Image Credit: Roosa Kulju / Unsplash. This image has been modified.

Updating Our Microbiome Software and Hardware

Good bacteria, those living in symbiosis with us, are nourished by fruits, vegetables, grains, and beans, whereas bad bacteria, those in dysbiosis with us and possibly contributing to disease, are fed by meat, junk food and fast food, seafood, dairy, and eggs, as you can see at 0:12 in my video Microbiome: We Are What They Eat. Typical Western diets can “decimate” our good gut flora.

We live with trillions of symbionts, good bacteria that live in symbiosis with us. We help them, and they help us. A month on a plant-based diet results in an increase in the population of the good guys and a decrease in the bad, the so-called pathobionts, the disease-causing bugs. “Given the disappearance of pathobionts from the intestine, one would expect to observe a reduction in intestinal inflammation in subjects.” So, researchers measured stool concentrations of lipocalin-2, “which is a sensitive biomarker of intestinal inflammation.” As you can see at 1:13 in my video, within a month of eating healthfully, it had “declined significantly…suggesting that promotion of microbial homeostasis”—or balance—“by an SVD [strict vegetarian diet] resulted in reduced intestinal inflammation.” What’s more, this rebalancing may have played a role “in improved metabolic and immunological parameters,” that is, in immune system parameters.

In contrast, on an “animal-based diet,” you get growth of disease-associated species like Bilophila wadsworthia, associated with inflammatory bowel disease, and Alistipes putredinis, found in abscesses and appendicitis, and a decrease in fiber-eating bacteria. When we eat fiber, the fiber-munching bacteria multiply, and we get more anti-inflammatory, anti-cancer short-chain fatty acids. When we eat less fiber, our fiber-eating bacteria starve away.

They are what we eat.

Eat a lot of phytates, and our gut flora get really good at breaking down phytates. We assumed this was just because we were naturally selecting for those populations of bacteria able to do that, but it turns out our diet can teach old bugs new tricks. There’s one type of fiber in nori seaweed that our gut bacteria can’t normally breakdown, but the bacteria in the ocean that eat seaweed have the enzyme to do so. When it was discovered that that enzyme was present in the guts of Japanese people, it presented a mystery. Sure, sushi is eaten raw, so some seaweed bacteria may have made it to their colons, but how could some marine bacteria thrive in the human gut? It didn’t need to. It transferred the nori-eating enzyme to our own gut bacteria.

“Consequently, the consumption of food with associated environmental bacteria is the most likely mechanism that promoted this CAZyme [enzyme] update into the human gut microbe”—almost like a software update. We have the same hardware, the same gut bacteria, but the bacteria just updated their software to enable them to chew on something new.

Hardware can change, too. A study titled “The way to a man’s heart is through his gut microbiota” was so named because the researchers were talking about TMAO, trimethylamine N-oxide. As you can see at 3:33 in my video, certain gut flora can take carnitine from the red meat we eat or the choline concentrated in dairy, seafood, and eggs, and convert it into a toxic compound, which may lead to an increase in our risk of heart attack, stroke, and death.

This explains why those eating more plant-based diets have lower blood concentrations of TMAO. However, they also produce less of the toxin even if you feed them a steak. You don’t see the same “conversion of dietary L-carnitine to TMAO…suggesting an adoptive response of the gut microbiota in omnivores.” They are what we feed them.

As you can see at 4:17 in my video, if you give people cyclamate, a synthetic artificial sweetener, most of their bacteria don’t know what to do with it. But, if you feed it to people for ten days and select for the few bacteria that were hip to the new synthetic chemical, eventually three quarters of the cyclamate consumed is metabolized by the bacteria into another new compound called cyclohexylamine. Stop eating it, however, and those bacteria die back. Unfortunately, cyclohexylamine may be toxic and so was banned by the FDA in 1969. In a vintage Kool-Aid ad from 1969, Pre-Sweetened Kool-Aid was taken “off your grocer’s shelves,” but Regular Kool-Aid “has no cyclamates” and “is completely safe for your entire family.”

But, if you just ate cyclamate once in a while, it wouldn’t turn into cyclohexylamine because you wouldn’t have fed and fostered the gut flora specialized to do so. The same thing happens with TMAO. Those who just eat red meat, eggs, or seafood once in a while would presumably make very little of the toxin because they hadn’t been cultivating the bacteria that produce it.

