Report on the American Society for Microbiology andNational Institutes of HealthWorkshop on Basic Bacterial Research

Basic Researchon BacteriaThe Essential Frontier

The National Institutes of Health (NIH)The Nationʼs Medical Research Agency, the NIH includes27 Institutes and Centers and is a component of the U.S. Department of Health and Human Services. It is theprimary federal agency for conducting and supportingbasic, clinical and translational medical research, and itinvestigates the causes, treatments and cures for bothcommon and rare diseases. For more information aboutNIH and its programs, visit www.nih.gov

The American Society for Microbiology (ASM)The ASM is the largest single life science society,composed of over 42,000 scientists and health profes-sionals. The ASM's mission is to promote research andresearch training in the microbiological sciences and toassist communication between scientists, policy makersand the public to improve health, economic well-beingand the environment. The ASM and its members workto identify and support research efforts that canaddress health and environmental problems.

Cover and Interior Bacteria ImagesStaphylococcus aureus—coccus prokaryote (MRSA bacterium)Mycobacterium tuberculosis—rod prokaryote (bacterium)E. coli (Escherichia coli)—dividing, hemorrhagic 0157:H7 strain.© Dennis Kunkel Microscopywww.denniskunkel.com

February 2007

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For many years the American Society for Microbiology (ASM) has been concerned about the need forincreasing basic research in bacteriology. This concern is based upon several premises, including:

1 the widespread perception that an adequate number of researchers in the U.S. in fields such asbacterial physiology and genetics are not being trained,

2 the importance of basic knowledge of bacterial physiology and genetics in the biotechnology industryand in applications including pathogenesis and biodefense,

3 the growing understanding of the impact of bacteria on human health, and on the development of chronic diseases.

To address these questions, the ASM and National Institutes of Health (NIH) jointly sponsored a workshop on Basic Researchin Bacteriology that was convened November 3-4, 2005 on the NIH campus in Bethesda, Maryland.

Introduction

Approach

The ASM-NIH workshop focused on scientific gaps andopportunities for research on bacteria. In order to stim-

ulate creative, goal-oriented interactions, the meeting inte-grated focused discussions within smaller working groupsand overarching sessions with entire group participation.Participants in the two-day workshop included scientistswith a variety of research expertise, representatives ofindustry, and representatives of federal agencies. Followingthe meeting, the groupʼs Steering Committee prepared thissummary of the discussions and recommendations toguide future research.

• What are the gaps in our knowledge, methodologies,and information access that must be addressed?What strategies would address these gaps?

• How has microbiological research at the basic andapplied levels been changed by technological advances(e.g., genomics, imaging, and computation)? What newopportunities have been revealed?

• How have these technological advances altered the per-ception of what problems are interesting and important?What are the benefits and drawbacks to these changes?

• What factors have changed the marketplace formicrobiologists over the years and how? Is this picturechanging again? What are the roles of the research insti-tutions in these shifts and how might they be influencedin the future? What are the roles of the microbiologicalsocieties in future shifts? What roles might the privateand public funding agencies play?

• What are the developments on the horizon that will affectmicrobiological research in the next five years?

Goal: The workshopparticipants focused on thefollowing discussion areas:

Basic Research on Bacteria The Essential Frontier

Overview

Bacteria and their phages are the oldest and mostabundant life forms on the planet. Bacteria have

co-evolved with us and are beneficial for human health. Thereare over 10 times more bacteria in our bodies than thereare human cells, and this natural microbiota is essentialfor proper development, nutrition, and resistance to disease.However, we also live in an environment replete with bacteriathat can cause a wide variety of human diseases withbacterial infections responsible for 25 percent of humandeaths globally, a number predicted to increase dramaticallywith the growing crisis of antibiotic resistance. We under-stand very little about the interactions between bacteriaand the environment that influence the delicate ecologicalequilibrium between humans and microbes and therebydetermine the balance between health and disease.

In addition to the bacteria that are in or on the human body,bacteria influence humans in many other ways. Bacteria arethe dominant occupant and architect of our entire biosphere.Bacteria sustain the metabolic cycles that are essential for alllife on earth. Bacterial metabolism sculpts our physical envi-ronment as well. Because they are ubiquitous and have suchdiverse metabolic capabilities, bacteria influence essentiallyall disciplines of science, including fields such as evolutionarybiology, ecology, immunology, cell and developmental biolo-gy, psychology, geology, chemistry, physics, climatology,computer science, and engineering.

Bacteria are also instrumental for understanding funda-mental life processes that are required by all organisms,including central metabolism, replication, transcription,translation, protein targeting, assembly and structureof macromolecular complexes, protein folding, stressresponses, error correction mechanisms, signal transduction,and developmental programs. These processes are moreeasily characterized in model bacteria and their phagesthan in other organisms because microbes provide suchtractable experimental systems. The large repertoire ofgenetic and biochemical tools and data that have beenacquired from basic research on bacteria is crucial fordissecting the complex metabolic and regulatory networksthat control these processes. This provides a launchingpoint for understanding the enormous diversity in thebacterial world and facilitates the understanding of theseprocesses in eukaryotes.

