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How to Increase Gut Bacterial Richness

We live in an “obesogenic environment,” with cheap junk food everywhere, thanks in part to subsidies going to the “‘food industrial complex,’ which manufactures obesogenic foods that foster addiction…The root causes…[may] make obesity difficult to escape,” but a lot of people do. If it were simply the external environment, why isn’t everyone obese?

“Some individuals seem to be more susceptible to the obesogenic environment…than others,” which suggests a genetic component, supported by studies of twins and adopted kids, but the genes that have been identified so far account for only 6 to 11 percent of the genetic variation in body mass index between individuals. Perhaps variation in our “other genome”—that is, all the different microbes that inhabit our body, known as the microbiome—may be playing a role. We have a hundred times more bacterial genes inside us than human genes.

As I discuss in my video Gut Microbiome: Strike It Rich with Whole Grains, a study found that people tend to fall into one of two groups: those who have lots of different types of bacteria in their gut (high “gut bacterial richness”) and those with relatively few types. Those with low bacterial richness had more overall body fat, insulin resistance, which is the cause of type 2 diabetes, high triglycerides, and higher levels of inflammatory markers, like C-reactive protein, compared to those with high bacterial richness. Not only did people with lower bacterial richness start out heavier, but the obese individuals with lower bacterial richness also gained more weight over time.

The question then becomes: Can a dietary intervention have any impact “A number of studies have associated increased microbial richness…with diets higher in fruits, vegetables, and fiber.”

Just giving fiber-type supplements doesn’t seem to boost richness, however, but the “compositional complexity” of a whole food, like whole grains, “could potentially support a wider scope of bacterial taxa,” types of bacteria, “thereby leading to an increase in diversity.” Human studies to investigate the effects of whole grains had been neglected, though…until now.

Subjects were given whole-grain barley, brown rice, or a mixture of both for a month, and all three caused an increase in bacterial community diversity. Therefore, it may take a broad range of substrates to increase bacterial diversity, and this can be achieved by eating whole plant foods.

Moreover, the alterations of gut bacteria in the study coincided with a drop in systemic inflammation in the body. We used to think that the way fiber in whole grains helped us was by gelling in our small intestine right off of our stomach, slowing the rate at which sugars were absorbed and blunting the spike in blood sugars one might get from refined carbs. We now know, however, that fiber is broken down in our colon by our friendly flora, which release all sorts of beneficial substances into our bloodstream that can have anti-inflammatory effects, as well. So, perhaps what’s happening in our large intestine helps explain the protective effects of whole grain foods against type 2 diabetes.

Interestingly, the combination of both barley and brown rice worked better than either grain alone, suggesting a synergistic effect. This may help explain “the discrepancy of the health effects of whole grains obtained in epidemiological [population-based] and interventional studies.”

Observational studies “strongly suggest” that those who consume three or more servings of whole grains a day tend to have a lower body mass index, less belly fat, and less tendency to gain weight, but recent clinical trials, where researchers randomized subjects to eat white bread rolls versus whole-wheat rolls, failed to provide evidence of a beneficial effect on body weight. Of course, whole grains are so superior nutritionally that they should continue to be encouraged. However, the “[i]nterventional trials might have failed to show [weight] benefits because they focused on a limited selection of whole grains, while in epidemiological trials [or the population studies], subjects are likely to consume a diverse set of whole grains which might have synergistic activities.”

Until recently, we knew very little about how powerfully our gut bacteria can affect our health. Catch up on the latest science with these related videos:

When it comes to rice, even white rice can be better than many choices, but brown rice is better and pigmented rice is probably the best. See my videos Kempner Rice Diet: Whipping Us Into Shape and Is It Worth Switching from White Rice to Brown? for more.

But what about the arsenic in rice? Learn more:

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.

45 responses to “How to Increase Gut Bacterial Richness

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  1. Some have suggested Fecal Implants to counteract all the Anti-biotics we have used over a lifetime. Probiotics don’t have enough variety. Do Beans and Greens promote diverse bacteria like grains?? Vegetables like Onions, Tomatoes, and Mushrooms should promote diversity in the gut microbiome as well.

    1. Harry Ploss,

      Most probiotics can’t colonize the colon; the colon bacteria, etc don’t grow outside of the type of environment of the large intestine, and the probiotics are grown outside the colon.

      That said, probiotics might have benefits, as they pass through the intestine, either intact or even degraded.

      I thought that the source of the gut microbiome is the mother, other humans, and food.

  2. Where do we mail donations to Nutrition Facts through the US mail? Encourage people to use IRA funds to send donations if they are over the age of 701/2. It can help with taxes.

  3. I have a very low grain intake in spite of being WFPB. Eliminating gluten-containing grains almost eliminated my psoriasis, and right around that time, the news about arsenic in rice came out. I never got around to replacing grains on a regular basis, though I occasionally eat quinoa, buckwheat, and rice. Do you think it’s important for the gut biome to include grains? Or do root vegetables, beans, vegetables, mushrooms, and fruits provide enough material?

