Microbial Diversity In The Genomic Era

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Microbial Diversity in the Genomic Era

Surajit Das,Hirak Ranjan Dash
Microbial Diversity in the Genomic Era Book PDF

Author : Surajit Das,Hirak Ranjan Dash
Publisher : Elsevier
Page : 840 pages
File Size : 54,8 Mb
Release : 2024-03-23
Category : Science
ISBN : 9780443133213

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Microbial Diversity in the Genomic Era by Surajit Das,Hirak Ranjan Dash Pdf

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

Microbial Diversity and Bioprospecting

Alan T. Bull
Microbial Diversity and Bioprospecting Book PDF

Author : Alan T. Bull
Publisher : Unknown
Page : 532 pages
File Size : 54,6 Mb
Release : 2004
Category : Science
ISBN : UOM:39015057583182

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Microbial Diversity and Bioprospecting by Alan T. Bull Pdf

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.

Genomics and Evolution of Microbial Eukaryotes

Laura A Katz,Debashish Bhattacharya
Genomics and Evolution of Microbial Eukaryotes Book PDF

Author : Laura A Katz,Debashish Bhattacharya
Publisher : OUP Oxford
Page : 256 pages
File Size : 45,9 Mb
Release : 2006-09-07
Category : Science
ISBN : 9780191513855

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Genomics and Evolution of Microbial Eukaryotes by Laura A Katz,Debashish Bhattacharya Pdf

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.

Diversity of the Microbial World

Angélica Cibrián-Jaramillo,Edder D. Bustos-Díaz,Francisco Barona-Gómez
Diversity of the Microbial World Book PDF

Author : Angélica Cibrián-Jaramillo,Edder D. Bustos-Díaz,Francisco Barona-Gómez
Publisher : Frontiers Media SA
Page : 86 pages
File Size : 54,6 Mb
Release : 2020-07-17
Category : Electronic
ISBN : 9782889636655

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Diversity of the Microbial World by Angélica Cibrián-Jaramillo,Edder D. Bustos-Díaz,Francisco Barona-Gómez Pdf

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.

The Science and Applications of Microbial Genomics

Institute of Medicine,Board on Global Health,Forum on Microbial Threats
The Science and Applications of Microbial Genomics Book PDF

Author : Institute of Medicine,Board on Global Health,Forum on Microbial Threats
Publisher : National Academies Press
Page : 429 pages
File Size : 50,7 Mb
Release : 2013-05-02
Category : Science
ISBN : 9780309268196

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The Science and Applications of Microbial Genomics by Institute of Medicine,Board on Global Health,Forum on Microbial Threats Pdf

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.

The Chemistry of Microbiomes

National Academies of Sciences, Engineering, and Medicine,Division on Earth and Life Studies,Board on Chemical Sciences and Technology,Chemical Sciences Roundtable
The Chemistry of Microbiomes Book PDF

Author : National Academies of Sciences, Engineering, and Medicine,Division on Earth and Life Studies,Board on Chemical Sciences and Technology,Chemical Sciences Roundtable
Publisher : National Academies Press
Page : 133 pages
File Size : 40,9 Mb
Release : 2017-07-19
Category : Science
ISBN : 9780309458399

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The Chemistry of Microbiomes by National Academies of Sciences, Engineering, and Medicine,Division on Earth and Life Studies,Board on Chemical Sciences and Technology,Chemical Sciences Roundtable Pdf

The 21st century has witnessed a complete revolution in the understanding and description of bacteria in eco- systems and microbial assemblages, and how they are regulated by complex interactions among microbes, hosts, and environments. The human organism is no longer considered a monolithic assembly of tissues, but is instead a true ecosystem composed of human cells, bacteria, fungi, algae, and viruses. As such, humans are not unlike other complex ecosystems containing microbial assemblages observed in the marine and earth environments. They all share a basic functional principle: Chemical communication is the universal language that allows such groups to properly function together. These chemical networks regulate interactions like metabolic exchange, antibiosis and symbiosis, and communication. The National Academies of Sciences, Engineering, and Medicine's Chemical Sciences Roundtable organized a series of four seminars in the autumn of 2016 to explore the current advances, opportunities, and challenges toward unveiling this "chemical dark matter" and its role in the regulation and function of different ecosystems. The first three focused on specific ecosystemsâ€"earth, marine, and humanâ€"and the last on all microbiome systems. This publication summarizes the presentations and discussions from the seminars.

