Skip to content.

Episode 16: What Is The Microbiome: Part 2

Episode 16: What Is The Microbiome: Part 2

We’re so excited to be back with new episodes of The Microbiome Report! To celebrate the re-launch of the show, we wanted to go back to basics with an episode that touches on the root of what the microbiome is and why it’s so important.   

To do that, we invited our resident researcher, Dr. Mahmoud Ghannoum, into the studio to talk to Andrea about the common language used around the microbiome, how people can decipher if they have a passing issue or a larger disease state, and what types of lifestyle factors are most important when we’re talking microbiome balance.

If you’re still confused about the world of the microbiome, this show will help clear the air and give you all the details you need to confidently talk about what’s going on in your gut.  


On this show, you’ll learn:

  • Common terms used to describe the microbiome (1:44)
  • What is dysbiosis and what affects gut balance? (3:56)
  • The percentage of people who have dysbiosis and how to know if you have it (6:32)
  • What’s “normal” when we’re talking gut health? (9:50)
  • How fat, protein, carbs and sugar impact the microbiome (10:55)
  • Are we born with a microbiome? (15:38)
  • Is there a “gold standard” for the microbiome? (17:23)
  • Critical lifestyle factors - the four “s’s” (18:50)

BIOHM gut quiz 


Andrea Wien: Welcome back to The Microbiome Report, a podcast made possible by BIOHM Health, a wellness company designed to balance and optimize your gut. After a brief hiatus, we're so happy to be back with monthly episodes all about the microbiome. I'm your host, Andrea Wien. And one of the things I still hear a lot when I talk about this show is the micro what? While many people are starting to hear about the microbiome, there are still plenty who have no idea what it is, which is why our relaunch episode is a back to basics show with scientist and BIOHM's co-founder, Dr. Mahmoud Ghannoum.

Dr. Ghannoum has been published over 400 times and cited close to 20,000 in his 40+ year career as a microbiome researcher. In this episode, I talk to him about the terms that are often used to describe the microbiome, the difference between annoying gastrointestinal symptoms like constipation and more serious states of disease, and the lifestyle factors that are critical for maintaining healthy gut balance.

If you've still been wrapping your head around what the microbiome is and why everyone's talking about it, this episode will shed some light on its importance and give you a solid grasp on what you need to know. Enjoy the show.

Our most popular episode is what is the microbiome? Today, I'm sitting down with Dr. Ghannoum to spend some time digging into a little bit more about the microbiome and giving everyone a better lay of the land. Thank you so much. Welcome back to the show.

Dr. Mahmoud Ghannoum: You are most welcome. Thank you for having me.

Andrea Wien: Can you give us a breakdown of the different lexicon or terms we're using when we're talking about the microbiome?

Dr. Mahmoud Ghannoum: Sure. The microbiome refers to the community of organisms that lives on our body, in our skin, [inaudible] on our skin, or on our gut and other parts of our body. And usually the microbiome, it's not just one community. It's a community of bacteria, fungus, as well as viruses. And you may have what this, what [inaudible] archaea. So there are a number of communities that live in different parts of our body and they interact together. Sometimes, you have terms called the microbiota, which refers to everything there, or bacterium, which refers to the bacterial community, and microbiome, which refers to the fungal community. And, finally, the virome which is the viral community.

Andrea Wien: Okay. So people may hear any of those terms when we're talking about these communities that are living in and on us, but they should really understand that it's the whole community as a whole, is the microbiome, everything that encompasses it.

Dr. Mahmoud Ghannoum: Yes, certainly. What happens at the beginning, a lot of people used to talk about the microbiome and, in fact, where they were only talking about the bacterial community. But now, with more knowledge, we're starting to realize that it is not just bacteria, but there is fungus as well, viruses and other organisms, which I mentioned.

Andrea Wien: And I think a lot of times when people say microbiome, they really mean the gut microbiome is what we're talking about. But there can be, as we've talked about on the show, so many different kinds, the skin microbiome, the vaginal microbiome, the mouth microbiome, but for the purposes of what most people are probably reading about, the gut microbiome is the hot topic of the moment.

