Prebiotic and Probiotic Foods for Gut Health

There are more microbes lining your colon and small intestine and covering your skin than there are cells in your body. Tens of trillions of bacteria and other microbes inhabit the large intestine, in particular, and they play a vital role in your health. In fact, some researchers have declared the collection of gut microbiota, called a microbiome, to be, effectively, another organ because of its function in the body. Without a healthy microbiome, your overall physical and mental health will suffer.

Your microbiome is unique to you, containing a combination of bacteria and other types of microbes that creates a mini ecosystem in the colon, or large intestine. Depending on where you live and what you eat, your dominant bacteria will be similar to those around you who live and eat similarly, but the exact combination of  microbe types your gut fosters will be unique to you.

Why is the Microbiome So Important?

Turns out Hippocrates was right when he declared, over two thousand years ago, that “all disease begins in the gut.” When your gut flora are imbalanced, a cascade of negative consequences is put into motion; over time, this leads to chronic diseases caused by inflammation and autoimmune disorders.

Your microbiome makes up 75% of your immune system, and signals from the gut travel to the brain along the vagus nerve. The vagus nerve controls the parasympathetic nervous system, which controls heart rate and intestinal and glandular activity, among other things.

The microbiome has so much influence on what happens in your heart, lungs, other organs, hormones, and the workings of the brain that it has been referred to as the gut brain. When your gut isn’t healthy, everything in your body—from your immune system to your mental health—suffers.

The Influence of the Western Diet on the Microbiome

White sugar

As you might have guessed, the Western diet—high in sugar, low in fiber—is the perfect recipe for an unhealthy gut. Without adequate food (fiber), the gut flora become imbalanced. Some bacteria and yeast flourish at the expense of others, and  these microbial thugs feed on the many types of sugar we ingest in processed, refined, and junk foods. In addition, they demand more sugar and refined foods in the form of cravings. Ever been helpless when faced with a donut or a pint of ice cream? It’s because the microbial thugs are in charge and they’re sending strong signals to your brain to feed them.

Over time, this imbalance leads to the breakdown of the intestinal mucosal cells, the tiny little fingers, or villi, that absorb nutrients and protect the gut lining. As these cells break down, the mucus lining of the gut dries and washes away, exposing the gut lining. Then the gut lining develops cracks, which allow tiny particles of undigested food to slip from the intestines into the bloodstream. This is called gut permeability, or leaky gut syndrome.

When particles of food enter the bloodstream, the body’s immune response is triggered as it attempts to deal with these unfamiliar food invaders.

The Western diet, then, keeps the body in a constant state of immune emergency, which leads to widespread inflammation inside the body. This constant state of emergency and inflammation leads to hundreds of chronic diseases, such as:

  • Rheumatoid arthritis
  • Fibromyalgia
  • Asthma and allergies
  • Skin conditions such as eczema, acne, and psoriasis
  • Irritable Bowel Syndrome (IBS)
  • Inflammatory Bowel Disease (IBD), Crohn’s Disease, and Ulcerative Colitis
  • Multiple Sclerosis
  • Lupus
  • Chronic Fatigue Syndrome
  • Schizophrenia, depression, and other mental disorders
  • Type 1 diabetes
  • Parkinson’s Disease
  • ADHD
  • Autism
  • Tourette’s Syndrome
  • Chronic kidney disease

The Western diet also leads to high incidences of overweight and obesity. 36.5% of adults in the United States can now be classified as obese, with many more landing in the overweight category.

Prebiotics and Probiotics: the Supermen of Gut Health

Fortunately, the terrible damage caused by the Western diet can be corrected and even reversed. Your gut microbiome is not a static thing: it can be changed depending on the food you consume. With proper feeding, you can help your gut microbes restore order and balance, restore and repair the gut lining and gut mucosal cells, and once again become diverse. The more diverse your gut flora are, the better off you’ll be.

Once again, Hippocrates, that ancient father of medicine, had it spot on when he intoned, “Let food be thy medicine and medicine be thy food.”

More recently, Michael Pollan said, “Eat food. Not too much. Mostly plants.”

Both were right.

