The Ultimate Guide To Eating For Your Microbiome

Written by Lynda Griparic
Lynda Griparic is a naturopath, nutritionist, writer, and speaker living in New South Wales, Australia, with over 14 years of experience in the health industry. Lynda specializes in gut health and weight loss, and has an Advanced Diploma in Naturopathy, Nutrition, and Massage from Nature Care College.

Photo by Nataša Mandić

Many of us are now aware that the state of our microbiome is a huge contributor to the state of our health—but between pebiotics, probiotics, and a host of other buzzwords, it can be hard to navigate actual action steps. What should you eat? What should you avoid? Let's dive into the world of microbiome-enhancing foods and get to the bottom of things.

Let's start with short-chain fatty acids.

While we all have very different-looking microbiotas, for all of us, optimal health lies in having a large diversity of bacteria in our guts. Our bacteria have specific functions that keep our systems humming along and protect us from illness, and the more strains there are, the more protection we have. These bacteria produce short-chain fatty acids, such as the well-researched butyrate, propionate, and acetate. They do this by fermenting "eating" dietary fibers.

Short-chain fatty acids are an impressive bunch. Not only do they play a crucial role in the human gut, but their impressive properties extend to our overall health, including:

All of that, simply from enhancing the quantity and diversity of your microbiome, and thus increasing your short-chain fatty acid production. But how do you actually do this? There are five main categories of microbiome-enhancing foods.

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FOS & Inulin.

Fructooligosaccharides (FOS) are oligosaccharides that occur naturally in plants. Inulins are a group of naturally occurring polysaccharides produced by many types of plants. These include:

  • Chicory root
  • Garlic
  • Jerusalem artichoke
  • Leek
  • Onion
  • Dandelion greens
  • Asparagus
  • Banana
  • Sugar beet
  • Honey
  • Tomato

Resistant starch.

This form of starch is resistant to digestion in the small intestine. It instead reaches the large intestine intact and goes on to feed our colonic bacteria, producing short-chain fatty acids. Resistant-starch-rich foods include:

  • Cooked, cooled potatoes
  • Green bananas
  • Cashews
  • Rolled oats
  • White beans
  • Cooked, cooled lentils
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Dietary fiber.

Dietary fiber is a group of food components that resist breakdown from digestive enzymes. This includes:

  • Flaxseeds
  • Vegetables
  • Fruit


Polyphenols are organic compounds found in plants that are involved in defense against ultraviolet radiation or attack from pathogens. These include:

  • Blueberries
  • Strawberries
  • Peaches
  • Plums
  • Grape seed extract
  • Resveratrol
  • Tea
  • Cocoa
  • Chocolate
  • Ginger
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Other prebiotic foods.

  • Kiwifruit
  • Beetroot
  • Fennel bulb
  • Green peas
  • Snow peas
  • Sweet corn
  • Savoy cabbage
  • Chickpeas
  • Red kidney beans
  • Cashews
  • Pistachio nuts
  • Peaches
  • Watermelon
  • Grapefruit
  • Pomegranate
  • Dates
  • Dried figs

How much is enough?

I always encourage my clients to eat at least eight servings of microbiome-enhancing foods every day. While that seems like a lot, it's actually quite doable. Here's what a day could look like:

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FOS and inulin-heavy sauteed onions, garlic, and asparagus perfectly season a simple egg scramble. Add artichoke if you want to bump up the healing properties even more.


Make a microbiome-feeding salad with dandelion greens, beetroot, fennel, cabbage, red onion, pomegranate seeds, wild-caught fish, olive oil, apple cider vinegar, pink Himalayan salt, and cracked black pepper.

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As the weather cools down, I love a hearty meal of slow-cooked grass-fed lamb shanks with FOS and inulin-rich sauteed leek and broccoli, with a resistant starchy sweet potato mash on the side.


A few squares of organic dark chocolate will up your polyphenol intake while satisfying that sweet tooth.


Sip on organic black tea, green tea, and white tea (without added milk or sugar) throughout the day. Try a glass of organic, preservative-free red wine at dinner.

Note: Those who have digestive disruptions such as SIBO, IBS, histamine, salicylate, or other food intolerances would benefit from consulting with a health practitioner as you’ll need to adjust your intake of certain foods on this list while treatment takes place.

This prebiotic soup is a great way to get in a few of those eight servings!

And are you ready to learn more about how to unlock the power of food to heal your body, prevent disease & achieve optimal health? Register now for our FREE web class with nutrition expert Kelly LeVeque.

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