Board of Governors, American Academy of Microbiology

Eugene W. Nester, Ph.D. (Chair) University of Washington

Kenneth I. Berns, M.D., Ph.D. University of Florida Genetics Institute

Arnold L. Demain, Ph.D. Drew University

E. Peter Greenberg, Ph.D. University of Iowa

J. Michael Miller, Ph.D. Centers for Disease Control and Prevention

Stephen A. Morse, Ph.D. Centers for Disease Control and Prevention

Harriet L. Robinson, Ph.D. Emory University

Abraham L. Sonenshein, Ph.D. Tufts University Medical School

George F. Sprague, Jr., Ph.D. Institute for Molecular Biology, University of Oregon

David A. Stahl, Ph.D. University of Washington

Judy D. Wall, Ph.D. University of Missouri

Colloquium Steering Committee

Timothy J. Donohue, Ph.D. (Co-Chair) University of Wisconsin-Madison

James K. Fredrickson, Ph.D. (Co-Chair) Battelle Pacific Northwest National Laboratory

Penny Chisholm, Ph.D. Massachusetts Institute of Technology

Nancy L. Craig, Ph.D. John Hopkins University School of Medicine

Jeremy S. Edwards, Ph.D. University of Delaware

Marvin E. Frazier, Ph.D. U.S. Department of Energy

Carol A. Colgan Director, American Academy of Microbiology

Colloquium Participants

John F. Alderete, Ph.D. University of Texas Health Sciences Center, San Antonio

Judith P. Armitage, Ph.D. University of Oxford, England

Jeffrey Blanchard, Ph.D. University of Massachusetts-Amherst

Patrick P. Dennis, Ph.D. National Science Foundation

Claire M. Fraser, Ph.D. The Institute for Genomic Research

Alf Game, Ph.D. BBSRC, Swindon, England

Carol Giometti, Ph.D. Argonne National Laboratory

Yuri Gorby, Ph.D. Battelle Pacific Northwest National Laboratory

James Hu, Ph.D. Texas A&M University

Julius H. Jackson, Ph.D. Michigan State University

Eugene Kolker, Ph.D. Biatech, Bothell, Washington

Allan E. Konopka, Ph.D. Purdue University

Frank W. Larimer, Ph.D. Oak Ridge National Laboratory

Robert A. LaRossa, Ph.D. E.I. DuPont De Nemours & Co., Inc.

Michael T. Laub, Ph.D. Bauer Center for Genomics Research, Harvard University

Jared R. Leadbetter, Ph.D. California Institute of Technology

Harley McAdams, Ph.D. Stanford University

George Michaels, Ph.D. Battelle Pacific Northwest National Laboratory

Julie C. Mitchell, Ph.D. University of Wisconsin-Madison

Hirotada Mori, Ph.D. Nara Institute of Science and Technology, Nara, Japan

Kenneth Nealson, Ph.D. University of Southern California

Martin Polz, Ph.D. Massachusetts Institute of Technology

Virgil Rhodius, Ph. D. University of California, San Francisco

Margaret Romine, Ph.D. Battelle Pacific Northwest National Laboratory

Lucia Rothman-Denes, Ph.D. University of Chicago

Lucy Shapiro, Ph.D. Stanford University School of Medicine

Thomas J. Silhavy, Ph.D. Princeton University

Heidi Sofia, Ph.D. Battelle Pacific Northwest National Laboratory

David A. Stahl, Ph.D. University of Washington

Jonathan Zehr, Ph.D. University of California, Santa Cruz

Why Systems Microbiology?

Systems microbiology is a specialization within systems biology, and to derive a parallel definition for systems microbiology only requires changing “studying biological systems” to read “studying microbiological systems” in the Ideker description. However, if systems microbiology is merely a subcategory of systems biology, then why does it deserve particular attention? Can systems microbiology offer lessons about life that inquiries into the biology of plants and animals cannot? The answer is an unqualified “ yes.” Clearly, studying microbes from a systems perspective can yield long-sought answers to questions about microbes and their roles in human health and the function of the biosphere. But perhaps more significantly, this approach can also lead to the development of the tools and insights that will eventually be applied to the systems analysis of non-microbial life.

