News headlines often paint E. coli as a vicious bacterium, capable of causing disease and death to those unfortunate enough to ingest it. But that is only a tiny minority of E. coli, and a very small part of the story of this remarkable bacterium; its relationship to human health and the food we eat is much more complex. Not all E. coli are bad - in fact most are not - and some are even beneficial. On September 1st 2011, the American Academy of Microbiology convened an expert panel of microbiologists, food safety experts, and bacteriologists to develop a more accurate picture of this often maligned bacterium. This report, the product of that meeting, tells the larger story of E. coli: its role in human health, in food, and even in our understanding of our own biology.

It has been over 150 years since the publication of On the Origin of Species, Charles Darwin’s landmark book based on his observations of animals in the Galapagos Islands. The two core principles he described in his work, descent with modification and natural selection, have helped us understand life’s tremendous diversity. But how do these same principles pertain to the microbial world that Darwin could not see? In 2009 the American Academy of Microbiology convened a colloquium in the Galapagos Islands to address this question. Based on that colloquium, this report summarizes the unique challenges posed by microbes, like vast evolutionary time scale, genetic promiscuity and rapid division, which complicate understanding microbial evolution. It also identifies areas of research and education where more information is needed to overcome these challenges. The report concludes that due to the power of microbes as model systems, tools in biotechnology, and drivers in biogeochemical and climate cycles, understanding microbial evolution may give us more than just the ability to understand microbial diversity; it will help understand the world around us.

Scientists can gain insights into new ways to use microorganisms in medicine and manufacturing through a coordinated large-scale effort to sequence the genomes of not just individual microorganisms but entire ecosystems, according to a new report from the American Academy of Microbiology that outlines recommendations for this massive effort. The report, “Large-Scale Sequencing: The Future of Genomic Sciences?” is based on a colloquium convened by the Academy in September 2008. The report outlines recommendations for large-scale microbial sequencing efforts directed toward cultivated isolates and single cells, as well as a community-scale approach to characterize a set of defined ecosystems of varying complexity.

Prepared by Merry Buckley, Thomas Slezak, and Thomas Brettin.

Bioinformatics, the application of computer analysis to molecular biology, is a fundamental corollary to biodefense research. As we face new security threats involving pathogens and infectious disease, bioinformatics databases must be improved and a plan must be made for integrating biodefense research throughout the world. This report outlines the recommendations made by the world's leaders in bioinformatics at a colloquium held in Baltimore.

Prepared by Merry R. Buckley.

Examines the current state of knowledge of microbial genomics, the technical challenges of using genomics in microbial systems, and the achievements that may now be possible by applying genomics to the study of microbiology. Makes recommendations for future directions in education and research.

Prepared by Richard J. Roberts, Peter Karp, Simon Kasif, Stuart Linn, and Merry R Buckley.

This report details the continued work in genome annotation that will likely lead to new applications and progress in healthcare, bio-defense, energy, the environment, and agriculture.  The report also discusses the critical challenges and ways to accelerate progress in the field of genome annotation.

Prepared by Merry Buckley.

Details the power of applying a systems approach to the study of biology and to microbiology, specifics about current research efforts, technical limitations, database requirements, education needs, and communication issues that surround the field of systems microbiology.

Prepared by Merry Buckley.

This report details the study of pathogenesis and how far we have come to having a complete understanding of pathogenesis and a phylogenetic framework for understanding the phenomenon.

Prepared by Paul Keim.

Surveys this new field and makes recommendations about how to move it forward.

Prepared by David A. Stahl and James Tiedje.

Examines the explosion of new information in microbial biology made available by recent advances in molecular technology--and looks at the important questions that remain. Recommends next steps for the integration of genomics with microbial systematics, evolution, and ecology.

Prepared by Joan B. Rose, Ph.D., and D. Jay Grimes, Ph.D.

Evaluates current status of water quality, discusses new and emerging issues, and examines shortcomings of current practices. Outlines gene probes, genotyping, antibody, and PCR (polymerase chain reaction) techniques that stand to replace outdated testing methods. Makes specific recommendations for risk assessment, technology use, data collection, research collaboration, and evaluation and development of best practices.

Prepared by David A. Relman, M.D., and Evelyn Strauss, Ph.D.

Details the enormous advances made possible through the genetic wealth and biological aptitude of microbes--and the new challenges arising from the advent of large-scale DNA sequencing. Discusses project selection and coordination, data management and analysis, training and education, funding, and ethics, and makes specific recommendations for future action.

The opinions expressed in this report are those solely of the colloquium participants and do not necessarily reflect the official position of our sponsors or the American Society for Microbiology.