Microbial Diversity In The Genomic Era

Microbial Diversity in the Genomic Era, Second Edition presents techniques used for microbial taxonomy and phylogeny, along with their applications and respective strengths and challenges. Though many advanced techniques for the identification of unknown bacterium are available in the genomic era, a far fewer number of the total microbial species have been discovered and identified to date. With that in mind, this book incorporates recently developed biosystematics methods and approaches to assess microbial taxonomy, with suitable recommendations for where to apply them across the range of bacterial identification and infectious disease research. Here, international researchers in the field first provide a broad overview of microbial genomics research and microbiome directed medicine, followed by sections on molecular tools for microbial diversity research, extremophilic microbial diversity, functional microbial diversity across application areas, microbial diversity and infectious disease research, and future directions for research. Step-by-step methodologies are provided for key techniques, along with applied case studies breaking down recent research studies into the practical components, illuminating pathways for new studies across the field. This new edition has been fully updated to address advances in the field of microbiome directed medicine, and whole genome sequencing for studying microbial diversity, considering both recent technological advances and new applications areas, from extremophile studies to the latest approaches in human microbiome analysis. Instructs in techniques used for microbial taxonomy and phylogeny, with discussions of their applications and respective pros and cons Reviews the evolving field of microbial typing and the genomic technologies that enable comparative metagenomic analysis of complex microbial environments Covers microbiome directed translational research, as well as whole genome sequencing for studying microbial diversity, with newly added research protocols and case studies Reviews future applications in the field of microbiome directed medicine Features chapter contributions from global experts in the field

Presents the diverse and complex sets of technology, data, knowledge, ideas, and objectives into an integrated and holistic approach to bioprospecting. * Explores the primacy of natural products for biotechnology, emphasizing the extraordinary resource that microbial diversity presents and how and where that resource, and the exploitable properties that it contains, can be found. * Demonstrates the need for modern microbiologists to have an integrated perspective of science in order to address the big questions in microbiology. * Serves as a reference for instructors and researchers in environmental microbiology, biotechnology, and microbial diversity as well as applied biologists.

Microbes, or microorganisms, are tiny living beings that cannot be seen by the naked eye. These little guys are one of the oldest living things on Earth, and are extremely diverse in how they live and what they can do. They, for example, can live in many places, from the freezing iciness of glaciers, to the insides of other organisms, like termites or humans. Since they are virtually everywhere, microorganisms are essential for the biological processes that allow plants and animals to breath, eat and thrive. But how were they able to endure, adapt and flourish constantly over millions of years? The secrets of their success are still within them, coded into their genomes, waiting for us to understand them. Now, genomes, bacterial or otherwise, are the repositories of life. These repositories store almost every bit of information that allows living beings to live in discrete units called genes. Genes are strung together like the sentences in a book, interacting with each other to create meaning, saving the story of that particular book—or that particular living organism’s genome—so it can be copied, modified, corrected or enhanced, and then passed on to new generations. After many, many years of studying these “books,” we have learned to read and understand them, thanks to the technological innovations of the last decade. Nowadays, it is possible to get the full genomic sequence of practically any organism, and compare it with thousands of genomes from other organisms, letting us peek at the secrets that make each organism who it is. With the current technical abilities, the challenge now is not to obtain the information but to interpret all those chunks of the story. Finding ways to untangle the riddles of genomic information is the work of Genomics, the science that allows us to obtain, analyze and prioritize information among the many stories that we sequence everyday. To do this, Genomics draws from many sciences, like mathematics and computing sciences, making it a truly interdisciplinary endeavor. Right now , genomics are one of the most important areas of biology, and many, if not most, of current biological studies use at least a little bit of genomics. For example, genomics can be used to identify a microbe and give it a name, to learn about what types of things it can do or places it can live, and to figure out the mechanisms that enable it to survive under particular conditions. Here, we will dwell on some of the basic questions about microbial adaptation, biodiversity, and their relationships with other living beings using a genomic approach. We will also focus on the environment, trying to understand how such tiny little creatures are capable of solving their daily problems, and how they can alter the places in which they live. Learning about these mechanisms will not only provide us with knowledge about life in general but will also help us to understand these organisms as a fundamental component of our ecosystem, including their harmful and beneficial effects in all aspects of our daily life, which can be translated into useful applications in almost any imaginable way.