Microbial Evolution

Howard Ochman
Microbial Evolution Book PDF

Author : Howard Ochman
Publisher : Unknown
Page : 0 pages
File Size : 40,7 Mb
Release : 2016
Category : Science
ISBN : 1621820378

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Microbial Evolution by Howard Ochman Pdf

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.

Spirochete Biology: The Post Genomic Era

Ben Adler
Spirochete Biology The Post Genomic Era Book PDF

Author : Ben Adler
Publisher : Springer
Page : 295 pages
File Size : 54,9 Mb
Release : 2018-08-21
Category : Medical
ISBN : 9783319896380

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Spirochete Biology: The Post Genomic Era by Ben Adler Pdf

Spirochetes comprise a fascinating group of bacteria. Although diverse in terms of their habitat, ecology and infectivity for vertebrate and non-vertebrate hosts, they are often considered together because of their similar cellular morphologies. This volume brings together an international group of experts to provide essential insights into spirochete biology, with an emphasis on recent advances made possible by the availability of genome sequences. As such, it offers a valuable resource for microbiologists and other scientists with an interest in spirochete biology.

Frontiers in Polar Biology in the Genomic Era

National Research Council,Polar Research Board,Committee on Frontiers in Polar Biology
Frontiers in Polar Biology in the Genomic Era Book PDF

Author : National Research Council,Polar Research Board,Committee on Frontiers in Polar Biology
Publisher : National Academies Press
Page : 187 pages
File Size : 43,7 Mb
Release : 2003-08-08
Category : Science
ISBN : 9780309087278

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Frontiers in Polar Biology in the Genomic Era by National Research Council,Polar Research Board,Committee on Frontiers in Polar Biology Pdf

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.

Science Needs for Microbial Forensics

National Research Council (U.S.). Committee on Science Needs for Microbial Forensics: Developing an Initial International Roadmap
Science Needs for Microbial Forensics Book PDF

Author : National Research Council (U.S.). Committee on Science Needs for Microbial Forensics: Developing an Initial International Roadmap
Publisher : Unknown
Page : 0 pages
File Size : 49,6 Mb
Release : 2014
Category : Law
ISBN : 0309302455

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Science Needs for Microbial Forensics by National Research Council (U.S.). Committee on Science Needs for Microbial Forensics: Developing an Initial International Roadmap Pdf

For these reasons, building awareness of and capacity in microbial forensics can assist in our understanding of what may have occurred during a biothreat event, and international collaborations that engage the broader scientific and policy-making communities are likely to strengthen our microbial forensics capabilities. One goal would be to create a shared technical understanding of the possibilities--and limitations--of the scientific bases for microbial forensics analysis. Science Needs for Microbial Forensics: Developing Initial International Research Priorities, based partly on a workshop held in Zabgreb, Croatia in 2013, identifies scientific needs that must be addressed to improve the capabilities of microbial forensics to investigate infectious disease outbreaks and provide evidence of sufficient quality to support legal proceedings and the development of government policies.

Uncultivated Microorganisms

Slava S. Epstein
Uncultivated Microorganisms Book PDF

Author : Slava S. Epstein
Publisher : Springer Science & Business Media
Page : 215 pages
File Size : 53,5 Mb
Release : 2009-09-01
Category : Medical
ISBN : 9783540854654

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Uncultivated Microorganisms by Slava S. Epstein Pdf

In 1898, an Austrian microbiologist Heinrich Winterberg made a curious observation: the number of microbial cells in his samples did not match the number of colonies formed on nutrient media (Winterberg 1898). About a decade later, J. Amann qu- tified this mismatch, which turned out to be surprisingly large, with non-growing cells outnumbering the cultivable ones almost 150 times (Amann 1911). These papers signify some of the earliest steps towards the discovery of an important phenomenon known today as the Great Plate Count Anomaly (Staley and Konopka 1985). Note how early in the history of microbiology these steps were taken. Detecting the Anomaly almost certainly required the Plate. If so, then the period from 1881 to 1887, the years when Robert Koch and Petri introduced their key inventions (Koch 1881; Petri 1887), sets the earliest boundary for the discovery, which is remarkably close to the 1898 observations by H. Winterberg. Celebrating its 111th anniversary, the Great Plate Count Anomaly today is arguably the oldest unresolved microbiological phenomenon. In the years to follow, the Anomaly was repeatedly confirmed by all microb- logists who cared to compare the cell count in the inoculum to the colony count in the Petri dish (cf., Cholodny 1929; Butkevich 1932; Butkevich and Butkevich 1936). By mid-century, the remarkable difference between the two counts became a universally recognized phenomenon, acknowledged by several classics of the time (Waksman and Hotchkiss 1937; ZoBell 1946; Jannasch and Jones 1959).