Dr. Mahmoud Ghannoum: Yeah, certainly, because most of the studies that have been really conducted on the microbiome, focused on the gut. And that's why when they talk, and you are absolutely right, when they're talking about the microbiome, they are really referring to the gut microbiome because we have the most understanding and the most research in that area.

Andrea Wien: And dysbiosis is something that we hear that comes up a lot too. What does that mean? What does that have to do with gut health?

Dr. Mahmoud Ghannoum: Well, to put it simply, dysbiosis is imbalance. Usually, as we mentioned, these organisms, the different bacteria viruses, they all live together and usually they are in balance, which means they working together to help [inaudible 00:04:08]. But, sometimes, you may have an imbalance which could be caused by, for example, use of antibiotics. And as if you have, instead of these organisms living happily, they'd start to change their niche and they may start even fighting together. And that's why you have imbalance.

And why is this important? It's important because if you have imbalance in our gut, you may have other parts of the body affected as well. So that's why, basically, when you say dysbiosis, you are talking about imbalance in the communities which usually is present in whatever site in our body, whether it's the gut, the skin and so on.

Andrea Wien: So it's like a bar fight on a Friday night, everything's going well, the guys are talking to the girls, everyone's getting along. The bartenders are serving drinks and then a bar fight breaks out and it might not... It doesn't only directly impact the people that are involved. It impacts the entire community, the whole atmosphere.

Dr. Mahmoud Ghannoum: Of course, of course. That's why you'll go to enjoy yourself, and then, suddenly, with all the fighting going around you, you are definitely in a state of what we call imbalance or dysbiosis.

Andrea Wien: And what are the risk factors for dysbiosis?

Dr. Mahmoud Ghannoum: There are a number of factors that could affect the microbiome. For example, if you are eating a diet, which is not... Unhealthy diets, the Western type of diet, a lot of processed food, a lot of sugar. If you are using certain type of medications, for example, as I mentioned before, antibiotics, or you are taking steroids, or you are taking some immunocompromising drug, all of this may affect your health and the balance of your microbiota, whether in your skin, as I said, or, in particular in the gut.

Also, there are other factors which could affect this balance. For example, if you don't sleep well, or if you are stressed out and there are studies which shows that this will also affect the balance of the microbiota and that's where Helter Skelter comes in to play.

Andrea Wien: All right, well, we're going to talk a little bit more about those lifestyle factors in a minute, but do we have an idea of the percentage of people who are affected by dysbiosis? Is that something that we know from the research?

Dr. Mahmoud Ghannoum: You know, and in general, I could tell you, for example, if we look at people who live on unhealthy diet, a vast majority of them have this. People who have, for example, a immune inflammatory disease, then maybe 60% of them are affected. So it depends on particular situation and the personal situation. But, in general, as you hear all the time, people are having some issues like constipation, diarrhea and this sort of thing. Clearly, they have some imbalance there. So if we take all this together, the percentage will be quite high to say maybe about 50% of people could have no level of imbalance where others could have some extreme imbalance. But, in general, a lot of people are affected by this viruses as you call it.

Andrea Wien: And it seems like it's more common, like you're saying in these Western cultures versus people who are living more indigenous cultures or eating a wider variety of foods who don't have the processed foods, we find lower levels of dysbiosis in those communities. Is that correct?

Dr. Mahmoud Ghannoum: Absolutely. There were studies actually conducted where they compared people who were living in the Western or developed countries versus those, let's say, who are living in Africa. And you find, because those people are living in Africa, they use more grains, more fibers, they have better balance than what we have in the Western world or developed world.

Andrea Wien: Now, is there a line between being uncomfortable and maybe having some digestive symptoms one day and actually having a disease state?

Dr. Mahmoud Ghannoum: Oh, definitely. Definitely. It doesn't mean that if you have sometimes constipation or diarrhea or other symptoms, bloating for example, it doesn't mean that you'll have serious disease, but you may have some imbalance which caused by the way we eat, the diet you had, if you are on antibiotic for a short period, this could be really a situation which affects you. But that doesn't mean that you have a serious infection, for example.

Andrea Wien: So can I have dysbiosis on Monday and not have it on Thursday?

Dr. Mahmoud Ghannoum: Sure, because it all depends. It's funny you should ask because sometimes our gut community could change very fast, especially the fungal portion of it, within 24 hours can change. So as you expect, if you have this change, then you have imbalance, then you may have some issues. The good news is that it's possible to rebalance it fast and feel good again soon. You are not going to live with it forever.

