THE MICROBIOME SUMMIT : The New Path to Health
Our Connection to the Microbial World Around Us
Dr. Rob DeSalle, PhD
Up until five years ago, most of what we knew about the human microbiome was the germs and pathogens that made us sick. But in the last five years, technology has allowed us to better understand the human microbiome – scientists have now identified and named 8,000 microbes! In this interview, Dr. Rob Desalle will talk about what it means to catalogue this microbial life for future study and research. Using brilliant metaphors, Dr. Desalle will help you understand more about how removing even harmful microorganisms can disrupt the ecosystem.
- Tracey:
- Hi Rob, thank you for joining me here today.
- Rob:
- My pleasure.
- Tracey:
- I’m really excited to speak with you today about the whole idea of the microbiome starting to catalog it and understand our microbes that are on us, in us and around us and the fact that we’ve only been able to really delve into this understanding within the last five years due to advances in technology. I mean before we only really understood what the pathogens were, but we didn’t understand all the rest. Can you explain to us what we’re trying to accomplish in science with the cataloging of the microbiome?
- Rob:
- Sure – sure. One of the things that we have to remember is that the reason that we know a lot about the pathogens is that they made us sick and we had a really good reason for trying to understand them better. So scientists spent a lot of time trying to grow them up in the lab and what this is called is culturing. And so, a lot of the microbes that caused a disease or causes discomfort we can culture. But the grand majority of microbes that are out there we simply can’t culture and so we don’t have a very good characterization of those microbes that we can’t culture. And as you pointed out, the technology came along five years ago, or maybe a couple years before that. And it allowed us now to identify every microbe that is in a particular ecosystem where we’ll get a handle on the diversity microbes that are in a particular ecosystem say like in our body, like in our mouth or in areas of our nose. So, this cultured versus unculturable microbes is very critical for us to understand when we’re trying to think about the diversity. So, there are about 8000 cultured microbes that we have given species names to and these 8000 cultured microbes a lot of them are either involved in our health or they’re important for industry so you can see the human centric focus on culturing those kinds of microbes. But now step back and think about this, there are about 10,000 species on that live in and on your body and maybe up to 10 times that many. So that’s a lot. But now let’s step back even further and look at that planet. There are about a 100 million species of bacteria on the planet. So, the grand majority of those we simply can’t culture. It becomes really important to understand this diversity without having to culture the bacteria and the way we do this is with barcodes. DNA barcodes so to speak, and we use the DNA sequences of different microbes to identify them and to get an idea of what kind of organisms are there. Now for the human body that’s very doable and that’s because as I said there’s maybe 10,000 species of microbes that we need to worry about that we need to have in our database in order to identify them. That means that we don’t have to cultural all 10,000 anymore unless we really want to unless you want to study molecular biology or the genetics of a strain that’s causing the disease, but now we can characterize the communities of bacteria that live in very specific parts of our body without having the culture anything, which is an amazing advance in science.
- Tracey:
- It is. It gives us a window into this invisible world, I mean it’s absently fascinating. I think of it kind of like outer space like the naming of stars, the naming of microbes, like trying to figure out who’s there
- Rob:
- Absolutely, some scientists also call it dark matter. This biological dark matter of our universe. These species that we haven’t been able to culture, but now can identify because we can get their genomes and look at their genetics. So, it is opening our eyes to this amazing amount of diversity on the planet. Again that the amount diversity in our bodies is only a fraction of what we see on the planet but the technology that we have is making what we see on in our bodies very precise, so precise that it’s going to help us a lot in trying to understand how those microbes interact and how they produce the ecologies on our body that are really important for our health you know so the ecologies of your mouth are important for tooth decay. The ecology of your gut is important for stomach disorders. The ecology of your underarm is important for body odor. Those kinds of things.
- Tracey:
- Right. Are we at the point of saying these are the ones that absolutely must be there and all the rest are just sort of players that are supporting the system, but they don’t necessarily have to be there. Like are there keystone species that need to exist?
- Rob:
- Yeah, that’s a wonderful question and that’s with the human microbiome diversity project is doing. What you first need to do is you need to have a baseline of species that live in healthy people, and so the baseline of healthy microbiomes for say people on the East Coast of United States is going to be different from the basic bottom-line or background microbiome for people who live in Africa and the people on the eastern coast of United States may even have a different microbiome than people who live in the Midwest of the United States. So we first need to understand that, and researchers are getting a pretty good idea of the background kind of baseline microbiome makeups for healthy people. Once you establish that then if you look at someone who’s sick say with as stomach disorder or skin disorder or something like you can compare that person’s microbiome to the baseline microbiome and get some insights into the the imbalance that’s caused by species composition and that might give you some information on what is actually causing the disorder. So this background stuff that we’re trying that researchers are trying to collect is very important. And it’s coming and it’s getting stronger and stronger with more and more samples that are collected.
