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Feeding Your Gut Microbes

Our microbiome or microbiota - are the trillions of microbes living in communities within and on a person (gut, nasal cavities, mouth, sinuses, etc.). They are incredibly  important to our health in many ways.

Our intestines (gut microbiome) are densely packed with microbes, with between 500 to more than 1000 species of bacteria. These microbes play a key role in our health - with digestion, getting nutrients and energy from food, in protecting against pathogens, and our immune system.

Research has found a link between some types of bacteria in the gut and chronic inflammation, some chronic diseases, and even cancer (e.g., colon cancer). On the other hand, the presence of other beneficial or good bacteria (e.g., especially Faecalibacterium prausnitzii) are associated with health and lower levels of chronic inflammation and chronic diseases.

It turns out our diets and lifestyle are a key element in whether there is good health or chronic inflammation in our bodies. Our modern western lifestyle, with a diet high in meat, fat, highly processed foods, low in fiber, little exercise, and frequent use of antibioticsis wiping out some of our beneficial gut microbes, as well as causing chronic inflammation.

THE ISSUE IS: Can one improve and nurture the beneficial bacteria in our bodies? 

Yes! Research shows that the diversity and balance of bacteria living in the gut can be changed and improved, and that changes can occur very quickly. Within a few weeks! The microbial communities fluctuate for various reasons (illness, diet, etc.), but diet is key to the health of your gut microbial community.

Think of the saying: "You are what you eat" in reminding yourself that what you eat feeds and nurtures bacteria, and different foods feed different bacteria.

A diet with lots of plant-based foods is the best way to feed and nurture beneficial microbes and lower inflammation that is linked to chronic diseases (e.g. diabetes, heart disease). This will also result in an increase of diversity of bacteria, which makes a person healthier and more able to resist diseases.

By the way, you may see three terms frequently mentioned, especially among companies promoting supplements: 1) prebiotics feed the beneficial bacteria in the gut, 2) probiotics are live beneficial bacteria, and 3) synbiotics are a combination of prebiotics and probiotics. But.. don't focus on these terms. Instead, focus on eating real foods, especially foods from plants. You don't need dietary supplements.

You can quickly improve your gut microbial community starting now. The following are some practical tips, based on what scientific research currently knows.


- Eat a wide variety of foods, especially whole foods that are unprocessed or as minimally processed as possible. Eat everything in moderation.

- Eat a diet rich in plant based foods: fruits, vegetables, whole grains, seeds, nuts, and legumes. Eat a variety of foods, perhaps along the lines of a Mediterranean diet. Think of Michael Pollan's advice: "Eat food. Not too much. Mostly plants."

- Eat at least 5 servings of fruits and vegetables each day. One serving is about half cup. Try to have some of these servings be fresh or raw produce (lots of microbes and fiber to feed and nurture the microbes in the gut). An apple contains millions of many species of bacteria!

Raw fruits and vegetables (as well as cheeses and fermented foods) all contain a variety of microbes that are ingested and so get into the gut. Some recent evidence suggests that bacteria in organic fruits may be especially beneficial.

- Eat more fiber, and increase how many servings you eat every day. A variety of fiber foods every day (to feed the variety of bacteria species in the gut), and several servings at each meal, is best. Think fruits, vegetables, whole grains, legumes (beans), nuts, and seeds. (Meat, dairy products, and seafood does not contain dietary fiber.)

Dietary fiber or roughage is the indigestible portion of food derived from plants. There are two types of fiberInsoluble fiber which doesn't dissolve in water and passes through the intestines (it provides bulking), and soluble fiber, which dissolves in water, and becomes a gel. Plant foods contain both types of fiber in varying degrees, depending on the plant's characteristics.

The latest research suggests that over 25 grams of fiber daily for adults is best for health (a recent study suggested up to 50 grams of fiber daily for men to reduce colon cancer risk). One could take fiber supplements, but real foods have many more benefits to them, and also provide a variety of fiber sources. {SCROLL DOWN FOR HIGH FIBER FOOD CHART }

Eat as many organic foods as possible. Research is finding some microbial and nutritional differences between organic and non-organic foods (for ex., organic produce has more beneficial species of bacteria). Pesticide residues in non-organic foods are ingested, but eating organic foods quickly lowers pesticide levels in a person's body. Pesticide residues in food may also kill off some beneficial bacteria in the gut (e.g., Roundup with the active ingredient glyphosate).

Even if you can't or won't eat organic foods, it is better to eat non-organic fruits, vegetables, legumes, seeds, nuts, and whole grains than to not eat them.

- Eat some fermented foods, ideally each day. Recent research shows that eating some every day is a quick way to increase gut microbial diversity (good!) and lower chronic inflammation that is linked to diseases. Examples of fermented foods: yogurt, kimchi, sauerkraut, fermented vegetables, traditional pickles, natto, kefir, buttermilk, and many cheeses.

Try to avoid or eat less of mass-produced highly processed foods, fast-foods, artificial ingredients, colors and dyes, additives, partially hydrogenated oils, and high-fructose corn syrup. Read all ingredient lists on labels!

