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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, cancer, and especially colon cancer. On the other hand, the presence of other bacteria (e.g. the beneficial bacteria Faecalibacterium prausnitzii) are associated with health and lower levels of chronic inflammation.

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

THE ISSUE IS: How can one improve, feed, and nurture the beneficial bacteria in our bodies?

While no one knows what exactly is the "best" or "healthiest" microbial composition of the gut, certain patterns or the mix of microbes are linked to either poor or good health. It looks like a diversity of bacteria is best (may make you healthier and more able to resist diseases), and that higher levels of certain beneficial microbes are good and linked to lower levels of chronic inflammation in the body, and to lower risk of certain diseases and conditions (e.g. heart disease).

Research also suggests that the diversity and balance of bacteria living in the body can be changed and improved, and that changes can occur very quicklyThe microbial communities fluctuate for various reasons (illness, diet, etc.), but diet seems to be 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 bacteria, and different foods feed different bacteria.

Three terms that are frequently mentioned are: Prebiotics feed the beneficial bacteria in the gut, probiotics are live beneficial bacteria, and synbiotics are a combination of prebiotics and probiotics. But don't buy supplements - all you need to do is to eat real, whole foods, especially foods from plants. It's the fiber in foods that feeds beneficial bacteria.

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 more raw fruits and vegetables (lots of microbes and fiber to feed and nurture the microbes in the gut). Some every day would be good. 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 (e.g. apples) 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 (a recent study suggested up to 50 grams of fiber daily for men to reduce colon cancer risk). One could take fiber supplements, but actual real foods have many more benefits to them, and also provide a variety of fiber sources. (See How Much Dietary Fiber Should We Eat? and Recent Studies Show Benefits of Dietary Fiber).  {SCROLL DOWN FOR HIGH FIBER FOOD CHART }

Eat as many organic foods as possible. There is much we don't yet know about pesticide residues on our foods. Pesticides are like antibiotics - they kill off microbes, both good and bad, and current thought is that pesticide residues in food may also possibly kill off some beneficial bacteria in the gut (especially Roundup with the active ingredient glyphosate), as well as some other health effects. Thus lowering the levels in your body of pesticides (as measured in blood and urine) is beneficial.

Also, organic foods don't contain added antibiotics and hormones, and there are some nutritional differences. (See post Eat Organic Foods to Lower Pesticide Exposures). But 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. It 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. Again, a variety of foods is best because each food has different microbial communities.

Try to avoid or eat less of mass-produced highly processed foods, fast-foods, preservatives, colors and dyes, additives, partially hydrogenated oils, and high-fructose corn syrup. Read all ingredient lists on labels, and even try to avoid as much as possible "natural flavors" (these are chemicals concocted in a lab and unnecessary).

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.


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,  ups exposure to bacteria to help develop and strengthen the immune system, and prevent allergies. Pets such as dogs and cats expose humans to lots of bacteria. One study found that with each furry pet (cat or dog) the risk of developing allergies drops more with each additional pet,  and drops to zero if a child is exposed to 5 or more pets in the first year of life.

Get regular exercise or physical activity. Professional athletes and ordinary people who exercise several times a week have more diverse gut bacterial community (considered beneficial) than sedentary people.

- Should one take probiotic supplements?  Probiotics  are generally considered beneficial, but much is unknown. However, some recent research has suggested 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.

Research shows that a healthy diet is the best way to feed and nurture beneficial microbes and lower inflammation that is linked to chronic diseases (e.g. diabetes, heart disease).

Supplements are unregulated, and 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 fruits and vegetables have hundreds of microbial species in and on them, and those that are organic may have more beneficial microbes.



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 September 2021.]

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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