Despite the broad impact of this field, basic researchon bacteria is at a crossroads. The research communityperceives that public funding for most areas of basicresearch, including bacteriology, has leveled off and thatincreased resources are being focused on infectious diseaseresearch prompted in part by biodefense concerns. Coupledto this, large multi-investigator projects have emerged as analternative to single investigator R01-type research projects.These developments raise the questions: What is the relativevalue of continued investment in basic research on bacteria,and is there a disproportionate emphasis on large scientificconsortia at the expense of research by smaller groups?

Evolving Priorities

Research on bacteria and their phages has led to manyfundamental scientific discoveries. Initial support for this

research was justified in part because of the role of bacteriain causing disease. With the advent of effective antibiotics itseemed like the war on microbes had been won. Hence, forseveral decades health-related research shifted to topicslike cancer, heart disease, and genetic diseases. Moreover,developments in molecular biology arising from research onbacteria made it possible to study many basic biologicalprocesses in mammalian cells, eliminating the argumentthat bacterial model systems were the only doorway toeukaryotic molecular biology.

Meanwhile, the microbes demonstrated how rapidly theycould evolve new traits. Microbial resistance to antibioticsdeveloped faster than new antibiotics could be developed,and the resistance spread throughout the microbial world.The global expansion of food distribution networks facilitatedthe rapid distribution of microbial pathogens. Simultaneously,emerging microbial pathogens filled new ecological niches,such as indwelling medical devices and the growing popula-tion of humans who are immunocompromised due to pri-mary infections (including HIV) or due to therapies used totreat chronic diseases. Furthermore, recent discoverieshave demonstrated that some diseases (including ulcers,certain types of cancer, heart disease, etc.) that were pre-viously believed to be caused by a genetic predispositionor exposure to environmental toxins are actually caused bymicrobes. This microbial offensive has summoned a

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renewed counter-attack on microbial pathogens.Meanwhile, new tools have become available that make itpossible to dissect the molecular basis of pathogenesisboth from the microbial and host perspectives. Recently,having the complete DNA sequences of bacterialpathogens has provided valuable insights into how micro-bial pathogens evolve and the extent of gene transferbetween pathogens. These advances have revealed newways to control infection, including the identification ofnovel targets for antimicrobials and novel approaches forvaccine development.

The value of basic research on bacteria has extended wellbeyond infectious diseases. Research on bacteria led tothe elucidation of important concepts of molecular biology,allowing developments in biotechnology that have yieldedtremendous benefits to many other aspects of humanhealth and well-being as well as providing new tools thathave facilitated our understanding of pathogenesis. Withthe advent of new tools that allowed us to extend beyondpure culture studies to identify bacteria in complex commu-nities in the environment, it became clear that bacteriahave many roles in human health that were previouslyunknown. These discoveries have opened important newopportunities for research on bacteria. Although these newtechnologies allow the rapid accumulation of data aboutbacterial genes and gene expression, interpreting thesedata relies on many basic aspects of bacterial genetics,physiology, and ecology that are not yet well understood.

Impact of New Technologies

New approaches like genomics, transcriptomics, andproteomics allow the identification of the entire genetic

complement of bacteria and which of these genes are turnedon under particular conditions. Comparative genomics led tothe discovery that gene exchange between bacteria is ram-pant and has dramatically influenced the acquisition of viru-lence, and had a major impact on our understanding of theevolution of pathogenesis. However, interpretation of datafrom these “omics” approaches relies on comparisons withdatabases rather than direct functional assays. Thus, thesenew approaches have not diminished the need for basicresearch because a detailed understanding of microbialphysiology and genetics is essential to interpret and test theresulting predictions. In fact, the ability of “omics” approachesto generate a tremendous number of predictions greatlyincreases the need for direct experimental tests basedupon genetics, biochemistry, and molecular biology.Furthermore, the detailed characterization of the mecha-nisms of discrete pathways and reactions, and molecularinteractions that modulate these interactions is required forunderstanding the integrated networks and for developingnew ways to modulate these processes for our purposes—a major goal of systems biology.

Imaging is another technological advance that has provid-ed useful insights into bacterial physiology and pathogene-sis. Sensitive new approaches allow the visualization ofmolecules within bacteria and bacteria within an infectedhost. The applications of these approaches in bacterialcell biology and ecology have only begun to be tapped.Coupled with an understanding of bacterial physiology andmolecular biology, and the ability to genetically manipulatethese processes, will lead to new therapies that directactive agents to particular sites in the host to combatdisease or stimulate health.

Because of sophisticated instrumentation requirementsand expense, efforts to develop these new technologicalapproaches are typically restricted to large groups ofscientists focused upon very specific problems. However,interpreting the vast amount of data generated by thesenew technologies and asking critical questions about whatit means typically relies on individual scientists with uniqueexpertise on a particular aspect of bacterial genetics, physiol-ogy, ecology, or molecular biology. To take optimal advantageof the intellectual capital spread across academia andindustry, individual scientists should have access to thefacilities needed to perform such experiments and thedata generated from these experiments.

