Microbiome Reset

I firmly believe that balanced blood sugar and a healthy microbiome together form the most important foundation of your long term health.  This applies to every system in the body.  I think the world started to pay attention to the microbiome when studies showed that when the microbiome from an obese mouse was transferred to a thin mouse, that thin mouse became obese.  After this shocking discovery, the field of study blew up.

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QuicK History

When I graduated from school, there were a few hundred studies about the microbiome, the organisms that we have a symbiotic relationship with, meaning we depend on each other to function.  At that time, working on the microbiome was considered pseudoscience.  Today, there are almost 150,000 studies, most of them completed in the last 5-10 years.  That number is growing exponentially.  In fact, as of today, there are 68,000 studies about metabolic factors and the microbiome published about obesity on PubMed, the national library of medicine.  10,300 studies about obesity.   Over 2,700 about depression. Almost 1,700 about anxiety.  Almost a thousand about fertility and the microbiome.  Over 1,100 about Alzheimer’s and the microbiome.  Over 1,700 about arthritis and the microbiome.  315 studies just about sinusitis.  Over 100 about cysitis,  Over 360 about acne.  When I speak to patients, I never wonder if their microbiome is healthy.  I wonder if their imbalanced microbiome is the cause of their illness.  I go from head to toe and ask about headaches, acne, sinus infections, dental problems, sore throats, chronic respiratory illness, digestive problems, genitourinary infections, joint pain, and athletes foot.  I also look for signs of neurologic, hormonal, and autoimmunity.  In my opinion, the longer the list, the more help the microbiome needs.  

The basic premise is very simple and of course, I didn’t invent it.  In school, we are taught a “eliminate, starve, and replace” approach.  This simple method will make progress in most people, although if your symptom list is very long, you may need more help.  The idea is simple.  Eliminate what we don’t want in the gut (excess yeast, unfriendly bacteria, and parasites), starve unfriendly bugs by removing foods they thrive on, and replace the good flora (and the fiber it eats to survive).  

There are many ways to do this, but if you follow these basic principles you should see a change in what survives in your body’s ecosystem.   I find that many microbiome diets are overly restrictive and complicated.  I have never seen a person have a major backslide from eating too much vinaigrette dressing or some of the other things the old books recommend.  People backslide from excessive highly processed foods with added starches, alcohol, and stress.  

First stage

For the first stage, eliminate as much as you can with an herbal formula like microbial defense or biocidin.  If this isn’t enough, and there are times in severe illness when I recommend pharmaceuticals.  I reference these studies 1 2  to point out that sometimes in the early stages of treatment,  the medicine may need to pack a bigger punch before herbs and probiotics can do their job.

Second Stage

In the second stage, we starve unfriendly organisms by removing sugar, flour, other sweeteners, and alcohol of any kind. It is totally normal to go through withdrawal for day 1 and 2.  On days 3,4, and 5, the “die off” stage can make all of your symptoms, especially digestive, worse.  If, by day 7, you are still feeling worse, you may need some extra help for the more complicated issues that go along with understanding how to address the microbiome.  

Third Stage

In the third stage, we replace what should be there.  I like to think of the digestive system as a yard full of weeds where someone wants grass.  Throwing a handful of grass seeds on top will not change that ecosystem.  It is established.  The weeds need to be removed, likely many times.  New seeds need to be added, likely many times and in large amounts.  Finally, the seeds need water and fertilizer to flourish or they still won’t grow.  In other words, you need good probiotics, and lots of them, with diverse food based fiber and starch to feed the new bugs.  Natural starches would include small portions of cooked carrots, beets, sweet potato, brown rice, legumes, or quinoa.  If these foods bother you, keep portions at ⅓ of a cup.  

Every January, after many people have supported the bugs that don’t help our immune system, we need to use something to kill those organisms off again so there is room for the friendly guys to grow.  

why is this so important?

