A colloquium was convened by the American Academy of Microbiology to consider issues relating to the blossoming field of microbial genomic science. The colloquium was held in New Orleans, Louisiana, on March 19-21, 1999. The principal findings of the colloquium are summarized below.

Microbes carry enormous genetic wealth and biological aptitude. Humans have already exploited these resources to enhance the quality of our lives in many ways. We have adopted the biochemical competence and versatility of these tiny creatures in medicine, agriculture, ecology, and studies of evolution.

The advent of DNA sequencing on a large scale brings with it the increasing ability to unravel and compile the genetic secrets of any living thing. Microbiologists are currently in a position to delve into these small organisms and to emerge with valuable information that can be put to both practical and theoretical use. This information will increase our understanding of how microbes contribute to health and disease of our bodies and of natural environments. It will also promote advances in food production, bioremediation, and drug design. It will extend our insight into how organisms weave the complex web that sustains them—and indirectly ourselves—and will allow us to reconstruct the origin of life and understand how it continues to evolve.

Investigators have already begun to tap into this tremendous store of knowledge. As the field of microbial genomic science has begun to grow, however, various problems have become apparent. Many of these are typical of a rapidly expanding enterprise; others are specific to this new scientific arena. The unique benefits of genomics can point to the importance of these problems and the need for coordinated attention. The colloquium participants discussed how to address these challenges so as to foster most effectively the expansion and vigor of this novel and invaluable endeavor.

Genomic science has the power to revolutionize microbiology, which in turn will transform and improve life on this planet. In order to realize this potential, strategic interventions are required now.

Front Matter

Executive Summary

A colloquium was convened by the American Academy of Microbiology to consider issues relating to the blossoming field of microbial genomic science. The colloquium was held in New Orleans, Louisiana, on March 19-21, 1999. The principal findings of the colloquium are summarized below.

Microbes carry enormous genetic wealth and biological aptitude. Humans have already exploited these resources to enhance the quality of our lives in many ways. We have adopted the biochemical competence and versatility of these tiny creatures in medicine, agriculture, ecology, and studies of evolution.

The advent of DNA sequencing on a large scale brings with it the increasing ability to unravel and compile the genetic secrets of any living thing. Microbiologists are currently in a position to delve into these small organisms and to emerge with valuable information that can be put to both practical and theoretical use. This information will increase our understanding of how microbes contribute to health and disease of our bodies and of natural environments. It will also promote advances in food production, bioremediation, and drug design. It will extend our insight into how organisms weave the complex web that sustains them—and indirectly ourselves—and will allow us to reconstruct the origin of life and understand how it continues to evolve.

Investigators have already begun to tap into this tremendous store of knowledge. As the field of microbial genomic science has begun to grow, however, various problems have become apparent. Many of these are typical of a rapidly expanding enterprise; others are specific to this new scientific arena. The unique benefits of genomics can point to the importance of these problems and the need for coordinated attention. The colloquium participants discussed how to address these challenges so as to foster most effectively the expansion and vigor of this novel and invaluable endeavor.

Genomic science has the power to revolutionize microbiology, which in turn will transform and improve life on this planet. In order to realize this potential, strategic interventions are required now.

The advent of DNA sequencing on a large scale brings with it the increasing ability to unravel and compile the genetic secrets of any living thing. Microbiologists are currently in a position to delve into these small organisms and to emerge with valuable information that can be put to both practical and theoretical use.

Introduction

Microbes live everywhere, including in deep-sea vents miles under the ocean, boiling hot springs, glaciers, and even rock, as well as more familiar settings such as soil, ponds, and animal intestines. Their ability to survive in diverse environments reflects an astounding array of biochemical aptitude.

The small size of microbes belies their powerful influence. They surround and inhabit us, and every creature on earth depends on them for life. In order to understand and exploit microbes, human beings must inventory and understand the vast repertoire of microbial activities. Because a creature's capabilities are reflected in and dictated by the DNA it carries, a microorganism's complete—or genomic—DNA sequence provides a blueprint for its biochemical and behavioral endowment.