3Basic Research on Bacteria The Essential Frontier

Challenges and OpportunitiesThere are many remaining challenges andcorresponding opportunities.

• Gene function—We need improved approaches for therapid biochemical and genetic confirmation of predictedfunctions, as well as improved computational methodsto accurately predict gene functions. A large number ofgenes have unknown functions. What are the “unknown”gene products doing?

• Annotation—Misannotation of genes, including the prob-lem of derivative annotations, is a pervasive problem thatcan result in misleading interpretations of genomic data.

• Metagenomics—Can we identify the roles of individualmicrobes present in complex microbial communities such asin the gut, in the oral cavity, on skin, etc.? To do so, we willneed better algorithms to analyze short-single reads,assemble partial sequences, and recognize mechanismsthat distinguish which functions rely on consortia of microbesvs. those that rely on individual microbes. This approach willallow us to identify which microbes comprise our normalbiota and which others cause diseases as well as what dis-eases result from interactions between multiple microbes.

• Metabolomics—We need new ways to quantify metabolicpools and flux through metabolic pathways to understandhow genetic information is realized through various func-tions, especially in differing host environments. Applicationsof this technology include microbial forensics and enhancedproduction of useful metabolites by industry.

• Systems biology—Because they are relatively simple andwell-characterized, bacteria provide an excellent modelsystem for systems biology. Multi-pronged studies onbacteria should allow us to couple the dynamics of metabolicpathways and regulatory networks to growth, adaptation,behavior, and population and community dynamics. Inmicrobiology, the microbial community is ultimately the func-tioning unit of the system. Studying such interactions willrequire close collaborations between microbiologists, com-puter scientists, mathematicians, physicists, and engineers.

• Evolution—Bacterial evolution is now an experimentalscience that addresses the questions how and why.Cumulative results to date have changed our understand-ing of the evolution and spread of antibiotic resistanceand emerging infectious diseases, but many fundamentalquestions remain. How do new strains evolve? Where dogenetic islands come from? How does the acquisition andloss of genes influence fitness in the host and the envi-ronment? Can we identify mechanisms that will lead tothe rapid identification of emerging infectious diseases?Can we impede this process?

• Normal microbiota—Over the last few years, we havedeveloped a better understanding of the impact of ournatural microbiota on human health and disease, butthese studies have also raised many new questions. Howdoes natural microbial biota affect human development,nutrition, and disease resistance? What is the role ofendogenous microbial biota in transfer of antibiotic resist-ance and virulence genes to potential pathogens? Whatdetermines whether metabolites produced by naturalmicrobiota are used as beneficial nutrients or cause tissuedamage in the host? How does the natural microbiotainfluence obesity, diabetes, and other chronic diseases?

• In vitro culture studies—Laboratory studies are invaluablefor studying bacterial physiology and genetics, facilitatingthe identification of new imetabolites, the manipulation ofbiochemical pathways for production of desired products,etc. However, the vast majority of bacteria are still uncul-tured. How can we culture previously uncultured organ-isms to allow studies in lab?

• Transmission—We have learned many details of viru-lence factors in a variety of bacteria, but we do not yetunderstand many aspects of microbial ecology andenvironmental adaptation that allow bacteria to survive inthe environment long enough to be transmitted to a newhost. Understanding this process will demand expertise inmicrobial genetics, physiology, ecology, and mathematics.

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• Antimicrobials—We desperately need innovativeapproaches for the development of new classes of antibi-otics (vs. simply modifying existing classes of antibiotics).Can we develop new methods to slow the development ofantibiotic resistance? Are the current regimes of antibiotictherapy optimal? What does ecology tell us about predict-ing and managing antibiotic effectiveness? Answeringthese questions will demand collaborations betweenmicrobiologists, chemists, and physicians.

• Immunity and tolerance—The human immune systemis constantly interacting with the thousands of bacterialspecies comprising our natural microbiota. Understandinghow the natural microbiota communicates with the immunesystem and how the immune system singles out harmfulmicroorganisms could lead to the development of drugsthat help the natural microbiota outcompete pathogens.

• Vaccines—We need new types of vaccines that provideeffective protective immunity and can be used in youngchildren and individuals with compromised immune sys-tems. Needs include more effective mechanisms of vac-cine delivery, vaccine targets that provide broad, long-lasting immunity, and vaccine formulations that are stableoutside a narrow window of temperature and humidityconditions. Development of these vaccines will requireintegration of the fields of immunology, bacterial genetics,comparative genomics, bioinformatics, and pathogenesis.

• Detection and identification—Rapid diagnostic tools toallow identification of the disease-causing agent and itsresistance profile would make it possible to reduce theuse of broad-spectrum antibiotics and encourage thedevelopment of targeted therapeutics that are less likelyto disrupt the natural microbiota.

• Chronic diseases—How do microbial infections stimulatechronic diseases? Once we understand how, can wedevelop new therapies to intervene and thus prevent thisprocess? These questions extend to dental microbiologyas well—for example, is there a relationship between peri-odontal disease and heart disease or premature births?

