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Episode 1: What’s the Microbiome?

Dr. Mahmoud Ghannoum talks about the Microbiome

In this three part series, we set the stage for the show with microbiome researcher, Dr. Mahmoud Ghannoum. In this first episode, we define the microbiome and get everyone on the same page before moving on to topic number two: fungus.

There was a time not too long ago when everyone was scared of germs. When scientists discovered bacteria, it set the world ablaze with news about how the microorganisms living in and on us caused disease – and therefore needed to be eradicated at all costs.

Today, we know that’s not true. Microorganisms like bacteria and fungi aren’t always friends, but they’re also commonly not foes either. In fact, researchers like today’s guest, Dr. Mahmoud Ghannoum, have identified thousands of gut organisms that live together and cooperate in ways both good and bad.

The average person could have anywhere from 300-400 species in our digestive tract at any given time, helping us to deal with stress, to act more courageously, or simply, to digest our food.

In this episode, we get very clear on exactly what the microbiome is, where different microbiomes are located around the body, and the exciting horizon of research as this field continues to expand.

If you’ve ever wondered what the microbiome is or what it does, this episode will bring it all into focus and offer some surprising tidbits on how using things like mouthwash could be disastrously squashing your buggy buddies.  


Episode 1 The Microbiome Report by BIOHM Health

Released Dec 6th 2018

In part 1 of our three part series, leading researcher Dr. Mahmoud Ghannoum sets the stage for future microbiome discussions on the show. In this first episode, Dr. Ghannoum explains what the microbiome is, where it’s located, and why it’s so critical to our existence.   

Here’s what you’ll learn in part 1:

What is the Microbiome? [2:00]

Impacts of Antibiotics [8:08]

The exciting future of personalized medicine [15:31]

What came first? Balance or disease? [21:23]

What are PREbiotics? [23:21]

biohm gut quiz


Andrea Wien: Welcome to the Microbiome Report powered by BIOHM Health. I'm your host, Andrea Wien. And to kick off the show, we're starting with a three part series on the basics of the microbiome. In episode one, we'll dive into what the microbiome is, where it exists around the body, and why it's important to study. In episode two, we'll talk about fungus, including specific fungi you may have heard about such as, penicillin and candida. And in episode three, we're breaking down info on biofilms and digestive plaque. If you haven't heard of these things, don't worry. You're not alone.

               My resident expert, Dr. Mahmoud Ghannoum will be joining me in the studio for this three-part series. Dr. Ghannoum is a Professor and the Director of Center for Medical Mycology at Case Western Reserve University and University Hospitals Cleveland Medical Center. Dr. Ghannoum has spent his entire 40 year career studying fungi. His research has been cited over 19,000 times, and he was the first researcher to coin the term microbiome, for the fungal colonies that coexist with bacteria around the body. Now, without further ado, let's jump right in. Dr. Ghannoum thank you so much for coming on the show.

Dr. Mahmoud Ghannoum: Thank you very much for having me.

Andrea Wien: So in preparation for this show, I asked a bunch of people on Facebook and different groups that I'm in, about what their questions were about the microbiome. And I was shocked because quite a few people said, "What's the microbiome." They didn't even know. And I think coming from this field where we're so entrenched in medicine and science and being on the cutting edge, it's easy to forget that a lot of the mainstream doesn't know what the microbiome is. So, tell me a little bit about what it is?

Dr. Mahmoud Ghannoum: Well, firstly, I'm not surprised that some people are not aware of the microbiome in spite of the fact that we have the media, the news these days talk a lot about the microbiome. But anyway, to make it more approachable to people so that they understand what the microbiome ...  When we talk about microbiome, we are referring to organisms or microorganisms that live in our body. For example, we all know if you have bacteria as well as fungus in our hands.

               So, that's all the time we think about it. "Oh, there are germs in our hands." But in fact, now recent studies starting to show that these microorganism not only in our hands, also they exist in our gut.

               They are in our hair, they are in our mouth all over our body we have these organisms. What's interesting about the recent studies is that we always are afraid, or at least we used to be afraid of germs. But now what we are learning with the new technologies that are available is that we also have some good organisms or beneficial bacteria, beneficial fungi that live in our body.

Andrea Wien: And I think interesting thing to think about is that there's not good and bad bacteria. It's all about the balance between the bacteria and the fungi and everything that's going on. So candida, for example, it's quite normal to have some level of candida in your system, but if it overpowers and becomes too much, that's when the problems come. So, talk a little bit about why it's dangerous to classify things as good or bad.