Microbes live everywhere, including in deep-sea vents miles under the ocean, boiling hot springs, glaciers, and even rock, as well as more familiar settings such as soil, ponds, and animal intestines. Their ability to survive in diverse environments reflects an astounding array of biochemical aptitude. They churn out the nitrogen that plants need for growth and emit gasses that create and maintain the critical composition of the earth's atmosphere. In our bodies, they help digest food, ward off attempts by harmful organisms to invade, provoke misdirected immune responses against our own tissues, and even shape the development of our immune systems.

Humans have co-opted microbial talents to enhance the quality of our lives. For example, many large-scale industrial processes depend on microbes. In addition, we exploit them for making food and medicines and put them to work cleaning up our sewage and industrial waste. Microbes can dramatically influence ecosystems because many possess unique abilities to recycle both organic and inorganic substances. As the world's human population increases and natural resources diminish, environmental challenges grow. Humans are trying to harness the vast metabolic potential of microorganisms to apply microbial solutions to some of these ecological problems.

Microbes are not only vital to our bodies, forests, factories, and all of life. They also represent a record of evolution. Because all life descended from tiny, single-celled creatures, microbes open a window into antiquity. By peering inside these simple organisms, we learn about our origins and those of every living thing. A comparison of new genome sequences with those previously known shows us aspects of biology unique to an organism, as well as features that are shared with others. Elucidating the patterns of particular genes (and the capabilities they confer) among microorganisms improves our understanding of how different creatures are related. This information is critical for attempts to study, capitalize on, and interfere with the activities of microorganisms. Discovering which microbes contain which genes reveals the capabilities demanded by particular types of environments or lifestyles, for example, and points to the deviations that allow organisms to adapt to unusual habitats or behaviors. It also provides the basis for predictions about what capacities a new microorganism might possess, based on the activities of its genetic neighbors.

Despite their importance, we know strikingly little about microbes. They compose greater than 50% of the living matter on this planet, yet we have identified far less than one percent of all the predicted microbial groups. The microbial world, therefore, represents a vast reservoir of untapped knowledge and potential utility. Microbes offer a view into the capabilities of living things that far exceeds the capabilities that will be revealed by, for example, the human genome sequence alone. The amount of DNA carried by a member of the human species is equivalent to the DNA cache of approximately 1,000 microbes, and there are far more than 10 times this number of different microbes in the world around us. Microbial genome sequencing, therefore, offers an extremely efficient way to generate a picture of the tremendous biological diversity that living creatures possess, particularly because microbes inhabit such an array of bizarre and extreme environments. To profit from this natural biological archive, we need to embark upon a coordinated, large-scale effort to uncover and interpret a comprehensive set of microbial genome sequences.

Already governmental, academic, and private agencies are deciphering the genetic code of many microbes. Since the debut of whole genome sequencing in the mid-1990s, the genomes of 29 microbes and three chromosomes from two lower eukaryotic parasites have been sequenced; more than 100 other sequencing projects are under way. Yet, inevitably for an enterprise that is advancing rapidly and generating an explosion of valuable information, problems have arisen. Organization and dissemination of technology and data have been haphazard. The absence of a broad discussion regarding priorities and goals has contributed to the lack of coordination and absence of generally accepted standards. Sequencing technology has matured at an unexpectedly rapid pace, making quite feasible goals that would not have been imaginable just a few years ago. But, funding is inadequate for the kind of large-scale, integrated effort that should be undertaken.

This colloquium was organized with the aim of directing attention toward the challenges that face this new and promising field in the hope of productively interceding while the enterprise is still young and malleable. Now is the time to conduct discussions that include people with a broad range of interests and expertise about current and foreseeable challenges. Already, federal agencies have begun to ask for guidance on these issues. It is essential that the sequencing efforts accelerate as rapidly and as smoothly as possible. With timely, well-aimed interventions, it should be possible to transform the vision of a large-scale microbial genome sequencing effort into reality, and to maximize the effort's efficiency and economy. The time is ripe for fruitful intervention.

Now is the time to conduct discussions that include people with a broad range of interests and expertise about current and foreseeable challenges.

Potential value of complete microbial genome sequences: vision for the future

Because the average length of a microbial gene is 1000 nucleotides, an amount of sequence equivalent to the size of the human genome (about 3.5 gigabases) carries about 3.5 million gene-sized pieces and should therefore contain at least 350,000 unique genes.