Microbial systems are important and ideal models

Bacteria, archaea, eukaryotic microbes, and viruses offer easier access to the workings of biology than do multicellular organisms, a fact that systems microbiology can surely exploit. The technical details of cultivation are undoubtedly less difficult for many microbes, which can be grown in petri dishes, tubes, and flasks, than they are for larger organisms, which require more complex growth conditions and more space. Microbes can also be grown asexually, allowing researchers to study clonal groups of cells, a feat that is often impossible with multicellular life forms. For decades these characteristics have allowed researchers to perform experiments under strictly controlled conditions. Systems microbiology is poised to capitalize on these aspects of microbes in order to provide new insights into their operation and to develop the platforms that can be applied to other living systems.

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Systems Microbiology in Action: Gene Regulatory Networks and Designer Microbes.

With the exception of fungi and certain other eukaryotic microbes, microorganisms carry relatively small genomes. The size of microbial genomes has enabled researchers to sequence the entire genetic material of thousands of viruses and hundreds of bacteria and archaea, and many more are sequenced every year. The ability to easily sequence major stretches of microbial genomes is particularly useful in studying the molecular and genetic basis of evolution, a phenomenon that is amenable to an experimental approach in microbial systems but is more difficult to explore in multicellular organisms.

Potential Applications of Systems Microbiology

The broad aim of systems microbiology is to acquire an understanding of the wiring diagrams of life – to grasp the relationships between the individual components that build an organism or a community. In seeking to move past the basic study of biological components (including molecules, enzymes, microbial species, etc.) and into a synthesis that can be used to predict the future state of biological systems, systems microbiology promises to provide powerful new tools and insights contributing to agricultural, medical, industrial, and environmental innovations.

The practice of agriculture stands to benefit in a number of ways from the information gathered through systems microbiology. For example, the procedures surrounding meat production could benefit from improved systems knowledge of microbial causes of cattle, chickens, and swine diseases, the epidemiology of those diseases, and the influences of pathogen transport. Similarly, high-density aquaculture could be improved through a parallel knowledge of the pathogens of fish and shellfish. The beneficial aspects of soil microbes or communities on plant productivity could be explored using systems techniques and could decrease our dependence on agricultural chemicals. Likewise, the impact of microbes on diseases of agricultural crops could be better managed with a systems understanding of the interplay of microbes, plants and pesticide application.

In medicine, systems approaches can offer strategies for identifying drug targets, overcoming antibiotic resistance, and managing the emergence of new diseases. A systems understanding of human pathogens will likely enable society to design antibiotics that target the weakest parts or Achilles heel of the organism. Alternatively, systems approaches could identify the appropriate antibiotics for use in multi-drug strategies that target pursue two or more steps simultaneously – an approach that promises to reduce the development of antibiotic resistance. An improved understanding of pathogens from a systems perspective will also facilitate management of hospital acquired infections. Using these methods to study pathogen ecology can offer insights into interventions that will prevent the emergence of new diseases from environmental sources.

Other applications where the predictive abilities of systems microbiology could be put to use include:

• Novel energy production systems. The development of commercial microbial hydrogen generation, BIO-batteries, and other technologies for energy production could be optimized by a better understanding of the microbial cell or microbial community as an integrated system.
• Metabolic engineering. Existing commercial bioreactors and the products derived from organisms inoculated into them could be optimized through a systems approach.
• Biocontrol. The use of ‘helper’ microbes to eliminate or control undesired microbial populations could be made possible through a systems understanding of their interactions in soil and aquatic communities.
• Pollution and bioremediation. Water and soil quality management systems could be optimized with systems approaches.
• Bioterrorism and decontamination. By identifying key steps in the function of potential bioterrorism agents, systems microbiology can help detect the release and prevent the spread of these microbes.
• Microbiological detection systems. Novel, highly specific, and sensitive detection systems and diagnostics can be easily developed using systems methods.
• Global monitoring. As the most numerous and diverse life forms on this planet, the activities of microbes and microbial communities can be used as sensitive reporters of local or planetary changes in temperature, greenhouse gases, pollutants, etc.