Here’s the link to my video on TMAO: Carnitine, Choline, Cancer, and Cholesterol: The TMAO Connection. For an update on TMAO, see How Our Gut Bacteria Can Use Eggs to Accelerate Cancer, Egg Industry Response to Choline and TMAO, and How to Reduce Your TMAO Levels.

Interested in more on keeping our gut bugs happy? See:

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.

42 responses to “Updating Our Microbiome Software and Hardware

Comment Etiquette

On, you'll find a vibrant community of nutrition enthusiasts, health professionals, and many knowledgeable users seeking to discover the healthiest diet to eat for themselves and their families. As always, our goal is to foster conversations that are insightful, engaging, and most of all, helpful – from the nutrition beginners to the experts in our community.

To do this we need your help, so here are some basic guidelines to get you started.

The Short List

To help maintain and foster a welcoming atmosphere in our comments, please refrain from rude comments, name-calling, and responding to posts that break the rules (see our full Community Guidelines for more details). We will remove any posts in violation of our rules when we see it, which will, unfortunately, include any nicer comments that may have been made in response.

Be respectful and help out our staff and volunteer health supporters by actively not replying to comments that are breaking the rules. Instead, please flag or report them by submitting a ticket to our help desk. is made up of an incredible staff and many dedicated volunteers that work hard to ensure that the comments section runs smoothly and we spend a great deal of time reading comments from our community members.

Have a correction or suggestion for video or blog? Please contact us to let us know. Submitting a correction this way will result in a quicker fix than commenting on a thread with a suggestion or correction.

View the Full Community Guidelines

    1. Sir my name is ifeanyi I live in UK. I have h pilory bacteria for almost 2yrs now and my doctors has been feeding me with antibiotics but I never get ride of them . Now I think I have ulcer as anything I eats burns my stomach. Pls can you help me with advice on what to do . I know you can help as you are more knowledgeable than these doctors .I am scared that this does not develope to colon cancer . Please come to my aid

    1. Zany,
      I would not assume that. Even in the Japanese market I go to, much of the seaweed is from China. That makes me worry about contamination and quality control.

  1. I’m in the middle of chemo and have experienced dreadful bouts of diarrhea. Being tested for c. difficile. I have been a plant based eater for many years but I am unsure now how to navigate back as I can have no fibre at the moment as it aggravates everything. Is there any guidance you could give those of us with compromised digestive systems who want to continue on the plant path? Thank you

    1. H,

      I will bring up fecal transplant and there are doctors you can talk to about it.

      It would need to be a professional because you would be re-introducing good gut bacteria but your immune system would be off from the chemo.

      I am just saying it because they say it has a very high success rate.

      My semi-joke would be or you could do a 30-minute kissing or love-making session with someone who is WFPB or share a vegan dog with them. Or slowly eat a wide variety of organic whole foods. Each fruit and vegetable from different locations would have their own good bacteria.

      But if you have a lot of bad bacteria you may have to deal with that first.,which%20further%20depletes%20good%20bacteria.

    2. @ H: My husband when through chemo and radiation for rectal cancer a couple years ago and when the doctor said no fiber, I panicked cause that’s all we eat! – I ended up buying a juicer and made him green juices everyday (cucumber, apple, kale, oranges/lemons, collard greens, carrots, celery and ginger root). The ginger root helped with nausea too. Best of luck to you – and FYI, my husband’s tumor completely disappeared!!!

  2. “H”, for c diff you will need an antibiotic. There’s a probiotic called s. boulardii that is helpful. You could also try the BRAT diet: bananas, rice (white), applesauce and tea.

    1. I heard an interview with the gastroenterologist who wrote this book:

      I’m sorry I dont remember where I heard it, or I would link to it.
      But I remember he talked about folks who are sensitive to grains/legumes can successfully transition to a WFPB diet, it just must be done gradually. I believe he said there was a chapter in the book about it: differet tips and tricks to make the process gradual and not too uncomfrotable. I was not listening closely, as this is not a problem I have.

      He absolutely is convinced everyone needs to be eating more fiber for better health.

      1. Mims,

        I have heard that, too.

        Slow introduction of foods.

        Just a few beans in a soup versus chili would be an example someone gave as a way to start

    2. CC,
      Do all grains make you ill? I doubt that. Plenty to choose from. Problem with lentils? Eat other legumes/beans, eg. split peas (high in protein and fiber).