Microbial genome sequences wield enormous power in their potential to touch and shape a tremendous range of human activities. Information and products gleaned from the sequences and associated studies will profoundly impact our health, environment, agriculture, and industry in terms of enhancing both quality and economics in these far-reaching areas.

Microbes contain an impressive repertoire of biochemical activities. This diversity far exceeds that of higher organisms, such as insects, plants, and animals. At least 10 percent (and usually closer to 30-40 percent) of the genes in every complete microbial genome sequence analyzed so far are “new”; they have not been previously discovered in another organism. Because the average length of a microbial gene is 1000 nucleotides, an amount of sequence equivalent to the size of the human genome (about 3.5 giga-bases) carries about 3.5 million genesized pieces and should therefore contain at least 350,000 unique genes. Furthermore, each microbial genome is small—about one thousandth the size of a mammalian genome. Because microbes occupy myriad environmental niches and a single human organism occupies one, the same amount of sequence from these tiny creatures represents a much wider array of function. We are surrounded by a deep pool of biochemically unique abilities. We have only begun to dip in.

Many molecules produced by living creatures can perform sophisticated feats. Natural selection over evolutionary time scales has honed the ability of biological molecules to carry out chemical deeds with extraordinary precision and specificity. Enzymatic reactions excel in their efficient use of raw materials, and in their production rates. In contrast to many human-made catalysts, enzymes can distinguish subtle differences in their substrates. This allows them to, for example, pick one of several identical chemical groups in a single molecule and add something to it or transform it into something else. Biological molecules can even discern mirror image molecules--a feat that is critical for designing and creating, for example, drugs that need to fit properly into the “glove” of some natural enzyme in the body. Furthermore, reactions performed by biological molecules far outnumber those performed by synthetic ones. Scientists have uncovered many natural reactions that have not been mimicked by laboratory methods.

Enzymes and the microbes that carry them exhibit useful behaviors. They naturally make methane and other sources of energy, fabricate useful chemicals such as antibiotics, and break down toxic substances to harmless products. Food engineers have added microbes (or, in some cases, their enzymes) to production vats in order to manufacture the high fructose corn syrup that sweetens our drinks. Cheese-makers use microbial rennin as a less expensive substitute for the calf version of the same enzyme. Microbes and their products permeate the baking, dairy, and alcoholic beverage industries. Furthermore, certain microbes thrive under harsh conditions, such as extremely high temperatures and pressures. These organisms contain hardy enzymes that can be used to carry out reactions that are currently beyond the reach of synthetic organic chemistry; some of these robust enzymes have already been applied in industry. Through genetic engineering, it is possible to adapt and fine-tune the already exquisitely sensitive and powerful microbial reactions to better serve human purposes.

Microbes also provide valuable information about evolution. Studying them has already revealed previously unknown mechanisms by which genes are “shared” among different branches of the tree of life, which are beginning to redefine the “topology” of this tree. Further investigations will undoubtedly reveal more secrets about how all creatures arose and developed.

Microbes, therefore, represent a veritable treasure chest of biochemical tricks and historical facts, most of which currently remain buried. Sequencing provides a tool with which to begin uncovering this mass of information (see Figure). A very small number of microbes have been discovered and even fewer of those have been, or are being, sequenced. Furthermore, because the function of up to 40 percent of microbial genes on average is unknown, scientists have not yet unraveled all the biochemical secrets of even one microbe.

Figure

Sequencing the genome of an organism entails spelling out the letters—the nucleotides, or bases—that compose the entire chromosome (or, in some cases, chromosomes). The sequence of these nucleotides allows scientists to predict where genes start and end, and the order in which amino acids are strung together to make the proteins that these genes encode. In many instances, the resulting pattern of amino acids resembles that of a protein with a known function. In such cases, scientists have a clue as to the new gene's—and its protein product's—role in the cell or its biochemical potential. Even if a gene does not resemble one with a known physiological job, investigators can still determine evolutionary relationships between organisms by discerning families of related genes.

In addition to these conventional uses of genetic information, sequencing can provide a doorway to creatures that are difficult to grow in the laboratory. Because DNA can be obtained from microbes whether or not they're viable, and whether or not we know how to propagate them in the laboratory, this method provides a powerful way to determine an organism's presence and genetic relatedness to other organisms. There is no demand for investigators to first figure out how to keep it healthy in a test tube instead of in its usual habitat miles under the ocean or some other odd and difficult-to-mimic environment. In some particularly productive circumstances, results from a sequence analysis might suggest ways to grow a previously uncultured microbe in the lab, by revealing relationships to organisms for which scientists have already solved this problem.