Disciplines That Can Contribute to Systems Microbiology

What fields can contribute to systems microbiology? Progress in this field needs the contributions of a diverse range of professionals. That is not to say that all problems will require the input of many different fields of expertise, as there are inevitably going to be goals that can be accomplished by individuals and goals that will require a consortium of scientists. Some of the professionals that are needed for these investigations include:

• Microbiologists,
• Biochemists,
• Evolutionary biologists
• Mathematicians,
• Computer scientists,
• Physicists,
• Chemists,
• Control theorists,
• Systems engineers,
• Geochemists,
• Atmospheric chemists,
• Chemical and physical oceanographers,
• Earth scientists, and
• Biostatisticians.

While specialists in each of these fields can make contributions to developing a systems approach to microbiology, interdisciplinary researchers familiar with microbiology will be in an excellent position to advance the field.

Regulation of Biological Systems

Due to the number and complexity of interactions involved in the biological pathways and regulatory networks, progress in understanding these systems has often been made by studying one isolated circuit at a time. As a result, limited progress has been made in describing the interactions between different components of interconnected regulatory networks. Systems microbiology may be the perfect approach for tackling this crucial subject. Using the tools of systems biology, researchers can begin to delve into the basic mechanisms of regulation, uncovering previously unknown types of interactions. Other, broader questions can also be addressed, including whether fundamental design principles exist in biological regulation and whether understanding these design principles offers insights into the in situ behavior of organisms.

Although a number of systems methods for addressing questions about biological pathways and networks already exist, new methods and approaches are needed. Investigators and technology development professionals need to consider which investments of time and money will have the greatest payoff in understanding these fundamental aspects of microbes and other living systems.

Applying a Systems Biology Approach to Microbial Communities

Current and future systems microbiology techniques can provide approaches to understanding the complex properties of microbial communities, their dynamics, and their impacts on natural and human systems. Systems approaches to microbial communities could answer the following fundamental questions: Which species are present? What are they doing? Where are they doing it? What is the environmental impact of the community? And finally, what happens to the community and its impacts in the event of a natural or society-generated disturbance?

As a first step in these investigations, it will be necessary to identify all the members of the community under study as well as all the interactions in which they engage. This is no small feat, and the ability to accomplish this kind of undertaking is likely to require new analytical and computational tools. The systems approach may at first find its greatest success by focusing on relatively simpler communities in which there is little overlap between the niches occupied by different members of the community. Stochastic effects may obscure the picture in communities in which there is a high degree of redundancy.

Spatial organization is another confounding factor in carrying out an analysis, but it may be avoided by studying laboratory communities in liquid suspension. In any event, and whichever community is selected for study using systems analysis, it is likely that single cell biochemical techniques will be needed as one of the key dissecting tools (see Technical Challenges in Systems Microbiology section –Single cell measurements).

Systems microbiology approaches should avoid treating the sum of all the genomes from a given environment, also known as the metagenome, as a single entity. Researchers should instead develop methods for assembling the individual genomes of the possible thousands of community members. The cell and its genome are critical units of organization in microbial communities and they should not be dissolved in research that hopes to achieve an understanding of these associations.

Hypothesis-Generating Research

By mining high throughput data, scientists can achieve new insights and derive novel hypotheses that would be time-consuming or impossible to develop through traditional reductionist approaches. Many successful examples of applying hypothesis-generating principles exist, including the genome mining work that uncovered motility and chemotaxis genes in Geobacter species. Prior to the genome mining work, these organisms were thought to be non-motile, but following the discovery of motility genes, experiments were implemented that confirmed their motility. Both tactics, hypothesis-generating research and hypothesis-driven research, are required for successful application of systems approaches.

