Metagenomics is a rapidly growing field of research that has had a dramatic effect on the way we view and study the microbial world. By permitting the direct investigation of bacteria, viruses and fungi irrespective of their culturability and taxonomic identities, metagenomics has changed microbiological theory and methods and has also challenged the classical concept of species. This new field of biology has proven to be rich and comprehensive and is making important contributions in many areas including ecology, biodiversity, bioremediation, bioprospection of natural products, and in medicine.
This book addresses in a coherent manner the diverse and multiple aspects of metagenomics and the multiplicity of its potential applications. Renowned authors from around the world have contributed chapters covering the new theoretical insights, the more recent applications, and the dynamically developing methods of data acquisition and analysis. Topics include: Conceptual frameworks, tools and methods, integration of complementary approaches, horizontal gene transfer, analysis of complex microbial communities, public data resources, plant-microbe interactions, bioremediation, industrial bioproducts, archaeal metagenomics, bioprospecting novel genes, the human microbiome, and philosophical themes in metagenomics.
The book is essential reading for all researchers currently performing metagenomics studies and is highly recommended for all students and scientists wishing to increase their understanding of this field.
Chapter 1 Metagenomics and Ecosystems Biology: Conceptual Frameworks, Tools, and Methods
Jianping Xu
Metagenomic analyses of natural biological communities are revolutionizing our understanding of the diversity, function, and inter-relationships among organisms in diverse ecological niches. The rapid advancements in metagenomics are largely due to the technical and analytical methods developed from high throughput platforms for cloning, DNA sequencing, robotics, high-density microarrays, 2D-gel electrophoresis, and mass spectrometry as well as associated bioinformatics softwares. In this chapter, I summarize a general framework of broad-sense metagenomics. The specific areas as well as the tools used are highlighted for identifying diversity, searching for novel genes and gene products, and investigating relationships among genes, mRNAs, and proteins in microbial communities. Of special notes are the recent developments in single cell isolation, whole-genome amplification, pyrosequencing, and database warehousing and the potential impact of these developments on our future understandings of microbial communities in nature. These exciting developments are bringing the dawn of a new era in biology, that of ecosystems biology.
Chapter 2 Beyond Metagenomics: Integration of Complementary Approaches for the Study of Microbial Communities
Andrés Cubillos-Ruiz, Howard Junca, Sandra Baena, Ivonne Venegas and María Mercedes Zambrano
Advances in genomics have had a great impact on the field of microbial ecology. Metagenomics in particular holds great promise for accessing and characterizing microbial communities. However, the high diversity and level of complexity present in microbial communities represent an obstacle to understanding these assemblages given the current approaches. The integration of microbial community structure with function, taking into account uncultured microbes in diverse environments, remains particularly challenging. The anticipated increase in metagenomic data available in the future will require high-throughput methods for data management and analysis of these large and complex microbial communities. Integration of complementing technologies like microarrays, high throughput sequencing and bioinformatics and of novel tools and "meta² approaches, such as metaproteomics, metatranscriptomics and meta-metabolomics, will be required to understand the role of microbes in different ecological habitats. In spite of the many challenges, the field offers promising perspectives for achieving a more comprehensive view of microbial communities and how microorganisms adapt to and function within their ecosystems.
Chapter 3 Horizontal Gene Transfer in Prokaryotic Microbiomes
Javier Tamames and Alex Mira
Horizontal Gene Transfer (HGT) is a very important force driving the evolution of prokaryotic species, since it allows the acquisition of new genes that can facilitate the adaptation to different environments and conditions. The availability of metagenomic sequencing can help to understand how HGT relates to community composition and environmental factors. Nevertheless, metagenomic sequences have particular characteristics that are not especially appropriate for the study of HGT, mainly their short length and their unknown origin. We describe here some methods to analyse the extent and nature of HGT in bacterial metagenomes, and study real-case examples of gene transfer in metagenomic sequences. The results show that the extent of HGT is influenced by the physical and ecological features of the environment.
