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Probiotics & Your Microbiome

Updated: Feb 5, 2020

Everything you've ever wanted to know about probiotics including who can benefit, which strains to look for, whether refrigeration required is better or not, and which brands have been clinically proven to be the most effective!

The microbes in our gut, also known as our gut flora or microbiome, have many roles. You may think their sole job is to absorb the nutrients we need to survive and thrive, however their impacts on our overall health are further reaching. Certain microbes in our gut are responsible for producing essential nutrients, like vitamin K, folic acid, biotin and butyric acid. Our gut microbiome also plays a very important role in protecting us from disease by limiting the growth of harmful bacteria and interfering with enzymes known to have cancer-causing effects. We also know that metabolic disease, such as obesity, diabetes and cardiovascular disease, are heavily impacted by our gut health. The flora itself is responsible for metabolizing and excreting cholesterol. And if the intestinal cells are compromised by downstream effects of dysbiosis, our innate immune system responds with increased inflammation that can progress to chronic disease over time.

Modern science has advanced in our understanding of the relationship between the microbes that live within us, but by no means is exhausted. What is clear is that one of the biggest components to a healthy gut is microbial diversity. Research has shown, time and again, the importance of having a diverse microbiome for overall health and prevention against disease. Outside of eating a good diet that supports healthy microbial diversity, one of the best ways to support a healthy microbiome is by supplementation with probiotics and prebiotics. In this article, we will focus on probiotics.

Not only have probiotics been shown to benefit common gastrointestinal disorders such as diarrhea, constipation, Ulcerative Colitis, Crohn’s, reflux, heartburn and intestinal ulcers, but they also play a role in vaginal infections, skin conditions, autoimmune disease, cold prevention and mood disorders. Personally and clinically, I have seen how helpful a quality probiotic can be with a wide range of conditions over the course of my career.

Understanding what to look before purchasing any probiotic product is key to ensuring you’re receiving what you need. The basic categories, or areas of distinction, are between strains, quality and quantity.

Lactobacillus & Bifidobacterium

These are the most common types of supplemental probiotics on the market, not because they are the most important, but rather because they are easier to keep alive in capsules as they can tolerate exposure to oxygen.

Both lactobacilli and bifidobacteria are groups of non-spore forming bacteria that each have various strains. For example, Lactobacillus rhamnosus and L. reuteri have been shown to be beneficial in preventing diarrhea. Lactobacillus rhamnosus is also one of the most well documented strains in preventing respiratory infections, antibiotic induced diarrhea as well as rotavirus induced acute viral diarrhea. It’s also specifically been shown to improve immune response to rotavirus vaccine. And Bifidobacterium strains, like B. infantis and B. breve, have been reported to be the most common species in healthy infants.

Saccharomyces boulardii

This is a fungal type of probiotic. It is not normally found in the human intestinal tract, but has been recognized for its benefit in treating antibiotic induced diarrhea. S. boulardii has also been shown to produce an enzyme that breaks down Clostridium difficile; a very nasty pathogen that is known for causing bloody diarrhea and being difficult to get rid of.

Bacillus spores

I am a big fan of Bacillus spore-based probiotics. These types of bacteria are encapsulated by protein shell which allows them to survive in harsh environments, like our stomachs. Our stomachs are highly acidic which is our first line of defense against pathogens. Any probiotic we take by mouth has to go through the stomach before making it to our intestines. Newer research has shown that the majority of probiotics do not actually make it past the stomach and into our intestines where they are meant to colonize.

Microbiome Labs developed the first 100% spore-based probiotic in response to this dilemma, called MegaSporeBiotic. MegaSporeBiotic contains 5 strains of bacillus spores. Bacillus Indicus HU36 have been shown to produce carotenoids at the site of absorption. Bacillus Clausii is great to take while on antibiotics because of its ability to resist being damaged by them. Bacillus Subtilis HU58 has many benefits. One amazing function is that it can produce 12 strong antibiotics that fight opportunistic and harmful bacteria. It also produces a compound called Nattokinase which has been shown to reduce blood pressure, cholesterol and excessive clotting. And, it produces a number of other nutrients like B vitamins and Vitamin K2. There are two other strains that are equally as fascinating and beneficial, but I think you get the point.

Microbiome Labs also conducted a clinical trial showing that MegaSporeBiotic can reduce intestinal permeability up to 60%, without any other diet or lifestyle interventions. Of course, we still need to pay attention to what we eat and put in and on our bodies, but it is encouraging to know how effective they are on their own.

Quantity / Dosing

If using lactobacillus or bifidobacterium based probiotics, a minimum dose of 2.5 billion live organisms per day would be the recommendation for mild, everyday care and maintenance. And for more serious conditions or infections, the dosing requirements would go up to around 50 billion CFU’s per day. Even though these numbers seem very high, they still are just a drop in the bucket when it comes down to the trillions of microbes in the gut at any given time.


Like most wellness trends, probiotic popularity has resulted in a number of companies looking to monopolize on the demand. Since they are a dietary supplement, there is no strict testing or approval process for manufacturers, making quality vary greatly across the market. Most brands available in health food stores can not be trusted as they are either contaminated with potential pathogens, have a lot of unhealthy fillers or do not even contain what they say they do! According to research, almost all probiotic supplements randomly sampled contain organisms and amounts of organisms different from their label claims. This is another reason I love Microbiome Labs. Their probiotics are tested four times before going into consumer hands. Not only do I respect their quality control, but they continue to be on the cutting edge of science and research for all things related to the world of microbiomes and give back to many organizations that are pushing the research further in this arena.

Can’t I just eat fermented foods?

Fermented foods like yogurt, kimchi, kefir, tempeh and sauerkraut are great for gut health but the benefit is not the same as a probiotic supplement that is meant to actually colonize and modulate the the gut microbiome. Rather, as foods are fermenting, many nutrients are made that help support the G.I. tract and immune system. By definition, fermented foods can be called probiotics, but their mechanism of action is different than what a supplemental probiotic can do.

Should I buy refrigerated or non-refrigerated probiotics?

My take is that spore-based probiotics are the best option available which do not require refrigeration. If deciding between lactobacillus based probiotics, refrigerated “live” versions are generally the better choice.

What if I feel worse after taking a probiotic?

This could mean that you’re taking too high of a dose or it could indicate that you have SIBO (small intestinal bacterial overgrowth). With SIBO, the addition of more bacteria, particularly lactobacillus strains, can cause excessive bacterial overgrowth and exacerbate symptoms of bloating, gas, etc. I recommend working with a healthcare provider if this has been your experience.

Since a healthy microbiome is critical to overall health, I almost always recommend supplementation with a probiotic. I concurrently always encourage my patients to get to the root of what is causing gut microbiome dysbiosis, but sometimes triggers are not always possible to avoid. Stress, lack of sleep, environmental toxins, antibiotics, sugar, alcohol and smoking are just some of the factors that damage our gut. We should do our best to avoid these but also take precautionary measures to protect ourselves with probiotics. Disease prevention is at the forefront of all my interaction with patients, and there is no better way to do this than by supporting a healthy gut!


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