Colloquium And Report On Systems Microbiology

The steering committee for the American Academy of Microbiology's colloquium, ''Systems Microbiology: Beyond Microbial Genomics'' met September 26, 2003, in Washington, DC, to plan the colloquium and discuss the report that would be produced following the colloquium. The steering committee developed the intellectual approach to the issues relating to systems microbiology, including drafting questions for the colloquium participants to work their way through. The committee then identified the scientists that should be invited in order to ensure a comprehensive and thorough analytical report. Dates and a venue were decided upon. The colloquium was held June 4-6, 2004 in Portland, Oregon. There were 35 scientists who spent the weekend discussing specific recommendations for how to capitalize scientifically on the advances in microbial genomics and progress towards a functional understanding of individual microorganisms and microbial communities. The issues discussed at the colloquium were timely and important, and we expect the report, which will be published in 2005, to be extremely well received. Once the report is available, a copy will be forwarded to you. The following items were discussed and will be included in our published report: The focus of this colloquium was on how to capitalize scientifically on the advances in microbial genomics and progress towards a functional understanding of individual microorganisms and microbial communities. Colloquium participants discussed where the field is heading and identify scientific opportunities, challenges, and benefits of this research. An important aspect was the identification of resource and technology gaps that must be addressed in order to advance the field. Making the Case for Systems Microbiology: (1) What can we learn about life processes through studying microbiological systems (sub-cellular, cellular, community)? (2) What important, new fundamental information and potential applications a re likely to emerge from studying systems microbiology (e.g., environmental, agricultural, energy production, medical)? (3) Who should be working on systems microbiology? Research Issues: (1) What kind of information is needed to understand how biological systems function? (2) What kind of information is currently available? (3) What information is not available? (4) How do we acquire additional information? (5) What defines a microbial species? (6) How do we measure ''noise'' in a biological system? (7) How are biological systems regulated? (8) How can a systems biology approach be applied to microbial communities? Technical Challenges: (1) What are the technical bottlenecks that limit advances in systems microbiology? (2) What are the quantitative issues and problems that need to be addressed? (3) How much data do we need? (4) How do we best get those data? (5) What kind of data do we need? (6) How do we assure the quality of the data? (7) How do we optimize utilization of the data? (8) How do we apply data from one system to another? (9) What are the questions we need to ask to determine functionality? Education, Training, and Communications Issues: (1) Are we currently training scientists to utilize existing and emerging technologies? If not, how do we? (2) Should new collaborations be initiated to study systems microbiology? If so, what are they and who should participate (academics, research foundations, industry, government, etc.)? (3) How can these collaborations be encouraged? (4) How important is international collaboration? Why or why not? (5) What should the public know about the potential of this kind of research? (6) Are there commercial potentials? If so, what are they? (7) What can the scientific community do to better communicate these issues? How? (8) Is there a role for professional societies? If so, what?

