Part I. Microbiome and Mealtime: Prebiotics, Probiotics, and Plant-Based Food

By Theophila Lee & Susan Im

This is the first of a three-part series on the microbiome. See Part Two for a discussion on the microbiome and mental health and Part Three for a discussion on the microbiome and maintaining skin health.

A diverse community 

Imagine a collection of 100 trillion bacteria, yeast, viruses, fungi, and parasites of different strains and varieties living in diverse, ever- changing environments around your skin, mouth, and gut (although the majority reside in the gut). This is your microbiome, a dynamic community of microorganisms that outnumbers nine times the number of human cells. Through new scientific advances, researchers are beginning to better understand the microbiome’s composition and implications on human health. 

Scientists believe that the microbiome, weighing as much as our three-pound brain, is a “second brain” just as important to understanding who we are. The organisms comprising the microbiome aren’t simply passive passengers in our body or disease-causing entities. They are integral to digesting food, educating our immune system, and resisting disease. An increasing number of studies are demonstrating that a diverse, balanced microbiome promotes health, longevity, and positive behavioral traits. Conversely, individuals with less healthy and diverse microbiomes have been shown to be more susceptible to a wide range of physical and mental illnesses. 

Microbiome impact 

Microbes around our body contribute to many of our differences. We leave traces of our microbial DNA on everything we touch, and scientists can match the palm of someone’s hand up with the mouse of the computer they use regularly with 95% accuracy. Your microbe has wide ranging implications including determining what drugs will be toxic to your system, whether your skin produces chemicals that attract certain mosquitos, and even influencing who you’re attracted to. 

Although the microbiome influences many diseases, particularly interesting is its implications on obesity, a conditioning affecting nearly 35% of adult Americans. In one study, obese mice were shown to have less diverse gut microbes than skinny mice. When gut microbes from obese mice were transplanted into the skinny mice, the skinny mice grew heavier and had more body fat. Furthermore, when microbial strains from skinny mice were transferred to the obese mice, these obese mice soon developed healthier weights. Researchers found that the microbiome of these obese mice were missing key gut bacterial strains integral for maintaining healthy metabolism that were present in the microbiomes of skinny mice. 

A healthy microbiome 

So what can you to do create the healthiest and most diverse microbiome? For one, sleep. When you don’t sleep, neither do your hard-working microbes. Give them the rest they need and make sure to get proper sleep each night. Secondly, exercise. It’s integral for stimulating a healthy balance of microbiome, so incorporate a range of strength and cardio exercises in your workouts. Thirdly, stress management. The gut and brain are inextricably linked, as will see in following article. Prolonged stress breaks down the lining of your gut and leads to inflammation and infection. Finally, limit antibiotic use. Antibiotics have been shown to decrease the richness, diversity, and evenness of the gut microbiome.  

Even more fascinating, however, are the implications of microbiome health on nutrition. Individuals with the most diverse diet have the most diverse gut bacteria. As the saying goes, you are what you eat. If you don’t eat the food, then your gut bacteria can’t access it. Here are some tips: 

  • Plant-based. Variety is key to creating a balanced microbiome. We typically regularly incorporate only 5-10 fruits and vegetables in our diet regularly, not giving our bodies access to a wider range of nutrients found in other plant-based fruits.  Try buying a new fruit or vegetable you’ve never tried before once every couple months. You might find something new you like sticks!
  • Prebiotic. Think of prebiotics as the water and fertilizer that help your microbial garden flourish. Prebiotic fiber is found in the non-digestible part of foods like garlic, onions, leeks, asparagus, bananas, barley, oats, cocoa, flax, seaweed and apples. They are fermented when they reach the large colon in a process that feeds microbiome communities and augments the number of healthy bacteria.  
  • Probiotic. Think of probiotics as the seeds that help your microbial garden grow. Probiotics are live, helpful bacteria naturally created in the process of making fermented foods like Greek yogurt, kefir, sauerkraut, miso soup, and kimchi. Probiotics like lactobacillus and Bifidobacterium help fermentation, seed the gut with new bacteria, and provide a boost to the immune system. 
    • Fermentation is a normal digestive process that occurs when bacterial break down food in the colon, producing short chain fatty acid crucial for digestive health. Fun fact- the colon actually produces the equivalent of a can of beer every day, which the liver detoxifies! 

Founder of Real Nutrition and NYC based dietician, Amy Shapiro, describes how probiotics and probiotics must work in harmony to maximize health and wellbeing: “They work together. Prebiotics are essential to keeping your health on track.  If you need to feed your gut flora then you can take a probiotic, but prebiotics are important to keep new and already established microbiomes on track.  Bacteria make up most of who we are and we want the good types to stick around!  Probiotics help with everything from skin inflammation to digestion and elimination, which are all huge parts in health and wellness.”

In short, respect your microbiome. Prioritize better stress management, proper sleep, sufficient exercise, limited antibiotic use and a varied diet full of different types of plant-based, prebiotics and probiotics foods. See if having happier bacteria leads to a happier you! 


  1. Wallis, Claudia. “How Gut Bacteria Help Make Us Fat and Thin.” Scientific American, Scientific American, 1 June 2014,
  2. “Prebiotics vs Probiotics: What Are the Key Differences & Health Benefits.” Prebiotics vs Probiotics: What Are the Key Differences & Health Benefits,

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