      1. Teresa, from what I can tell after 40 years of psoriasis, nothing works for everyone with psoriasis. There must be hundreds of pathways to our disease. Good luck finding your own lucky roadblock!

    1. That’s a good question Anne. I don’t know the answer. Perhaps one of the moderators can help.

      There was a big kerfuffle last year about grain-free diets (high in legumes and potatoes) in dogs causing heart disease but the picture with humans isn’t so clear.

      However, this study below might be of interest. In essence, it shows that gluten consumption increases the ‘good’ bacteria population in our gut and also boosts immune function. Since psoriasis is an autoimmune condition, it may be this boost in immune function that contributes to your psoriasis.

      Perhaps you could try to get the best of both worlds by eating very small amounts of grains on a regular basis?

      1. Tom,

        Thanks for posting that.

        I have also been very low grain even when I am eating WFPB.

        I am trying to switch and try higher grains because I want to understand the effects of each on things like weight loss.

        Mostly, the Blue Zones had some places like the Okinawans with high caloric intake from starchy vegetables – sweet potatoes, which I also don’t eat a lot of.

        At least one Blue Zone was only 11% vegetable intake, fruit wasn’t listed at all for that one, but that Blue Zone was high whole grains. This blog entry makes me understand that grains can also increase the diversity in the microbiome.

        High Carb Hannah is someone who comes to mind because she gained weight eating fruit, so not all diversity is the same. She was probably doing smoothies and wasn’t getting fiber. That is my guess.

        She lost weight and got to her ideal weight on the Starch Solution and she even does eat nuts and avocado with it.

        Mentally, It seems like there are various ways to do this process and that there may not be much difference in outcomes, as long as people stay away from too many animal products, refined carbs and oils.

      2. Thanks for the articles. I was reluctant to try or believe in gluten-free for psoriasis and tried it only when I started to have PsA (arthritis associated with psoriasis). GF got rid of joint pain within the month but took a full year before clearing my skin. Recent accidental ingestion and quick skin reaction just proved to me that I really do need to be completely GF. I think I will try to include small but regular grain and pseudo-grain servings. While I’m symptom-free on my WFPB diet, I had Crohn’s disease in my 50s, so gut biome cultivation seems very important!

        1. Anne S I recommend you try sourdough bread. A longer fermentation time allows the wild yeast to consume all the bad stuff, sugars and gluten, leaving the healthy stuff, prebiotic fiber. My husband has an autoimmune disease but tolerates sourdough bread.

    2. Hello Anne. Thanks for your comments.

      I think that all that we include in our regular diet matters for the gut microbiota diversity. This is a really interesting video which focuses specifically on grains and microbiome

      However, if you want to learn about the gut microbiome, you can check Dr. Greger’s videos about this topic. Go to:

      Hope it helps!

  4. I just had my microbiome tested and curiously I was shown to be low in bacterial diversity, despite not taking an antibiotic in over 40 years and eating a WFPB diet for last 30. But,my Prevotella copri ( a bacteria associated with people eating a plant based diet) fraction was almost 40%, compared to a population eating SAD who average 0.12% prevotella. My Bacteroides to Firmiculites ratio clearly reflected the fact I am a WFPB too. But not sure how good these DNA tests are…as I had no Lactobaccilus, yet, I eat cultured cashew yogurt, lactic acid fermented veggies, drink kombucha….

    Anyway, I did it through DayTwo, a new tests that helps folks normalize blood sugar by predicting glycemic responses to various foods based on your microbiome. I have been “prediabetic” for 15 years (HgA1C of 5.5). I would not recommend to a WFPB eater, as the database of foods are woefully inadequate to handle the choices of WFPB eaters (maybe in a few years?!) . BUt I can see that even eating a clean WFPB diet, my portion sizes are likely causing blood sugar spikes. I love a big serving of buckwheat with aduki beans or quinoa and pinto beans….but cutting serving size in half and bulking up with leafy greens/brassicas and adding a few nuts/seeds makes for better blood sugars.

    Always tweaking, never to old to learn new tricks.

    1. Whether WFPB or not, portion sizes are important and most people don’t stress this in any of the eating plans whether paleo, vegan or keto.

  5. Are you not aware of the negative effect all grains containing gluten have on the human system. Most of the functional medicine doctors attribute many of present day diseases to the over 400 gluten containing foods. I bought two of your books, “How Not To Die”, and found them informative. The glaring misrepresentation you continue to push that grains are not a problem is in stark contrast to the hundreds of Doctors I have read. I firmly feel that you do not wish to cause more disease, and yet you seem to be on the wrong side of the equation. Possibly, until NOW.

