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Understanding Microbiomes: Embracing the Hidden Heroes in Your Body for a Healthy Life

Written By Katie Di Lauro • 4 min read

When we refer to bacteria, fungi, and viruses, it’s usually in terms of sickness. But did you know that there are over 100 trillion microbes (living organisms) in your body? That’s right, we are a big bag of walking and talking bacteria! Much of this bacteria is beneficial and actually critical to our overall health, as it communicates with most cells in our body. In this respect, we need to understand, elevate, and maintain the good bacteria in our bodies. This explains why you might have been hearing a great deal about prebiotics and probiotics. 

First, let’s define a few terms:

Microbiome: our unique ecosystem of microorganisms that live in and on our body.

Microbes: a collective term for microscopic organisms that include bacteria, fungi, viruses, archaea, and protozoa.


1. Promotes regular bowel movements by enhancing motility, regulating intestinal pH levels, and influencing increased water content in the colon.

2. Improves immunity, which is essential for the development of our immune system by protecting us from pathogens. Beneficial gut bacteria can be pro-inflammatory or anti-inflammatory depending on our needs. Reduced bacterial diversity can cause the immune system to overreact, leading to autoimmune responses or allergies.

3. Supports mood because the bacteria in the gut can help create, synthesize, and modulate many of the same neurotransmitters as the brain, including GABA, norepinephrine, serotonin, melatonin, and acetylcholine.

4. Manages cravings and behaviors by sending regulatory chemical signals that control hunger and intestinal motility.

5. Manages inflammation – When your gut bacteria becomes unbalanced, it can frequently cause intestinal inflammation by altering the expression of the genes that regulate inflammation.

6. Modulates Vitamins – Gut bacteria help us extract nutrients from our food and produce essential nutrients such as antioxidants, B vitamins, and short-chain fatty acids.

7. Modulates and regulates human responses through chemical signals, including metabolism, fertility, and growth.

8. Influences genetic material by swapping genes or turning them on or off. If a substance is not ‘approved,’ the bacteria will send a signal to the immune system to eliminate it.

Development of Your Microbiome

The development of our microbiome actually begins in the womb; the umbilical cord, amniotic fluid, and the placenta have a microbiome. Whether you were born vaginally or via c-section, also influences your microbiome.  The birth canal exposures a baby to a diverse microbiome, further diversifying their microbial ecosystem therefore contributing to a stronger immune system. Throughout the rest of our lives, our exposure to foods, dirt, people and our general environment affects our microbiome richness and diversity. 


Many fermented foods may contain probiotics, which are naturally produced during the fermentation process or by adding probiotic strains during production. Note: the quantities of beneficial microbes found in dietary sources vary between brands due to differences in ingredients, preparation, packaging, and distribution methods.

  • Yogurt
  • Kefir
  • Sauerkraut
  • Pickles 
  • Kimchi 
  • Kombucha
  • Miso
  • Tempeh 
  • Supplements 


Prebiotics are important for feeding the probiotics, so they can continue to live, thrive, and multiply. Did you know that if we are not feeding the probiotic bacteria in our gut, it may actually start eating the lining of our gut (lumen) so it doesn’t starve? Prebiotics mainly come from carbohydrates in foods. Here’s a list of foods that contribute prebiotics: 

Cashews, cassava, green bananas, potato starch, potatoes (cooked and cooled), tiger nuts, artichokes, asparagus, chicory root, dates, fennel, figs, functional food products with inulin (e.g., high-fiber granola bars), garlic, kidney beans, onions, plums, ripe bananas, watermelon, wheat, chia seeds, legumes, pistachios, seaweed-derived products, soybeans, apples, apricots, cherries, citrus fruit (especially the peel), pectin used as a thickener in commercial foods as well as jams and jellies.


Diversity  – eat a varied diet, limited antibiotics and antibacterials and eating probiotics. 

Richness– how many bacteria genes you have (colonization- quantity). Feed the gut foods (fiber, probiotics)


Choose a high quality probiotics and probiotics that is stored shelf stable packaging or has remained refrigerated. Remember that probiotics are live organisms that can be degraded or killed when exposed to high heat, any extreme temperatures or light. Therefore I highly recommend a professional grade supplement. Pay attention to the storage instructions and the expiration date. When traveling, buy a shelf-stable formula. If you need to take an antibiotic, which will kill the good bacteria with the bad, repopulate your gut with probiotic foods and a high dose supplement – such as a 50 or 100 billion CFU (colony forming units). 

There are over 500 different kinds of probiotic species, each with their own speciality function in the body. Choose strains that meet your needs, such as gut health, cognitive, health, immune support, etc. If you need help choosing a probiotic that is right for you, please contact our Registered Dietitian Nutritionist and Integrative Functional Health Certified Practitioner, Katie Di Lauro. You may also refer to this Probiotic Reference Chart and order supplements from our preferred Provider: Designs for Health

The Bottom Line

The microbiome, consisting of trillions of beneficial microorganisms within us, plays a vital role in maintaining our overall health. Understanding the importance of nurturing a diverse and rich microbiome through the consumption of prebiotics and probiotics is key to supporting our immune system, mood, digestion, and well-being. By embracing a varied diet, limiting the use of antibiotics and antibacterials, and incorporating prebiotic and probiotic-rich foods or supplements into our routine, we can foster a balanced microbiome. Remember, a healthy microbiome contributes to a healthy you.

Katie Di Lauro, RDN

PFC Director of Nutrition

Learn more about PFC’s nutrition program and enroll in our weight loss camp today.

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