fatty acids (SFCA) as an energy substrate for the host, anti-tumor properties, neutralizing certain toxins, stimulating the intestinal immune system, reducing blood lipid levels and preventing obesity and type 2 diabetes.

Under normal homeostatic conditions, the intestinal microflora are of central importance in preventing colonization by pathogens, termed “colonization resistance.”  Predominant bacteria are considered to be beneficial when they are in balance.

The following tests results are mine:

As you can see in the graph above, my predominant bacteria are not hanging out singing Kumbaya together!  The bacteria I circled in red are too low and I need to work on increasing those numbers with probiotic supplements.  Ideally, all the bacteria should be in a similar range (in balance), falling within the 3rd and 4th quintiles.  If your beneficial bacteria are imbalanced, then you have a condition called Dysbiosis (related research article: Intestinal dysbiosis and reduced immunoglobulin-coated bacteria associated with coeliac disease in children).

I gave myself a star for no significant amounts of opportunistic bacteria, which are generally self-limiting and not normally considered pathogenic.

My husband’s results (his predominant bacteria aren’t happy either):

The following results belong to my 3 year old who has non-celiac gluten sensitivity.  Luke fully recovered from severe eczema and cradle cap after we received some much needed expert guidance using Dr. Rodney Ford’s e-Clinic last summer and we consequentially discovered his IgG casein intolerance and IgE egg white protein allergy.

Speake to an expert

While his skin totally cleared up, he continued having unpleasant bowel movements that often resulted in raised welts and open wounds on his bottom.  Not one of the several doctors we sought help from (his pediatrician, an allergist, a pediatric gastroenterologist and a dermatologist) ever suggested running a stool test on him.  Instead, I was told to potty train him (at 11 months old) so his stool would not come in contact with his skin (in the diaper) and handed a prescription for Elidel Cream (have you ever tried to potty train an 11 month old boy?  Needless to say, that didn’t happen!).

Luke’s entire test results had me on the verge of tears in Dr. Petersen’s office (there is much more to this test for Luke but I will save those findings until my next post).  In addition to his predominant bacteria being out of whack, his E. Coli level is too high and he was positive for an opportunistic bacteria called Citrobacter.

The following results belong to my 7 year old celiac son.  Sam has apparently inherited his mother’s uncommunicative immune system, because up until very recently, he has not complained of feeling poorly, in fact his disposition was energetic and happy.  It wasn’t until we began to get a weekly occurrence of clogged toilets that we discovered he was again suffering from severe constipation, to the point that his GI said his bowel was distended (again), most likely due to Sam ‘witholding’ and prescribed for him to take 2 capfuls of Miralax a day for the next year.  If that doesn’t work, he will need a colonic manometry, which I would like to avoid at all costs!

I just got a copy of Sam’s tests results yesterday (he didn’t take the test at the same time as the rest of us).  Let me just say that it took me a while to pick my jaw up off the floor.  Like Luke, Sam has several alarming underlying issues which I will be sharing sharing in my next post, but I have a strong feeling that we now know what is truly causing his constipation…and it’s not an issue with him ‘withholding!’

All of my guys are all being treated with stronger formulations of probiotics (dairy-free!) than they were taking previously.

To sum things up, here is more information from the Metametrix Gi Effects Profile Interpretation Guide:

Low Predominant Bacteria:

  • Predominant bacteria should be present at normal levels in the healthy gut.  Bacteroides sp. and Bifidobacter sp. should be present in the greatest amounts.
  • Low levels of beneficial fecal bacteria such as Bifidobacter sp. and Lactobacillus sp. and E. Coli have been associated with irritable bowel syndrome, characterized by alternating diarrhea, cramps and food intolerance.

(related abstract from the Journal of Leukocyte Biology: Pivotal Advance: Bifidobacteria and Gram-negative bacteria differentially influence immune responses in the proinflammatory milieu of celiac disease).

  • Low levels of predominant bacteria increase the likelihood of acquiring opportunistic and pathogenic organisms.

High Predominant Bacteria:

  • Blood infections of Mycoplasma have been linked to chronic fatigue syndrome and fibromyalgia.
  • Fusobacterium increases putrification in the colon.
  • Overgrowth of Lactobacillus sp. could produce D-lactic aciduria in those with short bowel syndrome.  Limit intake of carbohydrates.
  • Overgrowth of certain Clostridia sp. clusters may play a certain role in autism.
  • If Prevotella sp. is in the 5th quintile, suspect possible oral/throat infection.

Have you met your microbiota lately? 😀


  1. I took a similar test last year. My Bacteroids and Streptomyces were low and the Prevotella was high. The rest, fell into that 3rd/4th percentile. And while I had no opportunistic bacteria and the pathogenic bacteria were all in "clinically insignificant amounts", I had a positive test for parasites.