• Host-bacteria interactions—Genes that influence estab-lishment of microbial populations may influence the ability ofbacteria to cause disease. Identifying the host and bacterialgenes that influence colonization and virulence, and study-ing the mechanics of the host-bacteria conversation, mayprovide a novel approach for countering infections.

• Nanotechnology—To date most of our understanding ofstructure and function of bacteria comes from studies onpopulations of cells. However, averaging data from alarge number of cells obscures important processes thatoccur with single cells. Similar arguments can be madefor single molecules. Understanding structure and func-tion at the single cell and single molecule level hasimportant implications for nanotechnology. These ques-tions are enticing a new generation of physicists intomicrobiology, but they are often hindered by inadequateunderstanding of bacterial physiology and genetics.

• Bacterial physiology and genetics—Solving the problemsdescribed above demands a detailed understanding ofbasic molecular processes that mediate growth, metabo-lism, and regulation in microbial cells. Although commonlydescribed in textbooks as if they are completely understood,there are many important, unresolved questions aboutbasic bacterial genetics and physiology. For example,although when bacteria enter a host they must adapt to theincreased temperature and osmolarity, we do not know howgenes are regulated in response to these physical changes.

In addition to insights on diseases, basic research onbacteria also leads to discoveries that benefit humanhealth in other ways, including the development of newtools for cloning and gene expression, the modulation ofmetabolic pathways to overproduce useful end-products,the use of microbes for nanotechnology, the use of microbesfor bioremediation of toxic waste and radioactivity, and theuse of microbes for alternative energy production.

Individual investigators with smaller lab groups provide theexpertise needed to deal with the tremendous diversity ofmicrobes, approaches, and scientific backgrounds required tosolve these varied problems. However, human resources willneed to be leveraged with shared access to sophisticatedequipment to carry out research at the increasingly complexlevels now possible. In addition, major efforts will be neededto capture, analyze, and share the prodigious streams of dataalready resulting from modern technological approaches.Individual laboratories will need access to the most efficientalgorithms for such analyses, and access to tools that willallow them to create their own knowledge environments.

Basic Research on Bacteria The Essential Frontier

Is Larger Better?

Most of the important discoveries in bacteriology havecome from seemingly distant corners of basic

research driven by individual investigators with smallresearch groups. Some examples of such important dis-coveries include the growth of microbes in biofilms, therole of efflux systems in antibiotic resistance, the impact ofgene amplification on the development of antibiotic resist-ance, the role of metabolic pathways (e.g. the glyoxylateshunt) on persistent infections, the role of normal flora inanimal health, and the role of phage in the spread of bac-terial toxins. These discoveries did not come from researchefforts focused on a major initiative, but from research driv-en by basic scientific curiosity—a central premise of argu-ments by Vannavar Bush for the development of a federalresearch enterprise. Like travel on back roads vs. express-ways, both routes have important but different roles—theexpressway allows you to reach your destination faster butthe back roads are likely to reveal exciting vistas that arehidden from the expressway. Likewise, research by smallerresearch groups provides creative fodder for largerfocused research efforts aimed at countering infectious dis-eases, developing new antimicrobials, and detecting andthwarting potential bioterrorism agents.

Educational Needs

The fundamental concepts of bacterial physiology andgenetics are essential for both basic and translational

research. For example, an in-depth knowledge of bacterialphysiology and genetics is essential for effective develop-ment of new antibiotics, thwarting antibiotic resistance, con-struction of novel vaccines, and treatment of diseasesinduced by asymptomatic infections. Bacteria are also vitalto fields like chemical biology, biophysics, geobiology, andchemical engineering. However, newcomers from theseother fields often lack core knowledge of basic bacterialphysiology and genetics needed to integrate the disciplines.

Training in basic research on bacteria also provides theskills needed in biotechnology, the pharmaceutical industry,and clinical microbiology. Individualized research allows astudent to learn from mistakes and develop expertise introuble-shooting scientific problems in close collaborationwith a scientific mentor. However, there is concern in theresearch community that basic research in the microbialsciences has not flourished, resulting in fewer scientistsactively working in this area and fewer students trained torespond to future microbial challenges.

There is a widespread perception among microbiologiststhat enough scientists in bacterial physiology and geneticsare not being trained, seriously jeopardizing science,medicine, and industry. There are several potential reasonsfor this neglect. First, other than the widespread publicityabout the impact of antibiotic resistance, the communityhas done a poor job of explaining the importance of bacteriato the public. Because of this lack of awareness, there isno forceful public lobby promoting research on bacteria. Inaddition, this limits the exposure of young students to theexciting opportunities in this field. Second, over the lastseveral decades there have been shifts in emphasis withinacademic institutions that have led to a decline in departmentsupport, hiring, and curriculum emphasis on microbiology;in some cases microbiological research has been subsumedwithin other departments, e.g., cell biology. Thus, despitethe critical importance of microbiology research andeducation, many microbiology departments haveshrunk or disappeared.

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Summary

Basic research on bacteria has had significant impact onmany areas of science. This research has revealed

many fundamental features of all living cells, and hasproduced novel tools that allow us to study previously inac-cessible problems. Discoveries continue to be made usingmodel systems such as Escherichia coli and many othermicrobes with unique properties. Making discoveries oftenrelies upon insights from studying the physiology andgenetics of model organisms coupled with newly devel-oped experimental tools and creative ideas.

