BLACKSBURG, Va., February 28, 2007 – An international group of scientists has announced a major expansion of a lingua franca used to describe the activities of genes in living organisms. The expansion provides terms that scientists can use to describe the complex events that occur when a pathogenic or beneficial microbe encounters its host. 

Understanding these events is crucial for developing new interventions for preventing infections by disease-causing microbes while preserving or encouraging the presence of beneficial microbes. The unified language under development in this effort is called The Gene Ontology (GO). The new terms added to the GO will significantly bolster what is already a powerful tool for scientists to compare the functions of genes and proteins in a wide range of disease-related organisms. The ongoing initiative is part of the Plant-Associated Microbe Gene Ontology (PAMGO) project, a recently-established interest group of the worldwide Gene Ontology Consortium.

The GO Consortium has been working since 2000 to develop a common language of terms that can be used to describe how individual genes function in diverse organisms. The PAMGO project is supported by the National Science Foundation and by the National Research Initiative of the USDA Cooperative State Research, Education and Extension Service.

Candace Collmer, Professor of Biology at Wells College and one of the principal investigators on the project explained: “Microbes that associate with plants or animals can be pathogenic, neutral, or beneficial, but all share many common processes in their interactions with their hosts. For example, all must initially attach to the host. Accordingly, from the very beginning of the PAMGO project, we carefully tailored the new terms so that they would be useful for describing benign as well as pathogenic microbes in plant or animal hosts.”

Brett Tyler, Professor at the Virginia Bioinformatics Institute, and the PAMGO project leader, remarked: “Having a common set of terms to describe genes of pathogenic and beneficial microbes as well as the organisms they come into contact with is a critical step in understanding host-microbe-environment interactions. By providing a precise vocabulary for the functions of these genes, scientists can compare among microbes the many processes that make up the interplay between a microbe and its host.”

Dr. Tyler added: “PAMGO started out with the goal of creating terms to describe how microbes interact with plants. However, we quickly realized that almost all the terms were relevant to microbes that interact with animals and humans, and the response from researchers that study human and animal diseases has been very enthusiastic.”

"A common set of terms for the exchange of information about microbe-host interactions will help researchers communicate information, and expand concepts from the studies of microbes and their hosts," said Maryanna Henkart, Director of the National Science Foundation's Division of Molecular and Cellular Biosciences.

João Setubal, Deputy Director of the Virginia Bioinformatics Institute and one of the scientists on the project, commented “When the PAMGO project began, many GO terms existed for describing biological functions and processes found in microbes, but very few for describing the functions used by microbes in their associations with hosts.”

Trudy Torto-Alalibo, PAMGO Project Coordinator, remarked: “The GO Consortium has been set up in a way that allows all users to actively contribute to the ongoing refinement of the terms. When a scientist submits a new term to PAMGO it enables the entire community to participate in synthesizing a common understanding of how microbes associate with hosts. This is a tremendous open-source resource and a powerful way to advance our understanding of host-pathogen relationships.”

Michelle Gwinn-Giglio, Staff Scientist at The Institute for Genomic Research (TIGR) and a senior PAMGO member, remarked: “During the process of developing terms for PAMGO, it was immediately apparent that the mechanisms that microbes use to deal with hosts are really quite universal. The same terms can be used for species ranging from nematode worms to bacteria. Having these terms in place will greatly enhance research in this area.”

In the current update, the PAMGO consortium, in collaboration with Jane Lomax and Amelia Ireland of the GO Consortium’s editorial office at the European Bioinformatics Institute, has released more than 450 new terms for describing gene products involved in microbial-host interactions.

The PAMGO web site is available at

The PAMGO consortium is a collaboration between the Virginia Bioinformatics Institute, Cornell University, North Carolina State University, the University of Wisconsin-Madison, The Institute of Genomic Research (TIGR; a Division of the J.C. Venter Institute), and Wells College. The group works closely with the Gene Ontology Consortium. PAMGO is funded by the United States Department of Agriculture’s National Research Initiative-Cooperative State Research, Education and Extension Service and the National Science Foundation through the joint USDA-CSREES/NSF Microbial Genome Sequencing program.

About VBI
Virginia Bioinformatics Institute (VBI) at Virginia Tech has a research platform centered on understanding the “disease triangle” of host-pathogen-environment interactions in plants, humans and other animals. By successfully channeling innovation into transdisciplinary approaches that combine information technology and biology, researchers at VBI are addressing some of today’s key challenges in the biomedical, environmental and plant sciences.

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Barry Whyte,
Virginia Bioinformatics Institute, (540) 231-1767,

Cheryl Dybas,
National Science Foundation, (703) 292-7734,

Published by Barry Whyte, February 27, 2007