Dr. Mahmoud Ghannoum: You are Absolutely right. It's like if you take salt. If you take a little bit salt, this is good. But if you have a huge amount, any chemical could be bad. It's the same picture you can paint with microorganisms. Like for example, candida, we did a study, there are about at least 70% of the people have candida in their mouth and in their gut, but they have it at a very low level. In other words, they are there. They are happy campers. They are getting their food from our ... whatever side they are present, whether it's our skin or in the mouth or in the gut.

               The problem becomes an issue is when somebody take, let's say an antibiotic. If you take an antibiotic, what happens, you are killing the bacteria which keeps candida under control, and this leads to an overgrowth or an increase in number of candida. Once you have this increase in number, then we start having issues.

Andrea Wien: We're going to do a whole episode I know on Candida because it's such a hot topic right now, but to take a step back, what are some of the major players, when we're talking about bacteria? What are the ones that are colonizing the gut that we see most often in the gut and in the mouth and in any other of the microbiomes across the body?

Dr. Mahmoud Ghannoum: Well, again recent studies have started to show there is a large number of organisms in our body. In the gut for example, there are thousands of organisms, bacteria. Of these when you look at their classification, there are a lot of them which are good, and what I mean by good ... You are absolutely right, like if they increase the number of they could cause a problem. But in general, these good bacteria, they help us with our digestions and other things. But when we look at what is there, there is a wide number ... Like it could be the good bacteria as I mentioned, like bifidobacterium, Lactobacillus, you have other organisms which are really ...

               Faecalibacterium for example, these are good organisms. For example, faecalibacterium as I mentioned, it has anti-inflammatory activity which helps us. So, when you look at our gut, in addition to some of the organism which we mentioned, we have other bacteria which even though if they are present, as you mentioned before, in low numbers they don't cause trouble but when they increase in numbers, such as E coli for example, then they become an issue. So in general, you have about maybe 300, 400 different strains or species in our gut. They live together and they cooperate together in good and bad ways.

Andrea Wien: So I think a lot of people recognize Lactobacillus because we see it on yogurt, it's in a lot of food products that people may have picked up along the way. But when we look at the gut reports coming back at BIOHM, we don't see a lot of Lactobacillus in there. So, how is that possible that that one strain that seemingly is everywhere is not in our gut?

Dr. Mahmoud Ghannoum: The issues with this [inaudible 00:06:19] when you were trying to see what is the level of Lactobacillus, is we look at the stool and in the stool sometimes it shows that there is low abundance of Lactobacillus. However, Lactobacillus also has ability to adhere or stick to the lining of the gut and that's why sometimes we don't see it much because it is stuck to the gut lining. And when in the stool, we don't see it as much. So this really what tells you why sometimes you think you don't have any, but there are, as long as there is enough levels, where it tells you there is somewhere, some Lactobacillus, then you are fine.

Andrea Wien: Okay. And then could the same thing be for a pathogenic strain that those are also stuck to the gut. And so maybe in a soil sample, you wouldn't see that as much.

Dr. Mahmoud Ghannoum: Definitely the same could be applied to the pathogenic organisms. And again, we can talk about Candida since it's my favorite organism. It has a high ability to stick or adhere to tissues, but the problem when you have pathogenic organism, and the number is very high as you say, overgrowth, then in addition to sticking to the gut, we have enough in the stool that tell us there is a problem.

Andrea Wien: Why is candida your favorite?

Dr. Mahmoud Ghannoum: Well, I started the study in Canada over 40 years ago, and I spent all my life studying candida. So I love it. If you can say you love an organism.

Andrea Wien: Do you think that it has a personality if you had to give it a personality?

Dr. Mahmoud Ghannoum: Oh, definitely. It's a fun guy.

Andrea Wien: Just like you.

Dr. Mahmoud Ghannoum: Yes. That's a lot of the time when I give talks, people tell me, "Oh you seem to be happy when you are talking about fungus." I say, yeah of course. I make my living out of fungus and they are fun as well.

Andrea Wien: So you mentioned antibiotics as something that can throw off this balance. You've also done some research on things like artificial sweeteners. Can you talk a little bit about how what we're eating affects what's going on in our gut?

Dr. Mahmoud Ghannoum: This is really very important question because again, based on the recent studies, definitely our diet influence what microorganisms we find or what the microbiota exists in our gut. For example, if you have too much sugar, you have some organisms who love that, and they start to increase in number. If you-

Andrea Wien: They're like five year olds?