Andrea Wien: Is there some type of self assessment that people can do? So, for example, if they haven't had a normal bowel movement in X number of days, is that a sign that maybe there's some tweaking that needs to be done?

Dr. Mahmoud Ghannoum: Sure. I mean, you will start to feel uncomfortable, you know there is something wrong and then you need to say, "Okay, what am I eating? Should I change some of my food? Should I start doing some other lifestyle issues? If I'm so stressed out, for example, this could affect my gastrointestinal track causing some of these issues." So if you adjust these, you can really go back to normal.

Andrea Wien: What is normal? How many times should people be going to the bathroom every day? What should that consistency be like? What is normal?

Dr. Mahmoud Ghannoum: This is a very good question. Normal really varies depending on the person. Some people have different normals. But, to answer your question, if you go once or twice a day, for example, in the bathroom, that's normal. If you have sometimes slight, slight bloating, and then it goes, that's normal, it doesn't mean you are in a serious condition.

What you really need to do is "Okay. I don't feel. Let me watch what I am doing. Let me make sure I'm not taking, for example, this acid reflux drugs which I don't need." The good news about this, we are able to change the microbiota and, with that, balance it and become better. So it is not something which is impossible. And that's really what's so nice about it, is that the more we understand, the more now we have ways to try to bring it back to normality.

Andrea Wien: And how does, you've mentioned a couple of times changing diet and tweaking what you're eating, how does the microbiome react to macro nutrients like fat, protein, carbs?

Dr. Mahmoud Ghannoum: If you think about it, all this, what we eat, is basically feed not only us as a humans, but also it feeds the microorganisms in our gut. And by feeding the microorganism the wrong food, we are really doing disservice for our [inaudible 00:11:14]. So you are able to, for example, we've been thinking about what is the best diet to have to try to bring the spirits? It's a good idea to have, for example, low carbohydrates. It's good idea to have fibers. You need some resistance starch. Also, if you have proteins, take a plant proteins, for example. And so there are a number of good, healthy diets that you can follow, which is going to bring you back into a good, healthy wellness situation.

Andrea Wien: So if I go out, I'm at that bar with the bar fight, and we say, "Forget, this, I'm going to go have a bite to eat." And I have some greasy French fries and a burger. And the next day, I don't feel great, maybe balancing that out with some fiber, feeding my gut bacteria and fungi, some foods that they might enjoy more is a good way to start to get back on track.

Dr. Mahmoud Ghannoum: Absolutely.

Andrea Wien: Now you mentioned resistant starch. What is that, necessarily?

Dr. Mahmoud Ghannoum: Resistance starch, it's a starch that our body cannot break down, cannot digest. Whereas the microorganisms in our gut can. Which is the bacteria, for example, that it can break these starches and use it to produce metabolites, which are small molecules, which are really good toward our wellness. For example, if you have butyrate or short chain fatty acids, these have been shown to be secreted by these bacteria when you feed them the right type of food. And these affect our immune system and make us less inflamed situation, for example.

Andrea Wien: We did a whole show on the postbiotics and metabolites, so people should go back and listen to that if they're interested in hearing about that with Aubrey, love it. What are some foods that have resistant starch?

Dr. Mahmoud Ghannoum: Bananas, for example, some old oat, beans, for example, legumes are really full of those.

Andrea Wien: Okay. And the greener the banana, the higher it has resistant starch, right?

Dr. Mahmoud Ghannoum: Exactly. So if you want to eat banana, is a great idea, but try to eat it when it's under ripe a little bit, don't wait for it. They'll start to have these black spots and whatever.

Andrea Wien: Because then it turns into sugar. And let's talk a little bit about what sugar does to the microbiome.

Dr. Mahmoud Ghannoum: Sure. Sugar, in particular, affects fungus. For example, candida loves sugar. You eat sugar and refined sugar or all these drinks we have, which are full of sugar, 34 grams or 40 grams of sugar. All of these are good food for bad fungus, which is the candida, for example. That's why it's advisable not to eat this, try to deduce this because if you don't do that, you are going to support the growth of the fungus. And that will start to cause imbalance where it affects bacteria. And then you will start to have gastric issues.