    1. People were not as sensitive to Gluten 30 years ago, the use of Roundup and Glyphosate could be the cause of deteriorating Microbiome and the symptoms attributed to Gluten. Netflix has a new show on “un-natural selection” on how genetic engineering can be done in a garage by non-scientifically trained people. Of course in these non-sterile environments there may be some unintended natural selection going on too. In any case they talk about creating a Dog with a neon glow like fire flies.

      1. Harry, I thought I was reacting to the type of gluten in wheat. But found that organic bread is fine. Decided it was probably the glyphosate.

    2. Shyam Sasha’s,

      I don’t think that the practice of “functional medicine doctors” is evidence-based. In fact, I don’t even know where these practitioners get their information. Dr. Greger is presenting the results of nutrition research papers published in peer reviewed journals; these form the best available evidence to date about nutrition.

      Moreover, what is your scientific evidence that gluten has negative effects on the human system? I think major health problems result from the use of processed grain products, such as refined flours (white flour), in breads and pastries, etc. Furthermore, commercial bread making no longer includes long ferments (incubation with yeast) with bacteria included (both of which are parts of sourdough bread making), and instead adds all kinds of additives to speed the process of rising the bread dough and preservatives to keep the bread from molding or staling on store shelves. Yet making sourdough bread from whole grain flour was the norm for centuries, and even long ferments with yeast were typical until quite recently. Good bread is only water, whole grain flour, salt, and yeast or better yet sourdough starter culture.

      But the best way to eat grains is to eat them whole, or at best cut into smaller pieces (such as steel cut oats) and cooked. Basically, unprocessed.

      1. Dr.J, perhaps the view by some doctors that there is a problem with wheat gluten is because they see it over and over in their patients. I have seen the problem in a number of mine.
        Yes, wheat has been eaten for centuries. But I’m sure as a scientist you know that it’s not biologically the same wheat as centuries ago.
        I found this study interesting…

  6. Animals’ bodies are habitats for trillions of bacteria which essentially “farm” them. The digestion tube that most live in is integral with a body which is capable of ranging large distances to procure food.

    We are coated with a patia of bacteria; they occupy every surface both inside and outside the body. We are also THEIR farm.

    Bacteria regulate the bodies in which they live. Little “Mini Me’s” you might say. They also regulate life beneath the ground, which is many orders of magnitude more substantial than that above. Animal microbiomes are indeed universes unto themselves.

    Bacteria are at the top of the food chain, not the bottom.

  7. A Question: I took from Dr. med. Gregor’s book: “How not do the” among other things the reference to wash vegetables and fruits in salt water to rid them of environmental toxins.
    Is there an analogue indication for laundry / clothing, e.g. wool or silk, which you can not wash hot?
    Thank you so much!
    Carola Morell

  8. Question: I took from Dr. med. Gregor’s book: “How not do the” among other things the reference to wash vegetables and fruits in salt water to rid them of environmental toxins.
    Is there an analogue indication for laundry / clothing, e.g. wool or silk, which you can not wash hot?
    Thank you so much!
    Carola Morell

  9. Dr. Greger, does it bother you that so many posters spell your name wrong?

    My husband’s last name (as his widow, it’s also mine) could be spelled three different ways. Whenever I get something in the mail with the name spelled wrong, I toss it into the garbage bag, unread.

  10. How does your research on eating whole grain foods fit with the research of Cardiologist Dr. William Davis book Wheat Belly? There a great number of people suffering with auto immune diseases that might have their roots in consuming modern organic whole wheat products. Wheat products that have been hybridized to have a greater yield. Plant based eating is critical to health…..however I am wondering if we also need to warn consumers about the dangers of modern organic wheat.

    1. Cardiologist Dr William Davis suggests a diet that does not reverse Heart Disease. So he has written a popular book with no peer reviewed scientific support. Biggest problem with GMO plants is Glyphosate, gluten problems were very rare 30 years ago. Of course it is a free country and you can read whatever books you want and eat anything you want.

      1. Harry Ploss, wheat was mutated with radiation in the mid-80’s which increased the gluten and other unhealthy components. In addition, yeast was developed that shortened the fermentation time, replacing the wild yeast which consumed the sugars and reduced the gluten over a longer fermentation period. The solution must deal with all three issues – 1 buy organic wheat that has less glyphosate – 2 use an unmodified wheat with less gluten – 3 use long fermentation time to prepare bread to remove sugar and gluten.

    2. I defer to Dr Greger’s review of the literature. Seems to me Dr. William Davis book Wheat Belly, is his clinical opinion, and not peer reviewed research. Many of Dr Davis recommendations contradict Dr Greger literature review. Few people eat whole grains, they mostly eat processed genetically modified grains contaminated with Glyphosate. Dr Davis recommends eating Animal products that are contraindicated for many Auto-immune diseases.

