Why CSU is investing in microbiome science

By Anne Manning • Published March 22, 2019

Our bodies are brimming with invisible bugs – microscopic organisms, or microbes – such as bacteria, fungi, protozoa and viruses that inhabit our guts, our ears, our skin. This community of 100 trillion microbes regulates our immune systems, helps us digest food, and even plays a role in our mental health.

Under our feet, the soil in which we grow food teems with microbial life, including bacteria and fungi that regulate plant health and longevity. In just one cup of lake water, you’ll find thousands of bacterial species that quietly manage the functioning of a healthy waterway.

With apologies to Madonna, we are living in a microbial world – and we’re only just beginning to understand it.

The combined genetic material of all the microbes living in a particular environment – be that the human gut, the soil on a farm, or the bottom of a lake – is called a microbiome. And over the last two decades, microbiome science, and the federal funding that makes it possible, has made its grand entrance into the university research world. Thanks in large part to DNA sequencing technologies that allow researchers to get up close and personal with whole swaths of organismal communities, it is increasingly clear that our health, the health of animals, the longevity of our soils, and our very destinies, are tightly linked to microbes and their wider microbiomes.

Like the microbes living in our guts, microbiome science at Colorado State University is thriving. Building on a legacy of excellence in microbiological science and scholarship, several years ago the university’s leadership chose microbiome science as one of three strategic initiatives in which to invest significant resources (the others were aging research and air quality). The university has hired six faculty members who all specialize in the study of microbiomes, and together with other colleagues, they are part of CSU’s Microbiome Network.

What is a “microbiome?” And how is CSU leading the way in microbiome science? Watch a quick explainer.
Video by Savannah Waggoner

Microbes matter

“One thing we all know is that microbes matter,” said Ed Hall, assistant professor in the Department of Ecosystem Science and Sustainability, one of the six Microbiome Initiative faculty hires, and a member of the Microbiome Network. “Yet we have been struggling to connect all of this information into usable system-level insights. The Microbiome Network is a strategic answer to the question of why microbes matter, and how we can use those insights to improve humans, animals and ecosystem sustainability.”

First hooked on microbes through a faculty mentor while an undergrad at UMass Amherst, Hall now leads a lab examining the causes and consequences of microbial biomass, particularly in aquatic ecosystems like streams and lakes. He and his students are looking at nitrogen and phosphorus cycling in Lake Yojoa in Honduras, and how the presence of metals influences the watershed’s bacterial communities.

Researchers in the CSU Microbiome Network work in several colleges and disciplines – from microbiology to ecosystem science, and soil and crop sciences to animal sciences. They are connected by a common thread – tailoring their scientific endeavors to a systems-level understanding of the microbiomes of their chosen disciplines.

Kelly Wrighton, assistant professor in soil and crop sciences, came to CSU from Ohio State University to join the Microbiome Network. She and graduate student Kayla Borton are examining a specific microbe-mediated metabolism that occurs in the human gut.

“The question we are trying to answer is why certain people who have a high-protein, high-fat diet are susceptible to atherosclerosis, while other people who eat the same diet aren’t impacted,” Wrighton said. “One of the answers belongs in your host genome – your own DNA – but the other component could be the microbial component – how microbes in your gut convert those same chemicals differently than the microbes in another person’s gut.”

This, coming from a soil scientist? Wrighton calls herself and her students “ecosystem agnostics;” they look at fundamental metabolisms of microbe species, regardless of where they live. She’s examined soils, watersheds, and much more. For example, Wrighton and Borton have previously studied the methylamine metabolism they’re looking at in the human gut, but in a very different context: inside fractured shales in the Earth’s crust.

“We don’t really care what the ecosystem is,” Wrighton said. “Instead, we think about the functions and the chemical reactions that microorganisms catalyze. Then we can look across systems, and at how those microorganisms have these huge ecosystem-level consequences, and to track those differences across ecosystems.”

The network

The other faculty hired into the Microbiome Network illustrate the vastly different disciplines microbiome science can influence.

  • Jessica Metcalf, associate professor of animal sciences, studies microorganisms that inhabit the gastrointestinal tracts of vertebrates. One of her projects looks at the effects of captivity and domestication on animal health. She also is researching decomposition ecology and applying it to better understand meat shelf life and spoilage.
  • Pankaj Trivedi, assistant professor in bioagricultural sciences and pest management, explores interactions between microbiome and plant environments, including plant-microbe-insect interactions.
  • Joshua Chan, assistant professor in the Department of Chemical and Biological Engineering, focuses on modeling and engineering microbiomes. He considers such microbiomes as potential solutions to global challenges ranging from food security to climate change to human disease.
  • And Mike Wilkins, assistant professor in soil and crop sciences, is investigating the impacts of microbiomes on biogeochemical cycling in the environment.

Together with the larger web of microbiome and microbiology expertise across campus, including an assistant professor in the Department of English, these new faculty members are helping steer the direction of microbiome research and bringing new ideas to the table.

Symposium in April

One result of these efforts is the inaugural Front Range Microbiome Symposium at CSU’s Canvas Stadium April 18-19. The symposium has a heavy student influence, with the Graduate Researchers Across Microbiomes (GRAM) group recruiting student speakers and organizing events.

The symposium will feature a bevy of speakers, including keynotes from science writer Ed Yong and leading microbiome scholar Jill Banfield, who leads the Microbial Research Initiative within the Innovative Genomics Institute at the University of California, Berkeley.