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How to Foster a Healthy Gut Flora

What’s more important: probiotics or prebiotics? And where can we best get them?

“Virtually every day we are all confronted with the activity of our intestine, and it is no surprise that at least some of us have developed a fascination for our intestinal condition and its relation to health and disease.”

“Over the last years the intestinal microbiota [our gut flora] has been identified as a fascinating ‘new organ’” with all sorts of functions. Well, if the bacteria in our gut make up an entire, separate organ inside our body, what about doing an organ transplant? I discuss this in my video How to Become a Fecal Transplant Super Donor.

What would happen if you transferred intestinal bacteria from lean donors into obese subjects? Researchers figured that rebalancing the obesity-causing bacteria with an infusion of gut bacteria from a lean donor might help. They had wanted the study to be placebo-controlled, which, for drugs is easy, because the control subjects can just be given a sugar pill. But, when you’re inserting a tube down people’s throats and transplanting feces, what do you use as the placebo—or poocebo, if you will? Both the donors and the subjects brought in fresh stools, and the subjects were randomized to either get a donor’s stool or their own collected feces. So, the placebo was simply getting their own stool back.

What happened? As you can see at 1:32 in my video, the insulin sensitivity of the skinny donors was up around 50, which is a good thing. High insulin sensitivity means a low level of insulin resistance, which is the cause of both type 2 diabetes and prediabetes. The obese subjects started out around 20 and, after an infusion of their own feces, stayed around 20. The group of obese donors getting the skinny fecal infusion similarly started out low but then shot up near to where the slim folks were.

It’s interesting that not all lean donors’ stools conveyed the same effect on insulin sensitivity. Some donors, the so-called super-fecal donors, had very significant effects, whereas others had little or no effect, as you can see at 2:02 in my video. It turns out this super-donor effect is most probably conveyed by the amounts of short-chain fatty acid-producing intestinal bacteria in their feces. These are the food bacteria that thrive off of the fiber we eat. The short-chain fatty acids produced by fiber-eating bacteria may contribute to the release of gut hormones that may be the cause of this beneficial, improved insulin sensitivity.

“The use of fecal transplantation has recently attracted considerable attention because of its success in treatments as well as its capacity to provide cause–effect relations,” that is, cause-and-effect evidence that the bacteria we have in our gut can affect our metabolism. Within a few months, however, the bacterial composition returned back to baseline, so the effects on the obese subjects were temporary.

We can get similar benefits by just feeding what few good gut bacteria we may already have. If you have a house full of rabbits and feed them pork rinds, all the bunnies will die. Yes, you can repopulate your house by infusing new bunnies, but if you keep feeding them pork rinds, they’ll eventually die off as well. Instead, even if you start off with just a few rabbits but if you feed them what they’re meant to eat, they’ll grow and multiply, and your house will soon be full of fiber-eating bunnies. Fecal transplants and probiotics are only temporary fixes if we keep putting the wrong fuel into our guts. But, by eating prebiotics, such as fiber, which means “increasing whole plant food consumption,” we may select for—and foster the growth of—our own good bacteria.

However, such effects may abate once the high-fiber intake ceases. Therefore, our dietary habits should include a continuous consumption of large quantities of high-fiber foods to improve our health. Otherwise, we may be starving our microbial selves.

The microbiome is one of the most exciting research areas in medicine these days. For more information, see, for example:

For more on health sources of prebiotics, 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 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.

49 responses to “How to Foster a Healthy Gut Flora

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  1. Looking at this topic again, it is interesting that some thin people had very little short-chain fatty acids.

    “Some donors, the so-called super-fecal donors, had very significant effects, whereas others had little or no effect…..”

    Does that mean they are probably Keto?

      1. Good article Barb, and has link to best fiber foods also, beans, oatmeal, fruit, veggies. Foods that people resist eating unfortunately.

      1. True, the human holding the sheeeeeeeyet seems to have a lot more on the top of the head than Dr. G. (who has none). He does have similarly delicate hands, though, I noticed.