Dr. Mahmoud Ghannoum: Exactly.

Andrea Wien: They don't know when to stop.

Dr. Mahmoud Ghannoum: No. And of course the more you give them the happier they are.That's why we need to balance what we eat and watch what eat. It's like, what we say, you are what you eat. And you have other for example, organisms, they like to have fibers. And if you don't eat fibers in your diet, guess what they increase in number. And that's why we may start to see some imbalance in there. So that's really critical for us now with all this new information, to know what we eat, and how if we have imbalance what we need to do to bring it back and maintain it.

Andrea Wien: Is there a big difference in the type of microbiome someone would need if they were living here in North America and maybe even different parts of North America, Colorado versus Cleveland versus Miami, and then someone who might be living in Africa and living a completely different lifestyle and different food stuff.

Dr. Mahmoud Ghannoum: Oh, certainly. One of the studies I wanted to do once to look at the microbiota in HIV infected patients, and I want to do the study, use controls in the US and in Africa. And one of the main issues that came is that it depends on the diet. Your diet which as you know, what people eat in Africa or even what people eat in Texas versus what they eat in Denver. It could be completely different. Now, one interesting study looked at people who eat European or Western style diet, and they took a village in Africa and they try to compare what is their microbiota.

               And lo and behold, the people living in Africa because the type of food they eat that is an all natural. They don't eat too much meat and this thing. Their microbiota reflected our ancestors, where as for us here, we see different type of organisms or different type of microbiota which again, we are feeding them with what we eat and that's why we have differences.

Andrea Wien: How tied to our microbiome ... And this might be a big jump. I don't know if the science is there yet, is causing so much of our sickness.

Dr. Mahmoud Ghannoum: You are absolutely right. We are really living in an exciting time as far as the microbiome is concerned. We are starting to see a lot of studies published, and good studies in peer-review journal where it's linking different type of diseases with the microbiome. So, are we finished yet? I don't think so. I think within the coming five to 10 years, we are going to gain a lot of information and this information is going to allow us to manage our health differently, and not only this, I believe because of the knowledge that we are accumulating in the microbiome, we may start changing the way we manage our health.

               And we may follow for example, preventative measure instead of waiting to get sick to be treated. So, I think it's a wealth of information. Are we there yet? Not yet, but I tell you it's very exciting and promising.

Andrea Wien: Yeah. And I think that's why we want to do this show because there's so much research coming out every day. And so much of it is maybe misreported in the media or overblown in what we're able to do right now and what we really know about that's going on in our microbiomes. So, I think this show specifically is looking at, who's doing the research and how can we start to implement it in our lives. But it's a trial and error process. No one knows the completely how we're going to be able to balance exactly the microbiome for optimal health.

Dr. Mahmoud Ghannoum: I agree with you, but the good news from my point of view is that there is extensive literature being ... and the studies being done, and this is starting to help us to rebalance. But we really still need more and more in that direction. And we need good studies. We you need a good controlled studies. You need to make sure you have ... Let's say, if we want to look at a certain disease, how the microbiota affected? You will need to have the disease group and have the good control so that you can compare this. And then based on this knowledge and based on their data, it can start to tell you how to really adjust this microbiota towards the best.

Andrea Wien: You've been doing this research for 40 years. And I can imagine now that the microbiome has become a hot topic, that more and more researchers are starting to get involved. Where do you still see holes that you would love to be able to see a scientist working on?

Dr. Mahmoud Ghannoum: I think in my life, during this 40 years, I always find the new ways of like, I go to meetings and I think, "Oh this is very interesting." So that's where we should go. For example, I can tell you, I went to a meeting about 15 years ago and people are talking about the microbiome, and they're only talking about the bacteria. And then I said, but our body has a lot of fungus and that's why we should look at it. So now, we have not just my group, also other groups starting to look and seeing, you know  what there is ... Now we have communities of organisms, bacteria, fungus viruses, as well as parasites.

               But your question is where do we see this field going? I think we are starting to gain a lot of knowledge about how these organisms work together. So we spent time at the beginning to know what is there? Now we started to know that they will play together. So, we need to start the understanding, what are the mechanisms that allow them to help each other or inhibit each other? So this is an exciting area. It's what we call it, polymicrobial which means more than one organism playing together. That's one area.

