Preface

The advances in molecular biology, sequencing techniques, and data analysis tools in the past two decades have resulted in the evolution of metagenomics and enabled the study of uncultured organisms from different environments. Metagenomic analysis of the high-throughput sequences of a community sample has extended our understanding of the diversity, evolution, and functions of different organisms. This newly emerging science, which is one of the fastest developing fields in biology, is making important contributions to the fields of microbial ecology, bioremediation, discovery of industrial bioproducts, health, and many other areas.

This book is for the students starting their research projects in the field of metagenomics, for researchers interested in the new developments and applications in this field; and for teachers involved in teaching this subject. The book is divided into three sections as indicated from its title, namely; the basics of metagenomics, metagenomic analysis, and applications of metagenomics. It covers the basics of metagenomics from its history and background, to the analysis of metagenomic data as well as its recent applications in different fields. The book contains excellent texts at both the introductory and advanced levels, that describe the latest metagenomic approaches and applications, from sampling to data analysis for taxonomic, environmental, and medical studies.

The first chapter in this book, the introductory chapter, is a brief introduction on the basics of metagenomics, its background, and the metagenomic approaches. In the second chapter, the background on the application of different cultureindependent techniques and metagenomics to study the microflora of the changing environment of soil is introduced.

It is very important for students and researchers to understand the methods they are going to use in their research. With that in mind, the next section is on methodologies and data analysis. In Chapter 3, an overview of the different sequencing techniques is presented in terms of principles, advantages, and limitations. In addition, third-generation sequencing technologies are also addressed. Chapter 4 focuses on different available bioinformatic tools that are suitable for studying symbiosis and coevolution processes in any given sample. Chapter 5 addresses the current methodologies to carry out community structure profiling, using single-copy markers and the small subunit of the rRNA gene to measure phylogenetic diversity from next-generation sequencing data. Interestingly, this chapter also presents a compendium of open source tools, easy to use by biologists and non-specialists to study microbial diversity in a phylogenetic context.

The last section of the book highlights the applications of metagenomics in different areas. Chapter 6 presents a complete analysis of the microbial diversity in the polar glacier habitats and an overview of the metabolic potentials and biogeochemical cycles in these interesting and less-studied ecosystems. In Chapter 7 the current state and the future implications of studying intestinal microbiota associated with migratory birds are described. The authors of this chapter discussed the use of next-generation sequencing to comprehensively analyze the intestinal

microbiota of migratory birds, research on microbial communities traveling over long distances, that provides valuable information for the medical care, livestock industry, agriculture, and human health risks. Finally, in Chapter 8, the application of metagenomics as an emerging tool in aquaculture is discussed. This actual and potential application of metagenomics in aquaculture helps to understand the hosts-microbiota-pathogen-environment relationship underlying disease outbreaks and could be a key to develop strategies to improve productivity by increasing resistance to diseases and reducing the use of antibiotics with their negative environmental impact.

At the end, I would like to thank all the contributors for sharing their expertise in the field of metagenomics and for the appreciated academic integrity. I would like also to thank the reviewers for their precious time.

On behalf of all authors, I would like to warmly thank Ms. Sara Debeuc, the author service manager of this book, for her commitment, patience, and keen assistance which made this book possible. Our thanks are also extended to other staff of IntechOpen for their support.

Finally, the publication of this book was an interesting journey for me and I hope that the readers will enjoy reading it. I also hope this book will achieve its goals by contributing positively to the research community.

> **Wael N. Hozzein** Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt

Section 1