Andrea Wien: So after my meal of the greasy French fries and the hamburger, the next day, if I'm feeling bad, I shouldn't go out and have ice cream.

Dr. Mahmoud Ghannoum: I'm not going to try to limit you too much, but it would be a good idea. Have ice cream, but be in moderation. It's always in moderation. And a good idea about the carbohydrates and sugar is don't take a huge amount in one go, in one setting. So take a little bit in the morning. You can take it in the evening. Then it's much better than having a huge amount of five scoops of ice cream, for example. One scoop is enough.

Andrea Wien: The Microbiome Report is brought to you by BIOHM Health. Do you have a passion for gut health and want to change the lives of others? You could become a BIOHM Ambassador and start making a difference today. BIOHM Ambassadors are smart, health conscious, social entrepreneurs who get to work on their own terms, earn rewards, and make real money. To learn more about how to become an ambassador and hear from other ambassadors in the program head to, Now, back to the show.                                      

And are we born with a microbiome or are we sterile at birth? And then we get inoculated with it?

Dr. Mahmoud Ghannoum: What's so interesting is that babies, when they are born, as they come out, they already have some of the bacteria and fungus that are present in the mother. We will really start to have these organisms at birth. And then, clearly, they don't stay the same. They evolve, they change, but definitely we have the microorganisms in our gut, and I'm referring here to the babies, from the mother. And also if they have breast milk, all of this have some micro organisms, which make the body of the little baby their home.

Andrea Wien: Is it a jump to say that if the mom has dysbiosis, that we might see that in the baby too?

Dr. Mahmoud Ghannoum: Definitely. There are some sort of correlation. If the mom has, for example, an increase in proteobacteria and then it transfers to the child, it could affect the baby as well.

Andrea Wien: And how much is the microbiome changing in those first few months or weeks, even after birth?

Dr. Mahmoud Ghannoum: Oh, they change very quickly the first three, four months, but then they start to be stabilized, especially when you start giving them solid food and this sort of thing. Then you have a change of the microbiota there to become more like others, but it takes a little bit of time to happen. So it's not something set in stone. Again, it's going to vary between one baby and the other based on what type of food the mom feed them.

Andrea Wien: And I think that's an interesting point to make, too. From the beginning, our microbiomes are different and there's a lot of conversation now about what's the ideal diet? what's the ideal supplement protocol, probiotics, prebiotics, all of these types of things. Is there one right microbiome, one microbiome that's the gold standard that we should all be aiming for?

Dr. Mahmoud Ghannoum: You know, it's very difficult to define one microbiome that we should all sort of fit into. There are differences between people and between individuals, studies have shown, there are variability. As long as you have certain proportion or certain level of good organisms relative to the bad ones, then you are okay. But you don't have to be exactly the same. It's not possible because each child and each baby is fed different food. And that also helps to feed the microorganisms in your gut. So you're not going to have this ideal thing which everybody should have because otherwise we'd be clones.

Andrea Wien: Well, yeah, and the babies too, and even us, we're coming into contact with so many different bacterias, just from our everyday lives. One baby's eating sand, one's eating dirt ones-

Dr. Mahmoud Ghannoum: Playing with the dog.

Andrea Wien: Yeah, exactly.

Dr. Mahmoud Ghannoum: Sure, sure, the environment, that's another source for the microbiota, which you need to think about. And that's why it's very difficult to say this is the gold standard.

Andrea Wien: So let's talk a little bit more about those lifestyle factors that affect the microbiome. You mentioned a couple of them. We could call them the four S's sleep, smoking, stress, and a sedentary lifestyle.

Dr. Mahmoud Ghannoum: I like that.

Andrea Wien: Can you talk a little bit about each of those?

Dr. Mahmoud Ghannoum: So the studies have shown that... We'll start with stress. Stress definitely affects the microbiome and that, these days, it's very difficult to be not stressed with the way we live. We all try to work hard. We all have so many things to do. And then you have to also take care of the kids. And after you finish your work, you'll go. So we're all stressed out. That, and studies have clearly shown, that stress does affect the microbiota.