               The other area which I think is going to be very hot and it's starting people to look at it is, these organisms and they are working together, whether towards the good or the bad they secrete these metabolites. And these metabolites are small chemicals, which could affect your body. They go into the blood and they start affecting other parts of your body. So, this is where another area ... Now, in addition to this, we really need to harness the knowledge that we have so that we can come out with ways to control the microbiome.

               In other words, to maintain it in balance shape. And this could be from finding probiotics, which direct it towards a specific organisms in your gut. You need also sometimes maybe new therapeutic approaches, new drugs to maintain this balance. Okay. One thing which I think is going to be exciting and a lot of people hear about it these days, is about personalized medicine. From my point of view, this is very hot area. We need not only personalized medicine, also, we need a personalized nutrition.

               Because by what we eat, whether it is diet as well as nutritional supplements, including vitamins, probiotics, prebiotic is going to allow us to balance the gut or microbiota in our gut. And I think that's where the excitement is going to be.

Andrea Wien: It's very exciting. It's something I say to my clients all the time. There's 7 billion people on planet earth and there's 7 billion different diets that work best for all of us. So, I think too there's something called psychobiotics that are starting to come out and it's really how our microbiota is affecting our mood. And that's something that's so interesting to me, learning about how these other organisms can really start to control what's going on in the mechanisms of our body is so exciting.

Dr. Mahmoud Ghannoum: I really agree with you. I was in a meeting that's called the American Society for Microbiology, and one presentation was looking at how the microbiota affect our behavior. And it's amazing how certain microorganisms such as bifidobacterium was able by feeding mice, this bifidobacterium, it affected their mood. It made them more courageous. It made them less really [inaudible 00:16:57]. It's fascinating this area, I agree with you. The psychobiotic is going to be very exciting area, which will allow us to control our mood, our stress, and otherwise.

Andrea Wien: So many people have heard of the gut microbiome. They're familiar with it. They've eaten yogurt, they're drinking kombucha perhaps. These things that are very mainstream, but not many people think about the skin microbiome, the mouth, the vagina, even. So, when we're thinking about how to keep balance in those areas, what are your thoughts on different microbiomes that are outside of the gut?

Dr. Mahmoud Ghannoum: Well, I started working with the microbiome ... The first site in our body was the oral cavity. So I wanted to see, what is the microbiota that live in healthy mouth.

Andrea Wien: It's a little bit easier to get in there than the-

Dr. Mahmoud Ghannoum: Exactly.

Andrea Wien: ... the stomach?

Dr. Mahmoud Ghannoum: It's very easy to collect samples and that's what really one of the advantages of why we started. And what we found that in addition to understanding what is enhanced, we looked at HIV infected patients, and we found that there is disturbance in the balance, and we found really some organisms that can bring this balance the same way for example, for people with dental issues, periodontitis or [inaudible 00:18:15] and whatever. Studies are starting to show that there is imbalance in the oral microbiota.

               So, this is very important to address and people are starting to look at that as well. Now, with respect to the vagina, clearly the microbiome plays an important role in this, and a woman's health and this sort of thing. So now, people are starting to understand, and for a long time, for example, what is the imbalance that cause for example, the thrush? And they're finding that there is for example, your favorite organism lactobacillus is really less, and that's why some people develop thrush due to the fungi. And why?

               Because you have imbalance in the microbiota. We have less lactobacillus and when you have less lactobacillus, you have this other organism will grow and cause trouble. Also, we have the hormones in our body could affect also the balance of these organisms and encourage some of them to grow. So, understanding the microbiota, both in the oral, the vagina, as well as the skin is very important. So I just forgot to talk about the skin, because the skin ... I am in department of dermatology, and we have a lot of interest in understanding what [inaudible 00:19:33] microbiota?

               And we just published a paper about the gut-brain-skin connection. It seems there is a relation between the organism and our gut, which could affect our mood, our way or we behave ... As well as what skin live in our skin. Sorry. What organisms live in our skin, particularly, we are focusing on psoriasis, people with atopic dermatitis, and we are starting to see that not only bacteria has changed also fungus is changed. And now people are attempting to have a new research to identify how can we rebalance the skin or microbiota as well.

Andrea Wien: So is that to say then that there's a connection, if your skin microbiota is unhealthy, would it be possible to even have healthy mouth and gut microbiomes? Or is it they're either all in balance or they're all out of balance?

Dr. Mahmoud Ghannoum: This is a very complex question, but I can tell you, at least there are studies to show, when you have gut imbalance, there is concordance with respect to the balance of the microbiota in the mouth. It seems they reflect each other because remember, we eat the food or whatever it goes from our mouth, it go down into our gut. So there is some connection. Sometimes if you have imbalance in your mouth, it could be an indicator that you have imbalance in the gut as well. I don't think a lot of people studied the mouth, gut and the skin.

