Dirk Knemeyer

The Digital Life #168: The Microbiome

Episode Summary

This week on The Digital Life is the second in our special series of episodes put together in conjunction with our friends at the GET Conference, on the cutting edge of research science and technology. In this week’s episode we explore the topic of the microbiome, with interviews with Embriette Hyde and Justine Dubilias of American Gut Project and Brian Klein of the Forsyth Institute.

We’re only just beginning to understand the microorganisms that resides in, on, and around us. In the past it was estimated that we have 10x more non-human cells than human cells. More recent estimates lower that number to equal amounts of cells for both human and microorganisms. And, while we have a mutually beneficial relationship with some of the microbiota that colonize us, for some we just don’t understand what the relationship is, yet.

Jon : Welcome to Episode 168 of The Digital Life, a show about our insights into the future of design and technology. I’m your host Jon Follett.

This week on the podcast is the second in our special series of episodes put together in conjunction with our friends at the GET Conference, on the cutting edge of research science and technology.

In this week’s episode we’re exploring the topic of the microbiome, with interviews with Embriette Hyde and Justine Dubilias of American Gut Project and Brian Klein of the Forsyth Institute.

We’re only just beginning to understand the microorganisms that resides in, on, and around us.

In the past it was estimated that we have 10x more non-human cells than human cells. More recent estimates lower that number to equal amounts of cells for both human and microorganisms.

And, while we have a mutually beneficial relationship with some of the microbiota that colonize us, for some we just don’t understand what the relationship is, yet.

Let’s start with our interview with Embriette Hyde and Justine Dubilias of American Gut Project.

Embriette: I am Dr. Embriette Hyde. I am the Project Manager of American Gut Project at UCSD, University of California, San Diego.

Justine: I am Dr. Justine Dubilias. I am the Analyst on the American Gut Project at UCSD.

Dirk: Wonderful. Tell us a little bit about the American Gut Project and the work you are doing with it.

Embriette: It is a citizen science microbiome project, basically. Human microbiome research took off with the human microbiome, which was the first MIH funded effort to figure out what a healthy human microbiome looks like. We really realized after that study that it is really hard to define healthy because everybody is so variable. That pushed off researchers the world over and labs all over the world are looking at is the microbiome associated with this disease or with that disease or with this factor or with that factor. One of the things that we need to keep in mind is that to really accurately figure out where the associations are and get some statistical power in there, we need to get a good sampling of the population. We cannot just focus on, for example, a population in a single geographical location, which happens sometimes with research projects because the funding is limited, so you cannot sample a million people because you just don’t have the money to do that. That is what we are trying to do with American Gut, is reach out to the citizens [inaudible 00:01:27] as crowd sourced effort, where the participants themselves are not only providing samples to us but also the funding to do the work. Then we can get the sample sizes that we need for statistical power and to make some meaningful connections.

Dirk: That is great. For some of our listeners, even though microbiome is a hot term these days in the science community, maybe not all of our listeners know what the micribiome is. Could you explain it in a very basic way, what does that mean?

Justine: You are covered in bacteria.

Dirk: That is scary.

Embriette: It shouldn’t be.

Justine: They are actually your friends. Your body has about seventeen proteins that can break down carbohydrates, just in your human genome. Your microbiome, these bacteria that live in your stomach, can breakdown about seventeen or have about seventeen thousand ways to break down sugar. They are helping you digest your food. They are giving you vitamins. They are potentially protecting you against harmful bacteria that are coming in. They can help regulate whether you are obese or lean. They can contribute to auto immune disease. There is a whole variety of pathways they are involved in.

Embriette: I like what she said about helping fight against disease because some studies using germ free animal models, so these are animals that are basically sterile,, they have no bacteria in them what so ever. You can see that their immune system is basically non existent. I think that is a really elegant and powerful way to show that we need these micro organisms in our body or else we just cannot function appropriately and then we may actually succumb to some of those awful diseases that are such a small percentage of the ones that are actually out there.