Measuring Noise in Biological Systems

Noise is a problematic factor in all branches of experimental science, biology included. In biology, some of the difficulty lies in separating measurement noise, the irreproducible quantitative variation due to observational factors, from true biological noise, the irreproducible variation exhibited by biological systems. Moreover, stochastic processes have been shown to drive some biological phenomena, so biological noise cannot be dismissed from data analysis lest a significant underlying process be ignored. Hence, noise is an inescapable part of biological science and must be addressed in investigations that employ systems approaches. The ability to measure noise in a given biological system will depend upon the ability to quantify its relevant features.

Technical Bottlenecks

Since its inception, progress in microbiology has proceeded in lockstep with advances in technology. This dependence on technology also extends to systems microbiology, and a number of methodological difficulties must be resolved for the field to move forward. Many of these bottlenecks are universal and apply to multiple systems, but others are more system-specific.

Data accessibility

Enormous quantities of biological data have been accumulated over the years, including genome sequences, annotations, biochemical information, microarray profiles, and other types of information. These data could serve as an invaluable resource for developing a systems understanding of microbes, however, many important data sets are unavailable to public databases and others are not amenable to storage or comparison in a database format (video images etc.). Ideally, these data sets should be stored in searchable, cross-referenced databases that allow researchers ready access to information pertaining to their individual research efforts. For example, with new microarray data in hand, a researcher could access a relevant database to discover the location and context of a gene of interest, its place on a metabolic map of that organism, its relationship with or within regulatory networks, and related genes or pathways in other organisms. In order to make the best use of archival data and to move forward in the field, data of use in systems microbiology must be publicly accessible and encoded in a format that can easily be cross referenced. (Further discussion of this and other requirements for data formatting and databases are included in the section titled A Systems Microbiology Database.) The quantity of biological data is expanding daily, and the current state of disorder will only worsen if steps are not taken to organize data relevant to systems microbiology into a useful, convenient resource.

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Other technical bottlenecks in systems microbiology include:

Information and Data Gaps

While there are idiosyncratic differences in the type of type of information that needs to be gathered to characterize different biological systems, certain general requirements can be identified that are needed to characterize any given system. This information includes the “ parts list ”: a comprehensive accounting of the components of the system at many levels of organization, including the molecular, subcellular, taxonomic, and environmental levels. However, in many cases the entire list of components is not always needed to develop a thorough understanding of the behavior of a biological system. Even in the absence of complete knowledge, the systems approach can still work well.

There is also a need to obtain “global information,” or comprehensive measurements of cellular components, for each system under study. This may include, for example, the types and levels of regulation that occur in the system or the types, activities, locations and fluxes of cellular proteins, nucleic acids, metabolites, carbohydrates, and other cellular constituents. There is also a need to understand how an organism lives in its natural state. The evolutionary history of the system across multiple temporal scales is also necessary.

Once the systems approach begins to yield results, the information gathered is likely to feed back and indicate the most critical data that are needed to move forward in the analysis.

Acquiring Information and Data

Difficulties have arisen in collecting the data necessary for systems microbiology investigations. Existing disparities in formatting and data standardization between databases, for example, can hinder the ability of researchers trying to acquire information from prior investigations. Often, the necessary information is stored in a database or in the literature, but the representations or archive layout can prohibit easy access. These data are seldom subjected to a quality assessment, and researchers access these resources at their peril. Also, the representation of biological data in these databases often reflects a cultural gap in understanding between the computational scientists who design these databases and the biologists who use the data. In general, there is not enough support for the databases and other information sources critical to the advancement of systems microbiology.

The documentation of metabolic pathways poses a particular problem; there is a pressing need for standardization in these data sets. Scientific societies, journals and/or funding agencies should move to set standards for formatting of metabolic and regulatory pathway information. These formatting guidelines could apply to the type and organization of metabolic pathway information provided in research publications and submitted to public databases. It is also crucial that these data are stored in a “searchabl” way that allows researchers to explore pathways through a database interface.