Thus, multiple perspectives provide the same answers tothe two questions posed in the overview—there is a needfor continued investment in basic research on bacteria, anda continuing major role for research by individual researchgroups. This raises the question: How can these objectivesbe met in a time of limited resources? One approach wouldbe for the research community to tell its story in a mannerthat will make the points in this document clear to thepublic. Part of this story is a recognition of the significanceof bacteria in basic biology, genetics, chronic disease, andnutrition as well as infectious disease. In addition, researchon topics like evolution and ecology has a direct impact onthe advancement of human health. Increased interagencycooperation could promote progress in these critical areas.

Basic research on bacteria is a critical long-term investmentfor private and Federal research funding; it is vital to thedevelopment of applications that improve human health andwell-being, and impacts our nationʼs economy. Applicationsof basic research on bacteria are essential for medicine, thepharmaceutical industry, biotechnology, bioremediation, andalternative energy production. Developing these applicationswill demand integration of many scientific disciplines. Giventhe importance of this field for the Federal mission and theinterdisciplinary approaches required to exploit futurechallenges and opportunities, there is a continued needfor basic research on bacteria.

Basic Research on Bacteria The Essential Frontier

“...research on topics likeevolution and ecologyhas a direct impact onthe advancement ofhuman health.”

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Selected ReadingsAltman et al. An open letter to Elias Zerhouni. Science, 307:1409 (2005).

Backhed F., Ley R., Sonnenburg J., Peterson D., Gordon J. “Host-bacterial mutualism in the human intestine.”Science, 307: 1915-1920 (2005).

Bush V. Science: The Endless Frontier. United States Government Printing Office, Washington, DC (1945)[available at http://www.nsf.gov/about/history/vbush1945.htm].

Fauci A. S., Zerhouni E. A. “NIH response to open letter.” Science, 308:49 (2005).

Kaiser J. “Microbiology: Détente declared on NIH biodefense funding.” Science, 308:938 (2005).

Maloy S., Schaechter M. “The era of microbiology: a Golden Phoenix.” International Microbiology, 9: 1-7 (2006).

National Research Council. Treating Infectious Diseases in a Microbial World: Report of Two Workshopson Novel Antimicrobial Therapeutics. National Academies Press, Washington, DC (2006).

Overbye K., Barrett J. “Antibiotics: where did we go wrong?” Drug Discovery Today, 10: 45-52 (2005).

Schaechter M., Kolter R., Buckley M. Microbiology in the 21st Century: Where Are We and Where Are We Going?American Academy of Microbiology, Washington, DC (2003).

Schlegel H. “Continuing opportunities for general microbiology.” Archives of Microbiology, 182: 105-108 (2004).

Sleator R., Hill C. “Patho-biotechnology: using bad bugs to do good things.” Current Opinion in Biotechnology,17: 211-216 (2006).

“Applications of basic research on bacteria areessential for medicine, the pharmaceuticalindustry, biotechnology, bioremediation,and alternative energy production.”

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Appendix ISome examples that demonstrate theimpact of basic research on bacteria arelisted below.

Molecular Biology

• Cloning (plasmid and phage vectors;restriction enzymes)

• DNA sequencing• PCR (Temperature stable polymerases)• Protein overexpression (phage T7;

chaperones)• Protein secretion• Mutagenesis and DNA repair (discovered

in bacteria; including mismatch repairwhich plays major role in certain cancers)

• Recombination (including site-specificrecombination systems used for geneticengineering, and mechanisms of homolo-gous recombination)

• Transposons (initial work in maize, butmolecular understanding from work inbacteria)

Metabolism and Biochemistry

• Role of proton motive force in transport,energy (substrate coupled proton fluxesin bacteria)

• LacY as paradigm for secondary trans-porters (many now implicated in disease)

• Regulation of gene expression (via adiversity of mechanisms, including generearrangements, transcription, translation,turnover, etc.—most discovered byresearch in phage lambda and E. coli)

Ecology and Evolution

• Extent of microbial diversity (>99%microbes uncultured; use of rRNA fortaxonomy)

• Evolution of new traits (acquisition ofpathogenesis islands via horizontal genetransfer)

• Coordination of microbial populations(quorum sensing)

• Growth of mixed microbial consortia asbiofilms

Medicine

• Discovery of antibiotics (streptomycin,tetracyclines, vancomycin, bactricin, etc.)

• Antimetabolites (understanding of metabol-ic pathways led to improved therapies, e.g.trimethoprim plus sulfa)

• Inhibitors of resistance mechanisms(e.g. ß-lactamase inhibitors such asclavulanic acid)

• Discovery of gyrase and other topoiso-merases (led to quinolone antibioticssuch as ciprofloxacin, and anti-cancerdrugs such as etoposides that makeType II topoisomerases toxic in rapidlydividing human cells)

• Lipopolysaccharide structure (basis ofseptic shock)

• Function of eukaryotic genes (comparativegenomics of CFTR and P-glycoproteinsequences allowed prediction of their func-tion based upon similarity to bacterial ABCtransporters)

• Live, attenuated vaccines (e.g. Aromutants of Salmonella enterica sv. Typhi,required understanding of physiology)

In addition to the above discoveries thatemphasize the impact of microbiology priorto the last decade, some recent examplesof discoveries resulting from basicresearch on bacteria include the following.