Even emulsifiers (which are very hard to avoid) are linked to inflammation and effects on gut bacteria. Titanium dioxide in nanoparticle form is frequently added to candies and some foods and may disrupt gut microbes and cause gut inflammation.


Get regular exercise or physical activity. Both ordinary people and professional athletes who exercise several times a week have more diverse gut bacterial community (considered beneficial) than sedentary people. Brisk walking counts as exercise! Government guidelines say to aim for at least 1 1/2 hours per week of moderate exercise.

Avoid the use of triclosan or other "sanitizers" in soaps and personal care products (e.g., deodorants). Triclosan promotes antibiotic resistance and also kills off beneficial bacteria. Wash with ordinary soap and water.

Avoid unnecessary antibiotics (antibiotics kill off bacteria, including beneficial bacteria).

Vaginal births are best - microbes from the birth canal populate the baby as it is being born. If one has a cesarean section, some researchers suggest immediately taking a swab of microbes from the mother's vagina (e.g., using sterile gauze cloth) and swab it over the newborn baby. (See post discussing this research by Maria Gloria Dominguez Bello)

Breastfeeding is best - breastfeeding provides lots of beneficial microbes (up to 700 species) and oligosaccharides that appear to enrich good bacteria in the baby’s gut.

Live on a farm, or try to have a pet or two or more. Having pets, especially in the first year of life, increases exposure to bacteria which helps develop and strengthen the immune system, and prevent allergies. With each additional furry pet (cat or dog) the risk of developing allergies drops more, and drops to zero if a child is exposed to 5 or more pets in the first year of life.

- Daily probiotic supplements are not needed for a healthy gut microbiome. Probiotics are generally considered beneficial, but much is unknown. Some research suggests that there can be problems with routine daily use in healthy individuals (from ingesting too much of just a few species), and that taking probiotics slows down recovery of gut microbes after taking antibiotics.

The bacterial species available in stores are not those that are most commonly found in healthy individuals. Research the specific bacteria before taking any supplements, and only take when needed (for symptoms). Don't take routinely.

Researchers tend to stay away from daily use of probiotic supplements and instead focus on eating a variety of all the foods mentioned above (fruits, vegetables, whole grains, seeds, nuts, legumes, fermented foods) to feed and nurture beneficial bacteria.



Fresh & Dried Fruit  Serving Size Fiber (g)
 Apples with skin  1 medium 5.0
 Apricot  3 medium 1.0
 Apricots, dried  4 pieces 2.9
 Banana  1 medium 3.9
 Blueberries  1 cup 4.2
 Cantaloupe, cubes  1 cup 1.3
 Figs, dried  2 medium 3.7
 Grapefruit  1/2 medium 3.1
 Orange, navel  1 medium 3.4
 Peach  1 medium 2.0
 Peaches, dried  3 pieces 3.2
 Pear  1 medium 5.1
 Plum  1 medium 1.1
 Raisins  1.5 oz box 1.6
 Raspberries  1 cup 8.0
 Strawberries  1 cup 4.4
Grains, Beans (Legumes), Nuts, Seeds  Serving Size Fiber (g)
 Almonds  1 oz 4.2
 Black beans, cooked  1 cup 13.9
 Bran cereal  1 cup 19.9
 Bread, whole wheat  1 slice 2.0
 Brown rice, dry  1 cup 7.9
 Cashews  1 oz 1.0
 Flax seeds  3 Tbsp. 6.9
 Garbanzo beans, cooked  1 cup 5.8
 Kidney beans, cooked  1 cup 11.6
 Lentils, red cooked  1 cup 13.6
 Lima beans, cooked  1 cup 8.6
 Oats, rolled dry  1 cup 12.0
 Quinoa (seeds) dry  1/4 cup 6.2
 Quinoa, cooked  1 cup 8.4
 Pasta, whole wheat  1 cup 6.3
 Peanuts  1 oz 2.3
 Pistachio nuts  1 oz 3.1
 Pumpkin seeds  1/4 cup 4.1
 Soybeans, cooked  1 cup 8.6
 Sunflower seeds  1/4 cup 3.0
 Walnuts  1 cup 5.0
 Vegetables  Serving Size Fiber (g)
 Avocado (fruit)  1 medium 11.8
 Beets, cooked  1 cup 2.8
 Beet greens  1 cup 4.2
 Bok choy, cooked  1 cup 2.8
 Broccoli, cooked  1 cup 4.5
 Brussels sprouts, cooked  1 cup 3.6
 Cabbage, cooked  1 cup 4.2
 Carrot  1 medium 2.6
 Carrot, cooked  1 cup 5.2
 Cauliflower, cooked  1 cup 3.4
 Cole slaw  1 cup 4.0
 Collard greens, cooked  1 cup 2.6
 Corn, sweet  1 cup 4.6
 Green beans  1 cup 4.0
 Celery  1 stalk 1.1
 Kale, cooked  1 cup 7.2
 Onions, raw  1 cup 2.9
 Peas, cooked  1 cup 8.8
 Peppers, sweet  1 cup 2.6
 Pop corn, air-popped  3 cups 3.6
 Potato, baked w/ skin  1 medium 4.8
 Spinach, cooked  1 cup 4.3
 Summer squash, cooked  1 cup 2.5
 Sweet potato, cooked  1 medium 4.9
 Swiss chard, cooked  1 cup 3.7
 Tomato  1 medium 1.5
 Winter squash, cooked  1 cup 6.2
 Zucchini, cooked  1 cup 2.6

The tables are from

[Page updated February 2022.]