And also we did a study, we looked at the percentage of people, we had about 4,000 individuals. And when we looked at their level of stress, there was about 20% of the people have very high stress. So you can imagine these people, even though they eat good food, guess what? They still have terrible microbiota. It's because of the stress.

Andrea Wien: Let's talk about smoking.

Dr. Mahmoud Ghannoum: Smoking. We did a study in patients with HIV, with, and without, smoking. And definitely smoking can alter the microbiota. Also, not necessarily just HIV [inaudible 00:00:20:00], ordinary people who are in general healthy, when they smoke different microbiota have been shown. And usually what you do with smoke and you are encouraging the pathogenic organisms to increase in number. And that's why people who smoke, they have definitely different microbiota. And that's why they suffer with certain oral issues which other people don't.

Andrea Wien: Is it the tobacco, the nicotine, the preservatives, the chemicals that are in there, or a combination of all of it?

Dr. Mahmoud Ghannoum: It really is a combination of all of that. And also it depends on how much you smoke. Some people maybe take the two or three cigarettes, but there are people who smoke two packets a day. That obviously is going to affect them more. And also it's going to affect the microbiota not only in their mouth, also in their respiratory tract.

Andrea Wien: Is it similar if someone's chewing tobacco?

Dr. Mahmoud Ghannoum: Yes. There are studies, especially in certain areas of the world, where there are people tend to chew a lot of tobacco and they end up changing the microbiota. And also they develop oral cancer as well.

Andrea Wien: So is the microbiota changing because they're being suffocated because they are responding how maybe they would with sugar and that's a constant in someone's mouth? I'm wondering why we're seeing those changes.

Dr. Mahmoud Ghannoum: Those changes, if you think about it, you are smoking something, it has the nicotine, for example, it has definitely, we can see, if you look at the people's hands who smoke, there are all nicotine deposits. So these nicotine’s and other chemicals in cigarettes are deposited in the mouth. And then when they are deposited in the mouth, what they do, they affect the mucosa layer or the covering of our mouth. And by changing, discovering, you are also changing the organisms there.

Andrea Wien: Okay. What about sleep?

Dr. Mahmoud Ghannoum: Oh, sleep is very critical as a lot of people tend to sleep very little or they go to bed really late. And interesting, this morning I was listening to a program where they said people who go to bed late, let's say one or two o'clock in the morning. And they sleep. They have a lot of stress, a lot of inability to focus. And now what they did, they did an experiment where they had people go to bed two hours before that. And guess what? Their general overall health improved. And it's the same with the microbiota studies have been shown that if you don't sleep a while, you are causing imbalance in your microbiota, and obviously with imbalance, you are going to have gastric issues.

Andrea Wien: So it almost sounds like people aren't sleeping and then that's causing stress of the body internally and externally because we're not having the time to really power down, recharge, let all the systems that work when we're sleeping do their job. And then that's causing us more stress.

Dr. Mahmoud Ghannoum: Exactly. And that's where, as you mentioned later on, we'll talk about the gut brain access. And there is a clear connection between stress and the change in the microbiota.

Andrea Wien: All right. And our last one here, our last S is sedentary lifestyle. So not working out, not exercising, and I'm not necessarily talking about going to the gym every day of the week, but walking up and down the steps, gardening, those types of things.

Dr. Mahmoud Ghannoum: Oh, it's very, very important to exercise. We need to exercise because without that, again, we are affecting our body in general. Number one, if you don't exercise and you eat too much food, you are going to start to be obese. You are going to increase. And that itself affect our microbiota. But there are studies that shows if you have moderate exercise, as you said, walk more. For example, I go up the stairs in my work. I don't take the elevator at all. I exercise maybe half an hour a day, but I don't exercise at the weekend. You don't have to do it. Always moderation is the key in all these aspects. And in fact, if you have extreme sport, your microbiota will be also imbalanced. So that's why you need to be in the middle, try to do what you have to do to keep in shape. And by doing that, you are going to have a better gut health and better microbiome.