    3. Not sure if you are asking that question because you read a deceptive book or article that falsely claimed that grains and legumes are hazardous (very wrong! See: If you are asking because you’ve had symptoms when you tried eating grains and lentils there are several approaches you could take. With legumes like lentils, you may need to go slowly, introducing your body to beans and legumes slowly so your microbiome can adjust. Have you tried that? Usually lentils are more easily tolerated than other beans, but you could try beans again introducing slowly and building up.
      As far as grains, you may want to try different grains. You may have a gluten insensitivity, so you could go for gluten free initially, if you haven’t already (?) Once you can tolerate a small amount of grains, you could then through trial and error find which ones seem to agree more with you. Because our bodies are built for digesting complex carbohydrates and need the fiber legumes produce it is worth working through this so you can enjoy these healthy foods. Best of helath, despite your individual challenges on your plant based journey.

  3. I’ve been WFPB for many years and within the past year have developed worrisome bloating and an irritable bowel with all the symptoms. I simply don’t know what to eat anymore. GI docs want to do a colonoscopy and I am very reluctant to go through the harsh prep. A CT scan revealed stool throughout, nothing abnormal. I’ve tried FODMAPS on my own but I’d need help to do it properly. Any suggestions, given that we know that WFPB is the healthiest way to eat…? thank you….

    1. You could do a strict elimination diet, to find out what you personally are reacting to. It usually starts with a person eating only the one or two things they know is safe for them, such as, for instance, sweet potatoes, which is a food that hardly anyone reacts to. Wait for symptoms to subside while eating only that food. Then you eat a lot of just one other food, such as, for instance, broccoli, and then continue eating only sweet potatoes for a few days at least. If you react, you know broccoli is something you react to. If you don’t react, you know you can eat broccoli too. Then you try one more thing, such as apples. Eat a lot of apples once, and then wait several days… etc. etc.

      There is a lot of info on elimination diets online.

    2. Barbara,
      My husband has the same issue and it is a quandary as we have been on the WFPB diet for about 10 years. I’m wondering if it could partially be from eating grains that may have unseen mold spores or treated with pesticides? Hard to understand why. However, we have been using Jo Stepaniak’s Low-FODMAP and Vegan book the last month and it seems to help him. He plans to gradually reintroduce the “caution and non-safe” foods back into his diet at some point and hope it works. She has some quick, delicious recipes that have become many of our favorites. I hope this is helpful. Answers to this problem would be greatly appreciated!

  4. Thanks very much! I think if I had a coach I’d feel like I could take that on. I’ll check online though and maybe a good book to walk me through it. Thanks again…..

    1. Ifeanyi ojeah,
      You might try Stephen Buhner’s book, Herbal Antibiotics. He has some information about using Usnea, licorice, ginger, and/or artemisia for H. pylori. We are researching herbs and herbal supplements to help our daughter with her ALS and believe herbal remedies can be very healing. It just takes some researching from experts who have lots of experience and some experimentation. I wish you well.

  5. I watched the dolphins documentary and I have been watching sharks footage and there are bully, abusive dolphins who would hurt baby dolphins to have rough sex with females and there are sweet, loving, kind-hearted dolphins and same for sharks.

    That woman has sharks coming up to put their heads in her lap. They obviously love her.

    1. Can you imagine if that woman’s video had made it big instead of Jaws?

      The concept of the brokenness of sentient beings from trauma being healed resonates so much inside of me.

      1. The sharks are in pain from hooks. The fact that one woman removed 300 hooks and the fact that the sharks became so emotionally attached.

        Whoever the dummy was who didn’t think animals were sentient beings just never paid attention.

  6. Thank you Dr Greger and Everyone on the team! I spent hours per week watching your videos and reading your blogs! I am constantly learning and following all that I can. I appreciate you more than you could ever know!!

    I have your great Daily Doz app and love it.
    Ordered some Black Cumin, which I had never heard of, and as usual for me – figured if 1/4 t. was good I would add 3/4 t! I backed off of that amount after the 1st day. The 1/4t. is perfect!

    I just preordered your newest Cookbook! Will have it in 38 days!

    I am subscribed to all that I know is available of N Facts.

    Is there a schedule or way for me to know when Dr Greger is doing a live stream Q&A? (I watch YouTube. (No Facebook) I want to Try and get a question answered : )

    Thanks Again!

    1. Hi Dee,

      Thank you for all your support. We’re so glad these resources have been so meaningful to you. Please check out this page (found under the Video Library tab on top of the website) for upcoming Q&A dates. From there, I would recommend following our Facebook, YouTube, or Instagram pages for specific times, although lately it has been at 3pm ET on the last or second to last Thursday of each month on both Facebook and YouTube. We recommend tuning in as early as you can to get your question answered as they are answered in the order posted.