Development of New Antibioticsand Inhibitors

• Use of genomics to identify antibiotictargets and vaccine candidates

• RNA and DNA aptamers as therapeutics(resulting from work on phage T4,aptamer-based treatments are currentlyin clinical trials)

• Quorum sensing via homoserine lactones(required for virulence of some bacteria,inhibitors are being developed)

• Antibiotic resistance due to efflux pumps(new inhibitors in trials)

• Integrase inhibitors (studies on transposi-tion mechanisms in bacteria leading tothe understanding of the mechanism ofHIV integrase, and the appreciation thatthis enzyme is a good target for drugdevelopment; novel peptide antibioticsthat inhibit recombination)

• Antibiotic target interactions informingmodification of existing antibiotics (ribo-some structure allows development ofnew aminoglycosides; penicillin bindingproteins and mechanism of action ofpenicillins; mechanism of resistance tovancomycin; gyrase inhibitors, tRNA syn-thase inhibitor Mupirocin)

• Determined sites of action for pesticides(including Roundup and the sulfonylureaherbicides)

• Role of biofilms in antibiotic resistance andpersistence (targets for novel antibiotics;tissues, implants, etc.)

• Role of stress responses in antibioticpersistence and development of cross-resistance

• Phage therapy• Streptokinase as inhibitors of thrombosis

subsequent to myocardial infarction

Basic Research on Bacteria The Essential Frontier

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Virulence Mechanisms

• Cytoskeleton rearrangements modulatedby bacteria (e.g. Listeria, Salmonella, etc.)

• Growth of animal pathogens in plants(e.g. Salmonella)

• Role of metabolites in virulence (e.g.,Mg++ as signal of macrophage infection,relied upon basic studies of divalent iontransport)

• Previously uncharacterized roles of hostfunctions in defense (e.g. research inprogress implicates Pon1 in host defensein liver and spleen tissues)

Role of Bacteria in Chronic Disease

• Bacteria cause or contribute to particularchronic diseases (opposing roles ofHelicobacter in stomach and esophagealcancer; anaerobic consortia in periodontaldisease; periodontal bacteria in atheroscle-rosis; etc.)

• Role of periodontal bacteria in pretermbirths (previously overlooked becausebacteria could not be cultivated)

• Role of glyoxylate shunt in persistentinfections by pathogens, includingbacteria and fungi (relied upon basicunderstanding of pathway from workin E. coli)

• Role of osmotic stress mechanisms (e.g.glycyl betaine and proline accumulation)in infectious disease (e.g. E. coli UTI,Staphylococcus)

New Vaccines

• Use of minicells as vaccine delivery systems• Edible vaccines (cheaper, do not need

refrigeration, relied upon Agobacteriumgenetic engineering; e.g., hepatitis Bvaccine in potatoes successful in initialhuman tests)

• Use of live attenuated Salmonella strainsto invoke mucosal immunity (relied uponunderstanding of basic physiology)

• Use of Salmonella to deliver anti-cancertreatments (relied upon understanding ofattachment/secretion systems)

• Role of normal flora in development ofhost vascularization and immunity (e.g.Bacteriodes)

Biotechnology (over 40% ofbiotech products made in theUnited States and EuropeanUnion use E. coli as a host)

• Identification of novel enzymes fromextremophiles and “metagenomelibraries”

• Nutrients in genetically engineered crops(e.g. ß-catotene/Vitamin A in golden rice;plant genetic engineering relied uponbasic research on Agobacterium)

• Overproduction of membrane proteins inintracellular membranes of Rhodobacter(e.g. cystic fibrosis receptor)

• Production of leucine-rich proteins forchemotherapy (initially failed becausehigh level production leads to proteinswith norleucine substituted for methionine,understanding of pathways gave thesolution)

• In vivo substitution of unusual aminoacids (increased stability of therapeuticpeptides; required basic understandingtranslation)

• Tight on/off switches for gene expression

Detection of Pathogens

• Rapid detection methods demandunderstanding of extent of geneexchange (e.g. phage-mediated mobilityof exotoxin genes, transfer of antibioticresistance, pathogenicity islands)

• Array technologies to identify microbesand infections (required comparativegenomics)

• DNA-based rapid detection methodsbased upon comparative genomics

• Protein-based detection of antibioticresistance and toxins (based uponunderstanding physiology)

• Metabolic-based detection (forensicmicrobiology relies on ability to traceminute metabolites)

• Rapid breath tests for microbes (e.g.,urease test for Helicobacter, others indevelopment)

• Identification of genetic determinantsresponsible for changes in host specifici-ty associated with emerging infectiousdisease (relies on combination of genet-ics and comparative genomics)

Bioinformatics

• Correct annotation demands demonstra-tion of functionality (direct genetic andphysiological tests in model organisms,including bacteria and yeast; knowledgestill inadequate)

• Analysis of organisms that cannotbe cultured (e.g., causative agentof syphilis)

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Appendix IIASM-NIH Workshop on BacterialResearch participants.

