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What to Feed Your Gut Bacteria

For many years, it was believed that the main function of the large intestine was just to absorb water and dispose of waste, but “[n]owadays it is clear that the complex microbial ecosystem in our intestines should be considered as a separate organ within the body,” and that organ runs on a MAC, microbiota-accessible carbohydrates. In other words, primarily fiber.

One reason we can get an increase of nearly two grams of stool for every one gram of fiber is that the fiber fermentation process in our colon promotes bacterial growth. The bulk of our stool by weight is pure bacteria, trillions and trillions of bacteria, and that was on a wimpy, fiber-deficient British diet. People who take fiber supplements know that a few spoonfuls of fiber can lead to a massive bowel movement, because fiber is what our good gut bacteria thrive on. When we eat a whole plant food like fruit, we’re telling our gut flora to be fruitful and multiply.

From fiber, our gut flora produce short-chain fatty acids, which are an important energy-source for the cells lining our colon. So, we feed our flora with fiber and then they turn around and feed us right back. These short-chain fatty acids also function to suppress inflammation and cancer, which is why we think eating fiber may be so good for us. When we don’t eat enough whole plant foods, though, we are in effect starving our microbial selves, as I discuss in my video Gut Dysbiosis: Starving Our Microbial Self. On traditional plant-based diets, we get lots of fiber and lots of short-chain fatty acids, and enjoy lots of protection from Western diseases like colon cancer. In contrast, on a standard American diet filled with highly processed food, there’s nothing left over for our gut flora. It’s all absorbed in our small intestine before it even makes it down to the colon. Not only may this mean loss of beneficial microbial metabolites, but also a loss in the beneficial microbes themselves.

Research shows the biggest issue presented by a Western diet is that not leaving anything for our bacteria to eat results in dysbiosis, an imbalance wherein bad bacteria can take over and increase our susceptibility to inflammatory diseases or colon cancer, or maybe even lead to metabolic syndrome, type 2 diabetes, or cardiovascular disease.

It’s like when astronauts return from space flights having lost most of their good bacteria because they’ve had no access to real food. Too many of us are leading an “astronaut-type lifestyle,” not eating fresh fruits and vegetables. For example, the astronauts lost nearly 100 percent of their lactobacillus plantarum, which is one of the good guys, but studies reveal most Americans don’t have any to begin with, though those who eat more plant-based are doing better.

So it’s use it or lose it. If people are fed resistant starch, a type of MAC found in beans, within days the bacteria that eat resistant starch shoot up and then die back off when you stop. Eating just a half can of chickpeas every day may “modulate the intestinal microbial composition to promote intestinal health” by increasing potentially good bacteria and decreasing pathogenic and putrefactive bacteria. Unfortunately, most Americans don’t eat beans every day or enough whole grains, enough fruits, or enough vegetables. So, the gut flora—the gut microbiota—of a seemingly healthy person may not be equivalent to a healthy gut flora. It’s possible that the Western microbiota is actually dysbiotic in the first place just because we’re eating such fiber-deficient diets compared to populations that may eat five times more fiber and end up with about 50 times less colon cancer.

This is one of the reasons I recommend three daily servings of legumes (beans, split peas, chickpeas, and lentils) in my Daily Dozen checklist.

The microbiome connection may explain the extraordinary results in the study I featured in my video Is It Worth Switching from White Rice to Brown?.

More on the musical fruit:

More on the microbiome revolution in medicine:

For more on bowel health, check out:

In health,
Michael Greger, M.D.

PS: If you haven’t yet, you can subscribe to my free videos here and watch my live, year-in-review presentations:


Michael Greger M.D., FACLM

Michael Greger, M.D. FACLM, is a physician, New York Times bestselling author, and internationally recognized professional speaker on a number of important public health issues. Dr. Greger has lectured at the Conference on World Affairs, the National Institutes of Health, and the International Bird Flu Summit, testified before Congress, appeared on The Dr. Oz Show and The Colbert Report, and was invited as an expert witness in defense of Oprah Winfrey at the infamous "meat defamation" trial.