The American Academy of Microbiology convened a colloquium June 4-6, 2004 to confer about the scientific promise of systems microbiology. Participants discussed the power of applying a systems approach to the study of biology and to microbiology in particular, specifics about current research efforts, technical bottlenecks, requirements for data acquisition and maintenance, educational needs, and communication issues surrounding the field. A number of recommendations were made for removing barriers to progress in systems microbiology and for improving opportunities in education and collaboration. Systems biology, as a concept, is not new, but the recent explosion of genomic sequences and related data has revived interest in the field. Systems microbiology, a subset of systems biology, represents a different approach to investigating biological systems. It attempts to examine the emergent properties of microorganisms that arise from the interplay of genes, proteins, other macromolecules, small molecules, organelles, and the environment. It is these interactions, often nonlinear, that lead to the emergent properties of biological systems that are generally not tractable by traditional approaches. As a complement to the long-standing trend toward reductionism, systems microbiology seeks to treat the organism or community as a whole, integrating fundamental biological knowledge with genomics, metabolomics, and other data to create an integrated picture of how a microbial cell or community operates. Systems microbiology promises not only to shed light on the activities of microbes, but will also provide biology the tools and approaches necessary for achieving a better understanding of life and ecosystems. Microorganisms are ideal candidates for systems biology research because they are relatively easy to manipulate and because they play critical roles in health, environment, agriculture, and energy production. Potential applications of systems microbiology research range from improvements in the management of bacterial infections to the development of commercial-scale microbial hydrogen generation. A number of technical challenges must be met to realize the potential of systems microbiology. Development of a new, comprehensive systems microbiology database that would be available to the entire research community was identified as the single most critical need. Other challenges include difficulties in measuring single-cell parameters, limitations in identifying and measuring metabolites and other products, the inability to cultivate diverse microbes, limits on data accessibility, computational limitations associated with data integration, the lack of sufficient functional gene annotations, needs for quantitative proteomics, and the inapplicability of current high throughput methods to all areas of systems microbiology. Difficulties have also been encountered in acquiring the necessary data, assuring the quality of that data, and in making data available to the community in a useful format. Problems with data quality assurance and data availability could be partially offset by launching a dedicated systems microbiology database. To be of greatest value to the field, a database should include systems data from all levels of analysis, including sequences, microarray data, proteomics data, metabolite measurements, data on protein-protein or protein-nucleic interactions, carbohydrate and small RNA profiles, information on cell surface markers, and appropriate supporting data. Regular updates of these databases and adherence to agreed upon data format standards are critical to the success of these resources. It was recommended that educational requirements for undergraduate and graduate students in microbiology be amended to better prepare the next generation of researchers for the quantitative requirements of applying systems microbiology methods in their work. Systems microbiology research is too complex to be the sole property of any single academic discipline. The contributions of microbiologists, computer scientists, control theorists, biostatisticians, and others are all required to move the field forward. Since research in systems microbiology demands the contributions of a diverse array of professionals, collaboration across disciplines and national borders should be strongly encouraged by research bodies and funding agencies. Although the details of systems microbiology research are probably not of interest to the average individual, the potential applications and benefits of these types of investigations should be conveyed to the lay public.

This volume contains cutting-edge reviews by world-leading experts on the systems biology of microorganisms. As well as covering theoretical approaches and mathematical modelling this book includes case studies on single microbial species of bacteria and archaea, and explores the systems analysis of microbial phenomena such as chemotaxis and phagocytosis. Topics covered include mathematical models for systems biology, systems biology of Escherichia coli metabolism, bacterial chemotaxis, systems biology of infection, host-microbe interactions, phagocytosis, system-level study of metabolism in M.

People's desire to understand the environments in which they live is a natural one. People spend most of their time in spaces and structures designed, built, and managed by humans, and it is estimated that people in developed countries now spend 90 percent of their lives indoors. As people move from homes to workplaces, traveling in cars and on transit systems, microorganisms are continually with and around them. The human-associated microbes that are shed, along with the human behaviors that affect their transport and removal, make significant contributions to the diversity of the indoor microbiome. The characteristics of "healthy" indoor environments cannot yet be defined, nor do microbial, clinical, and building researchers yet understand how to modify features of indoor environmentsâ€"such as building ventilation systems and the chemistry of building materialsâ€"in ways that would have predictable impacts on microbial communities to promote health and prevent disease. The factors that affect the environments within buildings, the ways in which building characteristics influence the composition and function of indoor microbial communities, and the ways in which these microbial communities relate to human health and well-being are extraordinarily complex and can be explored only as a dynamic, interconnected ecosystem by engaging the fields of microbial biology and ecology, chemistry, building science, and human physiology. This report reviews what is known about the intersection of these disciplines, and how new tools may facilitate advances in understanding the ecosystem of built environments, indoor microbiomes, and effects on human health and well-being. It offers a research agenda to generate the information needed so that stakeholders with an interest in understanding the impacts of built environments will be able to make more informed decisions.