               But I'm sure there are ... because of the gut, the skin brain connection or access as we call it, definitely a change in the gut microbiota will also influence the skin microbiota, but we need more studies in this area.

Andrea Wien: So you mentioned your HIV patients that you were studying, their microbiomes of their mouth were imbalanced. What came first? The imbalance or the disease?

Dr. Mahmoud Ghannoum: Honestly, you are difficult. You give them difficult questions because we really don't know these answers. I think that we don't know. It's the chicken and egg situation, but at least from my research, if we have an immunity defect or you are compromised in one way or another, such as HIV infected patients, you have problem with that immunity. So, our body is very efficient in controlling germs when we have good immunity. So when you have a deficient immunity, then these organisms, there is nothing to control them.

               So to me, I would say if you have deficiency in your immunity comes first and then that will lead to the imbalance as well, because then there is nothing to control these organisms there.

Andrea Wien: That makes sense. Okay, great. I was reading the other day about gut microbiome. I'm sorry, the mouth microbiome and its relation to vasoconstriction, and when we eat certain nitrates foods are turned into nitrite and then nitric oxide in the blood. And so, it can actually reduce blood pressure, but if people are using things like mouth washes or maybe chewing tobacco, and they're altering their microbiome of their mouth, perhaps that could have some effect on their internal structure as well.

Dr. Mahmoud Ghannoum: Definitely. This again takes us back to the idea of the metabolites. When you have these nitrates, you then end up with nitric oxide and this sort of thing. This is good. That's where we need to start looking at the metabolites because absolutely, if we interfere with this balance, we are affecting these metabolites or these little chemicals which could go through the blood and cause issues somewhere else.

Andrea Wien: Before we end the show, I want to talk just briefly about prebiotics, because that's an area that most people don't really know much about. They're starting to hear more about the importance of prebiotics. What are they?

Dr. Mahmoud Ghannoum: Prebiotics unlike probiotics, which are really probiotics alive organisms, or which as we mentioned Lactobacillus for example. The prebiotic are basically fibers. Okay. They are certain fibers which we can eat and the fibers are important. Why? Because they feed the good bacteria in our gut, which start to help the breakdown of our food to keep the bad bugs under control. So  it's type of fibers basically, which ... and also there are different prebiotics and some of them, for example the inulin have been shown to be a really very good prebiotic. So some of them are polysaccharides and ...

Andrea Wien: And I would assume different ones feed different probiotics. So it really is all about if you already have an over abundance of one thing, you might not want to eat that prebiotic that could feed that.

Dr. Mahmoud Ghannoum: Sure. And that's why really, when you do the gut report or you understand what is in on your gut microorganism, you know where there is balance or imbalance, and then based on this, you are able to use the right fiber, the right probiotic and the right diet to bring it back into balance and that as well.

Andrea Wien: And at least in that area, the science is clear for the most part on which bacteria are fed by which things maybe more plant matter, maybe animal fats, etc. So it's a little bit clearer in that regard of what we're eating and how that can affect the individual bacteria, correct?

Dr. Mahmoud Ghannoum: Correct. We are really getting there. We are really getting there. There are a lot of published work now where it shows if you have imbalance in certain organism, like for example, if you have imbalance in proteobacteria having prebiotics in particular is very good or fiber, okay? Also having Vitamin D3 will be also very good. So yes, once you know what organism's in your gut, you will be able to select what type of food you need to eat, what type of fibers or prebiotic, probiotic and vitamins to take so that you really restore and maintain your balance.

Andrea Wien: Dr. Ghannoum, this has been great. Thank you so much for coming on to set the stage of the microbiome discussion. And we look forward to talking to you more about fungi and biofilms and everything else that you've been researching. Thank you so much.

Dr. Mahmoud Ghannoum: Thank you very much. This was great pleasure to meet you.

Andrea Wien: Thanks so much for listening to the show. If you enjoyed what you heard, don't forget to tune back in next week for episode two of the Microbiome Report. Until next time, I'm your host Andrea Wien.


The microbiome. It dictates so much of how we move through the world – from how we digest our food to the mates we choose as we spin around the globe. On this show, we’re investigating how the things we do everyday impacts the bugs of our bodies.

The Microbiome Report is powered by BIOHM Health.


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