Soil Biological Communities and Ecosystem Resilience

Martin Lukac,Paola Grenni,Mauro Gamboni
Soil Biological Communities and Ecosystem Resilience Book PDF

Author : Martin Lukac,Paola Grenni,Mauro Gamboni
Publisher : Springer
Page : 347 pages
File Size : 52,5 Mb
Release : 2017-10-06
Category : Technology & Engineering
ISBN : 9783319633367

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Soil Biological Communities and Ecosystem Resilience by Martin Lukac,Paola Grenni,Mauro Gamboni Pdf

This volume explores current knowledge and methods used to study soil organisms and to attribute their activity to wider ecosystem functions. Biodiversity not only responds to environmental change, but has also been shown to be one of the key drivers of ecosystem function and service delivery. Soil biodiversity in tree-dominated ecosystems is also governed by these principles, the structure of soil biological communities is clearly determined by environmental, as well as spatial, temporal and hierarchical factors. Global environmental change, together with land-use change and ecosystem management by humans, impacts the aboveground structure and composition of tree ecosystems. Due to existing knowledge of the close links between the above- and belowground parts of terrestrial ecosystems, we know that soil biodiversity is also impacted. However, very little is known about the nature of these impacts; effects on the overall level of biodiversity, the magnitude and diversity of functions soil biodiversity generates, but also on the present and future stability of tree ecosystems and soils. Even though much remains to be learned about the relationships between soil biodiversity and tree ecosystem functionality, it is clear that better effort needs to be made to describe and understand key processes which take place in soils and are driven by soil biota.

Beneficial Microorganisms in Agriculture

Ram Prasad,Shi-Hong Zhang
Beneficial Microorganisms in Agriculture Book PDF

Author : Ram Prasad,Shi-Hong Zhang
Publisher : Springer Nature
Page : 357 pages
File Size : 48,6 Mb
Release : 2022-07-04
Category : Technology & Engineering
ISBN : 9789811907333

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Beneficial Microorganisms in Agriculture by Ram Prasad,Shi-Hong Zhang Pdf

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.

Genomics and Evolution of Microbial Eukaryotes

Laura A Katz,Debashish Bhattacharya
Genomics and Evolution of Microbial Eukaryotes Book PDF

Author : Laura A Katz,Debashish Bhattacharya
Publisher : OUP Oxford
Page : 256 pages
File Size : 52,8 Mb
Release : 2006-09-07
Category : Science
ISBN : 9780198569749

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Genomics and Evolution of Microbial Eukaryotes by Laura A Katz,Debashish Bhattacharya Pdf

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 majorlineages), 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.

The Pangenome

Hervé Tettelin,Duccio Medini
The Pangenome Book PDF

Author : Hervé Tettelin,Duccio Medini
Publisher : Springer Nature
Page : 311 pages
File Size : 55,9 Mb
Release : 2020-04-30
Category : Science
ISBN : 9783030382810

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The Pangenome by Hervé Tettelin,Duccio Medini Pdf

This open access book offers the first comprehensive account of the pan-genome concept and its manifold implications. The realization that the genetic repertoire of a biological species always encompasses more than the genome of each individual is one of the earliest examples of big data in biology that opened biology to the unbounded. The study of genetic variation observed within a species challenges existing views and has profound consequences for our understanding of the fundamental mechanisms underpinning bacterial biology and evolution. The underlying rationale extends well beyond the initial prokaryotic focus to all kingdoms of life and evolves into similar concepts for metagenomes, phenomes and epigenomes. The book’s respective chapters address a range of topics, from the serendipitous emergence of the pan-genome concept and its impacts on the fields of microbiology, vaccinology and antimicrobial resistance, to the study of microbial communities, bioinformatic applications and mathematical models that tie in with complex systems and economic theory. Given its scope, the book will appeal to a broad readership interested in population dynamics, evolutionary biology and genomics.