  7. I have a host of digestive and autoimmune disorders and have been on a whole-food, plant-based diet for almost a year. However, my conditions conflict in what I’m supposed to eat (for some, a high fat diet is recommended, but for others, a low fat diet is recommended; some need a high-fiber diet, some need a low fiber diet). Trying to find the right foods is sometimes frustrating. I try to eat foods that are known to be anti-inflammatory, but a recent test to see if my microscopic lymphocytic colitis had disappeared revealed that it’s still active. Is a plant-based diet, which tends to be high in fiber, actually a bad idea for me?

    1. “Recommended” by who? A talking head on the internet selling supplements? or a neighbor? or the conclusion of a peer-reviewed clinical study in which 5000 patients with your disease were fed a particular food that caused them to deteriorate? There is a big difference! The source of your information is important. Accepting advice from anyone (including doctors) without high quality evidence (real published science) supporting that advice will usually keep you searching for the right answer. Dr. Greger reports on the real evidence, so you won’t find any conflicts here. If you don’t find your answers on this site, it might not even have been researched yet. Please keep in mind that a WFPB diet is beneficial in the vast majority of cases, but it’s not a cure-all. We also see many people THINKING they are eating healthy, but they are not. Best to read Dr. G’s books carefully and keep in mind that food-like items like oils and flour and juices are NOT whole foods. It’s a common mistake that is made by many.

  8. Some health practitioners have recommended take L-carnitine with acetyl-l-carnitine. Based on this article, would this be ill advised even if I am on a plant-based diet? I am concerned I am doing myself more harm by taking this.

  9. I’ve subscribed to your blog and even have a couple of your books. I am gluten free (IBS), dairy free, vegetarian. A year ago I was diagnosed with acid reflux. A very annoying health issue. I don’t have heartburn, regurgitation, just an annoying cough. It’s worse in the evening than during the day, although when I talk the cough shows up many times and very annoying when in meetings. They call it esophageal reflux. I’ve read many books and websites about what not to eat, so my diet became even more limited than before. I’ve never seen any of your videos or blogs on this. Do have one? Do you have any insight or new ways that are being looked at to treat this. One day I didn’t have it and then boom the next day I was coughing. I’m 65. In decent health besides this very annoying issue.



  10. Joyce,

    A few considerations, including an allergy to something you’re eating to too little digestants and more.

    And yes Dr. G has a number of videos worth watching on the subject: and to start the conversation.

    Using a raised bed, at the head of the bed, may also afford some comfort. And there are some physical therapy techniques to consider.

    Although it might be the opposite of what you’re thinking, your reflux may be due to an inadequate amount of digestive enzymes. You can experiment with some over the counter products, used at meals. Or go a scientific route using the Heidelberg test ( and see if your low on hydrochloric acid.

    Start with these suggestions and see if your finding some relief.

    Dr. Alan Kadish moderator for Dr. Greger

  11. Hello!

    I’ve been experiencing some digestive issues for a few years — bloating, gassy stomach, mild constipation. I tried the low-FODMAP diet, but it didn’t help completely. I recently met with a functional medicine physician and I did a SIBO (Small Intestine Bacteria Overgrowth) breath test, which came back positive — I was high on both methane and hydrogen. My physician recommends an herbal antimicrobial treatment (instead of antibiotics) to treat the SIBO and rebalance my gut bacteria — specifically using Biocidin and Olivirex.

    My physician also had me take an IgG Food Sensitivity/Allergy Test, and I was positive for several foods, which means I might be sensitive to those foods. My physician recommends temporarily eliminating those foods and then re-introducing them to see which I am actually sensitive to. I’m hesitant to do that though because I recently decided to do a plant-based diet, and the foods I would have to eliminate are things I eat a lot of — soy, nuts, wheat, some beans, etc.

    I’m wondering if Dr. Greger / NutritionFacts has any experience with IgG Food Sensitivity tests and/or how to treat SIBO. Any advice would be appreciated!

    1. Hi, Zoe! I do have experience with IgG Food Sensitivity tests. My take on them is that they tend to simply tell you what you have eaten recently. I have had clients whose doctors ordered those tests, leading them to completely change their diets, and then retest only to find that the tests listed all the new foods they were eating as sensitivities. In my opinion, these tests have little or no value. SIBO has not yet been covered here on NutritionFacts, but you might find this video to be of interest to you: I hope that helps!

Leave a Reply

Your email address will not be published. Required fields are marked *

Pin It on Pinterest

Share This