Due to the high costs of many of the technologies necessary for carrying out the work of systems microbiology, it may be advisable to develop central “locations of excellence” to serve as a resource for the scientific community. High resolution microscopy, other imaging or modeling technologies, and high throughput data production facilities, for example, which are too costly for many labs or universities to provide, could be housed in collective centers to the benefit of researchers and the field in general.

Assuring data quality

The problem of how to ensure and validate the quality of data available in public databases has become more and more challenging with the genomics data explosion of recent years. Physics and other fields have grappled with large data sets in the past and the manner in which the dilemma was solved in those areas may offer lessons to biology today. The contributions of computer scientists and information specialists will be crucial in resolving the issue of information management, but it is important that biologists work closely with these professionals to ensure the utility of the information systems that are developed.

Genomic data should not be treated as static; mechanisms need to be put into place to continuously update the sequence and annotation data available in public databases. One serious impediment to maintaining data timeliness is the inability or reluctance of most scientists to commit to the long-term upkeep of their publicly available data. When a student graduates, or the funding for a project is exhausted, the impetus to continue updating and actively curating small databases is often lost.

The manner in which genomics and other critical data are generated should be standardized and reported in both the archival databases and publications. For example, microarray data are more useful only if the details of the experimental conditions and analyses are recorded and documented in an accessible format. This type of information must be included with genomics data sets to ensure the results are interpreted properly.

Quality assurance and reproducibility standards for systems microbiology data that are consistent across all the relevant journals and agencies need to be established. Once proper standards are developed they could be implemented through peer review and incentives from funding agencies.

In applying for funding, researchers are strongly advised to allot money and personnel time to quality assurance tasks.

Making Systems Data Applicable and Available

Efforts to standardize experiments, analyses, and biological materials across microbiological fields will aid in efforts to develop the field of systems microbiology. For example, defined cultivation practices can be standardized to enable the reproducibility of experiments from lab to lab. The results from experiments carried out under such standard conditions can be integrated across many labs in a coherent framework. In addition, the selection of model organisms or model communities for particular broad areas of research would help to standardize the collection of information in a manner that would be useful to a systems approach. Ideally, model organisms would be selected to represent different evolutionary histories so that data obtained from one phylogenetic branch could be applied to other line-ages to determine the biological consistency and universality of particular theories.

It is recommended that a commission on data exchange be established to determine standards for data analysis that would promote exchange of data resources. Finally, a reference microorganism repository with original samples and libraries as well as information on the field sites and environments from which the microbes were derived would also enable researchers from different labs to build effectively on the work of others.

Properly designed databases are pivotal in making the data of systems microbiology widely available. A general standard should be instituted by the professional societies and scholarly journals that requires data to be submitted to an appropriate public database.

A Proposal for a Systems Microbiology Database

How can researchers in systems microbiology, as a community, make the most out of the data that has already been collected? What is the best way to ensure that data from one system can be applied to learn something about other systems? The key to optimizing the use of systems microbiology data lies in sharing quality data openly. The value of a given investigation in systems microbiology is trivialized if the resulting data are not made available to the scientific community in a standardized and accessible format.

Currently, however, protocols for ensuring that quality systems microbiology data are widely disseminated among researchers are absent and, as a result, data are not effectively shared among researchers. Microarray data, for example, are scattered among numerous different repositories, personal websites, and often partly reported in publications and there are no mandatory standards or consistency in their analysis. Moreover, there is no unified way in which to query these and other data. The success of systems microbiology will be limited unless the data of past and present is shared promptly and structured in a way that it can be used effectively. To accomplish these twin goals of dissemination and organization, it is recommended that a central, curated database for systems microbiology be established.

A number of unconnected data resources are available to researchers in systems microbiology, but they are inadequate to address the needs of the field. Databases of raw data and personal data usually lack a quality control framework. Other databases house data that are out of date, are not indexed or searchable, or are not available to the research community at large. A new database is clearly needed. Assembling a database for use by the systems microbiology community represents a central challenge for the field and for systems biology in general.

