Feed Your Gut Microbiome With Food - Lakeside Natural Medicine

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Feed Your Gut Microbiome With Food

ByJoanne Aponte, ND March 19, 2019

Your gut microbiome is made up of all the micro-organisms (bacteria) that live in your digestive tract. There are likely 10 times more bacterial cells in your body than there are human cells! In other words, we are mostly bacteria (not human!). A majority of these bacterial cells live in your digestive tract. There are hundreds of different types of bacteria in the gut and each person’s microbiota (aka bacteria) makeup is unique.

What do the bacteria in the gut do?

The bacteria in your gut protect the digestive tract from damage and help keep the gut lining healthy; support the immune system and help maintain immune system balance; protect against allergy development; make vitamins (such as vitamin K and B vitamins); inhibit the growth of pathogenic bacteria that can cause health issues; they help the body make neurochemicals such as serotonin and GABA that impact our moods; and they modulate and control inflammation throughout the body.

They key is to promote a healthy microbiome is with food.

While probiotic supplements are helpful and replace health beneficial bacteria quickly (I use these a lot with good results). The effects of probiotic supplements are only temporary. In other words, you only benefit from the probiotics while you are taking the supplement. Once you stop the supplement, your gut bacteria go back to the way they were. For permanent change, you need to grow your own beneficial bacteria, and this is done through diet and lifestyle

A healthy gut is one in which there is a diverse amount of bacteria in the gut (lots of different kinds of bacteria) and low levels of pathogenic bacteria (disease causing bacteria). Having plenty of “good” bacteria is key to keeping the “bad” bacteria in check.  Here are some things you can do to nourish your microbiome.

How to promote a healthy gut microbiome:

  • Eat a wide diversity of multi-colored, whole plant foods and plant fibers. Plant food diversity = microbiota diversity.
  • Live on a farm and/or do lots of organic gardening (get your hands in the dirt!!)
  • Eat more raw fruits, vegetables, nuts and seeds
  • Exercise moderately – too much or too little can be a problem.
  • Manage stress
  • Get adequate sleep
  • Avoid medications known to negatively impact the microbiome – proton pump inhibitors (for acid reflux), antibiotics and NSAIDs such as Advil and Tylenol.

Foods that feed a healthy and diverse microbiome:

  • Legumes/lentils
    • eat these cold (leftovers) to gain the benefit of the resistant starch. This is especially a good idea if you are trying to manage your weight.
  • Cruciferous vegetable – broccoli, kale, cauliflower, Brussel sprouts, cabbage
  • Beet root
  • Foods rich in FOS and GOS – artichokes, burdock roots, garlic, onions, leeks, asparagus.
  • Sunflower seeds, pumpkin seeds, almonds
  • Soak grains overnight – such as oats, brown rice, quinoa and millet.
  • Resistant Starches
    • Boil potatoes and other root veggies and eat cold
    • Cook black beans, red lentils and other beans and eat cold.
  • Polyphenol rich foods – THINK COLOR! And think Red!
    • Dark cocoa powder
    • Green tea
    • Fruits – blueberries, cherries, strawberries, blackberries, plums, raspberries, apples with skin (red), grapes with skin, pomegranates.
    • Nuts and Seeds – Flax seed meal, pecans, hazelnuts, black tahini
    • Vegetables – Purple/red/orange carrots, purple/red potatoes, red cabbage, spinach, red onions, red lettuce
    • Grains: rice (brown, red, black), red and white quinoa, sourdough rye bread (
    • Black olives & olive oil


For patients with a lot of digestive symptoms I often run a comprehensive stool panel to get a thorough picture of what kind of bacteria are living in the gut. Everyone’s balance of gut bacteria is different and thus tolerance to the above foods will vary. Testing helps tailor the diet recommendations specific to the individual person. Consider seeing a naturopathic doctor to help you with this aspect.

Editor’s Note: The information in this article is intended for your educational use only. Always seek the advice of your physician or other qualified health practitioners with any questions you may have regarding a medical condition and before undertaking any diet, supplement, fitness, or other health program.

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