69 responses to “What to Feed Your Gut Bacteria

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  1. Dr. G., how many times do you run to the toilet every day? I happened to watch a recent Bobby’s Perspective, and he said that when he used to follow a WFPB diet he’d sit on the royal crown a good 16 or so times a day.

    Which sounds like a stretch. (There’s gotta be a pun in there somewhere.)

    1. Am thinking I meant to write “throne,” not crown. How does one sit on a piece of head apparel? I guess anything’s possible.

      (Mercury does direct again in a coupla days. Yaaaay.)

        1. Laughing

          Yes, I have that problem, especially on my cell phone.

          My new phone is slightly better at spelling than my last iPhone, but they didn’t optimize it with Grammarly.

          It drives me crazy because the letters are so small and when I type “sub” as an example, it offers me

          -stitution -stance -traction

          rather than saying

          substitution substance subtraction

          I find it harder to figure out what they are offering as suggestions.

          The good part is that it is trying to learn what I want to say. I like that part, but I don’t like it just showing the endings.

          Plus, when I push on the ending I want, it doesn’t always give it. That has happened several times and I think it changed it, but it only added on a random letter, rather than changing the word.

          It still changes things without my permission.

          But it is still better than my old phone.

          My old phone would wait until the very last second when I would push send and suddenly it would do things like changing the word “prostate” to “prostAte” as it was sending.

  2. I love the simplicity of evidence-based eating! When I was working at whole foods, I would see people spend 50-200 on a small bottle of pro-biotic pills. As a poor college student, I’ll definitely take the 99 cent can of organic chickpeas.

    1. Linda,

      Yes, I have a friend who has such gut problems and she has been on antibiotics over and over again, followed by probiotics over and over and over again.

      It costs a fortune and doesn’t work.

      Allergists have had her doing the elimination diet for decades and it has just made her have crazy theories of what she might be allergic to. She has spent decades saying, “I think I am allergic to…. soy, wheat, yeast, nope, I can eat wheat, but I can’t eat nuts or fruit or maybe it is….”

      Not one doctor has said, “Fix your gut microbiome.”

      Beans, the other elimination diet.

    2. Or, Linda—who wrote, “As a poor college student, I’ll definitely take the 99 cent can of organic chickpeas”—how about ca. $1.49 for a pound bag of dried garbanzos, with which you could make the equivalent of four (!) 15-oz. cans of chickpeas?

  3. This is great information—imagine, 50 times less colon cancer, and just for eating five times more yummy beans! But Dr. Greger seems to be in need of new ideas. How about looking into fasting and its benefits?

  4. Qustion: So food in the resistant starch group like plantain and my favorite plantain flour is equally good for healthy flora biomes?

    1. How important is it to buy organic greens? I see that some greens are in the dirty dozen list. Does a salt water rinse or soak help with that?

      1. hi Don DiSciascio,
        The following 2 videos would be worth the few minutes for you to watch. They suggest ways to clean the produce we buy, and also give perspective on the ‘is organic food worth it’ question. For us, even non-organically leafy greens are too expensive to buy in the off season. Winter time means spending over $6 for a small half dozen chard, kale, or whatever leaves! The Environmental Working Group (the watch dog that issues the dirty dozen and clean thirteen lists) says, eat your veggies no matter what. Dr Greger illustrates why in the second video. (if It is organic and on sale, we buy it, and if it isn’t we don’t)

    2. Sammy,
      I’d assume so, at least I’ve never seen a statement to the contrary. Cf.

      Heat is also an important consideration. From the link above:

      “The amount of resistant starch changes with heat. Oats, green bananas, and plantains lose some of their resistant starch when cooked. Another type of resistant starch is made in the cooking and cooling process. Cooked rice that has been cooled is higher in resistant starch than rice that was cooked and not cooled.

      How to Add Resistant Starch to Your Diet

      Try cooking rice, potatoes, beans, and pasta a day in advance and cool in the refrigerator overnight. It’s ok to reheat the starch before eating. Reheating doesn’t decrease the amount of resistant starch. In place of cooked oatmeal, try uncooked oats soaked in yogurt, milk, or a non-dairy milk and refrigerate overnight (often called overnight oats).
      Add lentils to a salad or soup.

