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The Ever-Expanding Importance of the Gut Microbiome

Your body is home to trillions of bacteria (as well as viruses and fungi) that make up a complex ecosystem known as the microbiome. These microorganisms work alongside our own cells supporting and enhancing our biological systems and overall health. The best way to support the microbiome is by diet and lifestyle but often, we find ourselves in need of more. Let’s take a deeper dive into what probiotics do, how to keep them happy and decipher what personal options we may have. That way we can all optimize our own very specific microbiomes and reap the profound health benefits.

What do probiotics do?

The probiotics that specifically make up the gut (GI) microbiome, play an intricate role in the promotion of wellbeing including but not limited to…

Epithelial cell growth and repair (restoration of the gut lining)

Preventing the entry of pathogens (“bad bugs”)

Anti-inflammatory activities

Immune system regulation and cytokine (immune signaling molecules) balance

Digestion and absorption of nutrients


Production of vitamins (vitamin K and B12)

Biotransformation of heavy metals and other toxins (conversion to more readily excreted forms)

Bile salt transformation (to help balance the microbiome, for detoxification and digestion)


How do I keep them happy?


To keep these probiotics happy and healthy (so that we can be happy and healthy), we must feed them what I like to refer to as the 3 P’s…


Prebiotics (undigested fibers)

Polyphenols & Phytonutrients

(brightly colored plant-based foods – mostly vegetables and low glycemic fruits)


In addition, we must attempt to avoid known disruptors of the microbiome such as unnecessary antibiotics, excessive alcohol consumption, inflammatory and overly processed foods as well as chronically unmanaged stress.

Certain medications are also notorious for disrupting the microbiome like…


NSAIDs (Non-steroidal anti-inflammatories)

Acid suppressors (Proton pump inhibitors (PPIs) and H2 blockers)

Oral contraception (OCPs)

Metformin (Antidiabetic drug)

Steroids (Prednisone)

Antimicrobials (Antibiotics and Antifungals)


It is imperative that these medications be used wisely, for the minimal effective dose and duration only under the supervision of a trained clinician while maintaining an open dialogue about natural, less disruptive alternatives.


In doing so, we can reap the benefits of a more diversified microbiome, the multitude of functions that they provide or augment and the “postbiotics” that they create for us, in particular, short chain fatty acids (SCFAs). Put differently if we feed them, they feed us, and we all benefit. Diversity is key (of diet and of the microbiota) and these very special “postbiotics” can supply fuel to our intestinal cells, act as anti-inflammatories, promote detoxification, decrease cancer, cardiovascular and metabolic risks.


So, what should I eat?


Two of the main probiotic bacteria that reside in the digestive tract are Lactobacilli and Bifidobacteria.

These can be taken as supplements or included in the diet in the form of fermented (or probiotic rich) foods. Fermented foods are those changed by the desired action of microbes, usually bacteria or yeast. Fermented foods aren’t the same as probiotics, however. Probiotics are specific strains of live microbes with proven health benefits. Choosing fermented foods with “live and active cultures” may benefit you most. Some fermented foods are heat processed which destroys live microbial cultures. Still, fermentation itself changes foods in many beneficial ways. In addition, we must eat a diet rich in prebiotics to support the microbiome that we are repleting, balancing and protecting.

Some examples of common probiotic and prebiotic foods:

Dairy probiotic foods: acidophilus milk, buttermilk, cheese (aged), cottage cheese, kefir, sour cream, yogurt (plain, no added sugar, active cultures)

Non-dairy probiotic foods: fermented meats, fermented vegetables, kimchi, kombucha, kvass, miso, natto, pickled vegetables (raw), sauerkraut, tempeh, non-dairy “yogurt” (plain, no added sugar, active cultures)

Prebiotic foods: apple, asparagus, banana, burdock, chicory, cocoa, dandelion greens, eggplant, endive, flaxseed, garlic, honey, Jerusalem artichoke (sunchoke), jicama, konjac, leek, legumes, onion, peas, radicchio, whole grains, yacon

To maintain colonization of the digestive tract, probiotics must be taken or eaten regularly. To get the maximum benefit from fermented foods, it’s important to read product labels and choose only those that contain “live and active cultures” and preferably raw, unpasteurized, perishable ingredients.

What are my options if I need a probiotic supplement?

The benefits of one probiotic strain may be completely different from another and the more that we learn about the microbiome, the more therapeutically specific we can be. It is best to select the right probiotic for the right condition. Perhaps the simplest and best thing you can do is to make sure to eat a variety of probiotic dense foods to cover all grounds (remember, diversity if the key).

When you are planning on purchasing probiotics, it is imperative that you read the label so that you can identify the genus, species and strain in addition to the number of colony forming units (CFUs). Pay attention to shelf life/stability and any other specific information listed on the product.

“Regular” probiotics

As previously mentioned, two of the main probiotic bacteria that reside in the digestive tract are Lactobacilli and Bifidobacteria and some of the well-studied species-specific strains are…

Bifidobacterium bifidum

Lactobacillus plantarum

Lactobacillus acidophilus

Lactobacillus rhamnosus


Another class of well-studied and therapeutically beneficial probiotics is Saccharomyces boulardii which is actually a type of yeast that can be very helpful to combat not only bacterial imbalances, but pathogenic yeast overgrowth as well.

Soil based probiotics

Soil based probiotics have a natural, seed-like structure, making them tougher than “regular” probiotics. Therefore, they can withstand stomach acid and digestive enzymes better, and have been proven to contribute to the diversity of the microbiome. All this can be accomplished with fewer CFUs.

New kid on the block

There is an explosion of data around a new kid on the block called Akkermansia muciniphila which has been shown to be extremely beneficial for treating metabolic syndromes like diabetes and obesity due to it’s influence on short chain fatty acid (SCFA) production.

As you can see, there are many options to choose from and when doing so, it is best to understand what you are trying to accomplish. Regardless of the condition being treated or reason for probiotic use, there are some very important items to pay attention to like…

Brand quality – look for reputable, established supplement brands

Survivability – look for strains that are better able to make it to the gut to colonize it

Diversity – review the number of strains present within the product or determine if it is a probiotic that inherently contributes to diversity like soil based organisms

Stability – does the product need to be refrigerated or not

Prebiotics – does it contain prebiotics and can therefore be classified as a synbiotic


Everything starts at the beginning…

It has become increasingly clearer that gut health is the gateway to overall health. This is the inevitable truth whether we are discussing cardiometabolic benefits, cancer risk or even autoimmunity. Subtle simple daily habits can begin to unlock the potential of our microbiome. The key is to stay informed, ask appropriate questions, become an advocate for your own health and make the necessary changes to your diet and lifestyle as guided by the information above. Food is medicine and you do not need a medical degree to practice the art of eating for health.