  11. On the study done on whole wheat vs white rolls, please note that “whole wheat” rolls contain 1/3 whole wheat & 2/3 white flour. Therefore, not much difference and could explain the non-significance of the study.

  12. I wonder if you could comment the following: in the healthy gut fiber works to populate more of a good bacteria , however , if there is presence of dysbiosis gut and bad bacteria grow equally well and contribute to the existing digestive issues unfavorable .
    Appreciate it .

    1. Marina,

      The microbiome is a soup of different bacteria and other constituents all fighting for dominance, all the time going forward looking for nutrients and trying to optimize their growth.

      By increasing the diversity with a number of different inputs, such as organic apples and other fruit and veggies which are highly colonized, we effectively allow the “good” group to move toward achieving dominance.

      With that said some bacteria are very virulent and don’t get displaced, even with our best efforts. Occasionally using a bit of artificial biology in the form of antibiotics and or other inputs is essential.

      It appears clear from the literature that the principle constituents to our milieu, from the positive point of view, is from the WFPB diets vs the common refined and or meat-based approach.

      Dr. Alan Kadish moderator for Dr. Greger

  13. My wife developed gluten sensitivity about 25 years ago. It was NOT from a change in “modern” wheat. I purchase wheat in large lots (a habit from an old Mormon friend of mine) of 1000 pounds or more so it lasts many years. We had eaten copious amounts of home made WW bread for several years from the same batch of organic wheat. When we finally figured out that my wife had become sensitive to wheat, we dated it back to immediately following a bladder infection and a round of antibiotics. That temporary loss of gut flora, removed the nutrients that gut flora provide to the intestinal wall and she developed gut porosity. I theorize that the combination of a difficult to digest protein along with gut porosity led to her sensitivity. Her case did NOT develop from Glyphosate residues. Her case did NOT develop from some sort of franken-gene modified “modern” wheat. I strongly believe it is something else in the food environment that causing more frequent gut porosity, that has caused the widely perceived “gluten” and/or “wheat” problems. The changes in wheat over time have been extremely gradual verses this dramatic rise in sensitivity publicized today. I say this based on my work with a local wheat farmer and our discussions about varieties and changes over time. So just as Dr. John McDougall says, I suspect there is something else going on with this gluten/wheat issue. Something else producing gut porosity in some people, that brings about these problems. Now I’m going to have my usual large bowl of wheat berries with home made oat milk (I don’t make bread very often any longer – that would be cruel!)

    1. Dane, I have exactly the same issue : gluten-UTI – antibiotics. But I wanted to say that gluten is NOT the only thing that triggers UTI. It seems rice, all pseudo grains (though I can not fully commit to a later just yet ) and casein. It is much broader issue for me but it was crucial to stop gluten and dairy.

      1. Marina,
        I may have confused you. My wife’s UTI had nothing to do with being “triggered” by gluten. It was her use of antibiotics to deal with UTI that produced gut porosity – allowing some undigested gluten (which is a protein) to be presented to the immune system as a possible invader. Now her body will no longer tolerate a similar “threat” and clears out gluten within a few minutes. I love my wheat but if I ever have to have an antibiotic, I abstain from wheat for a few weeks to allow my gut to heal before presenting wheat again. So far that has worked wonderfully.

        1. Hi Dane,

          I am sorry. But that is so amazing that you and your wife are able to have wheat ! I was not able to re-introduce it no matter what I did and I was clear of antibiotics for many years … gluten was still a trigger for me.

          Thank you for clarification !

      1. Thank you Dr. Kadish for your comment and the article link. I’ve always been of the mind that it is the food presented to my digestive system that determines the eco system for helpful microbiota to develop. From this article, maybe that is not entirely true. More study is in order.

        Dr. Kadish, could you please email me directly. I have been wanting to connect with someone at Nutrition Facts to request a topic of pregnancy preeclampsia for a future video/series. After my daughter had a recent problem with preeclampsia I did lots of research. Sadly I found only a couple of Nutrition Facts videos that even mentioned the topic. And I’m pretty sure there is sufficient indication in the literature that would justify such a video.
        Thanks Much

  14. With differing information out there about diatomaceous earth–food grade, of course–I wondered about how safe it might really be. I’d love to see a video or blog post about this topic, please.

    Many, many years ago, I ingested water from Jamaica. I had had a bacterial something or another lay dormant in my system for about 6 months before it started making me very sick. I eventually found a doctor who helped me, after having had numerous blood tests that couldn’t come up with anything conclusive. Long story short, ever since having gotten sick from that experience, I have had problem absorbing many nutrients; often showing deficiencies too. I now eat WFPB but still seem to have those deficiencies. I had hoped maybe DE would help my gut health somehow, but would really like to know before trying this, if would make me worse or better. I trust Dr. Greger implicitly.

    Thank you for your time and consideration!

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