      As a partial flour replacement try green banana flour, plantain flour, cassava flour, or potato starch. Resistant starch will be lost when baking or cooking with these flours. “

    3. Hi Sammy,

      I am a volunteer for Dr. Greger. Thank you so much for your question.

      Plantains are likely very good for your gut bacteria. However, it is possible that plantain flour may not be as good, although I cannot say this for certain. Foods that are turned into flours (like wheat flour, almond flour, etc.) or nut butters (e.g., peanut butter) is absorbed at a much greater rate in the small intestine. Therefore, less is left over for the bacteria in our large intestine to feed on. This can result in less favorable gut bacteria diversity.

      This concept is explained well in Dr. Greger’s video here:

      I hope this helps answer your question!

  5. I was SO hoping Dr. Oz would be doing another of his “What Does Your Poop Look Like” shows, but it’s True Crime Tuesday. The show is supposed to be about how how somebody’s husband tried for three years to poison her.

    1. Must be poison week. I ended up watching “Murder She Solved” yesterday and that was about poisoning, too. It didn’t end up being her husband. It ended up being a neighbor with a murder mystery serial killer wish. (He hosted “murder mystery parties” in his house and also killed his neighbor the same way as the death in the party.”

      The one before that was good. A woman detective felt like her dead body seemed to be somehow related to a dead body in another town, which she was told to drop the case, but she did it on her spare time. Turned out that the murder for hire got off the freeway in the wrong direction and murdered the wrong person. She went up to see where the person had lived and made the same wrong turn and got the revelation to the case.

      The second one was a stubborn reporter who connected two cases on her spare time, and that one was a poisoning case, too. That one hit home because the woman murdered her husband and boyfriend with antifreeze.

      The science is fascinating in them. So is the logic.

      I have a relative-relative (by marriage twice removed, but we celebrate the holidays together) who is a police detective who solved a big case out of just being stubborn.

      That was the only time I was ever jealous of his job. I would love to do a trying to figure things out type job.

  6. There is some evidence probiotics are harmful, at least if taken to after a course of antibiotics. Small study of 21 people but still, I found it an eye-opener.

    Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT

    Bottom line seems to be once again that whole food trumps pills.

    1. For those that aren’t in the life sciences field, Cell is considered the to be one of the most prestigious peer reviewed journals of biological research (if not the most). That doesn’t mean that all its articles are well designed research, but it does increase the odds.

  7. Being a serial short-cut taker, I add a quarter tsp of Inulin to a 12 oz glass of mango or guava juice, along with a quarter tsp of brewer’s yeast and 3-5 shakes of angustora bitters.

    Nothing but well-formed softies when doing this.

    Oh, forgot to mention… I also eat a half-green banana once or twice a day.

    1. “Nothing but well-formed softies when doing this.”

      – – – – – –


      Perhaps you could film a video and post the link showing us the size and shape of some of your little softies. I’m sure all the folks would be thrilled to death to watch it. :-)

      Dr. Oz would, anyway.

      1. Perhaps you could film a video and post the link showing us the size and shape of some of your little softies. I’m sure all the folks would be thrilled to death to watch it. :-)
        Heh, due to the fact I’m capturing my stool in one of those stand-alone camping toilets (to compost as fertilizer for my future Industrial Hemp plot) I am unable to observe my stool until I empty the unit. But when they come out they appear soft and well formed plus I visualize their shape and feel as I expell the cute little turds.

        And while I’m discussing my biologics, (and since I’m not using my real name on this forum ‘-) I’ll also admit to capturing my urine in a gallon glass jug both in order to observe the clarity (sometimes I can fill an entire jug and observe no cloudiness whatsoever… suggests my kidney are functioning properly. When it gets cloudy at about a half gallon, I revert to drinking more water and less tea and other thick drinks)… and to use as fertilizer on the various trees on my property. Since doing that, my trees have become healthier and stronger.