  2. “inserting a tube down people’s throats and transplanting feces”
    Is this correct?
    I thought fecal transplants were done via enema or colonoscopy?

    1. The places that do it tell how they do it. Some use capsules and they tell people.

      Honestly, I looked it up for my friend and I couldn’t mentally think which would be harder.

      Trying to swallow the capsules or doing it the other way.

      I think I will eat the vegetables.

  3. Hi Doc, I registered just so I could tell you thanks for what you’re doing. I appreciate it and the best of health to you and yours :)

  4. Hello,

    I am a supporter of and a big fan of Dr. Greger’s work and have read both of his 2 latest books, How Not to Die and Diet. I have been a 100% whole food, plant-based eater for a decade with an extremely high fiber diet, up to 150 grams a day, however, as of quite recently, I have had a large hiccup in my microbiome health. Hoping Dr. Greger could help me understand if eating TOO much fiber could cause deleterious health effects and gastrointestinal issues.

    Thank you very much!

    1. Mark,

      Could you explain what a microbiome hiccup means?

      Did you have a test with too many bad gut bacteria or too few good guys

      Or are you having GI problems?


      Are you drinking high alkaline water or taking natural antibiotics?

      1. I have seen writings that cause me to ask:

        Did you switch your diet recently?

        Do you know that you have enough B12, D3, and Omega 3?

        Do you eat a lot of dried fruits?

        Are you eating sugary vegan foods?

        I am not a doctor. I have watched videos from people like Gojiman and Plant-Based Science.

        Dr. Greger will have your question on his list because you brought the topic up here, but Plant-Based more often heals gut microbiome.

        If it is recent, maybe you need to try to figure out what changed in your diet during that time.

      2. Hi Deb,

        Thank you for your speedy and thoughtful reply. What I meant by a microbiome hiccup was 10 days ago, I began experiencing constipation and diarrhea (2 things that I have NEVER experienced on my 10 year, whole food, plant-based diet). Currently, I am still having these same symptoms. My diet consists of oatmeal, sprouted grain bread and cereal, raw walnuts, chia, hemp and flax seeds daily, berries and a variety of fruits, leafy greens, vegetables, avocados, legumes, salads, tofu, tempeh, mushrooms, onions. Truly, I am the healthiest eater you’ll find. My wife, daughters and I (even my dog Max) are 100% whole food, plant-based. My splurge is 88-100% dark chocolate with a handful of cashews or peanut butter in the evening. I follow a strict 16 off, and 8 hours on eating program. My eating window if from 10-11am to 6 or 7pm. I have always had fantastic bowel movements, 2-3 a day and I eat between 150-175 grams of fiber a day ( my wife and I did the calculations earlier this week). During those 8 hours, I am a voracious eater and have a large appetite. For a living, I am a Health Psychologist/ nutritionist and am extremely active with clients walking, jogging, lifting weights and playing hours of tennis a day. I am 5′ 10” and weigh 160lbs. Two-three days a month, usually on Mondays, I do a 24-36 hour fast as well. This has always kept me full of energy, regular and feeling great. A colleague ( a dietician) examined my diet and said my fiber consumption was the highest she has ever seen and that I should switch to a low fiber diet for a couple of days. I love my high fiber diet, ( although tonight I had white angel hair pasta for the first time in 10 years and it melted in my mouth), and want to get back to it, but when researching too much fiber on the web, my symptoms of diarrhea, constipation, sore belly and bloating are consistent with the overconsumption of fiber). I understand the science behind the microbiome, I teach it at University and want to continue to feed it high quality fiber in order to receive those SCFAs. I would NEVER eat meat, dairy or eggs, do not want any part of the TMAO, and also want to get back to lentils and the like fast!

        I take a B12 supplement, 1,000mcg every other day, get plenty of sun and take a low dose algae omega 3 supplement every other day with 300 mg of DHA and 150mg of EPA.