6 thoughts on “Feeding Your Gut Microbes

  1. Rhonda Witwer

    You don't talk much about resistant starch as a way to feed your gut microbes, which surprises me. There is a huge body of evidence showing that this type of fermentable fiber has a huge impact on shifting the microbiome to health-promoting varieties. Its fermentation produces more butyrate than any other fiber tested, has been shown to shift expression of more than 200 genes within the large intestine, and is directly connected to significant improvements in insulin sensitivity. A recent study by Stephen O'Keefe from the Univ of Pittsburgh showed improvements in inflammation and reduced colon cancer biomarkers. My website,, is a great place to start learning about it. With warm regards, Rhonda

    1. Sima

      Yes, resistant starch is absolutely important to the diet, but as long as a person eats a variety of plant based foods, it will include resistant starch. In my post of August 5, 2014 I included the excerpt from a study that said: "Good examples of natural sources of resistant starch include bananas that are still slightly green, cooked and cooled potatoes [such as potato salad], whole grains, beans, chickpeas, and lentils."

      The Stephen O'Keefe study is excellent in showing the importance of a high-fiber diet for health (as opposed to a low fiber, high fat and meat, high processed foods westernized diet). Some of the typical low-fat, high fiber foods (associated with good colon health) eaten in the study were: hi-maize corn fritters, beans, salmon croquettes, spinach, red pepper and onions, homemade tater tots, mango slices, okra, tomatoes, corn muffins, black-eyed peas, and pineapple.

  2. Leon Kaliniec

    I found your article very informative and making good common sense, but it's totally dedicated to "Feeding your gut microbes", what, you've nothing to feed? In extreme case where one one has been fed an overdose of various antibiotics there are so few bacteria left there is nothing to feed. Is Fecal Transplant the only option? Isn't there a pro/pre biotic containing a representative culture gut bacteria?

    1. Sima

      Once beneficial gut bacteria species have been totally eliminated - then they're gone (see post). Unfortunately probiotic supplements on the market contain only several species (while the gut has hundreds of species), research suggests they don't stick around in the gut, and the microbes are not some that are thought to be "keystone species" - such as Faecalibacterium prausnitzii.
      But don't despair. You can definitely improve on the microbial gut communities that you do have by feeding and nurturing them... and you can also ingest many more by eating a variety of raw fruits and vegetables, fermented foods, cheeses, going outside and gardening or being active, being exposed to animals, drinking water, etc.
      A research article I posted about found that each raw fruit and vegetable tested had a variety of bacterial communities - from 17 to 161 families of bacteria. Which is why eating a variety of unprocessed foods is so important.
      And try to eat as many organic foods as possible (because pesticides kill microbes - not just on the fruits and vegetables, but research suggest that residues of pesticides such as Roundup/glyphosate kill beneficial gut microbes).
      I suspect that the longer one is off antibiotics, the better the gut microbiome looks (even if you originally took them for years). A study looking at this has not yet been done.

  3. Janice Cattanach

    Oh my. Years of antibiotic use for acne has increased my chronic sinusitis, and made me antibiotic resistant. Although I was born in the 50's and never took an antibiotic until I was 17, after that I lived on them for the cystic acne. I am an RN and was advocating probiotics in yogurt before doctors were. I reasoned that killing the bacteria in the gut was responsible for post-antibiotic diarrhea. Now all the doctors are on the bandwagon! I went on an anti-inflammatory diet at age 62, and my cystic acne disappeared in 3 days. Gluten was what was causing my acne even at this age! Last year I was unable to get rid of my sinus infections. I would get off a 14 day round of antibiotics and in a month I was sick again. I have done much research but a couple of months ago, I found an article on L. sakei and ordered it. I was already sick; I put the powder in my nose, and in 5 minutes felt a difference. Within 24 hours I felt normal! Praising Christ Jesus for this discovery! I just shared some of the bacteria with a cancer survivor that can't get over her sinus issues. She never had them before chemo, but says it is like allergy sensitivities now. So, now learning how to feed the bacteria. Hoping to do the oral capsules of fecal microbiome at some point. Thank you so much for all this research you continue to do.

  4. Laura

    I really appreciate the information, I think we still have a lot to know about probiotics. I have had problems in the intestinal flora after having to take many antibiotics, a friend recommended me Lactoflora probiotics and the truth is that they were very well for me.


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