Genomics and Evolution of Eukaryotic Microbes synthesizes the rapidly emerging fields of eukaryotic diversity and genome evolution. Eukaryotes (cells with nuclei) evolved as microbes and have existed on Earth for approximately two billion years. The tremendous diversity of eukaryotic microbes (protists) is often overlooked by those who study the macroscopic eukaryotic lineages: plants, animals, and fungi. Yet, eukaryotic microbes are of critical importance to ecosystems, human health, and our desire to understand biodiversity on Earth. By bringing together groundbreaking data from genome studies of diverse eukaryotic microbes, this book elucidates the many novelties among eukaryotic genomes and provides a single resource for otherwise widely dispersed information. Eukaryotic microorganisms impact both our health and our environment. These organisms include some of the deadliest known pathogens such as Plasmodium falciparum, a causative agent of malaria, and Entamoeba histolytica an agent of dysentery. Eukaryotic microbes also play a significant role in environments through their involvement in global biogeochemical cycles. Such roles are perhaps best exemplified by the coccolithophores, including the species Emiliania huxleyi, which can create 'blooms' in the oceans that are visible from outer space (i.e. as large as the state of Alaska). Despite the great importance and breadth of eukaryotic microbes (the vast majority of major ukaryotic lineages are microbial, with plants, animals and fungi representing just three of an estimated 60-200 major lineages), our understanding of their diversity and phylogeny is only now rapidly expanding, in part bolstered by genomic studies. This book presents analyses and interpretations from experts in the field. Recent advances, particularly in DNA sequencing technologies, have made eukaryotic microbes more accessible to genome analyses. Unravelling the wealth of information on eukaryotic genomes will invariably revolutionize our understanding of eukaryotes, including their physiology, systematics, and ecology.

Over the past several decades, new scientific tools and approaches for detecting microbial species have dramatically enhanced our appreciation of the diversity and abundance of the microbiota and its dynamic interactions with the environments within which these microorganisms reside. The first bacterial genome was sequenced in 1995 and took more than 13 months of work to complete. Today, a microorganism's entire genome can be sequenced in a few days. Much as our view of the cosmos was forever altered in the 17th century with the invention of the telescope, these genomic technologies, and the observations derived from them, have fundamentally transformed our appreciation of the microbial world around us. On June 12 and 13, 2012, the Institute of Medicine's (IOM's) Forum on Microbial Threats convened a public workshop in Washington, DC, to discuss the scientific tools and approaches being used for detecting and characterizing microbial species, and the roles of microbial genomics and metagenomics to better understand the culturable and unculturable microbial world around us. Through invited presentations and discussions, participants examined the use of microbial genomics to explore the diversity, evolution, and adaptation of microorganisms in a wide variety of environments; the molecular mechanisms of disease emergence and epidemiology; and the ways that genomic technologies are being applied to disease outbreak trace back and microbial surveillance. Points that were emphasized by many participants included the need to develop robust standardized sampling protocols, the importance of having the appropriate metadata, data analysis and data management challenges, and information sharing in real time. The Science and Applications of Microbial Genomics summarizes this workshop.

As we enter the twenty-first century, the polar biological sciences stand well poised to address numerous important issues, many of which were unrecognized as little as 10 years ago. From the effects of global warming on polar organisms to the potential for life in subglacial Lake Vostok, the opportunities to advance our understanding of polar ecosystems are unprecedented. The era of "genome-enabled" biology is upon us, and new technologies will allow us to examine polar biological questions of unprecedented scope and to do so with extraordinary depth and precision. Frontiers in Polar Biology in the Genomic Revolution highlights research areas in polar biology that can benefit from genomic technologies and assesses the impediments to the conduct of polar genomic research. It also emphasizes the importance of ancillary technologies to the successful application of genomic technologies to polar studies. It recommends the development of a new initiative in polar genome sciences that emphasizes collaborative multidisciplinary research to facilitate genome analyses of polar organisms and coordinate research efforts.

Microorganisms are a major part of the Earth’s biological diversity. Although a lot of research has been done on microbial diversity, most of it is fragmented. This book creates the need for a unified text to be published, full of information about microbial diversity from highly reputed and impactful sources. Recent Advancements in Microbial Diversity brings a comprehensive understanding of the recent advances in microbial diversity research focused on different bodily systems, such as the gut. Recent Advancements in Microbial Diversity also discusses how the application of advanced sequencing technologies is used to reveal previously unseen microbial diversity and show off its function. Gives insight into microbial diversity in different bodily systems Explains novel approaches to studying microbial diversity Highlights the use of omics to analyze the microbial community and its functional attributes Discusses the techniques used to examine microbial diversity, including their applications and respective strengths and weaknesses

This book discusses genetic engineering of both plants and microbes for making agricultural practices more productive and sustainable. It chapters explore the understanding of the interaction between plants and microbes, and genomic information to modify the metabolism of plants or microbes to further enhance the beneficial interaction. The book covers the development of commercial inoculants including selection of appropriate plant growth-promoting rhizobacteria/ phosphate solubilize bacteria based on target host plant, soil type, indigenous microbial communities, environmental conditions, inoculant density, suitability of carriers and compatibility with integrated crop management. This is a relevant content for scientists and researchers working on soil biology, sustainable agricultural and plant physiology. Also, this book is a useful read for graduate and post graduate students of agriculture, botany and microbiology.