        Really nothing new in my diet. The Algae supplement is the latest thing, but I started that 2 months ago. I am on zero medications, take no drugs, no alcohol and have wonderful spiritual practices like meditation and prayer that I do daily. My stress is minimal and my life is phenomenal!

        Any help would be greatly appreciated. I teach the importance of eating more fiber and less cholesterol in my practice, and do not expect my clients to eat half as much fiber as I do. My clients call me the fiber king.

        I appreciate your time and thoughtfulness,

        1. Mark,

          Thank you for your amazing answer.

          You have a mystery on your hands.

          I am tending to not think it would be fiber, after all of these years.

          I read your whole post but I have already forgotten if you are 100% organic.

          I wonder if there could have been some contamination.

          Also, a few of us on the site have had Methyl B-12 fails because it isn’t always shelf-stable.

          I started having a lot of symptoms that seemed like it could be B-12 related when I lowered my fortified plant milk intake and the symptoms went away when I switched back to Cyano.

          Also, one woman who was vegan who started having problems turned out to be low in Lactobacillus.

          No new pets or romantic partners or spouse cheating on a plant based diet or taking oil of oregano or drinking too much high ph water?

          That part is based on studies Dr Greger had posted where the half hour of kissing or having a dog would give you the other persons gut bacteria.

          If it keeps going maybe get checked for yeast overgrowth/ SIBO. A lot of the YouTube ex-vegans got things like SIBO.

          One person ended up needing to lower their grains but it wasn’t about fiber it was leaky gut related.

          Drink your cabbage juice and eat your broccoli sprouts is what I told my cousin who had stomach ulcers.

          Broccoli sprouts helped something like 80% of h pylori cases, I think.

          He and I walked through that part about 2 years ago.

          Right now, I have him eating Foods for nitric oxide because Dr Burke reverses gangrene using nitric oxide as one of his mechanisms.

          But I am pretty sure about the broccoli sprouts.

          Again, I am not a doctor.

          Gojiman said that a lot of the people who have digestive problems like SIBO had done long fasts.

          You mentioned fasting so I will send you to Gojiman’s Site and he talks about fasting as being able to mess things up.

          He is a nutritionist I think. Or one in training.

          He sells SIBO testing kits but I am not sending you to him for that. Just that there are ex-vegans who left because of GI problems and I am pretty sure fasting long periods of time and alkaline water were 2 factors.

          I will be praying for you but I know that you are doing so great that this is just a learning curve moment. Small tweaks or time.

          Also don’t forget COVID can have those symptoms.

        2. Mark

          My understanding is that a high fibre intake can actually result in constipation if fluid intake is low. Exercise can also help fibre move through the system.

          if increased fluid intake (and/or prunes) does not improve matters within three or four days, it may be prudent to consult your family doctor to rule out more serious causes.

          1. Fumbles, your points about drinking fluids and maintaining exercise were key in my case. I get around 60 to 75 gm fiber/day, but then I probably eat less than half of what Mark does. I average about 4 or 5 gm per 100 calories I eat in a day.

            Mark’s question caused me to look up more info, and sure enough, there can be consequences to eating too much. Developing (rare) a phytobezoar is one possibility. Anyway, these links may be helpful to Mark too:


    2. Hello Mark,

      In the case of a “microbiome hiccup,” it’s difficult to determine what the issue is, since that simply is not enough information. I would suggest having a proper evaluation from your doctor and possibly a gastroenterologist to further diagnose the issue. As for your question about “too much fibre,” high fibre diets aren’t the cause of gut concerns, but can reveal underlying issues. In some people, a slow increase in fibre is recommended. However, in your case, I really can’t get to the bottom of what is going on without a proper medical evaluation.

      I hope this information helps and that you can take the time to have a proper evaluation.
      Dr. Matt

  5. To Dr Greger

    Dr Burke talked about nitric oxide is something infrared increases as part of his reversing gangrene.

    I see his case studies with photos on YouTube, but are there studies other than case studies?