Andrea Wien: Yeah. In one of our earlier episodes with Eve Guzman, the ambassador for one of the ambassadors for BIOHM, she talks about how, when she became a bodybuilder, and really started competing, that's when she noticed that her gut microbiota were way worse than when she was overweight. So having those extremes-

Dr. Mahmoud Ghannoum: Oh, definitely this is the case. And also there was a study from Ireland, the Republic of Ireland, where they looked at rugby player. It's like our football player here in the US and guess what? They really are similar to our players here, football players, they are extreme exercise. They eat food, which is unbelievable and definitely not healthy a lot of the time. And that in itself is affecting their gut microbiome. And remember when you are exercising, a lot of the blood rushes to, for example, your muscles in your hand and your thighs and this sort of thing. And we are in a way depriving our gut from the blood that is needed there. And that's why it really caused this imbalance of the microbiota.

Andrea Wien: Yeah. And again, it could come back to stress, extreme exercise, puts a stress on the body internally.

Dr. Mahmoud Ghannoum: Exactly, exactly. And that's, in a way, what I'm trying to say is that the extreme exercise you are putting stress in your gut because you are not giving them enough aeration, enough oxygen by having the blood supply become less and less and focused more in our periphery rather than in our gut, as you would say.

Andrea Wien: So, I know so much of the microbiome science is new. You've been doing research for 40 years, but we're really starting to learn so much more. How much do we still have to learn? Is there a comparison in science of where we were with something else on a different topic of where we kind of are now with the microbiome research?

Dr. Mahmoud Ghannoum: I mean, the good news is we have advanced a lot in the understanding of the microbiome in the last few years, but the story is not ending here. What you need to do, it is a really dynamic situation. And now we are starting to see, "Okay, we know that it's a change in the gut microbiota, how can we rebalance it? What can we do to give you back your health?" And that's where, really, the science is going to be going. So I would say in the coming five to 10 years, we hope to have a better really sort of understanding of how we can help people to balance their gut.                          

And the good news is we are starting to do that. We have, really, in the last year or so, we developed a diet where it will help people to balance their gut. And then we tested it in people and guess what? We were able to change the microbiota so that it becomes more beneficial than harmful one, but also people who were a part of this study start feeling better. Gastrointestinal symptoms, less inflammation, they slept better. They had more energy, as well as less constipation and this sort of thing. This gives me hope that, in the coming, as I mentioned, five to 10 years, hopefully you will be able to prevent a lot of these issues that we suffer, daily issues, basically, that we suffer from.

Andrea Wien: And is there somewhere that this information is going to be published, that people will have access to that research and the diet that you've come up with?

Dr. Mahmoud Ghannoum: Oh, sure. We tend to publish our work in peer review journals and biomedical journals, but also we have a book that is going to come for total health balance and control, and this should come out in December of this year, hopefully.

Andrea Wien: Great. Well, we will definitely be looking for that. Dr. Ghannoum, thank you as always for coming on the show and we'll talk to you soon.

Dr. Mahmoud Ghannoum: It's always my pleasure to be with you. Thank you very much.

Andrea Wien: Thanks so much for listening. Again, I'm Andrea Wien and The Microbiome Report is powered by BIOHM Health. To learn more about the company or to become an ambassador, head to That's We'll see you next time.


Tune in every month on iTunes here:  

Thanks for listening!

Thanks so much for listening to the show. If you enjoyed this episode and think others could benefit from listening, please share it.  

Do you have feedback or questions about this episode?

Email us at  

Subscribe to the podcast

If you would like to get automatic updates of new podcast episodes, you can subscribe to the podcast on iTunes, Stitcher, or from the podcast app on your mobile device.  

Leave us an iTunes review

Ratings and reviews from our listeners are extremely valuable to us and greatly appreciated. They help our podcast rank higher on iTunes, which exposes our show to more awesome listeners like you. If you have a minute, please leave an honest review on iTunes.

Related Articles

  • Episode 77: How Crohn's and Ulcerative Colitis Are Wildly Different Than IBS

    The terms inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) get used interchangeably, but as we’ll learn in this episode, they are wildly different diagnoses with very different treatment...

  • Episode 76: Are You Doing Everything "Right" And Still Sick?

    It can be frustrating when you feel like you’re “doing everything right” and still not improving.  On this episode, Dr. Ami Kapadia joins Andrea to talk about persistent yeast overgrowth...

  • Episode 75: One Species' Trash Is Another's Treasure

    Typically, we don’t think about picking up the waste byproducts of another species and using them to our advantage. But when it comes to short chain fatty acids - the...