    Though, the report said, "Parasite present; taxonomy unavailable. A taxonomy unavailable finding likely indicates an ingested protozoan and not a human parasite. It does not indicate treatment unless patient symptoms and other inflammatory markers are consistent with parasite infection." Considering the fact that I regularly foster cats and kittens that come from less than ideal circumstances (and have to be treated for parasites), I guess it's not totally surprising to have a positive on that test, especially since I can't help smothering the little fur balls with kisses (they are just so freakin' cute!).

    Unfortunately, the focus of the chiropractor was more into his "brain based therapies" and not into fixing the biochemistry of my body. So little was done to address this. There were also some other negative metabolic test results that were mostly ignored. While I'm happy to have had someone willing to have me tested (and finding out about the gluten and soy intolerances) I felt like there was little followup to those issues. So, I've stopped seeing him (it doesn't help that I still have a large bill that I'm ever so slowly paying off of stuff not covered by insurance).

    Once I clear some of this debt, I'll have to try finding another doctor that is more focused on balancing out my body's systems.

    • Janet,

      I was positive for a parasite too and it said the same thing, "taxonomy unavailable." I also have a slight overgrowth of Saccharmyces and a few other fairly minor issues.

      I'm sorry that the doctor you saw wasn't all that helpful in addressing each of your issues, I hope that you can get into see someone that will give you better attention. I have been so impressed with HealthNOW, they've already called me 3 times since we've been home to check up on us and go over Sam's test results, they really hold your hand through the process. I've never received this level of attention from any of our local physicians. I think they need to start some satellite offices around the country! 🙂

  2. Michelle Olejar says

    I am so happy you got some vital information. Your Sam sounds like my Sean and your Luke my Erik. I was also told the whole "potty train early" line of crap and "Miralax daily".

    We are attempting the probiotics as well. It has been difficult up to this point though due to the dairy intolerances and texture issues with the boys. Good luck!

    • Thanks Michelle! The first time Sam's GI put him on Miralax, I blindly followed his advice and I'm so thankful to have received a second opinion this time around (and additional tests to look for the root problem).

      My boys are on a dairy-free probiotic and I either pour it in a smoothie, or mix into some food (like mashed potatoes), so far, they've been doing really well with it.

  3. Thank you Heidi for putting all of this information together. I know it takes time, but your sharing the story is helping so many. We are right behind you in testing. Just dropped two bags of pee off at Fed-ex and in the mail to France. We have so much to talk about!


    • It's my pleasure to share Lexie, and you're right…it does take time to put these posts together, especially when you find yourself getting sucked into all the fascinating research!

      Can't wait to talk with you this weekend! I'm anxious to hear about everything going on with you and your peeps!



  4. Hi Heidi

    Thank you for writing this great article which has a wealth of information and an eye opener to what we have been missing out all this time. I met a doc today who practices Integrative medicine, probably on the same lines as Dr Peterson and Dr Hayman. The doc herself has been through breast cancer and 9 different surgeries and has gone through tons of tests and all possible medications. I am keeping my fingers crossed that this is probably the doc that can help my 7 yr old son who is on GF/CF/EF diet and other autoimmune disorders. We will be doing a comprehensive stool and pee test through , hopefully the test results will help us get in the right direction.

    Once again, thank you for all the hard work you do in helping so many people. keep up the good work.

    Thanks and Take care


  5. My autistic son who is 3 had this test done and he was off the charts…lol. He is on so many different supplements. Thank goodness he loves applesauce, because everything gets dumped in there 3 times a day! The gut is such a fascinating part of our body. Thanks for sharing your results and extra info!

  6. Heidi,

    I LOVE that you are so dedicated to your family and their health–and so willing to pass along what you are learning! I have a brother who so needs to hear this and I have the hardest time finding the right words to get through to him–without upsetting him. Our sister has Celiac his nephew (my son) has it. He says he was tested (blood test–but hasn't shared "what" test) that he reports was negative. He has every symptom and then some–I just know that even if he doesn't have Celiac–there is something going on. It's the running joke in our family (has been for years) about who's still in the bathroom–it's HIM! He misses everything because he's in the bathroom. There's a problem! 🙂

    Thanks for putting this out there!


  7. Rebecca Bochenek says

    What probiotics are recommended that do not contain dairy?

  8. I had just finished typing up a long comment here and my computer died. Ugh. Anyway, what I wanted to say was that you are doing an amazing job of sharing such wonderful information with everyone!! Would you have ever expected to become such an expert on all things bacteria and poop? LOL

    I am so glad that you are getting closer and closer to your optimal health! What brand of probiotics are you all taking?

    Cannot wait to pick your brain in person this weekend!



  9. Hi Heidi,

    Your posts have helped me decide to make an appt at the HealthNOW clinic for my family. I hope to receive the same great care that you describe in your posts. Thanks for the detailed and informative updates!

