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

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.

The first bacterial genome, Haemophilus influenzae, was completely sequenced, annotated, and published in 1995. Today, more than 200 prokaryotic (archaeal and bacterial) genomes have been completed and over 500 prokaryotic genomes are in va- ous stages of completion. Seventeen eukaryotic genomes plus four eukaryotic chro- somes have been completed. The concept of achieving better understanding of an organism through knowledge of the complete genomic sequence was first demonstrated in 1978 when the first bacteriophage genome, X174, was sequenced. Complete genomic sequences of prokaryotes have led to a better understanding of the biology and evolution of the microbes, and, for pathogens, facilitated identification of new vaccine candidates, putative virulence genes, targets for antibiotics, new strategy for rapid diagnosis, and investigation of bacteria–host interactions and disease mec- nisms. Recent increased interest in microbial pathogens and infectious diseases is largely attributed to the re-emergence of infectious diseases like tuberculosis, emergence of new infectious diseases like AIDS and severe acute respiratory syndrome, the problem of an increasing rate of emergence of antibiotic-resistant variants of pathogens, and the fear of bioterrorism. Microbes are highly diverse and abundant in the biosphere. Less than 1% of these morphologically identified microbes can be cultured in vitro using standard techniques and conditions. With such abundance of microbes in nature, we can expect to see new variants and new species evolve and a small number will emerge as pathogens to humans.

Presents an integrated view of the expression of bacterial genetic information, genome architecture and function, and bacterial physiology and pathogenesis This book blends information from the very latest research on bacterial chromosome and nucleoid architecture, whole-genome analysis, cell signaling, and gene expression control with well-known gene regulation paradigms from model organisms (including pathogens) to give readers a picture of how information flows from the environment to the gene, modulating its expression and influencing the competitive fitness of the microbe. Structure and Function of the Bacterial Genome explores the governance of the expression of the genes that make a bacterium what it is, and updates the basics of gene expression control with information about transcription promoter structure and function, the role of DNA as a regulatory factor (in addition to its role as a carrier of genetic information), small RNAs, RNAs that sense chemical signals, ribosomes and translation, posttranslational modification of proteins, and protein secretion. It looks at the forces driving the conservation and the evolution of the dynamic genome and offers chapters that cover DNA replication, DNA repair, plasmid biology, recombination, transposition, the roles of repetitive DNA sequences, horizontal gene transfer, the defense of the genome by CRISPR-Cas, restriction enzymes, Argonaute proteins and BREX systems. The book finishes with a chapter that gives an integrated overview of genome structure and function. Blends knowledge of gene regulatory mechanisms with a consideration of nucleoid structure and dynamics Offers a 'DNA-centric' approach to considering transcription control Views horizontal gene transfer from a gene regulation perspective Assesses the opportunities and limitations of designing synthetic microbes or rewiring existing ones Structure and Function of the Bacterial Genome is an ideal book for graduate and undergraduate students studying microbial cell biology, bacterial pathogenesis, gene regulation, and molecular microbiology. It will also appeal to principal investigators conducting research on these and related topics and researchers in synthetic biology and other arms of biotechnology.

The genetic information contained in DNA is not static, especially in bacterial DNA. It is capable of recombining with other DNA sequences and transferring to other bacteria. These processes allow bacteria to rapidly respond to their environment and are also important in production of disease and the spread of antibiotic resistance. This book is concerned with the mechanisms underlying these dynamic processes in bacterial DNA.

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 all 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. Key Features Genetics, genomics, and bioinformatics integrated in one place Over 400 full-colour illustrations explain concepts and mechanisms throughout and are available to instructors for download A section dedicated to the application of genetics and genomics techniques, including a chapter devoted to laboratory techniques, which includes useful tips and recommendations for protocols, in addition to troubleshooting and alternative strategies Bulleted key points summarize each chapter Extensive self-study questions related to the chapter text and several discussion topics for study groups to explore further This book is extended and enhanced through a range of digital resources that include: Interactive online quizzes for each chapter Flashcards that allow the reader to test their understanding of key terms from the book Useful links for online resources associated with Chapters 16 and 17

The study of bacterial genetics has revolutionised with the development of genome sequencing, which let us catalogue the gene content of various clinically and industrially important bacteria and opened up the field of comparative genomics. The research findings on bacterial genetics were further enhanced by the development of allied techniques that allowed interrogation of the interactions and functions of the many components of the genome. These developments accelerated with the widespread adoption of quantitative deep-sequencing approaches. This process allowed both comparative and functional genomics on an unprecedented scale by presenting powerful tools to investigate multiple layers of bacterial adaptation and evolution. This book presents the application of genomic tools to examine bacterial adaptation. The emphasis is on data analysis and interpretation. Much of the material is drawn from the recent, primary literature, which is the most powerful tool in the cutting-edge and fast-growing field of bacterial research.