Chapter 4 Analysis of Complex Microbial Communities Through Metagenomic Survey
María-Eugenia Guazzaroni, Peter N. Golyshin and Manuel Ferrer
Microbes are important for the Earth System, playing a very important role in maintaining the wellbeing of our global environment. Despite the obvious importance of microbes, very little is known of their diversity, how many species are present in the environment, and what each individual species does i.e. its ecological function. Until recently, there were no appropriate techniques available to answer these important questions. The vast majority of these organisms cannot be cultured in the laboratory and so were not amenable to study by the methods that had proved so successful with known microorganisms throughout the 20th century. It was only with the development of high-throughput technology to analyze and sequence DNA from the natural environment that information began to accumulate that demonstrated the exceptional diversity of microbes in Nature in fact, most microbes are entirely novel and have not previously been described. Following on from this, in this chapter we provide an analysis of the basic aspect of culture-independent tools to study microbial communities, the methods available to isolate environmental DNA and to establish metagenomic libraries which can further be used for extensive activity screens, and a number of the recent applications of this technology.
Chapter 5 Public Data Resources as the Foundation for a Worldwide Metagenomics Data Infrastructure
Guy Cochrane, Maria J. Martin and Rolf Apweiler
The public data resources serving nucleotide and protein sequence, functional annotation and sampling information provide the foundation for a worldwide bioinformatics data infrastructure. The traditional paradigm of genomic-level studies on isolated and identified organisms lies at the centre of these data resources. While metagenomics takes advantage of this existing paradigm, new methods and concepts are also required to rise to the many novel challenges presented by metagenomic data. In this chapter, we cover primary raw nucleotide sequencing data repositories, the annotated nucleotide sequence databases and the management of protein information from metagenomics studies, taking as example resources the European Nucleotide Archive and the UniProt Universal Protein Resource. We provide details of the information that is available from these resources, tools that support the use of the information, resources for data providers and the analytical pipelines that enrich these largely unannotated datasets.
Chapter 6 The Potential for Investigation of Plant-microbe Interactions Using Metagenomics Methods
Trevor Charles
The interactions between microbes and plants make the major contribution to the biotic components of soils, the most diverse habitats on Earth. Plants play central roles in providing nutrient input into the soil, both through microbially-mediated decomposition of plant matter, and through the direct provision of photosynthate derived root exudates. These nutrients support large and diverse microbial communities, many of which provide direct benefit to the plant. The interplay between plants and their microbial co-habitants is regulated by extensive chemical signalling. Most of what we know about these complex community interactions has been derived through study of organisms in pure culture, but it is well known that the vast majority of microbes have not been cultivated. We now have the opportunity to explore the interactions between plants and microbes through cultivation independent study of the microbial communities. While high-throughput DNA sequence analysis will be an important tool for these studies, the immense richness and diversity of such communities present a strong mandate for the use of functional metagenomics strategies that involve a broad variety of screening methodologies to discover and study the currently unknown key biological processes.
Chapter 7 Application of Metagenomics to Bioremediation
Isabelle George, Benoît Stenuit and Spiros Agathos
In this chapter, we discuss the potential of metagenomics to boost the development of improved strategies for monitoring the impact of pollutants on ecosystems and for cleaning up contaminated environments. Increased understanding of how microbial communities cope with pollutants could help to assess the potential of contaminated sites to recover from pollution and increase the chances of bioaugmentation or biostimulation trials to succeed. Moreover, by providing direct access to the pool of environmental genomes without the bias of cultivation, metagenomics offers the possibility to explore the vast diversity of degradation pathways of environmental microorganisms, which remain to a large extent poorly characterized (if not totally unknown). This could lead, among others, to the design of more efficient customized strains/consortia for targeted use in bioremediation applications. Finally, we provide an overview of the obstacles encountered in the implementation of metagenomic-based knowledge into field applications and propose solutions to facilitate such a technology transfer.