    His pictures are enough but I am trying to get my cousin to eat his beets and greens, etc.

    The grotesque photos seem to have worked.

    He is using infrared and PEMF.

    But food increases nitric oxide and there was a person on Forks Over Knives who didn’t have an amputation, too.

    1. Here are cases where they used things like sepia, silica, and sulfur.;year=2015;volume=9;issue=2;spage=114;epage=122;aulast=Mahesh

      Silica and Sulfur, to me, is Fiji Water and cruciferous, allium, and beans.

      I have to look all of it up in relationship to dialysis, but if I can buy him a case of Fiji water and a basket of broccoli and cauliflower and cabbage, I will be very happy.

      I still don’t know what sepia is or if it is necessary. I think they said, “sequentially” and I wonder if that is necessary. Or if I understood it properly. For the silica and sulfur would that mean a week of drinking Fiji water followed by a week of high cruciferous?

    2. I am trying to understand the arginine and Homocysteine part of gangrene.

      Getting there.

      How to lower homocysteine in a meat eater is going to take a process.

      1. Deb,

        You truly amaze me with all the things you are “trying to understand” — most of which I couldn’t care less about. Seriously!

        1. YR,

          You probably don’t have a relative who has been told he needs an amputation.

          I found studies on All sorts of things that speed wound healing or prevent amputation but his doctor won’t tell him even one thing.

          Today, I found that pineapple might help him. The enzyme has been studied.

          I have found 10 things already and his doctor only knows surgery.

  6. I think about the Blood Sugar Rising documentary and how they ended up with a whole department related to amputations.

    Is it that they don’t know or is it that they make more money if things go toward amputations and dialysis, and blood sugar meds, etc?


    That is one of my particular crises of trust issues.

  7. Another off-topic post (sorry RB)

    ‘The American Cancer Society has updated its cancer prevention guidelines to emphasize a shift away from a “nutrient-centric” approach to what’s characterized as “a focus on dietary patterns” — or the way people actually eat. In addition, the group stresses the need to maintain a healthy body weight throughout life.

    The dietary advice favors eating a variety of fruits, vegetables, and whole grains. Red and processed meats, sugar-sweetened drinks, and highly processed foods should be limited or avoided entirely. Alcohol consumption should be kept to one drink per day for women and two for men, although the authors note that “it is best not to drink alcohol.”‘

    1. “Alcohol consumption should be kept to one drink per day for women and two for men, although the authors note that “it is best not to drink alcohol.”‘
      – – – – – – –

      Not only because I’ve never been interested in alcohol, but I consider them wasted calories. Would rather drink black coffee or tea.

        1. Hey, the authors of the link you posted even said “it is best not to drink alcohol.”‘ I eat my alcohol ….handful of purple grapes every day.

          I take it you are/were a boozer. *hic* ? :-)

          (My halo never needs polishing.)

  8. Dr. Greger compared taking the Small Pox to eradicate it and taking a vaccine for the Covid-19.
    The former had proteins suspended in a mineral oil, which was a safer way. The modern vaccines with antigens and adjuvants are injected directly into the bloodstream. Whats the point in eating the right … people have to do their own research on whats in these vaccines ..keep the immune healthy!

