Bacterial Genomics

This book presents the application of genomic tools to examine bacterial adaptation. The emphasis is on data analysis and interpretation.

Our understanding of bacterial genetics has progressed as the genomics field has advanced. Genetics and genomics complement and influence each other; they are inseparable. Under the novel insights from genetics and genomics, once-believed borders in biology start to fade: biological knowledge of the bacterial world is being viewed under a new light and concepts are being redefined. Species are difficult to delimit and relationships within and between groups of bacteria – the whole concept of a tree of life – is hotly debated when dealing with bacteria. The DNA within bacterial cells contains a variety of features and signals that influence the diversity of the microbial world. This text assumes readers have some knowledge of genetics and microbiology but acknowledges that it can be varied. Therefore, the book includes all of the information that readers need to know in order to understand the more advanced material in the book.

Overview and Goals This book describes how to visualize and compare bacterial genomes. Sequencing technologies are becoming so inexpensive that soon going for a cup of coffee will be more expensive than sequencing a bacterial genome. Thus, there is a very real and pressing need for high-throughput computational methods to compare hundreds and thousands of bacterial genomes. It is a long road from molecular biology to systems biology, and in a sense this text can be thought of as a path bridging these ? elds. The goal of this book is to p- vide a coherent set of tools and a methodological framework for starting with raw DNA sequences and producing fully annotated genome sequences, and then using these to build up and test models about groups of interacting organisms within an environment or ecological niche. Organization and Features The text is divided into four main parts: Introduction, Comparative Genomics, Transcriptomics and Proteomics, and ? nally Microbial Communities. The ? rst ? ve chapters are introductions of various sorts. Each of these chapters represents an introduction to a speci? c scienti? c ? eld, to bring all readers up to the same basic level before proceeding on to the methods of comparing genomes. First, a brief overview of molecular biology and of the concept of sequences as biological inf- mation are given.

Foodborne illnesses caused by various bacterial, viral, and fungal pathogens lead to a high number of morbidity and mortality in the U.S. and throughout the world. Recent advances in microbial genomics have significantly improved our understanding of the physiology, evolution, ecology, epidemiology, and pathogenesis of different foodborne pathogens. This book focuses on the genomics of foodborne bacterial pathogens. It begins with a brief overview of the recent advances in microbial genomics and the impact of genomics on food safety research. Then, eight chapters follow that elaborate some in-depth reviews on the genomics of several common foodborne bacterial pathogens including Bacillus, Campylobacter, Clostridium, Escherichia coli, Listeria, Salmonella, Staphylococcus, and Vibrio. Finally, the last four chapters focus on some current genomic, transcriptomic, and proteomic technologies and their applications in studying the epidemiology, evolution, and pathogenesis of foodborne bacterial pathogens. Genomics of Foodborne Bacterial Pathogens can be used as a reference by scientists and professionals in academia, government, and industry who are interested in understanding microbial genomics and using genomics tools to study foodborne bacterial pathogens. This book can also be used as a textbook for instructors and professors who teach food microbiology or microbial genomics-related courses at the post-graduate level.

A wide range of microbiologists, molecular biologists, and molecular evolutionary biologists will find this new volume of singular interest. It summarizes the present knowledge about the structure and stability of microbial genomes, and reviews the techniques used to analyze and fingerprint them. Maps of approximately thirty important microbes, along with articles on the construction and relevant features of the maps are included. The volume is not intended as a complete compendium of all information on microbial genomes, but rather focuses on approaches, methods and good examples of the analysis of small genomes.

'Microbial Pathogenomics' contains a unique collection of reviews demonstrating how genomics has revolutionized our understanding of virulence, host-adaptation strategies and the evolution of bacterial pathogens. Current technologies - computational tools and functional approaches to genome analysis - are carefully documented and clearly illustrated. These include visualization tools for genome comparison, databases, in silico metabolic reconstructions and function prediction as well as interactomics for the study of protein-protein interactions. The concepts of pan-genomics and reverse vaccinology are introduced as strategies when addressing the challenge presented by bacterial diversity in the prevention and treatment of infectious diseases. The authors explore individual bacterial pathogens and discuss the mechanisms that have contributed to their evolutionary success. Special cases of host adaptation, for example, are illustrated by Helicobacter pylori and 'Mycobacterium tuberculosis' which are human-specific and highly persistent; further bacteria discussed include 'Escherichia coli, Campylobacter, Pseudomonas, Legionella, Bartonella, Burkholderia' and 'Staphylococcus'.'Microbial Pathogenomics' provides the reader with a global view of key aspects and future trends in bacterial pathogenomics and evaluates their impact on the understanding and treatment of infectious diseases. Well illustrated and accessible to both specialists and nonspecialists, it is recommended not only for researchers in microbiology, genomics and biotechnology, but also for lecturers and teachers.

"Understanding of bacterial genetics and genomics is fundamental to understanding bacteria and higher organisms, as well. Novel insights in the fields of genetics and genomics are challenging the once clear borders between the characteristics of bacteria and other life. Biological knowledge of the bacterial world is being viewed under a new light with input from genetic and genomics. Replication of bacterial circular and linear chromosomes, coupled (and uncoupled) transcription and translation, multiprotein systems that enhance survival, wide varieties of ways to control gene and protein expression, and a range of other features influence the diversity of the microbial world. This text acknowledges that readers have varied knowledge of genetics and microbiology. Therefore, information is presented progressively, to enable all readers to understand the more advanced material in the book. This second edition of Bacterial Genetics and Genomics updates the information from the first edition with advances made over the past five years. This includes descriptions for 10 types of secretion systems, bacteria that can be seen with the naked eye, and differences between coupled transcription-translation and the uncoupled runaway transcription in bacteria. Topic updates include advances in bacteriophage therapy, biotechnology, and understanding bacterial evolution"--