The field of microbial genomics will give rise to large amounts of information about microbes’ biochemical talents. Our understanding of complex microbial communities in diverse environments will advance.

The past five years have seen the complete sequencing of about 30 organisms, most of them microbes. Within the next decade, the genetic blueprints of hundreds more organisms—including humans—likely will be fully spelled out. As the sequencing enterprise picks up steam, however, greater coordination for projects will be essential and challenges of appropriate storage, analysis, and dissemination of the data they produce will need to be met.

In the next five years, the rate of sequencing will accelerate; a simple bacterial genome sequence may be completed in a day! Colloquium participants hope that scientists will be able to enter and manipulate data easily within widely accessible databases that include up-to-date information about sequence and associated biology from all over the world. Computer tools will help investigators analyze their data rapidly; researchers will be able to ask sophisticated questions and obtain reasonable answers. This will allow them to proceed quickly from new sequences to testable hypotheses that will reveal biological function. Numerous affordable technologies will exist for analyzing gene expression and protein action on a genome-sized scale. As a consequence, the amounts and types of data about gene function will explode.

The field of microbial genomics will give rise to large amounts of information about microbes’ biochemical talents. Our understanding of complex microbial communities in diverse environments will advance. We will understand much more about the role of microbes in keeping our bodies and surroundings healthy as well as in making us sick. This amassing knowledge will fuel a significant increase in the number and types of commercial products in the fields of agriculture, medicine, industry, and environmental cleanup.

CURRENT STATUS

As of July 2000, scientists have published genome sequences of 29 microorganisms; over 100 more are in progress. So far, the bulk of sequencing has been performed by a few, dominant centers. These include governmental, as well as private, agencies. Sequencing technology is advancing rapidly. Methods for generating sequences have become faster and more efficient. As a result, costs per nucleotide of sequence have decreased. They still, however, prohibit most smaller groups, such as individual academic laboratories, from tackling entire genome sequences. Eventually, individual investigators will likely enjoy the option of sequencing an entire microbial genome by themselves, in a reasonable period of time; this would greatly expand the breadth and depth of the gene and gene product discovery effort. However, at the present time, most investigators cannot consider this a realistic possibility.

Coverage of the microbial world has been spotty. In particular, genome projects have focused on organisms that cause human disease. Microbes of agricultural importance or those that associate harmlessly with animals (commensals) have not received nearly as much attention. Similarly, organisms that inhabit the nether regions of our planet, and which therefore represent the great diversity in the microbial world, have largely been ignored.

Much of the information about the function of genes has not been demonstrated directly; rather, it has been inferred from the sequence. Genes that share a large amount of sequence identity or similarity encode proteins that commonly perform the same or related functions. As a result, comparison of a sequence to a gene with a known function can provide clues as to the new gene's activity. However, this method has its limitations. Nature can use similar amino acid sequences (represented in genes by similar nucleotide sequences) for different biochemical activities, and relying on sequence information alone to reveal a gene's properties can lead researchers astray. Furthermore, cells employ similar biochemical reactions in different ways. For example, an investigator might infer from a particular sequence that the gene product in question adds a phosphate group to another protein. However, the target protein and the biological effect of that phosphate will remain a mystery until experiments are performed that directly probe the function of the unknown gene.

Scientists have a long tradition of unearthing what a gene product does by direct experimental inquiry. Decades-old techniques, as well as methods that exploit tools that have been developed in the last few years, can reveal a gene product's function. Conventional procedures and modern, whole genome-level approaches are converging in some new technological schemes. For example, several powerful new strategies represent a convergence of conventional genetic techniques and rationale with a modern, high-throughput twist.