  9. I realize this is a bit off-topic, but since Mark has brought up something similar already, I’m hoping that it’s not totally irrelevant. I have a similar issue, thought my constipation is recurring and not just a recent phenomenon. I’m also a WFPB vegan of long duration (vegetarian since childhood, vegan since college, and whole foods eater for many years now). I eat between 80 and 90g of fiber per day–oatmeal, ground flax seeds, lots of other seeds (pumpkin, chia, sunflower, sesame), nuts, lots of greens and cabbage, other crucifers, berries, citrus, bananas, dried fruits, beans, tofu, root veg, onions, etc. I’m female, in my late 30s, 5’11, 127, very active (hiking, rock climbing, cycling, running), and I notice that, contrary to internet advice, exercise seems to bring on rather than cure constipation. It could be a hydration issue, though there are no indications of dehydration during or right after exercise (urine is clear and light), and I drink water during exercise of any significant duration. In some cases, though, I can’t find any correlation with either exercise or diet: I just don’t have to poop for a few days in a row. I wonder if it could be a hormonal thing, since I’ve noticed over many years that it seems to get worse in the second half of my cycle. I also wonder if there really is such a thing as too much fiber (or, more precisely, too much fiber relative to other components of one’s diet). One other thing I’ve noticed is that, on the rare occasions that I consume a processed fat (e.g., olive oil added on a salad instead of just a vinegar/mustard based dressing, or olive oil on whole wheat pasta, or some store-bought hummus), that seems to help. So I wonder if only consuming fat in whole food form (nuts, seeds, avocado) might be contributing? At any rate, I’m frustrated because all of these studies that Dr. Greger links to show that vegans poop all the time! I seem to be a weird vegan outlier.

    1. That is interesting about the hummus.

      I love hummus but I buy the oil-free.

      Starbucks green tea latte with soy milk always worked quickly for me (and, no, I wasn’t having constipation. I work about 20 minutes from Starbucks and if I drank it on the ride home, I would have to stop at a store with a bathroom. 5-minutes flat.

      I am thinking their soy milk probably has oil in it.

      Maybe start with hydration because it sounds like you are probably exercising enough to sweat some of your fluid out.

      1. Thanks for your thoughts, Deb. I appreciate that you are very thorough and really try to understand not just study results but the mechanisms of action/underlying explanations. Maybe I need to try the Starbucks green tea soy milk latte!

        I definitely drink water when I’m sweating, but the occasions where I actually pee less and have more concentrated urine are not consistently correlated with follow-on constipation. Sometimes the more intense/vigorous exercise (think HIIT) is both more dehydrating and yet not constipating, while climbing a long, technical multipitch route up a mountain for 14-16 hours is not dehydrating (I consume plenty of water as I go and pee normally), and yet… then I won’t poop for days after.

        It seems to be a motility issue, I think? Things just get very slow sometimes–perhaps due to rising progesterone, or maybe (this is my hypothesis with the oils) a weak gastrocolic reflex. It’s like, if I eat fat in the form of ground flax mixed into oatmeal, or as an avocado and handful of walnuts on a huge pile of greens/cabbage/carrots, it doesn’t register? I wonder if it’s a brute quantity thing, or a type of fat/degree of processing thing. (I also haven’t really tried to track this info, so my earlier estimate about fiber might be off–it could be even more, and I’m not actually sure how much fat I’m consuming. I’m sure it varies according to hunger, etc. But I do eat a LOT of nuts and seeds.)

    2. It looks like you’re doing a lot of things right! In your case I would highly suggest seeing your doctor for a proper evaluation. There may be something going on structurally with your digestive tract, or you may be experiencing symptoms as a result of poor thyroid function. Either way, it’s something that will require investigation.

      I hope this helps,
      Dr. Matt

          1. And your gut instinct perceived their gut instinct as BS. So which really IS bull? We all see our worlds differently.

            My husband told me he was going to marry me after only one date. And somehow, my “gut instinct” knew he was right. We were married till (his) death after 30 years.

  10. Switching to a plant based diet basically de-activated my autoimmune disease (dermatomyositis) , since then I’ve suspected it’s because of gut flora and permeability and the improvement of those with a plant based diet. I appreciate all the info on here regarding these topics, thank you!

    QuickQ as I’m currently listening to the pod about garlic right now- is roasted garlic as effective as raw garlic in terms of gut benefit and overall health benefits?

    Thank you!

  11. So is it good to take metamucil? I know it’s good to get fiber from a variety of plant sources but just asking about the prebiotic.

    1. The Gastroenterologist who wrote “Fiber Fueled” likes small amounts of prebiotic fiber supplements and fermented foods.

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