Chapter 8 Applications of Metagenomics for Industrial Bioproducts
Dominic Wong
Recent progress in mining the rich genetic resource of non-culturable microbes has led to the discovery of new genes, enzymes, and natural products. The impact of metagenomics is witnessed in the development of commodity and fine chemicals, agrochemicals and pharmaceuticals where the benefit of enzyme-catalyzed chiral synthesis is increasingly recognized. Recovery of metabolic pathways and gene clusters involved in biosynthesis of antibiotics and bioactive molecules has increased the prospect of identifying useful natural and synthetic products for drug development. The discovery of biocatalysts operating optimally with high efficiency in conditions amenable to industrial processes requirements are key to successful development of food products, detergent additives, bioactive compounds, fuel alcohol and biodiesel, as well as optically active intermediates for chemical and drug synthesis.
Chapter 9 Archaeal Metagenomics: Bioprospecting Novel Genes and Exploring New Concepts
Alexander M. Cardoso, Maysa M. Clementino, Janaína J.V. Cavalcante, Ricardo P. Vieira, Rodolpho M. Albano and Orlando B. Martins
Microorganisms are responsible for sustaining life on Earth but how they do so is still poorly understood. The readily cultured microorganisms represent only 0.1% to 1% of the total microbial communities present in most habitats. Until the advent of metagenomics tools, which allow the investigation of microorganisms that cannot be cultured in the laboratory, we were unable to study the entire genetic makeup from particular environments, thereby losing a fruitful source of microbial biodiversity and functional novelties. Within microbial communities, the archaeas harbour an excellent repertoire of novel genes for biotechnological applications and represent a key step for understanding evolution and to comprehend metabolic pathways. In this chapter, we used selected examples of archaeal metagenomics to illustrate the impact of metagenomics on our current understanding of microbial ecology and its potential implications for future research.
Chapter 10 Metagenomics and Its Applications to the Study of the Human Microbiome
Karen E. Nelson and Bryan A. White
Genomics came of age when we began to witness a greater level of microbial diversity within species than previously anticipated. This laid the foundation for generating genomic sequence data from whole environments without first using a culturing step, a field of research now known as "metagenomics². The term metagenomics was first used in the late 1990's, and was defined as the genomic analysis of microorganisms by direct extraction and cloning of DNA from an assemblage of microorganisms. The availability of "next generation² sequencing technologies such as 454 pyrosequencing have made it such that a cloning step is no longer essential for metagenomic projects (see http://www.454.com/). The National Institutes of Health launched a Human Microbiome initiative (http://nihroadmap.nih.gov/hmp/) with primary goals to determine if there is a core human microbiome, to understand the changes in the human microbiome that can be correlated with human health, and to develop new technological and bioinformatics tools to support these goals. Initial sequencing initiatives for this program are in place and include metagenomic sequencing to characterize the microbial communities from 15-18 body sites from at least 250 individuals. This effort has expanded to become a worldwide initiative and will be described in this chapter.
Chapter 11 Philosophical Themes in Metagenomics
Maureen O'Malley and John Dupré
From a philosophical point of view, metagenomics offers a wealth of ontological and epistemological insights. Ontologically, metagenomics has implications for how we understand biological entities and their functions, as inquiry extends from more traditionally bounded entities, such as molecules and organisms, to multi-level communities interacting with planetary chemistry and geology. We will focus in particular on how metagenomics affects concepts of organism and living entity, and the connections between the older notion of superorganism and the emerging one of metaorganism. When examined within an evolutionary framework, the concepts of metagenome and metaorganism may also transform the way in which evolutionary processes are understood, especially in regard to the nature of competitive and cooperative interactions between different entities. In addition to generating fundamental questions about biological ontology, metagenomics is leading a transformation of standard life-science epistemology into multi-level systems-based understanding. Metagenomics also raises questions about the relationships between hypothesis-driven and data-driven science, and how biological meaning develops out of metagenomic sequence. Overall, we conclude, metagenomics is a scientific approach that vindicates pluralism and has profound philosophical implications for fields within and without the life sciences.