June 14-16, 2018 London, UK Key Topics : Plant Physiology, Microbial Transformation, Microbial Physiology And Genomics, Microbiology Research And Advancements, Infectious Diseases And Diagnostic Microbiology, Clinical Microbiology And Antimicrobials, Microbial Ecology And Eco Systems, Mycology, Phycology And Mushrooms, Medical And Molecular Microbiology, Nosocomial And Healthcare Associated Infections, Viral Outbreaks And Epidemiology, Microbes And Beneficial Microbes, Microbial Diseases, Diagnosis And Prevention, Applied Microbiology And Biotechnology, Water Microbiology And Novel Technologies, Bioremediation, Biodegradation And Biodeterioration, Predictive , Preventive, Personalized Medicine And Molecular Diagnostics, Fungal And Infectious Diseases, Pharmaceutical Microbiology, Microbial Infections, Bacterial Pathogenesis, Soil Microbiology, Agricultural Microbiology, Industrial, Food And Fermentation Microbiology, Veterinary Microbiology, Systems Biology And Bioinformatics, Clinical Virology And Infectious Diseases, Cell, Molecular Biology And Molecular Genetics, Microbial Biofilms, Infection And Immunity, Microbial Diversity, Microbial Genetics, Current Trends In Microbiology, Microbial Immunology And Infection Control, Environmental Microbiology, Microbiology And Microbes World, HPV And Cancer, Cancer Immunology And Immunotherapy, Clinical And Medical Case Reports, Antimicrobial Resistance And Infection Control, Applied Microbiology And Biotechnology, Molecular Ecology, Petroleum Microbiology, Bacteriology, Parasitology, Pathology, Protozoology, Protistology And Virology,

Examining the enormous potential of microbiome manipulation to improve health Associations between the composition of the intestinal microbiome and many human diseases, including inflammatory bowel disease, cardiovascular disease, metabolic disorders, and cancer, have been elegantly described in the past decade. Now, whole-genome sequencing, bioinformatics, and precision gene-editing techniques are being combined with centuries-old therapies, such as fecal microbiota transplantation, to translate current research into new diagnostics and therapeutics to treat complex diseases. Bugs as Drugs provides a much-needed overview of microbes in therapies and will serve as an excellent resource for scientists and clinicians as they carry out research and clinical studies on investigating the roles the microbiota plays in health and disease. In Bugs as Drugs, editors Robert A. Britton and Patrice D. Cani have assembled a fascinating collection of reviews that chart the history, current efforts, and future prospects of using microorganisms to fight disease and improve health. Sections cover traditional uses of probiotics, next-generation microbial therapeutics, controlling infectious diseases, and indirect strategies for manipulating the host microbiome. Topics presented include: How well-established probiotics support and improve host health by improving the composition of the intestinal microbiota of the host and by modulating the host immune response. The use of gene editing and recombinant DNA techniques to create tailored probiotics and to characterize next-generation beneficial microbes. For example, engineering that improves the anti-inflammatory profile of probiotics can reduce the number of colonic polyps formed, and lactobacilli can be transformed into targeted delivery systems carrying therapeutic proteins or bioengineered bacteriophage. The association of specific microbiota composition with colorectal cancer, liver diseases, osteoporosis, and inflammatory bowel disease. The gut microbiota has been proposed to serve as an organ involved in regulation of inflammation, immune function, and energy homeostasis. Fecal microbiota transplantation as a promising treatment for numerous diseases beyond C. difficile infection. Practical considerations for using fecal microbiota transplantation are provided, while it is acknowledged that more high-quality evidence is needed to ascertain the importance of strain specificity in positive treatment outcomes. Because systems biology approaches and synthetic engineering of microbes are now high-throughput and cost-effective, a much wider range of therapeutic possibilities can be explored and vetted.

Bacteria have been the dominant forms of life on Earth for the past 3.5 billion years. They rapidly evolve, constantly changing their genetic architecture through horizontal DNA transfer and other mechanisms. Consequently, it can be difficult to define individual species and determine how they are related. Written and edited by experts in the field, this collection from Cold Spring Harbor Perspectives in Biology examines how bacteria and other microbes evolve, focusing on insights from genomics-based studies. Contributors discuss the origins of new microbial populations, the evolutionary and ecological mechanisms that keep species separate once they have diverged, and the challenges of constructing phylogenetic trees that accurately reflect their relationships. They describe the organization of microbial genomes, the various mutations that occur, including the birth of new genes de novo and by duplication, and how natural selection acts on those changes. The role of horizontal gene transfer as a strong driver of microbial evolution is emphasized throughout. The authors also explore the geologic evidence for early microbial evolution and describe the use of microbial evolution experiments to examine phenomena like natural selection. This volume will thus be essential reading for all microbial ecologists, population geneticists, and evolutionary biologists.