Maximizing Microbiome Knowledge


Microbiomes – communities of diverse microorganisms that live together in different environments – are invisible to the naked eye.  But these communities play an enormous role in maintaining the health of ecosystems found in plants and soils, the ocean and atmosphere, and systems within the human body, like our digestive track.

The White House Office of Science and Technology (OSTP) has recently announced a new National Microbiome Initiative to advance research into microbiome behavior and function. The effort promises to yield not just a better understanding of our natural world, but also insights into how microbiomes can be tapped to improve the health of humans, plants, animals, and ecosystems. Although there are tens to hundreds of millions of different types of microbes, there is little current understanding of how they interact in communities or with their environments and the different disciplines that study the microbes in humans, animals, plants, and the environment tend to be disconnected.

“We live in a microbial world,” says Jeff Dangl, University of North Carolina, Chapel Hill Professor of Biology, Investigator of the Howard Hughes Medical Institute,  and co-author of several key journal articles that have helped fuel the OSTP initiative. “You would not be alive today were it not for the microbes in the ocean that provide half of your oxygen, microbes in soil that make production of food possible, and microbes in your gut that help you break down that food and help you fight off infection.”

The White House initiative will fund research into unanswered questions common to all microbiomes.  It will also fund better tools to study microbiomes and create opportunities for industry to commercialize discoveries. It aims to achieve coordinated research – linking scientists who study plant microbiomes with those studying human and environmental systems, and drawing in bioinformatics and data scientists essential to this area of research.

Sound familiar? It should, because that type of work fits squarely within UNCChapel Hill’s core research strengths. Faculty at Carolina are already leaders in these fields, and are excited about the opportunities the new OSTP initiative could provide.

“We need to mine the wealth of knowledge and depth of experience already present at UNC– the exceptional faculty, staff and students conducting cutting-edge research on microbiomes from many different environments – by unifying it with a larger vision,” says Adrian Marchetti, UNC professor of Marine Science. “This federal initiative may be the catalyst for us to do so.”

UNC-CH Microbiome Commitments

In August of 2015, Dr. Elizabeth R. Stulberg, Senior Policy Advisor for Food and Life at OSTP, visited UNC. The University’s reputation as a top-tier research institute drew her to campus. She met with microbiome scientists and university leaders to learn more about what makes UNC-CH and the Research Triangle a preeminent destination for microbiome work.  She charged scientists to examine the microbiome assets on campus and take steps to prepare for a federal initiative that could foster greater collaboration.

She also met with companies in the Research Triangle like Novozymes and AgBiome – which counts Dangl as a co-founder – along with scientists from neighboring institutions. She encouraged the region to leverage its collective strengths to compete for opportunities from the federal initiative.

Following her visit, UNC’s microbiome researchers and data scientists came together and agreed to establish MµNC, a new research collaborative on campus that will serve as a convening point for faculty from all disciplines to pursue multidisciplinary microbiome research and tackle questions common to all microbiomes. UNC boasts more than 60 UNC faculty and staff throughout its departments, schools, and centers that research various microbiomes. Since the OSTP visit, the University has added five more faculty positions with an emphasis on microbiome research, and a new research computing platform will dedicate a portion of its resources and personnel to microbiome analysis bioinformatics.

The MµNC hub will sponsor multidisciplinary on-campus seminars and partner with Research Triangle Park institutions to host intellectual exchange events for North Carolina microbiome scientists. Plans are in the works to pilot a data science training program that will groom graduating life science students as postdoctoral scholars providing bioinformatics support to UNC microbiome faculty.

Microbiome Research at Carolina

Work being done by UNC scientists includes the investigation of how plant microbiomes are organized and contribute to a plant’s sophisticated immune system. Dr. Jeff Dangl’s Lab seeks to discover how plants communicate with growth-promoting microbes and differentiate them from pathogens in complex plant-associated microbial communities.

Microbiota in humans are being explored by UNC researchers seeking to understand the role they play mediating diseases like colorectal cancer, cystic fibrosis, Crohn’s disease, and diabetes. UNC’s Multidisciplinary Inflammatory Bowel Diseases Center, led by Dr. Balfour Sartor, works to directly translate their discoveries into better patient care and prevention programs.

At the Carolina Population Center, Dr. Penny Gordon-Larsen is currently incorporating gut microbiome data into her complex, longitudinal analysis for the Coronary Artery Risk Development in Young Adults (CARDIA) and China Health and Nutrition Study (CHNS) datasets. “We all host microbiota that live in our guts,” Larsen says, “some of which are potentially helpful and others harmful. There is some suggestion that microbiota may be related to obesity and other cardio metabolic diseases.”  Her research looks for patterns that signal how microbiota can be used to promote health.

Marine scientists at UNC are investigating how marine microbes are affected by their environment and how they influence the biogeochemistry and ecosystem dynamics of our oceans. Dr. Adrian Marchetti’s biological oceanography lab currently studies trace metals, such as iron, that are essential for phytoplankton nutrition and works to predict the impact climate changes have on phytoplankton distribution and abundance.

The federal initiative aims to pull these specialties together to unlock larger microbiome mysteries. “Despite the differences in ecosystems that UNC’s microbiome researchers study,” says Dangl, “we use an overlapping set of sophisticated technologies. Coordination helps us learn from each other more efficiently and it saves money because we share tools.”

Tools of the Trade

Carolina has developed robust infrastructure to address the needs of microbiome research teams. UNC’s Microbiome Core Facility provides space, equipment, and expertise to analyze and characterize complex microbial communities in a wide variety of environments.

Established 2009, the facility is the only one of its kind in the world. “The platforms and analysis pipelines change all the time,” says Andrea Azcarate-Peril, the facility’s director and UNC Professor of Cell Biology and Physiology. “We are able to keep up with these ever-evolving changes and advise researcher on the best methods for their projects.”

Additionally, the Center for Gastrointestinal Biology and Disease (CGIBD)  – a collaborative GI research center at UNC Chapel Hill and North Carolina State University, originally established in 1983 – promotes and enhances multidisciplinary digestive disease research. UNC has also completed a new multi-million dollar computational cluster, Longleaf, which includes features dedicated to the growing computational and information processing needs of the University’s microbiome researchers.

UNC’s strength in tackling the mysteries of the microbiome builds on much more than its facilities and infrastructure. “We are a unique institution,” says Gordon-Larsen. “We have a campus culture that facilitates collaboration and supports interdisciplinary study. Plus we have extremely talented faculty who are world-renowned in their expertise. It’s a great place to engage in team science.”