Dirk: You mentioned this is part of the citizens science movement so of course you are looking for all of us to, or as many of us who are willing to contribute. My wife is a scientist and she in fact did contribute to the American Gut Project. I find it very interesting but I was not compelled to contribute because I found the sample submission, re-exposes me as a little weak stomached perhaps. Maybe you could explain to our listeners, what is a sampling look like and then more importantly, how do you use that and how is that vital to the research that you are doing?

Embriette: The sampling process itself, it isn’t too difficult. I know some people get a little queasy because they think, oh gut, does that mean I have to poop in a bucket or something like that. It is really not so bad. We have just a double headed swab and if you do want to provide a stool sample you just swab a piece of used toilet paper. Most people are using toilet paper in the bathroom anyway, I would hope. It is just that one extra step of just you swab it and then put the swab back in the tube and that’s it. For skin and mouth it is even easier, you are just rubbing the swab …

Dirk: Is that just USPS?

Embriette: It goes through the regular mail, yeah. We provide envelopes that are addressed already for participants to send their samples back. Just a regular 92 cent stamp will do it and you can put it through the mail.

Dirk: You get a lot of information from these samples, right. Talk about that and how you translate it into your work.

Justine: We get about, is it six million sequences on a sample?

Embriette: On a typical run we are getting about forty thousand sequences per sample. We have a little over 500 of those each time we run a sequencing run.

Dirk: Wow.

Justine: Then, we are able to take those sequences and map them to bacteria using a reference set of data that has been developed over a set of years. Then, we take that table of information, we take information about the participants, we put those together, and start to look for patterns and trends in the data. One of the things that we noticed in the data is that we have people tell us about how frequently they drink alcohol. Do you never drink, do you drink less than once a week, once a week up to daily. Looking at adults over the age of 21, of course …

Dirk: Of course.

Justine: .. we were able to find this trend where we saw the more people drink alcohol, the more types of bacteria in their gut. This sounds sort of scary to some people that more bacteria seems bad. In fact, we find that in disease states, like inflammatory bowel disease, you have fewer types of bacteria.

Embriette: It kind of makes sense, if you think about it a little bit. If you go back to what we were discussing before. Like Justine said, the ones that typically live in us can help us fight off the pathogens. If you have a more diverse community with a lot of different types there, they can do a lot of different things. The community itself is just a little more robust and can experience those potential pathogens in a much healthier way. They can stand up to it better and fight it off better. If you think about it that way, it does actually make sense rather than the initial thought which is, more bacteria, that cannot be good. But it actually really is in a vast majority of cases.

Dirk: That is very interesting. There are a few themes that are futurist themes that we are interested in that I would like to ask you about in the context of your work. In terms of human life expansion, what are ways the microbiome and the research you are doing will contribute to people living longer in the future?

Embriette: That is a really loaded question, actually.

Dirk: Unintentionally.

Embriette: It is hard to say now because the research is still so young. Ideally, what we would like to do, the best way to think about it is, you are creating a map of the human microbiome. You can identify the areas on the map that are bad. You can identify areas that are good. The key is going to be how do we move from the areas of good to bad or bad to good. Of course, if you are moving from the areas of bad to good you can think health quality is going to be better. Of course, if I get hit by a bus tomorrow it didn’t help. It is really hard to say how and in which context we are going to be able to achieve that because the research isn’t there yet. That is why it is so important that we get more people into the project because the more people we get, the faster we can determine those associations and those connections.

Justine: I think chronic disease management will also be a big issue. There is some gourdeous work showing that microbial metabolite is associated with cardiovascular disease and vascular degeneration. If we can understand which microbes are contributing to that molecule, we can sort of prevent heart disease. In type one diabetes, they are finding that there is a point at which your microbiome predicts, this is a preliminary study, but it predicts that you see kids who are about to go into a full blown clinical diabetes have a different trajectory in their microbiome then kids who are either healthy or kids who are not in danger of getting … I am not phrasing this well … In danger of getting the disease but are not actually sick yet.

