Cultivating, not hacking, the Microbiome

In this recent New York Times article, biohacker Josiah Zayner decided to attempt to fix the imbalance in his microbiome by consuming antiobiotics and then ingesting a friend’s sweat, saliva and feces in order to recolonize his digestive tract. You can watch the short film and read more here:

In the past five years of evaluating thousands of patient’s microbiomes before and after treatments, while recording their subjective and objective response to various treatments, I have learned that there is no one size fits all approach to treating the microbiome.

Good medicine always starts with a good diagnosis. Bad medicine always starts with a generic approach that is attempted instead of a thorough analysis of the problem and its underlying causes. In a field that doesn’t have enough strong research to support any standardized approach, I can already tell you that any standardized approach would be missing the point.

In Traditional Chinese Medicine, the insight is to always look at the patient fresh, the color of their skin, coating on their tongue, tone of their voice, body type, emotional tone, quality of the pulse. When we attempt to interact with the microbiome, it is these levels of attention to detail that help to guide us towards a successful treatment of microbial imbalances and other sources of inflammation such as food sensitivities or pesticides that may be effecting our microbiome as well.

The sad part of this film is that Josiah felt this was his only option since he had seen conventional gastroenterologists who had no experience working with the microbiome. He was displaying IBS-D symptoms and potentially he could have found a gastroenterologist to prescribe Xifaxin, which is an FDA indicated antibiotic for the treatment of Irritable Bowel Syndrome- Diarrhea type. This is simply 14 days of antibiotics which will help to lower bacterial overgrowth effectively. I have used this in many cases of bacterial overgrowth that were resistant to more natural antibacterial agents such as Thyme and Oregano oil, goldenseal, or colloidal silver. I never use it without attempting to recolonize with high dose probiotics. Many gastroenterologists will use VSL #3, which is a prescription strength probiotic. Even recolonizing doesn’t prevent a return of the previously overgrown species. They are never completely wiped out and always have the potential to return, especially early on in the treatment process. One component of the treatment that can reduce the likelihood of recurrence is reducing dietary sugars that are summarized by the acronym FODMAP. In my experience, after 14 days of xifaxin, and high dose probiotics, if patients return to a diet high in FODMAP foods, they will often have a recurrence in bacterial overgrowth. The drug company that makes Xifaxin showed that there was often a recurrence of symptoms every 42 days, which may require subsequent rounds of the same antibiotic in order continue to be free from the symptoms of IBS-D. I have found that after prolonged periods of maintaining a low FODMAP diet and a retest confirming the correct balance of the digestive flora, patient may re-introduce FODMAP foods slowly. The Monash group has more data on this approach. But this is just one of many potential imbalances that could lead to the symptoms that fall under the ICD-10 diagnosis of IBS-D.

IF however, Josiah had a parasite or yeast overgrowth or as I commonly see on tests, all three, then simply taking an antibiotic would not treat his problem and may make his yeast problem worse, for instance. Often times, antibiotics are how patients end up with a digestive imbalance in the first place. It is because the antibiotics that are used for upper respiratory infections (most were viral anyways) kill off beneficial flora like lactobacillus and bifidobacteria, while leaving other strains, such as the bacteroides phyla, unaffected. Yeast flourishes during antibiotics as well and often finds time to root itself into the soil of the digestive tract. Detecting yeast can require more than just doing a stool test. Often times it will not culture out on the test but patients will have many of the symptoms of yeast overgrowth in the digestive tract. I couldn’t help but think about that at the end of this Short Film where it shows that Josiah has developed a sweet tooth. Maybe those antibiotics + an unknown stool transplant cultured yeast in his digestive tract, which is notorious for giving patients a sweet tooth.

I always make the analogy of farming to teach patients how to relate to manipulating the digestive tract. A conventional doctor looks at the same stool test results that I order, sees “weeds” growing in the soil and simply tries to use the most effective “weed killer” to remove the weeds. A holistic medical doctor sees weeds and looks to the soil to determine why the weeds are growing in the first place. What feeds those weeds? Do they like sun or shade? Dry or damp soil? High in phosphorus or nitrogen? When I look at the microbiome, it is about using the safest and most effective “weed killer”, while cultivating the soil to grow a healthy flora and fauna. In order to do this correctly, it requires an understanding of the environment in the present and in the future as it is changing dynamically, which involves a combination of science and collective wisdom derived from experience.

When attempting to manipulate the microbiome, which can affect everything from autoimmune disorders to dermatologic conditions and joint inflammation, it is important to do so in a controlled manner under the guidance of a professional with the capacity to understand the complete picture, to read between the lines of the tests and look at the person, as well as use the most effective and safe treatment. I always tell patients who shy away from more potent treatments in favor of less effective but “safer” treatments, that the safest treatment is to do nothing. To attempt to manipulate the microbiome uneffectively through herbal combinations can often result in further imbalance. Many patients become dejected by the process but in my experience even patients who have suffered from problems for many years and have many failed prior attempts can do well when a fully informed approach is used.

Sometimes the biggest contributors to gut health can be mind-body, hormonal, dental, or environmental. Stepping back and looking at the patient as a whole can often times change the context in which the unsolvable condition arises so that it no longer becomes unsolvable. The San Francisco Institute For Integrative and Regenerative Medicine utilizes a synthetic approach that brings together multiple systems and offers systems-based treatment that changes both the context and cause of the problem. Come in for a consult to learn more about what this means for you.


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