        1. forgot to mention (must have been the proponol ‘-) I also add a small amount of Kombucha to start things on their way to breaking down.

        2. My grandmother was a nurse, so I grew up with a lifetime of discussions about what stool and urine looked like.

          I look and make sure that it isn’t black and that it flushed down my non-composting toilet.

          We don’t have a water shortage where I live.

          When I lived in California, the rules of people’s houses were:

          If it’s yellow, let it mellow, if it’s brown, flush it down.

          It took a while to adjust to coming back to a place where we had a well with plenty of water after years of not washing cars and not flushing toilets.

          My elderly relatives had piss pots and an outhouse. My friends father’s house still has an outhouse and piss pots.

          My dog peeing on the grass got less damaging when I switched his diet, but my friend’s father used to pee wherever he happened to be outside and he had tell tale grass yellowing. Must be diet.

          My dog used to be the biggest lawn murderer I had ever seen.

      1. I worked for 10 years in a building with no running water. We had portapotty’s.

        I have also camped with outhouses.

        I have never used a composting toilet.

        I have used a commode when my uncle used to fall asleep in the bathroom for an hour.

  8. We installed an air compressor in my gut that runs on plants, put beans in and it doubles it’s output. Fruit makes it go really good too.

      1. Tonight was a news night to remember.

        Round up officially caused cancer. That is huge!

        Waiting for the dominos to start falling. Organic, here everybody comes!

        I hope they help the small farms go organic. They can’t afford the process.

  9. I have ulcerative colitis. I have tamed it completely with diet, but if I eat the wrong foods it quickly flares up.

    I do not each sugar, gluten, yeast AND I AVOID LEGUMES.

    This is based on my own personal experience, not and science.

    I personally find all legumes leads lead to bowel inflammation. Lentils are the worst, closely followed by chick-peas (which is a shame, as I used to love hummus).

  10. Rinse dried beans and pulses in cold water. Soak over night or at least 6-8 hrs. during the day. Empty water, rinse beans again for several minutes. Then cook on high until the water boils, turn down to low and simmer for about 10 minutes. Remove from heat rinse thorougly. Place in cold water, bring to boil, turn down heat and simmer for about 20-35 min, This helps remove the chemicals in the beans that cause gas.

    1. Joan,
      That’s quite a process, and I am sure it is effective. From your description, it seems that cooking in an Instant Pot as I do would not be effective. Do you happen to know?

  11. I would like to know what alternative food options there are to to feed good Bacteria besides beans. I have many food allergies including Legumes, Beans and Tree nuts as well as many healthy vegetables such as Squash, Tomato and Cauliflower. I take a probiotic supplement but would prefer to build my gut health with healthy food. I bought your “How not to Die” Cookbook and realized I am allergic to most of the ingredients, (sigh)..

    1. Hello,

      The best foods for feeding gut bacteria will be fiber rich foods. Fortunately for you, all whole plant foods contain fiber! Also, if you’re allergic to beans, but not lentils, then lentils could be a great way to check off the legume section on Dr. Greger’s Daily Dozen.

      Matt, Health Support

    2. D Grl, I would suggest Inulin. The one I use is the NOW brand, made from Organic Blue Agave. IIRC, it can also come from Artichoke.

      Of course there are things like green bananas that will fuel your lower gut. I eat those in addition to stirring a small amount of Inulin into a drink.

      Another good one is raw potatoes or even cooked potatoes that are refrigerated. If they are something like new potatoes they form a hard outer shell, but I’m guessing that mashed potatoes, refrigerated, will do the job.

        1. This brings up a question… I’ve got some packaged mashed potatoes in my freezer I haven’t tried yet. Your pointing out that the unmodified potato starch needs to be used cold for resistance… I think I read somewhere that cold potatoes otherwise prepared could be reheated.

          I’m curious if someone has info about heating up the aforementioned mashed potatoes (since they are frozen) still being resistant?

          1. Good question. In the case of white rice, I previously posted a study concluding that reheated retains some but not all of the resistant starch (forget the %s).