Embriette: The pre-diabetic. If you want to go directly to actual life span prediction, just in the absence of chronic disease or any other disease, we do have some collaborators who are really interested in looking at that. The work they are doing shows there is some connection to diet. We do know that there is a connection between diet and the microbiome. I think if one day we can make a connection between those two and wrap it together that would awesome. That is something that we have and something that we will be working on in the future. There is a lot of exciting stuff out there for us to do. Job security. We are not going to be done with this anytime soon.

Dirk: From a microbiome perspective, I mean this as a very serious question, should I not be using soap when I bathe? The shampoos and detergents and the soaps that we have obviously have chemicals that may be deleterious to us. What would be the healthiest approach to staying hygienic while still being as healthy as possible for the microbiome?

Embriette: We have this whole thing that came out, I don’t know if you have heard of the hygiene hypothesis?

Dirk: No.

Embriette: It is a really elegant hypothesis that looks at the lifestyle now in Western countries and how we are really germaphobic. We wash everything in an OCD type manner. Our counters, our houses, ourselves, our kids, and our animals. As that change in the way we live occurred, we noticed that the incidence of some chronic diseases is also increasing. The hypothesis that since we are killing off all of the diversity that is important for fighting off bad things or making sure that our immune systems functions correctly, we are actually setting ourselves up to be a more sick society.

One of the things that we like to say is don’t go overboard. You don’t have wash your kitchen counter every three minutes, you know. Wash it, of course, after you prepare meat on it because we know that meat contains pathogens. Let your kid go outside and get a little dirty, you know. It is okay if he is playing in the dirt. You don’t have to freak out, oh my, he is going to die. I think it is a balance. Obviously washing is good and it serves it’s purpose but let’s not go crazy with it. Let’s walk that fine line of getting rid of the bad but also maintaining the good and not hurting the good while we are at it.

Justine: I actually think from a hygiene perspective, another big one is pets. There is a study showing that pets help increase your microbial diversity and that if you have a dog, you share more of your bacteria with your partner, via your dog, than you do if you have an infant.

Dirk: Wow. That is interesting. You talked about not going overboard or crazy with the cleanliness. To bring that into very concrete, adult terms, right. Anytime I get home, the first thing I do is wash my hands. I go into the office, first thing I do is pump the sanitizer and wash my hands before I start working. Is that on the overboard side or is that on the okay side? What is healthy microbiome behavior?

Embriette: I guess it depends on what you were doing before you did that, right. Again, it is hard to say and this would be my own personal opinion so I don’t want anyone who is listening to think that this is, you know, what everyone should be doing. What I tend to do is wash before I eat, wash before I am going to be doing something that involves a lot of, you know, if my hands are going to be near my face.

Dirk: Hand and mouth stuff?

Embriette: Yes, exactly. Otherwise, I am not too frightened about what is is.

Dirk: Okay. Fair enough.

Embriette: Do you have anything to …?

Dirk: You’re both here for the GET conference, from San Diego. Thank you for making the trip. It is wonderful to have you. What are the things that you are excited to learn about or share in your time here?

Justine: There are a ton of cool projects here. This is our third year at the conference with American Gut and it has been amazing to see it grow over the three years. There are a lot of really cool projects that come back year after year. It is exciting to see everything continue to go along.

Embriette: I totally agree with that. There are so many awesome projects here, in learning about what they are doing but also seeing the excitement of the people who come to the conference to learn about all of the labs is also really cool because that is something I think all of us have in common here, regardless of what our project is. That is getting people excited about science and about the work that we are doing, bringing it out to people and showing people that it is not just something that is only for the PhD scientists that went to school for 10 million years. No, you can help contribute too, to what we are doing, and that’s really a cool thing.

Dirk: Wonderful. Thank you both so much for coming on.

Embriette: Thank you for having us. It was great.

Brian: My name is Brian Klein and I’m with the Forsyth Institute in Cambridge, Mass.

Dirk: Excellent. Brian, what is the kind of work you’re doing at the Forsyth Institute?

Brian: At the Forsyth, I’m studying actually indoor track microbiomes and the salivary and nostril microbiomes of athletes that use these indoor environments. The Forsyth Institute studies dental, cranial, facial work in general and it kind of fit in there with the salivary and the nostril work that we are doing.

