The next big thing for the human microbiome

By

Beth Giudicessi

The White House Office of Science and Technology Policy announced today a new National Microbiome Initiative to foster the integrated study of microbiomes across different ecosystems.

Ferran Garcia-Pichel, dean of natural sciences in Arizona State University’s College of Liberal Arts and Sciences, attended the event in Washington in his role as founding director of ASU’s Biodesign Center for Fundamental and Applied Microbiomics , which was launched in concert with the White House’s new initiative. The center will bring together researchers from diverse fields to identify the basic governing principals of microorganisms and how they may affect health, food production, climate change, forensics and other issues.

We asked Garcia-Pichel to explain microbiomes, from where they come, the reasons they are important and why it is the right time to studying them more closely. Video and text below.

Question: What is a microbe?

Answer: The microbe part is really easy. It is a living organism that you cannot see with your naked eye.

Q: Where do microbes live?

A: They live everywhere. You cannot find a place easily without any microbes. Microorganisms cover what we call the fringes of habitability.

What’s the hottest temperature in which a microorganism can live? It’s a 121 degrees. The first large organism you could see, you’d probably have to go down to about 45 or perhaps 50 degrees Celsius, so there’s a 70 degree difference in which only microbes inhabit.

The same is true for acidic environments and basic environments — only microbes have learned to live under those conditions.

Q: If microbes live on humans, from where do they come?

A: That’s an interesting question. We don’t quite know in all cases where microbes come from or if there is a single answer in all cases. We know, for example, that microbes in the human microbiome do not necessarily get transmitted directly from mother to child.

There is a certain dynamic of interactions between ourselves and our environment so that what we call a “succession” occurs where eventually our organism gets seeded with the right kinds of microbes that create a stable environment.

Q: If a microbe lives in me, is what’s good for it also good for me?

A: Not necessarily. Within microbes, like in good movies, there’s all sorts of characters.

Most microbes are beneficial. We evolved together, we learned to live with each other, and we learned to what we call in biology, “have a symbiosis.” But sometimes, some of them do things that ae not so good, and they are what we call pathogens. Some microbes actually take advantage of the host in a way that is only beneficial to them and detrimental to the host. Those are microbes we call “germs,” and those are the ones that cause disease and are the ones we tend to fight.

Perhaps what’s coming to the fore now is that people are realizing, “Huh, maybe we can now understand ourselves and our environment with our understanding of the part of our world that surrounds us, that’s sort of hard to focus on because we can’t see it. But it’s important.”

Q: Why is it important for researchers from different fields to work together to understand microbiomes?

A: Like in most areas of science, we are trained in a particular area, and we’re good at that. We’re not very good at thinking with the mindset of other disciplines. That’s where bringing people from different areas of science together with a common mission can be very successful. ASU has been extremely successful in gaining a foothold in those interdisciplinary areas that nobody has claimed, so we thought that gave us an advantage.

Let me give you an example. [The complexity of microbiomes] is very hard to do for a microbiologist alone, like myself. So perhaps it would be a good thing to team up with bioinformatician and an applied mathematician to see if we can create some parity out of the complexity. I will make sure that they get the biology right. They will make sure that I get my complexity straightened into what’s simple. What’s important is how we put that together into something that attains predictability.

Q: Why is this only now emerging?

A: Beats me! This is what I’ve done my whole life. And yet, it came as a surprise when it started breaking through that the impact of our own microbiomes was really important in our own health — that’s the part that’s really new. Of course, as humans we worry about our own health, so that has come to the fore. Now, more and more disciplines are realizing it. I think that’s what’s been happening in the last decade or so.

The other thing that has also helped has been techniques. What has changed in the last 20 years or so is we have developed methods for High-Throughput Sequencing. Essentially, we can get lists of [what’s in a microbiome] by looking at what we call the community DNA. We go into a soil or we go into a plant root or we go into human feces and we sequence all the genes of all the bacteria and then we get a listing of what is there.

Q: What research is ASU doing on microbiomes?

A: At ASU we have a long history of work in different microbiomes. There’s been several groups working in different colleges and in different departments on the role of microbes. We were pretty convinced that we needed to something bigger than what we were doing. There was a collection of leaders that worked in these various areas of microbiomes but they didn’t really have a hub, they didn’t really have a club, they didn’t really have a place to come together regularly. So we thought: it would be great if we could bring together the expertise we have at ASU with this common goal of bringing together people from different areas into one single center.

The center will be called the Center for Fundamental and Applied Microbiomics. It brings together this idea of wanting to get the fundamentals of how microbial communities work; meaning, those common rules that would apply generically to all groups and would predict the emerging properties from the sum of the parts. Very much like ASU, we would like to push the applied — the relevant immediacy — of our research for our everyday life.

Q: Can you tell us about the need to coordinate this research on a national level and beyond?

A: Microbiomes are everywhere. It is endless! We can start talking about our own microbiomes, the diversity of microbiomes, the diversity between human microbiomes in children versus older people versus sick people — there’s a diversity in every aspect of microbiomes. There is no way that one single institution can tackle the whole complexity of microbiomes. The task is daunting. That’s why we need to really tap into finding this common thread that goes through microbiomes because that’s going to give us the most bang for the buck. At the same time, there may be important things that need to be developed and there’s really room for a lot of people here. So I think that it’s not just a national initiative that will be needed but also an international one, and some of it is brewing both in the U.S. and in Europe — and I think others will join really soon.

Interview transcript edited for length and clarity.

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