    • Tami,


      My husband and I were just talking the other day and we both agree, spending the money to fly to California to go to HealthNOW was the best money we every spent, hands down. It frightens to me think of what could have been in our future, had we not gotten to the bottom of our ongoing health saga, and our local physicians were obviously not interested in finding the root cause of our problems…just wait till you hear about the rest of this test and what we were able to discover about our little boys…makes me a bit hot under the collar that their local doctors never thought to order such a simple test, but one that can tell you so very much.

      I would recommend HealthNOW to anyone!


  10. Thanks for the very informative post! We've had extensive stool testing in my household and have found it to be instrumental to dealing with our food sensitivities. I hope it helps your family, Heidi.

    A couple people asked about probiotics.. we have had really good luck with Custom Probiotics. We buy the six strain powder ( I think it's important to get tested before spending an arm and a leg on probiotics so you know what you are short on, and what bad guys you are fighting.

    • Thanks Megan and I am so happy to hear that the stool test was helpful to you and your family too, it's amazing the amount of information one can get from poo, LOL!

      Thanks for the info on custom probiotics and I couldn't agree with you more about getting tested before spending an arm and a leg on probiotics, they have different formulations for a reason (just wish I had known that several years ago!).


  11. Someone at Metametrix sent this link to me. I'm an old scientist who is not much into blogging. But, having been involved in the concepualization, design and doctor education for the Metametrix GI Effect profile, it is very gratifying to see it's use explained so clearly. It's even more heart-warming to hear of how it has helped people overcome health problems.

    Heidi – Congratulations on your accurate and clear explanation about how to use the data on predominant bacteria to see a problem and to track progress toward wellness. Once you see the basic concepts about the need for robust, balanced growth of all those little critters, you can enjoy a casual conversation with them, such as "Hello Flora, how you doin?"

    Richard Lord, Ph.D.

    Chief Science Officer

    Metametrix Clinical Laboratory

    • Dr. Lord,

      Thank you so very much for your kind comment, I really appreciate it. I spent quite a bit of time trying to word my explanation in a clear and accurate way; it means a lot to have your seal of approval!


  12. Thank you !!!! A blog reader who has never posted before, my daughter is CF/EF and I am GF/CF… I will be doing this test for sure:-). This is a long winding road, but help is out there- your post is proof! I am treating myself for adrenal fatigue via neuroscience products and I am sure both my kids, my son age 4.5 CF, could benefit from the info in this post and metametrix. best wishes to your kiddies….

    • Hi Dana!

      I hear ya on the long and winding road! It's taken me 6 years just to get to this point. It would be really nice if there were a comprehensive textbook that taught us about all the nooks and crannies that can accompany many of the underlying health issues that lead people to a gluten-free, allergen-free lifestyle! The Metametrix GI Profile test is probably the single most important test we've taken thus far (since getting our family's celiac and non-celiac GS test results).

      Best wishes to you and your kiddos too, please keep me posted on how you're doing!


    • Heidi,

      Once again thanks for the detailed post and sharing your family's results. I always look forward to these to learn more and then follow the path you are paving. Also if you don't mind please share the probiotics you are using, we have to be dairy free here too.


  13. My 4 year old and I are both gluten and dairy free. Can you recommend a pro biotic that is dairy free and well as gluten free until we could get test like this done? I'm having a hard time find dairy free ones.

  14. Hi Heidi!

    My 4 year old just got her metametrix back..
    Can I email you a cpoy to get your opinion? She is constipated and has leaky gut..allergies..Uc…
    I am sure there is more to it than what they are telling me…She sounds similar to your older son sam. I am guessing she has parasites, but they cant nail down which ones
    I would apprecitae the “fecalologist” opinion!!
    Thanks csssie

  15. OrganicBabyU says

    I just called them as well because I was considering purchasing. The man was very curt with me when I asked what medium he grew the probiotics on and said it was proprietary and he has no idea. I find that VERY concerning. I asked if it was GMO as many like Jarrow use GMO soy. He said no but then I asked how he knew that if he had no idea what the medium was…he said he has thousands of customers and if I didn’t believe him not to buy from him and hung up on me. I wouldn’t buy from a company who doesn’t know about their product and hangs up on people when they ask legit questions…ESPECIALLY to my children. 


  1. […] of having balanced microbiota in our intestines.  In case you missed that post, you can read it here.  In today’s post I will be covering parasites, pathogenic bacteria and […]

  2. […] of having balanced microbiota in our intestines.  In case you missed that post, you can read it here.  In today’s post I will be covering parasites, pathogenic bacteria and […]

  3. […] : hate to digest from Mysteries Internal • Heidi’s incredibly detailed and informative post Hello Flora, How You Doin‘ from Adventures of a Gluten-Free […]

  4. […] can learn more about these issues in the following posts where I shared some of our problems with poor intestinal fauna (the good bugs), parasites (Sam had a pinworm and Luke had a hookworm infection), and adrenal […]