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Influence on the Microbiome and Health






The human gastrointestinal microbiome is a complex ecosystem, it is a “microbial organ” within the gastrointestinal tract.  The human Microbiome is home to more than 1000 species of bacteria, yeast and other microorganisms.  The genome of our microbiome contains more than 100 times more genes than our own human genome.  Balance within our microbiome is essential to our health.  When our intestinal ecology is altered, so too is the health of our bodies.  These microbes influence our metabolism, immunity, inflammation, digestion and absorption of nutrients. The beneficial bacteria help us to digest food, synthesize vitamins, absorb nutrients from food, and detoxify chemicals and toxins.  The microbiome also helps to regulate our weight and metabolism, produce neurotransmitters and anti-inflammatory hormones.  Health of our Microbiome is foundational to our overall health and resilience.

Our microbiome is a dynamic living organism that is influenced by our diets, lifestyle and environments.    Things such as infections, toxins, stress, emotions, and diets can influence the balance of the microbiome.   And the balance of our microbiome can make the difference between health and disease.   To maintain optimal colonization in the digestive tract, it can be helpful to consume probiotic-rich foods or take probiotic supplements.  There is now a trend towards supplementing with pre-biotics and pre-Biotic foods.     The long terms benefits of the probiotic balance in our digestive system are now attributed to the metabolites of these beneficial microbes and their influence on our health.   These metabolites are known as post-biotics.    Let’s take a deeper look at the spectrum from Pre-biotic to Pro-Biotic to Post-Biotic and see how they differ and what they do.





Pre-Biotics are nutrients from plant based, fiber rich foods, which act as food for the Probiotics and Gut Microflora.   Soluble and insoluble fibers are indigestible carbohydrates that are available in plants and plant-based foods. While insoluble fibers benefit a healthy system by aiding in the efficient elimination of wastes, soluble fibers promote fermentation by the gut microbial community.Some examples of prebiotics that naturally exist in foods are: Fructans, including inulin and fructo-oligosaccharide, Galacto-oligosaccharides and trans-galacto-oligosaccharides, Resistant starches and oligosaccharides, and Polyphenols and cocoa-derived flavanols.

And while a diverse, whole food, plant-based diet that is fiber-rich contains an array of prebiotics, some prebiotic foods that are selective to known beneficial gut bacteria include:  Artichoke, Asparagus, Avocado, Banana, Barley, Beans, Beets, Chicory, Garlic, Honey, Milk and Yogurt, Onion, Peas, Rye, Seaweeds, Soybean, Tomatoes, Whole wheat.   Although pre-biotics can be taken as supplements and included in probiotic formulas, they are abundant in a diet rich in soluble fibers.   Getting them in your diet is the best method of establishing a healthy microbiome. 



Prebiotic Foods



Probiotics are live microorganisms that are intended to have health benefits by supplementing our digestive tract with microbes in a healthy microbiome.  Pro-Biotics may be found in Fermented foods and specific supplements.  Many of the microorganisms in probiotic products are the same or similar to the microorganisms that are in our bodies.   They help digestion, absorption, detoxification, vitamin manufacture, and immune health.   Probiotic Supplements and Foods contain a variety of microorganisms, and each probiotic may have a different effect on the body.   The most common probiotics are from the groups Lactobacillus and Bifidobacterium.   To be effective in benefitting the immune system and digestive tract, they must be taken or eaten regularly.

Fermented foods are rich sources of Pro-Biotics.  Some great probiotic foods are Sauerkraut, Kimchi, Pickles, Beets, Chutney, Yogurt, Kefir, Buttermilk, Relishes, Miso, Tempeh, Tamari Sauce.   While probiotic foods may be easily incorporated into your diet, they are commonly supplemented.    When choosing supplements, it is best to include probiotics that contain Lactobacillus and Bifidobacterium.    There can also be specialized probiotic supplement for specific organisms to help a specific function.   


Probiotic Foods 



Postbiotics are the metabolites of probiotics, or the components that result from probiotic activity in the gut, like fermentation. As intestinal microbes consume prebiotic fiber, the result of that fermentation or consumption is what is known as postbiotics.

Recent research presents evidence that most of the positive effects we used to attribute to probiotics are actually due to postbiotics.  They may also provide the bases for the proper processing of prebiotics, promoting a healthy prebiotic population. 

As commensal gut microbes break down prebiotics through fermentation, various metabolites and by-products are generated that contribute to system-wide health benefits. These postbiotics demonstrate positive health effects from their potential effects on the immune system, inflammation, antioxidants, infection control and anti-cancer properties.  

Some examples of postbiotics include organic acids, bacteriocins, carbonic substances and enzymes. They result naturally from the existence and survival of microorganisms living in our gut, though they can also be added directly through therapeutic processes. The short-chain fatty acids (SCFAs) butyrate, propionate, and acetate are examples of postbiotics.


Postbiotic Foods 

Benefits of Postbiotics

  1.  May help lower blood sugar and prevent obesity
  2. A lack of intestinal microbe balance has been shown to contribute to obesity and insulin resistance. A postbiotic bacterial component called muramyl dipeptide, has been shown to relieve glucose intolerance by increasing insulin
  3. Supports probiotics
    Probiotics and postbiotics work together to exhibit beneficial effects on human health. Probiotics produce postbiotics which often produce the immune effects that have been deemed beneficial for our health.
  4. Treats Diarrhea
    It has been long known that probiotic foods and supplements are effective in treating diarrhea. With The effect is not due to a direct interaction between the “good” bacteria and the intestinal lining, but rather to the metabolic products released by probiotics.
  5. Antimicrobial properties
    One of the main functions of probiotics and postbiotics is to populate the gut with an ecosystem that favors the growth of good bacteria, thus not allowing the population of infectious bacteria
  6. Helps Support Immune System in Infants and People with Difficult Conditions
    For people with conditions that result in immunodeficiency (immune system deficiency or weakness), or infants, probiotics may not be tolerable or safe. Postbiotic compounds are more tolerable and may reduce problematic inflammation.
  7. Reduces Inflammation
    people with inflammatory bowel disease (IBD) may not benefit from probiotics, and in fact may be detrimental to inflammation. In fact, postbiotics, when administrated, may protect against inflammation caused by some infections.



To put it simply, prebiotics proceed probiotics, which proceed postbiotics. Postbiotics, in turn, promote the use of prebiotics. Prebiotics are like the “food”, probiotics are the microorganisms themselves, and postbiotics are the results of probiotics consuming that “food”. Postbiotics, while being a sort of probiotic waste, are what may be exerting many of the health effects on humans. This helps us understand the symbiotic relationship between gut microorganisms and humans on an even deeper level.

A balanced and healthy gut microbiome is essential for optimal immune function and digestion, and both the intestinal microbial community as well as their metabolites impact our entire system. Supporting gut microbes through a diverse, plant-based diet of fibers and prebiotic foods may ensure abundance of not only beneficial bacteria, but also those fermentation by-products, or postbiotics, that demonstrate nutritional, metabolic, and immune health benefits.




Dr. Gabrielle Francis is a New York City Naturopathic Doctor, Chiropractor, and Acupuncturist.

Learn More about her practice, The Herban Alchemist HERE!