- Tracey:
- Right. Is anybody worried that all that maybe environmental practices that aren’t so friendly to microbes that we’ve destroyed some that maybe are there any that are on the verge of becoming extinct. Is anyone raising any alarms?
- Rob:
- As extinction goes, there are a couple cases where we’ve removed certain microbes from our body ecology. For instance one helicobacter pylori is the microbes that was associated with ulcers and over the last 20 or 30 years’ antibiotics have removed effectively removed helicobacter pylori from our guts. So, that’s a huge extirpation event that’s ecological word, which means you just remove most of that particular species from the ecology and this has stopped ulcers, but at the same time it has caused other problems. The removal of that species from the ecosystem now causes GERD, the esophageal problem, and also some stomach cancers have started to arise as a result of the removal of this bacterium from the gut. And in addition, children who don’t have this microbe are developing asthma in higher frequency. So like any ecosystem you remove a keystone species like helicobacter pylori and you disrupt the ecology. You correct the one problem but you now cause a slew of other problems or a set of other problems. The things that other people are looking at are more about the balance of major kinds of microbes that exists in say your gut or in your mouth. Things like that and they’re not really about extinction of driving these things to extinction, but they’re worried more about disrupting the balance that’s there.
- Tracey:
- Right. In your book, “Welcome to the MicroBiome” you spend a great deal of time trying to explain the ecosystem’s approach. I like what you have to say in your epilogue. Food for thought for all of us. Would you mind elaborating on that?
- Rob:
- Sure. We took a silly little example from a movie – the Princess Bride – that fantastic movie which I guess it’s about two decades old. It’s a movie about a princess who is kidnapped and taken to be married to a prince in some other country and she’s followed by a man dressed in black, who was trying to rescue her, and at one point the man in black confronts these three villains bandits who were or kind of taking her to the new land. One of them is a giant, one, and one is swordsman, and one’s a self-proclaimed genius. And the man in black dispatches with the giant and with the swordsman and now he’s got to dispatch the third guy who’s name is Vizzini and what he does is he proposes a game of wits and the game wits is based on putting poison in one glass and moving them around and then having the two guys choose which glass they want to drink from or Vizzini choses the glass that he was to drink from. And what happens is Vizzini points to the glass and says “oh you would not put the poison in that class because it would been too simple for me to figure it out but then if you think I think it’s simple that you must’ve put the poison in that glass” And back and forth in the reasoning is more about trying to anticipate what’s going on and he finally makes a decision takes a sip and keels over dead and that the man in black takes a sip from his and he’s okay. The idea there that is relevant to microbiomes is that’s what we kind of do with microbiomes. We try to reason – how back and forth, back and forth in kind of a arms race in trying to get these things under control. It turns out in the movie the reason that the man in black won the game of wits was that he had made himself immune to the poison and it did not matter which glass he would drink from both glasses had the poison it. So, the second moral to the story is that we need to be like the man in black. We need to anticipate and we need to think of new ways of overcoming the kinds of crises and the kinds of challenges that microbes make for us in interacting with us. And by thinking about this immune thing and thinking in more clever ways I think we can overcome some of the problems that we’re seeing. We won’t be able to do it however, without knowledge about the microbiome.
- Tracey:
- Absolutely. Absolutely. I love that example. It is so true. I mean the way that you described it as arms race. I mean here we killed H. pylori thinking we were being so smart about it, and you mentioned we killed it off because we thought leading to stomach ulcers and then ultimately cancer and then you point out “oh well it’s the eradication of it actually might have contributed to the exact same problem.”
- Rob:
- Yeah. In the ecology and in evolutionary biology this is a recurring theme with how humans try to deal with pathogens and how humans try to deal with inconveniences. So we eradicate something in order to make our lives easier or in order to take inconvenience out of our life and by eradicating something, whether it be a microbe or a rodent or some other small mammal or rather we’ll eradicate a plant. By removing those things from the ecosystem we’re having an impact on system and that impact on the ecosystem may have very detrimental consequences down the road. So, the whole idea is just like the man in black to understand the entire picture and to try to think of how to manipulate the ecology to get rid of the inconvenience or to tone down inconvenience, but not at the same time not disrupting the ecology, which then can cause all kinds of bad things down to road.
- Tracey:
- To me that is one of the key messages that we all need to take home from that is we need to have a different approach or a rethink of how we look at illness and health.
- Rob:
- Absolutely. Some of the more important cures or therapies that we’re going to think of in the next decade or two with respect to how microbes are affecting our bodies are not going to be antibiotics. At least I’m going to predict this. I don’t think they’re going antibiotics. I think they are going to be manipulations of the ecology of the microbes that live in and on us and not eradication but manipulation of the ecologies to again overcome some of the inconveniences but at the same time maintain the status quo with respect to the ecology so that we don’t cause a ripple effect of problems downstream.
- Tracey:
- Absolutely. It’s so important. Thank you so much for sharing and imparting all of your knowledge today. We really appreciate it.
- Rob:
- Okay. You take care.
