Penn State Microbiome Center's DAWG chews on microbiome data sets

Cole Hons
September 17, 2019

UNIVERSITY PARK, Pa. — While developing her winning USDA-NIFA fellowship in the summer of 2018, Mara Cloutier, a doctoral candidate in Penn State’s Soil Microbiology and Biogeochemistry program, approached Carolee Bull, the director of Penn State’s Microbiome Center. Cloutier wanted to brainstorm ways that she could make a lasting impact on the center, equal to the impact the center had on her.

Among the numerous possibilities they considered, Cloutier latched onto the need to help others improve their data analysis skills. The idea inspired her to launch a new initiative — one that could help Penn State’s Microbiome Center achieve its mission to support transformative, interdisciplinary research.

“A big goal of the center is to provide structured educational opportunities unique to Penn State, to increase the diversity and breadth of microbiome research at Penn State,” Cloutier said. “To assist with that, we pulled together a group of graduate students and postdocs called the Data Analysis Working Group⁠ — or DAWG.”

“Many faculty are looking for an easy entry into microbiome research and analysis,” Bull noted. “This initiative gives faculty with great questions and little experience a way to learn with their students and postdocs as they further their research.”

All scientific research requires the collection of data, and lots of it. But any collection of information is meaningless until it’s organized, analyzed and interpreted. With a multitude of data sets being collected across disciplinary boundaries, sophisticated tools and methods of analysis and interpretation are required to pull it all together in a relevant and useful way. The Penn State Microbiome Center’s DAWG seeks to facilitate this process, so that more members of the Penn State community can produce research deliverables related to microbiomes.

“DAWG is led by four postdocs/graduate students each semester,” explained Cloutier. “When we launched in spring 2019, DAWG was led by myself, Fabricio Vieira (postdoc in plant pathology and environmental microbiology), Sofia Roitman (doctoral student in biology), and Taejung Chung (doctoral student in food science).”

To date, DAWG has presented five workshops, educating students, postdocs, and lab technicians about software and best practices for analyzing microbiome data. The group also analyzed a dataset for Professor of Biology Bert Eardly at Penn State Berks.

“I had been investigating the devastating effects of a 100-year-old zinc smelter on the local forests and ecosystems in a small town near my campus in east-central Pennsylvania,” said Eardly. “Although I had collected a large amount of genetic data on the affected ecosystems, I was unfamiliar with the most recent web-based systems and software that are currently used to analyze this type of data.”

With DAWG’s help, Eardly was able to collaborate with students working in microbiology, environmental science, ecology and bioinformatics.

“These students were able to provide me with invaluable assistance by analyzing and interpreting my data,” Eardly said. “We're currently summarizing this work for publication.”

The resulting co-authored manuscript is a clear product of the efforts of the team and the platform provided by the Microbiome Center.

DAWG workshops benefit not only the participants, but also the presenters.

“As a group leader, I not only learn a lot of different aspects of microbiome data and its analyses, but also enjoy discussions with other students who are on the same page as me,” said Chung.

In fall 2019, the Microbiome Center plans to offer a DAWG workshop every month, open to anyone with an interest in microbiome research. These workshops aim to:

  • Provide unique opportunities for students and postdocs to teach faculty, staff and students microbiome processing and data analyses.
  • Train graduate students and postdocs on bioinformatic software useful for microbiome research.
  • Help build collaborations between the members already associated with the Microbiome Center and Penn State researchers who are interested in microbiome research.
  • Use the skills of Microbiome Center members to help a researcher at Penn State process data and analyze results, culminating in a publication or potentially being used as preliminary data for a grant application.

Ultimately, DAWG organizers hope to assist with one major research project each semester. To learn more about workshops, potential collaborations, and the possibility of bringing a project to the team, contact Cloutier at muc345@psu.edu.

The Microbiome Center is a member-driven community providing many opportunities to develop meaningful broader impacts with lasting outcomes. To brainstorm real contributions for your next grant, contact Bull at ctb14@psu.edu

Last Updated September 18, 2019