Despite the fact that genomic investigations hold the potential to transform microbiology, the sequenced genomes have so far impacted the field less than expected. In part, this is because often the sequencing community has failed to plan for how genomic data would be integrated into the experimental biology; as a result, the necessary links between gene sequences and function are lagging. The microbial sequencing endeavor currently lacks a mechanism for establishing a broad discussion of priorities about all aspects of the effort. Which microbes should be sequenced? How should scientists ensure that there is good coverage of important microbes from a wide variety of fields? Which technologies and approaches should be put in place to use the genomic information being generated, in an optimal fashion? What kinds of innovations are most needed to generate and interpret the data? How should quality control standards be developed? When during a project should sequence be released? How will funds be generated to support this ambitious, yet tractable and valuable, endeavor? All of these questions and many more are critical to the success and productivity of microbial sequencing projects, yet they have not been considered in a well-orchestrated way.

Moreover, current sequencing efforts are not coordinated. Groups are duplicating each other's efforts by sequencing the same organisms. Once completed, the raw data from publicly funded projects are available, but not always from commercial projects. However, additional information—for example, results investigators might have about the physiological role of particular sequences—is not entered in any standardized format. For this and other reasons, it often remains hidden to the scientific community at large. Furthermore, dissemination of information about new technology has not been optimal, in part because no centralized entity is charged with the responsibility for this task.

Better database management tools would greatly enhance efforts to make optimal use of the data that are pouring in from the various sequencing projects, but there has been little organized discussion of the specifications and development of such tools. The field of bioinformatics—where biology and computer science intersect—is booming. Funding organizations are beginning to support this new enterprise and those conducting it, but it will require more concerted support to thrive. Financial support for improved informatics tools and for sequencing per se is not currently sufficient for the kind of large-scale efforts that should be undertaken.

Multiple funding sources exist for various microbial sequencing projects, and each has its own perspectives and priorities. These include the Department of Defense (DOD), Department of Energy (DOE), National Aeronautics and Space Administration (NASA), National Institutes of Health (NIH), National Institutes of Standards and Technology (NIST), National Science Foundation (NSF), and the Department of Agriculture (USDA). Together, the different agencies cover a great deal of intellectual and practical territory. However, their combined potential could be strengthened by coordination between them in terms of long-term management or thinking. The enterprise could become more efficient and powerful than it is now.

Challenges, Opportunities, and Potential Solutions

Specific Recommendations

Colloquium participants developed a number of recommendations for the future. Those that were unanimously endorsed are the following:

• Develop a large-scale, coordinated, multi-agency, microbial genome sequencing effort. Stimulate collaborative projects between a sequencing group and a group that understands the biology of the organism and is well equipped (in terms of training and tools) to probe hypotheses that arise from the new sequence information with experimental approaches. Create a mechanism for open discussion within the scientific community about evolving needs, priorities, and planning.
• Coordinate all aspects of microbial genome projects among interested parties. This should aim to organize efforts to gather, disseminate, and use microbial genome sequence information. It should also cultivate efforts to promote all aspects of necessary continued support: funding, development of data management tools, creation of ethical and practical guidelines and standards, smooth input and access to data, constant examination of all aspects of planning appropriately for the next phase, and efficient use of all types of resources (human, financial, technological) to hone the genome sequencing endeavor and ensure its success.
• Provide a central and easily accessible location for completed genomic sequences and associated information about the biology associated with it. Create standardized and easily accessible sequence annotation and computational tools so users can efficiently and productively use the data.
• Devise new guidelines for data release, other issues of standardization, and for ethical issues related to public electronic databases. Establish a multi-agency committee that will organize a discussion among interested parties.
• Organize a mechanism with which to address societal concerns and inform the public about the benefits and implications of a large-scale microbial genome sequencing effort. Ethical issues that might be discussed include whether and to what degree sequences and their products could become private property, how to curb attempts to exploit microbial genome information for malevolent purposes, and whether and how to preserve microbial diversity.
• Modernize the K-12 educational curriculum to cultivate a society whose members understand the importance and ramifications of microbial genomics.
• Enhance high-level training and education in genomics and associated technologies. Encourage academic programs and departments to submit training grants that focus on some aspect of microbial genomics. Encourage funding of postdoctoral work in this area by stimulating the creation of fellowships.
• Nurture the development of methodology that reveals the biological role of microbial DNA sequences. To help speed movement from sequence to function, create funding opportunities for new experimental methods as well as for development of data management tools. These technologies and approaches should include novel ways to infer gene and protein function at the level of the individual gene/protein as well as at the level of all the genes/proteins within an organism. It is vital to fuel enthusiasm for new approaches without discouraging the use and development of the old.