Alan Brown, writer and blogger for the Kavli Foundation, contributed this article to Live Science's Expert Voices: Op-Ed & Insights.
From inside our bodies to under the ocean floor, microbiomes — communities of bacteria and other one-celled organisms — thrive everywhere in nature. Emerging at least 3.8 billion years ago, they molded our planet and created its oxygen-rich atmosphere. Without them, life on Earth could not exist.
Yet we know surprisingly little about the inner workings of nature's smallest and most complex ecosystems.
Microbiomes have a great deal to teach us. By learning how members of microbiomes interact with one another, scientists might discover innovative green chemistry and life-saving pharmaceuticals, or learn how to reduce hospital infections, fight autoimmune diseases, and grow crops without fertilizers or pesticides.
The sheer complexity of microbiomes makes them difficult to study by conventional biochemical means. Nanoscience provides a different and complementary set of tools that promises to open a window into this hidden world. [The Nanotech View of the Microbiome]
Earlier this month, The Kavli Foundation hosted a Google Hangout with two leaders in the emerging applications of nanoscience for studying microbiomes. They discussed the potential of natural biomes, why they are so difficult to understand, and how nanoscience may help us unlock microbiome secrets.
Joining the conversation were:
Eoin Brodie, a staff scientist in the Ecology Department at Lawrence Berkeley National Laboratory. He was part of the team that pioneered a device capable of identifying thousands of the bacterial species found in microbiomes, and is currently developing ways to combine data from many different types of measurement tools into a more coherent picture of those ecosystems.
Jack Gilbert is a principal investigator in the Biosciences Division of Argonne National Laboratory and an associate professor of ecology and evolution at the University of Chicago. He has studied the microbiomes of hospitals and is working on ways to use nanostructures containing bacteria to help infants fight immune diseases.
Below is a modified transcript of their discussion. Edits and changes have been made by the participants to clarify spoken comments recorded during the live webcast. To view and listen to the discussion with unmodified remarks, you can watch the original video.
The Kavli Foundation: So let's start with an obvious question, what exactly is a microbiome?
Eoin Brodie: A microbiome is a connection of organisms within an ecosystem. You can think of the ecosystem of microbes in the same way you think of a terrestrial ecosystem, like a tropical forest, a grassland, or something like that. It is a connection of organisms working together to maintain the function of a system.
Jack Gilbert: Yes. In a microbiome, the bacteria, the archaea (one-celled organisms similar to bacteria), the viruses, the fungi, and other single-celled organisms come together as a community, just like a population of humans in a city. These different organisms and species all play different roles. Together, they create an emergent property, something that the whole community does together to facilitate a reaction or a response in an environment.
TKF: How complex can these microbiomes? Are they like tropical forests? Are they more complex, less complex?
J.G.: The diversity of eukaryotic life — all the living animals and plants that you can see — pales into insignificance beside the diversity of microbial life. These bacteria, these archaea, these viruses — they've been on the earth for 3.8 billion years. They are so pervasive, they have colonized every single niche on the planet.
They shaped this planet. The reason we have oxygen in the atmosphere is because of microbes. Before they started photosynthesizing light into biomass, the atmosphere was mostly carbon dioxide. The reason the plants and animals exist on Earth is because of bacteria. The diversity of all the plants and animals — everything that's alive today that you can see with your eyes — that's a drop in the proverbial ocean of diversity contained in the bacterial and microbial world. [Can Microbes in the Gut Influence the Brain?]
E.B.: We tend to think of the earth as being a human planet and that we're the primary organism, or the alpha species. But we're really passengers, we're just blow-in's on a microbial planet. We're recent, recent additions.
TKF: You both wax so poetic about it. Yet we know so little about microbiomes. Why is it so hard to understand what goes on in these ecosystems?
E.B.: Jack eluded to it. The first problem is that microbiomes are very small. We can't see them, and it's very difficult to understand how things work when you can't see them. So tools are needed to be able to see these organisms.
We also can't grow them. It's very hard to bring them from the natural ecosystem into the lab for study. Probably less than one percent, depending on the ecosystem, can actually be cultivated on growth media in the lab so that we can do experiments and understand what functions they carry out. That leaves 99 percent — the vast majority of the microbes on Earth and most of their ecosystems — unknown to us, apart from their DNA signatures and things like that.
Now, Jack has pioneered DNA analyses. When you look at the DNA signatures from these environments, there are all these new organisms, new proteins, and new functions that we have never really seen before. This has been called earth's microbial dark matter. Just like dark matter and energy in the universe, this has been unknown to us, but it is extremely important if the planet — and humans — are to continue to function.
TKF: So, what makes it so hard to grow these microbes in a Petri dish?
E.B.: They're very fussy. You can think of it that way. They don't like to eat the food that we give them, in many cases. They eat things that we don't know they can eat. They breathe things that we don't know that they can breathe.
We breathe oxygen, they breathe oxygen, but they also breathe nitrates, iron, sulfur, even carbon dioxide. Getting the right concentrations and combinations of what they eat and breathe is very difficult.
In some cases, even if you can work that out, there may be something that they need to get from another member of the ecosystem. That member may supply an essential nutrient or a cofactor for them to grow.
So getting all of those possible permutations and combinations right is extremely challenging. A lot of people are working on it, and there's a lot of expertise being put into this, but it's extremely difficult and complicated.