The two components of a healthy gut are probiotics and prebiotics. By taking care of these two things, you’ll be on your way to a healthy, happy gut.


Probiotics are the beneficial bacteria and yeast that make up your microbiome. Think of them as the happy, energetic workers of your gut.

Probiotics line both the small intestine and the colon (large intestine), but they are concentrated in the colon. After partially digested food moves from the stomach into the small intestine, nutrients are removed and absorbed into the blood stream. By the time the food has moved into the colon, all that remains is water and the indigestible fiber from your food. While the colon lining absorbs the water, probiotics get to work on the fiber, munching away ecstatically. During this process, they secrete short-chain fatty acids such as butyrate, which builds the mucus lining of the gut. They also manufacture vitamins and interact with your hormones, immune system, and cells. The particular balance of gut flora you have also determines how aggressively calories are extracted from the food you eat (an imbalance actually causes your body to absorb more calories, thus contributing to overweight and obesity!).

It’s important to eat foods that contain probiotics—especially in a society where antibiotics are a commonly prescribed solution to illness and caffeinated beverages are used for energy. The more diverse your gut flora are, the healthier your gut will be.

Foods that contain probiotics will help restore and rebuild a healthy microbiome. They include:

  • Plants: high quality vegetables and fruits can help build a diverse gut flora. Whenever possible, choose certified organic or grow your own using composted soil or another growing medium that provides a wide range of nutrients and minerals to the plants.
  • Fermented foods: fermentation allows probiotics to pre-digest a substrate (the substance that is being fermented) while multiplying and flourishing. Eating fermented foods is like giving yourself a whopping dose of ready-to-go beneficial microbes that will begin their work in your gut right away. Sauerkraut, fermented (not merely brined) cucumber pickles, kimchi, tempeh, and aged hard cheeses are examples of fermented foods that contain plenty of probiotics.
  • Cultured foods: cultured foods like kefir and yogurt introduce trillions of beneficial bacteria into the gut. While yogurt cultures enter the gut, do their good work, and then die off and are excreted within about 24 hours, kefir cultures stick to the gut lining and continue to flourish. Both milk kefir and water kefir are easy to make at home and require no heat for culturing. Yogurt, which does require a little heat for culturing, is also simple to make at home.
  • High quality probiotic supplements: supplements that contain dried, powdered probiotics are a good addition to a healthful diet.


If probiotics are the happy critters that populate your gut microbiome, prebiotics are the food upon which these critters thrive and flourish. While you’re building a diverse and robust microbiome, it’s important to continually Leeks fuel it with prebiotic goodies.

Prebiotics are, essentially, fiber. Fiber cannot be broken down and absorbed by digestive enzymes in the stomach and small intestine, but it is essential for moving food through the digestive system, cleaning out waste, and feeding gut flora. When chyme (partially digested food sludge in the small intestine) finally makes it into the colon, all that’s left of the sludge is water and fiber. This is when the microbiota feast.

Prebiotic foods include a diverse range of raw and cooked vegetables and fruits. These foods provide plenty of fiber for probiotic feasting. The higher the fiber content, the happier your gut flora will be.

While you should make it a goal to eat as many different types of vegetables and fruits as you can (the more diverse your consumption, the more diverse your microbiome will be), here are some powerhouses of the prebiotic world:

  • Raw and cooked onions
  • Jerusalem artichokes (also called “sunchokes”)
  • Raw garlic
  • Raw leeks
  • Bananas
  • Raw wheat bran
  • Dandelion and other dark leafy greens

Going from a typical low-fiber Western diet to a diet plan that packs a huge fiber punch can be hard on your recovering digestive system. Add prebiotic foods gradually until you can consume five or more grams of fiber per day without excess gas, bloating, or stomach pain. In terms of servings, a good goal is to get seven cups of plant food each day—five from vegetables, and two from fruit—according to Jeanette Hyde, nutritional therapist BSc, and author of The Gut Makeover.

By working to increase your probiotic count and feed them with prebiotics, you’re working to make your gut happy, healthy, and able to function effectively in your body. A happy microbiome is one of the basic keys to a healthy mind and body.

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