Steering Committee

James Anderson, Ph.D.Program Director, Division of Geneticsand Developmental BiologyNational Institutes of General Medical SciencesNational Institutes of Health

Dennis M. Dixon, Ph.D.Chief, Bacteriology and Mycology BranchDivision of Microbiology and Infectious DiseasesNational Institute of Allergyand Infectious DiseasesNational Institutes of Health

Stanley Maloy, Ph.D.Professor and DirectorCenter for Microbial SciencesSan Diego State University

Carol A. Nacy, Ph.D.CEO, Sequella, Inc.

James M. Tiedje, Ph.D.Professor, Center for Microbial EcologyMichigan State University

General Meeting Participants

Frederick M. Ausubel, Ph.D.Professor of GeneticsDepartment of Molecular BiologyMassachusetts General HospitalHarvard Medical School

Jonathan Beckwith, Ph.D.American Cancer Society ProfessorDepartment of Microbiology andMolecular GeneticsHarvard Medical School

Jorge Benach, Ph.D.Professor, Center forInfectious DiseasesStony Brook University

Martin J. Blaser, M.D.Chair, NYU Department of MedicineNew York University Schoolof Medicine

Laurie Comstock, Ph.D.Associate Professor of MedicineChanning LaboratoryBrigham and Womenʼs HospitalHarvard Medical School

J. Stephen Dumler, M.D.Professor of PathologyDivision of Medical Microbiology,Department of PathologyThe Johns Hopkins UniversitySchool of Medicine

Richard H. Ebright, Ph.D.Professor and InvestigatorHoward Hughes Medical Institute atRutgers University

Claire M. Fraser-Liggett, Ph.D.President and Director, TIGR

Nancy E. Freitag, Ph.D.Associate Professor, Seattle BiomedicalResearch Institute andDepartment of Pathobiology & Microbiology,University of Washington

George Georgiou, Ph.D.Cockrell Regents EndowedChair in Engineering #9Chemical Engineering, BiomedicalEngineering and Institute for Cell andMolecular BiologyUniversity of Texas at Austin

William R. Goldman, Ph.D.Professor of Molecular MicrobiologyWashington University School of Medicine

Jeffrey Gordon, M.D.Professor and Director, Center forGenome SciencesWashington University

Everett Peter Greenberg, Ph.D.Professor and ChairDepartment of MicrobiologyUniversity of Washington

Eduardo A. Groisman, Ph.D.Professor and InvestigatorHoward Hughes Medical Institute at theWashington University School of Medicine

G. Wesley Hatfield, Ph.D.Professor, Department of Microbiology andMolecular GeneticsUniversity of California, IrvineSchool of Medicine

Darren E. Higgins, Ph.D.Associate Professor, Department ofMicrobiology and Molecular GeneticsHarvard Medical School

Ann Hochschild, Ph.D.Professor, Department of Microbiologyand Molecular GeneticsHarvard Medical School

William R. Jacobs, Jr., Ph.D.Professor and InvestigatorHoward Hughes Medical Institute at theAlbert Einstein College of Medicine

Samuel Kaplan, Ph.D.Professor and Chair, Microbiologyand Molecular Genetics DepartmentUniversity of Texas Health Science CenterHouston Medical School

Paul Keim, Ph.D.Professor and DirectorPathogen GenomicsTranslational GenomicsResearch Institute (TGEN)Northern Arizona University

Linda J. Kenney, Ph.D.Associate Professor, Department ofMicrobiology & ImmunologyUniversity of Illinois-Chicago

Roberto Kolter, Ph.D.Professor, Microbiology andMolecular GeneticsHarvard Medical School

Robert Landick, Ph.D.Professor, Department of BacteriologyUniversity of Wisconsin-Madison

Robert A. LaRossa, Ph.D.Research Fellow, Central Research &DevelopmentDuPont Company

Richard Lenski, Ph.D.Hannah Distinguished ProfessorDepartment of Microbiology &Molecular GeneticsMichigan State University

Mary E. Lidstrom, Ph.D.Associate Dean, ProfessorUniversity of Washington

Sheila A. Lukehart, Ph.D.Professor of MedicineUniversity of Washington

Basic Research on Bacteria The Essential Frontier

12

Joe Lutkenhaus, Ph.D.Professor, Department of MicrobiologyUniversity of Kansas Medical Center

Jeffery F. Miller, Ph.D.Professor and Chair, Department ofMicrobiology, Immunology and MolecularGeneticsUCLA

Charles P. Moran, Jr., Ph.D.Professor, Department ofMicrobiology & ImmunologyEmory University School of Medicine

Shelley M. Payne, Ph.D.Professor, Department of Molecular Geneticsand MicrobiologyUniversity of Texas at Austin

Kit Pogliano, Ph.D.Associate ProfessorBiological SciencesUniversity of California, San Diego