Dirk: Okay, so when you say indoor … When you said indoor, I though of like an indoor exercise area. I think you’re talking about something different.

Brian: No. Actually, indoor exercise area so … Especially here at this conference, a lot of people have studied the microbiome of indoor environments kind of on a healthcare setting like the hospital microbiome project. There is an office microbiome project. They kind of did like the live-in work but no one had ever actually studied how play environments affect the people who use them in an microbiological … From a microbiological standpoint. We wanted to be one of the first on that.

Dirk: That’s very interesting. In a general way, how are these different microbiome environments different? From work to play to home, what are the characteristics of those differences?

Brian: Yeah, so when you think about how the temperature settings are put up. If you think about how the room is lit, how large these rooms are, how many people fit into them. Indoor tracks and I’m working specifically in greater Boston right now and we have four indoor tracks for studying. The temperature ranges that I’m seeing, I see as low as 50 degrees which you would never see in an office environment or hopefully, a hospital and hopefully, not your house to as high as 85 degrees Fahrenheit. Sometimes it’s within the same day. Some tracks are very stable, some are not. These tracks can fit up to 6,000 people, sometimes a standing room to 10,000 so you have like a … How many people are you cramming in to one room and air exchange cycles would be very different from other indoor environments.

Dirk: My understanding is that the more diverse the microbiome environment is, the healthier it actually is for the individual. Is that correct?

Brian: I think we’ve … The gut is extremely diverse and for the most part, they’re seeing … When they see a non-diverse gut, you have an ailment usually. I think that’s where a lot of that thinking comes from but there are definitely niches that are dominated by very few things especially with humans. I think we haven’t quite explored enough to say that it’s usually super diverse is good especially because you could have a super diverse, weird microbiome whether or not that’s good for you.

Dirk: Yeah. Do you have answers or at least, hypotheses of what are the characteristics of healthy microbiome environments from the standpoint of … You mentioned temperature earlier, number of people, like what are the characteristics of a healthy environment?

Brian: Yeah. In terms of indoor environments and looking at the athletic indoor environments I’m staring to look at, it would really depend on trying to cultivate like a healthy environment rate and the … You’re going to affect what viruses stay around, what fungi proliferate or even just come in based on whether or not you … The temperature would be a big factor. Also as been shown in some of the studies so far, opening the windows so mechanical ventilation is huge in terms of what is actually in the air inside your building. If you open the window, it’s going to look a lot like what’s outside. You’re not just recircing that’s already in there.

Dirk: Yeah. Any last words or things you’d like to share with our audience or … ?

Brian: Sure. I just … I think that studying our microbial world is really important and getting participation … Moving from just studying the environment which we have to study but also studying how the host interact with the environment is where I want to go and where I think a lof the science is going to be moving. You define these physical places first, whether it’s a hospital, it could be the soil. You say what’s in the soil but then the next question, to me, would be well, how does the soil … If I’m digging in the sand affect me the next day or down the line? Like do these things change because people always talk about let your kid play in the dirt. Well it might not only be from an immunological standpoint, it could also be from a microbial standpoint like changes what’s on your skin or changes what’s in your mouth if you are really playing in the dirt.

Dirk: This has really been great. Thank you so much for your time.

Brian: No, thank you.

Jon: Listeners, remember that while you’re listening to the show you can follow along with the things we are mentioning here in real time. Just head over to thedigitalife.com – that’s just one “L” in thedigitalife – and go to the page for this episode. We’ve included links to pretty much everything mentioned by everybody, so it is a rich information resource to take advantage of while you are listening or afterward if you’re trying to remember something you liked.

You can find links to the complete interviews, and others from the conference in the resources section for this episode. You can find the Digital Life on iTunes, Soundcloud, Stitcher, Player.fm and Google Play.

And if you want to follow us outside of the show, you can follow me on Twitter @jonfollett. And of course this whole show is brought to you by Involution Studios, which you can check out at goinvo.com, that’s g-o-i-n-v-o dot com.

That’s it for Episode 168 of The Digital Life. I’m Jon Follett and I’ll see you next time.

Tagged on:     

Leave a Reply

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