    1. Yes! But please read the ingredients to make sure there aren’t a bunch of additives.

      Matt, Health Support

  12. I am MACRO tracking my diet, (Carbs, Fats, Protein, Fiber). The maximum fiber intake is 25g per day. I have been taught that to much fiber, more than 25g per day for women, leaches out important micronutrients from the gut and is counter productive. What do the scientific facts say? It is very challenging for me to eat a plant based diet without having to add some sort of meat and dairy to gain the benefits of muscle development! I have been struggling with this dilemma. HELP!

  13. The data overwhelming finds that at least 40g of daily fiber, up to 65g daily, has increasing health benefits across many health outcomes. These include: lower diabetes risk, lower cholesterol, lower risk of colorectal cancer, lower blood pressure, lower heart disease, lower heart failure.

    Fiber does not leech out micronutrients, thankfully.

    Here is the search result for Dr Greger’s many videos on protein, harms of animal protein vs plant protein, data demonstrating that plant protein is of higher quality and associated with far better health outcomes, and that entirely plant based eaters get nearly the same amount of dietary protein as omnivores, which is still several times the protein necessary for all bodily functions including muscle growth.

    There are also many entirely plant-based strongmen, MMA fighters, and bodybuilders you can seek out for advice on professional bodybuilding entirely on the far healthier protein from plants. Just search online.

    Best to you!

  14. The final sentence in the blog “What to Feed Your Gut Bacteria” states: “It’s possible that the Western microbiota is actually dysbiotic in the first place just because we’re eating such fiber-deficient diets compared to populations that may eat five times more fiber and end up with about 50 times less colon cancer.” This has raised questions in my mind.

    The article referenced in the above statement (Am J Clin Nutr. 2013 Jul; 98(1): 111–120.
    Published online 2013 May 29. doi: 10.3945/ajcn.112.056689. Ou, et al “Diet, microbiota, and microbial metabolites in colon cancer risk in rural Africans and African Americans”) identifies differences in gut flora, but I did not see where it compared how much fiber each group ate. And I also noted that it is a very small study group (12-15 men in each group)

    In that article, I do see where Dr. Gregor has come up with “decrease by 50 times”, but in the context of talking about fiber that seems a bit misleading. The reference uses WHO statistics on incidence of colon cancer in native Africans compared to African-Americans. The article also notes there is a huge difference in amount of protein and fat in the two diets. And one must also ask what other differences there are in lifestyle, longevity, access to health care, etc exist to make that such a dramatic difference. One of the studies referenced actually mentions there is no difference in fiber content (J Nutr. 2007 Jan;137(1 Suppl):175S-182S. doi: 10.1093/jn/137.1.175S. O’Keefe et al “Why do African Americans get more colon cancer than Native Africans?”), although I find that hard to believe.

    Most of studies with which I am familiar (such as Adventist Health studies and Nov 2011) Aune et al. Dietary fibre, whole grains, and risk of colorectal cancer: systematic review and dose-response meta-analysis of prospective studies) put decreased risk at 10% for each 10 g added fiber. I have not seen where that is a linear relationship beyond total risk lowering by 35-40%, although it is possible it is out there. It is possible, I suppose to round off and suggest that there is a 50% decrease in risk in response to dietary fiber. But a 50% decrease in risk is much different than “50 times”.

    It is also interesting to note that Aune et al state that fibers from cereals are more helpful than that from legumes. The focus of the blog seemed to be “eat more legumes to make your gut bacteria happy” when cereal fiber may do a better job. (Although I do admit there are references to fruits an grains found within the blog as well)

    So it would seem to me that there are many other factors leading to this wide difference in colorectal cancer between native Africans and African Americans. In the interest of not misleading the public as to the real decrease in risk with increased fiber and improved gut flora, would it not be better to state 40% (which is well-documented) rather than 50 times (which is a difference in incidence between two widely divergent groups with many, many differences in risk factors not taken into account with pure incidence numbers). If you have further references on this issue, I would be happy to read them.

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