Underlying Dysfunction in Digestive Diseases

A common dysfunction in physical disease – digestive and many others including everything from obesity to Autism – is a compromised microbiome. Very few doctors understand how to correct it, and this includes conventional and alternative practitioners alike. This isn’t new information, but how to address it, is. 

There are pathogenic bacteria, yeast, and parasites, and then there are commensal bacteria. The commensal phylum are meant to be in our guts, and when balanced carry out a multitude of functions in our favor. They make vitamins we need, help digest our foods, promote a strong immune system, and even elevate our moods.  

Yet you would be hard pressed to find anyone who has a truly healthy microbiome these days. Even one course of antibiotics can shift the balance, permitting one phylum to grow at another’s expense. The commensal distribution can shift so significantly that pathogenic infection results, but often more subtle changes allow for a disproportionate combination of commensal bacteria that can wreak havoc and set the stage for disease. High, low, or absent phylum can contribute to IBS, IBD, metabolic sydrome, chronic fatigue, auto-immune disease, type 2 diabetes, high blood pressure, mood disorders and more.

Extreme numbers result from obvious offenders such as chlorine in the water and antibiotics in conventionally raised meat.  Lesser knows is the impact from “healthy” diets like ketone, low carb, high fat, some versions of paleo, and low FODMAP. Each of these generally incorporate low fiber or low diversity fiber. This can feed microbes that eat bile salts but starve those that eat resistant starches, for example. Or it may feed those that eat putrefying protein but starve others needed for a homeostatic and health protective balance. Each of these diets can and should be supplemented with targeted prebiotics, oligosaccharides, resistant starches, polyphenols, and plant food fibers, but they usually are not. 

People feel great on these diets, because they also share in common the elimination of processed foods and emphasize whole foods. But in the long term, if not supplemented appropriately, unintended consequences ensue.

If the gut is out of balance, then probiotics, sadly, are not the answer. They don’t colonize the gut and are out of the system in one to two weeks. Relying on a good probiotic to replace the good guys killed off during the latest round of antibiotics won’t work. You can, however, use prebiotics like partially hydrogenated guar gum and GOS to regrow small numbers, assuming they haven’t been eradicated. When they have been, fecal transplants are an option, because they do colonize the gut. 

This isn’t to say that probiotics aren’t useful, and in fact, amazing. They do wonderful things for our bodies while they are working their way though and should definitely be taken while on antibiotics. Significant research data show probiotics are beneficial for a multitude of conditions and illnesses.  Dr. Jason Hawrelak is a superstar on everything microbiome – from how to treat microbial dysfunction to restoring, regrowing and balancing the gut microflora.  His focus is on prebiotics and using foods to correct imbalance, and he also routinely uses probiotics for specific conditions. He has created a web site, Probiotic Advisor, that can be searched by condition to find the probiotics that have been found through published studies to be of benefit. There are also a number of courses on the microbiome and how to manage conditions, such as peptic ulcers, naturally. 

Finally, it’s important to know where you stand in terms of microbiome health.  A Ubiometest is by far the best for this purpose. It’s also the least expensive and can be ordered online without a prescription.  Genova Labs GI Effects Comprehensive Stool profilecomes in second but is less useful, more costly, and must be obtained through an integrative physician. A benefit of the Genova test is that it also looks at potentially pathogenic bacteria and yeast. For a comprehensie assessment of pathogens the Doctor’s Data Comprehensive Parasitologytest is best.   

Assessment of pathogens can be useful when there are specific problems, in which case they must sometimes be treated before successful microbiome restoration. But a note of caution is that each of these tests are a snapshot in time and will show most of what is in a stool sample on a particular day, which can change from day to day. They are also mostly useless for parasites unless one has a new infection, as opposed to one that has become chronic.

I’m personally in a challenging place. Because of pathogenic infections I am not able to eat most of the foods necessary to regrow a strong and protective microbiome – yet. Paradoxically in such a situation as mine they can worsen things and certainly intensify symptoms.  In fact, I am using multiple, long term treatment options that challenge the microbiome even more.  It’s a horrible catch 22 – needing to both treat infection and needing a stronger, more protective microbiome to prevent such infections. Fecal transplant is also not yet an option for me as one needs a clean slate. 

Many are in a similar predicament and find that these “health” foods tend to wreak havoc. It’s usually because of small intestinal bacterial overgrowth (SIBO) or parasites, the subjects of upcoming blogs. Stay tuned for a deeper discussion on each of these and the controversies surrounding various treatment options. 

3 thoughts on “Underlying Dysfunction in Digestive Diseases”

  1. I would be interested in future information related to Crohn’s disease. I suffer from it and have been doing research as to how I can manage the disease better. I am certain my gut flora is not sufficient to control the disease and the symptoms I continue to have regularly. If you find new supplements or probiotics that would significantly aid in the process of healing this disease, I would appreciate it.

    Thank you for your assistance.


    Tana Stoiberg

    1. Hi Tana –

      Crohn’s is not an area of expertise for me, but I will certainly keep you in mind as I’m writing blogs and researching these difficult GI areas. I do know that diet is key in managing the disease, and I’ve also heard that fecal transplant can be of benefit for some. It may be worth reaching out to the Taymount Clinic for feedback on their success rates with fecal transplants for Crohn’s. I will keep you in my thoughts and prayers Tana and wish you the best on your healing journey. Please keep me updated.


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