Steve J. Projan, Ph.D.Vice President, Biological TechnologiesWyeth

Peg Riley, Ph.D.Professor, Biology DepartmentUniversity of Massachusetts Amherst

Martin Rosenberg, Ph.D.Chief Scientific OfficerPromega Corporation

Lucia B. Rothman-Denes, Ph.D.Professor, Department of MolecularGenetics and Cell BiologyThe University of Chicago

Molly Schmid, Ph.D.Keck Graduate Institute

Olaf Schneewind, Ph.D., M.D.Professor, Department of MicrobiologyUniversity of Chicago

David H. Sherman, B.S., M.S., Ph.D.Professor, Life Sciences InstituteUniversity of Michigan

Thomas J. Silhavy, Ph.D.Warner Lambert-Parke Davis ProfessorMolecular Biology DepartmentLewis Thomas LabsPrinceton University

Melvin Simon, Ph.D.Division of BiologyCalifornia Institute of Technology

Magdalene So, Ph.D.Professor and Chair, Department ofMolecular Microbiology & ImmunologyOregon Health & Science University

Gisela Storz, Ph.D.Senior InvestigatorCell Biology and Metabolism BranchNational Institute of Child Healthand Human DevelopmentNational Institutes of Health

Malcolm E. Winkler, Ph.D.Professor, Department of BiologyIndiana University Bloomington

Ryland Young, Ph.D.Professor, Biochemistry/Biophysics DepartmentTexas A&M University

Federal Meeting Participants

Patrick P. Dennis, Ph.D.Program Director Molecularand Cellular BiosciencesNational Science Foundation

Daniel Drell, Ph.D.Program Manager, Life Sciencesand Medical Sciences DivisionOffice of Biological andEnvironmental ResearchU.S. Department of Energy

Judith H. Greenberg, Ph.D.Director, Genetics andDevelopmental BiologyNational Institutes of General MedicalSciences/National Institutes of Health

Maria Giovanni, Ph.D.Assistant Director for MicrobialGenomics and Advanced TechnologiesNational Institute of Allergy andInfectious DiseasesNational Institutes of Health

Maryanna P. Henkart, Ph.D.Division Director Molecularand Cellular BiosciencesNational Science Foundation

Dennis Mangan, Ph.D.Chief, Infectious Diseasesand Immunity BranchNational Institute of Child Healthand Human DevelopmentNational Institues of Health

Barbara Mulach, Ph.D.Communications andPolicy Team LeaderNational Institute of Allergyand Infectious DiseasesNational Institutes of Health

Ann Lichens-Park, Ph.D.National Program LeaderCompetitive ProgramsU.S. Department of Agriculture

Sam Perdue, Ph.D.Program Officer Bacteriologyand Mycology BranchNational Institute of Allergyand Infectious DiseasesNational Institutes of Health

N. Kent Peters, Ph.D.Program Officer Bacteriologyand Mycology BranchNational Institute of Allergyand Infectious DiseasesNational Institutes of Health

Alexander Politis, Ph.D.Chief, Infectious Diseasesand Microbiology IRGCenter for Scientific ReviewNational Institutes of Health

Norka Ruiz-Bravo, Ph.D.Deputy Director for Extramural ResearchNational Institutes of Health

Michael Schaefer, Ph.D.Program Officer Bacteriologyand Mycology BranchNational Institute of Allergyand Infectious DiseasesNational Institutes of Health

Diane Stassi, Ph.D.Scientific Review AdministratorCenter for Scientific ReviewNational Institutes of Health

Starting with bottom row, left to right:Row 1: Linda J. Kenney, William R. Jacobs,

Jr., Michael Schaefer, Magdalene So,

Barbara Mulach

Row 2: Frederick M. Ausubel,

Stanley Maloy, Dennis Dixon,

Melvin Simon, Laurie Comstock,

William R. Goldman,

Nancy E. Freitag

Row 3: Roberto Kolter, Lucia B. Rothman-

Denes, Ann Hochschild,

Patrick P. Dennis,

J. Stephen Dumler

Row 4: George Georgiou, Ryland Young,

Richard Lenski, Shelley M. Payne,

Everett Peter Greenberg

Row 5: James M. Tiedje, James Anderson,

Gisela Storz, Robert A. LaRossa

Row 6: Thomas J. Silhavy, Sheila A. Lukehart,

Dennis Mangan, Mary E. Lidstrom

Row 7: Charles P. Moran, Diane Stassi,

Malcolm E. Winkler,

David H. Sherman, Robert Landick,

Ann Lichens-Park, Daniel Drell,

Peg Riley

Row 8: Jeffrey Gordon, Molly Schmid,

Kit Pogliano, Alexander Politis,

Carol A. Nacy, Richard H. Ebright

Row 9: N. Kent Peters, Claire M. Fraser-

Liggett, Martin J. Blaser,

Joe Lutkenhaus

Row 10: Eduardo A. Groisman,

Olaf Schneewind, Jeffery F. Miller,

Darren E. Higgins,

Jonathan Beckwith

American Society for Microbiology1752 N Street, NWWashington, DC 20036Tel: 202-737-3600www.asm.org