To be effective, a systems microbiology database should be all-inclusive, searchable, current, and authoritative. The accumulated data should include many levels of information from the different analytical and experimental techniques relevant to the field. To accomplish this goal, a coordinated effort will be required on the part of researchers and those responsible for maintaining the existing data sets and databases to integrate the available information into a logical configuration. This configuration should be easily queried and searched – capabilities that would facilitate the optimal use of the data resources. Efforts to ensure that the data remains up to date would be critical to the success of the database. Also critical are the development of data formatting standards that will streamline submission, searching and retrieval of data. Format standardization must be made a high priority for the field. It is critical that biologists, as the end-users be the driving force behind the design and construction of the database and the contributions of scientists from all nations should be welcomed to the database effort. A database that demands quality and accommodates data from all quarters could serve as the “gold standard ” source of information for the field.

The appropriate dimensions of the database are open to debate. Smaller databases that focus on single organisms, for example, may better capture the attention and efforts of professionals who are invested in a particular system. As a result, small databases may be easier to maintain and keep up to date. On the other hand, a larger database could be more efficient and cost effective with respect to administration and hosting issues.

Preparing Microbiology Students to Use Systems Approaches

System biology holds great promise for the future of microbiology. Considering the power of these approaches, microbiologists should be trained with an eye to the skills that are necessary to understand and apply systems concepts to microbiological problems. To prepare them for systems microbiology applications, the core curriculum for microbiology students should include:

• Microbiology,
• Quantitative biology and mathematics,
• Biostatistics,
• Biochemistry,
• Physiology, and
• Modeling of biological systems.

Instrumentation Training

Progress in biology is paced by instrumentation; steps forward are enabled by new technologies, and the field can be stymied if new tools are not made available or are unused. Broader training in the high throughput techniques and new analytical, microscopic and modeling instrumentation associated with systems microbiology is highly recommended so that more microbiologists can take advantage of the most current technological advances. In their training, students should be exposed to a number of techniques and approaches so that they can learn to choose appropriate methods to address a given hypothesis.

It is imperative for biologists to communicate with the physicists and engineers who design and construct instrumentation for use in systems microbiology. Oftentimes, the different vocabularies of biology and physical science can stand in the way of effective communication between these professionals. Engineers and physicists who develop biology instrumentation need to be exposed to more biology training to facilitate the necessary collaborations and design the appropriate user-friendly devices to support research activities.

Collaboration in Systems Microbiology

Collaboration is a key ingredient for success in systems microbiology. However, the details of collaboration, including communication between distant institutions, questions of where to situate collaborating scientists, student co-mentoring, co-authorship, and issues to do with funding, tenure or promotion can hamper effective cooperation and career development of involved researchers. These challenges must be dealt with to enable effective interdisciplinary research and collaboration.

Modes of Communication

A number of modes of communication are open to those interested in conveying systems microbiology lessons to non-scientists. For example, commercial space on television would be an effective, albeit expensive, vehicle for communicating with the public. Educational programs that center on interviews with key scientists in the field could be recorded on DVD and sold to schools for use in the classroom, or targeted for use by public radio and television. Children's or young adult books that convey the excitement of microbiology to the lay population could be a useful vehicle, especially when one considers the scientifically literacy of the average citizen. Microbiology could also be integrated into high school curricula; experimentation with microbial systems can offer relatively low-cost, high-impact lessons for young people. A program that encourages graduate students in microbiology to reach out to the community could establish a long-term commitment to conveying the importance and excitement of microbiology research to the public.

The Role of the Scientific Community

Communication between the scientific community and the general public needs improvement. Scientists can be ineffective communicators when it comes to reaching a lay audience. Hence, a greater emphasis on coursework in writing and presentation is recommended for microbiology students. Also, scientists and the relevant scientific societies need to be more proactive in conveying important science to writers and journalists.