Penn State creates new center for microbiome research

Novel tools such as this GFP-labeled strain of the coral pathogen V. coralliilyticus (shown as a green aggregate) are being used to clarify the role of individual microbes in the onset and spread of coral diseases that have altered Caribbean coral reef ecosystems. A new Penn State research center will provide a focal point for the study of such communities of microorganisms that live on or in people, plants, soil, oceans and the atmosphere. Credit: F. Joseph Pollock, Medina Lab, Penn StateAll Rights Reserved.

UNIVERSITY PARK, Pa. — A University-wide effort to promote the study of microbiomes has led to the creation of a center for microbiome research at Penn State. Microbiomes are the communities of microorganisms that live on or in people, plants, soil, oceans and the atmosphere.

Announced by Neil Sharkey, the University's vice president for research, the center — housed in the Huck Institutes of the Life Sciences — will support transformative, interdisciplinary research on microbiomes, a fast-growing area of scientific inquiry.

"Researchers have been studying the interactions between communities of microorganisms and their environments for over a century, but microbiome research has exploded recently with the emergence of new and relatively affordable technologies, allowing us to test hypotheses that previously were difficult to examine," Sharkey said.

"Penn State has a tremendous opportunity to be transformative in this field because of the presence of early adopters, a range of unique expertise, significant investments in new faculty, and outstanding facilities," he said. "This center will provide infrastructure and resources needed to increase the diversity and breadth of microbiome research across all Penn State locations and will offer new opportunities for researchers from divergent disciplines to collaborate."

Microbiomes maintain optimal function of diverse ecosystems, influencing human health, food security, environmental quality and other factors. Dysfunctional microbiomes are associated with human chronic diseases such as obesity, diabetes and asthma; local ecological disruptions such as the hypoxic zone in the Gulf of Mexico; and reductions in agricultural productivity.

Numerous industrial processes, such as biofuel production and food processing, also depend on microbial communities. Although new technologies have enabled significant discoveries about the importance of microbiomes, scientists still lack the knowledge and tools to manage microbiomes in a manner that prevents dysfunction or restores optimal function.

The University's focus on microbiomes dovetails with increased recognition of the importance of this field within the scientific community and by the public. In May 2016, the White House Office of Science and Technology Policy announced the National Microbiome Initiative, aimed at fostering the integrated study of microbiomes across different ecosystems.

That announcement coincided with commitments for federal agency investments of $121 million in the first two years. Agencies supporting microbiome research include the Department of Energy, the National Aeronautics and Space Administration, the National Institutes of Health, the National Science Foundation and the U.S. Department of Agriculture. In addition, $400 million in financial in-kind support was committed by other organizations, including Penn State.

Carolee Bull, head of the Department of Plant Pathology and Environmental Microbiology, represented Penn State at the kick-off event for the national initiative. Bull, a professor of plant pathology and systematic bacteriology in the College of Agricultural Sciences, is chair of the planning committee that drafted the proposal for the new center and will lead the center until a director is named.

"Several Penn State colleges and institutes have robust microbiome-related research programs and have made commitments to participate," said Bull, who is part of a new Food and Agriculture Microbiomes research cluster at Penn State.

"We expect that a core group of about 30 researchers and their teams will be actively involved in the center's activities," Bull said. "Researchers from a broad range of social and behavioral sciences, including communications, are involved to develop unique research questions and strategies that will be distinctive to the Penn State approach to microbiome research."

She noted that more than 100 faculty members have been involved either on the planning committee or as participants in preliminary meetings and workshops. Units represented have included the Colleges of Agricultural Sciences, Communications, Earth and Mineral Sciences, Engineering, Health and Human Development, Information Sciences and Technology, Medicine, and the Eberly College of Science, as well as the Huck Institutes of the Life Sciences, the Social Science Research Institute, the Institutes of Energy and the Environment and the Institute for CyberScience.

Faculty, staff, postdocs and students discuss microbiome research during a networking event in October 2016. Scientists from 12 Penn State colleges and research institutes participated in microbiome initiative planning or events. Credit: Penn StateCreative Commons

A microbiome workshop in June 2016 — spearheaded by Gary Thompson, the College of Agricultural Sciences' associate dean for research and graduate education, and organized by Siela Maximova, research professor of horticulture and faculty fellow in the college's research office — attracted more than 50 representatives from 10 Penn State colleges and research institutes. In October, a networking event drew more than 55 researchers and featured 17 posters and five "lightning" talks featuring a wide range of research related to microbiomes.

To encourage participation, the planning committee holds weekly meetings that are offered as webinars to allow interaction with those who cannot attend in person, including researchers at other Penn State locations across the state. "Members of the faculty at the Hershey campus already have been participating, and we look forward to engaging more scientists from other Penn State campuses going forward," Bull said.

The Food and Agriculture Microbiomes research cluster, which engages faculty primarily from the College of Agricultural Sciences and the Huck Institutes of the Life Sciences, has been a catalyst in bringing the University-wide center to fruition, according to Bull. Supported by the college's Office of Research and Graduate Education, this cluster — the goal of which is to develop biological tools for improving human health and enhancing plant and animal health and productivity — will benefit from the interdisciplinary collaboration the new center will foster.

To further strengthen microbiome research at Penn State, the Department of Plant Pathology and Environmental Microbiology has hired two new faculty members, Kevin Hockett (microbial ecology) and Terrence Bell (phytobiomes), Bull said. Searches also are underway to fill positions in the Department of Food Science (microbial ecology) and the Department of Plant Science (root biology and rhizosphere interactions). In addition, she said, the College of Medicine plans to fill five new positions as part of its commitment to microbiome research.

In an effort to reach those not yet affiliated with the center, the Office of the Vice President for Research will circulate a University-wide survey to identify research strengths related to microbiomes and gauge relevant areas of interest among research faculty and staff.

Penn State faculty, students and staff interested in receiving the microbiome center's email updates or information about planned weekly events can contact Erika Stover at

Reef-building corals, like the one shown here, and other ecosystems harbor diverse communities of microorganisms collectively called a microbiome. Penn State's new microbiome research center will foster collaboration across several academic colleges and institutes to study microbiomes relevant to human health, plants and soils, food science, energy, the environment and other domains.  Credit: F. Joseph Pollock, Medina Lab, Penn StateAll Rights Reserved.

Last Updated April 21, 2017