So why is this so important?  If you don’t care, skip this paragraph!  We have what is called a mucin layer that covers our intestinal walls.  Under that mucin layer, we have a very complex neurological and immune system.  If an organism touches that tissue, it starts a process called “signal transduction”.  This means that the whole body gets a signal that there is an invader and the immune system is signaled.  This could cause an astounding variety of systems to malfunction.  What’s worse, while the immune system is busy doing the wrong thing, it’s not doing the right thing, like protecting our sinuses, gums, throat, skin, etc.  The more the unnatural inhabitants in our gut touch that sensitive tissue, the more systemic problems we have beyond just bloating or gas.  Even the metabolism changes.  The biggest mistake I see people make when they are trying to heal the gut is cutting all starches.  We know now that our friendly bugs will actually eat our mucin later if there is no starch, making us much more sensitive to foods in the long run.  We also know that totally cutting out diverse fibers (like those in beans and grains) limits our ability to develop a complex ecosystem of good bugs.  We just need to control portions of both.  We know that probiotics alone don’t “heal the gut”, although they do help release byproducts that are anti-inflammatory.  It’s actually including the liquid probiotics grew in, like Kombucha or Sauerkraut with juice, that speeds up the gut healing process.  I am also a big fan of any treatment that increases glutathione, which regulates the immune response and promotes the development of a normal mucin layer and reduced inflammation in the gut.

What’s truly remarkable is that we have a unique microbiome throughout the whole body.  As a person who primarily sees complex endocrine conditions, the most fascinating thing that I stumbled across was the microbiome impact on hormone balance.  It’s barely been studied.  We know diet and exercise impact hormone related symptoms, but most people don’t know that treating the microbiome can transform many women’s conditions.  This is likely because of the gut and liver role in hormone metabolism.  But one area of study that is in its infancy is the microbiome in the female anatomy.  We don’t know enough yet, but my clinical experience has taught me that if we treat the microbiome that we do understand, the rest of the body balances out.  And if you want to add further support, at minimum we know that L Rhamnosus is in many products that are used locally to help balance the flora in the pelvic area.

There are ALWAYS ways to do more.  

Check out my blog on dental health to understand how you can improve your oral microbiome.   

Check out my blog on my morning drink to see what you can add to speed up the process and build your energy.  

Check out my blog on stress management to reduce the impact on stress on your flora.  

After about 3 weeks, you should feel substantially better.  If you don’t, it may be time to ask a professional to help.  If you do, you will want to stop, but continue.  You must consistently foster the growth of this new ecosystem or you will not maintain your results.  If you must have sugar, make sure you don’t exceed 10 grams at a time (unprocessed fruit is fine).  Don’t eat more than 2 fruits per day.  Don’t swap out artificial sweeteners.  If you must occasionally have alcohol, never have more than 2 drinks a time, and not more than 2 times in a week.  Never have sweet alcoholic drinks.  Once you are done, your body will tolerate breaking these rules better.  But I do suggest that after you finish the diet, you follow a basic structure of a healthy microbiome.  I will list this below. 

For the replace portion, the concept is simple.  At least 20 billion guaranteed (on the self not at the factor) per pill per day.  You’re not likely to get that online or at a grocery store.  Usually only health care providers have their probiotics shipped in temperature controlled environments to keep them stable.  I like Probiotic 225.  I would use 1 packet daily for 5 days, then one weekly until gone.  Want half the price tag?  Try probiotic pearls instead.  The dose  is lower, but it is cost effective and better on a budget.  I am always surprised to see how many people will only re-purchase the probiotic 225 over all of the others, even though it is the most expensive supplement I keep in my office.  

Breakfast should contain fiber, about 30 grams of protein, and about 30 grams of fat.  If you fast in the morning, you should try to include some form of fat or protein if you are a woman.  Friendly organisms can digest your mucin layer if you fast too long.  

Lunch should contain about 2 cups of veggies, ½ cup of starch, 30 grams of protein, and 1-2 tbsp of plant based fat.  

A mid afternoon snack should contain 2 tbsp of nuts and 1 cup of fruit.  

Dinner should have about the same format as lunch.  

Stick to the 2/2 alcohol rule if you begin drinking again, and consider a high dose probiotic after alcohol.  The rest of the time, if your diet is clean, you might be able to maintain your good flora with food based probiotics and fiber.  

When I see people doing literally everything right and it’s not helping it is usually one of 4 things.  It could be a drug.  They may have a parasite in a hard to reach place and truly need a short term medication.  They may eat perfectly and have terrible stress / trauma, which will literally cause enterobacter, a friendly bug, to become a pathogen and there is no test for that.  They also may have a really complicated mix of bacteria and yeast and treating one makes the other worse.  In these cases, it doesn’t hurt to get help.  The right provider will empower you to learn how to balance your gut and keep it healthy.  

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