Encyclopedia of Metagenomics

Encyclopedia of Metagenomics Karen E. Nelson Editor Encyclopedia of Metagenomics Genes, Genomes and Metagenomes: Basics, Methods, Databases and Tools With 216 Figures and 64 Tables Editor Karen E. Nelson J. Craig Venter Institute Rockville, MD, USA ISBN 978-1-4899-7477-8 ISBN 978-1-4899-7478-5 (eBook) ISBN 978-1-4899-7479-2 (print and electronic bundle) DOI 10.1007/978-1-4899-7478-5 Springer New York Heidelberg Dordrecht London Library of Congress Control Number: 2014954611 # Springer Science+Business Media New York 2015 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher’s location, in its current version, and permission for use must always be obtained from Springer. Permissions for use may be obtained through RightsLink at the Copyright Clearance Center. Violations are liable to prosecution under the respective Copyright Law. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. While the advice and information in this book are believed to be true and accurate at the date of publication, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made. The publisher makes no warranty, express or implied, with respect to the material contained herein. Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com) Preface Welcome to the Encyclopedia of Metagenomics. It is anticipated that the Encyclopedia will become a resource for tools, tool development and all things metagenomic. Volume 1 encompasses Genes, Genomes and Metagenomes. It covers a range of approaches to conduct metagenomics surveys including descriptions of analysis tools. Several of these approaches, including databases, have been under development from the beginning of the metagenome era and are enabling the analysis and interpretation of large microbial data sets from various environments. “Genes, Genomes and Metagenomes” also covers DNA extraction, various cloning and sequencing approaches, quality control and experimental designs: all essential components of the microbiome and metagenomic sequencing process. These approaches have continued to evolve and be refined, and several improvements have been incorporated over the past few years. This has also been driven by a switch to next-generation sequencing (NGS) platforms including Ion Torrent, 454 and various Illumina technologies. Post-sequencing genome assembly, alignment tools, gene prediction and annotation are also critical to successful data interpretation. Deeper dives in Vol. 1 discuss codon usage, clustering programs and functional gene characterization. MD, USA Karen E. Nelson September 2014 v About the Editor Dr. Karen E. Nelson is the President of the J. Craig Venter Institute (JCVI). Prior to being appointed President, Dr. Nelson held a number of other positions at the Institute including Director of JCVI’s Rockville Campus and Director of Human Microbiology and Metagenomics in the Department of Human Genomic Medicine at the JCVI. She is also a Professor at JCVI with an active research program in genomics and metagenomics. Dr. Nelson has led several genomic and metagenomic efforts including those of several reference microbial genomes and the first human metagenomics study that was published in 2006. Additional ongoing studies in her group include metagenomic approaches to study the ecology of the gastrointestinal tract of humans and animals, studies on the relationship between the microbiome and various human and animal disease conditions, reference genome sequencing and analysis primarily for the human body, and other omics studies. Dr. Nelson also heads the microbiome group at Human Longevity Inc., which was recently formed in La Jolla, California. Dr. Nelson received her undergraduate degree from the University of the West Indies and her Ph.D. from Cornell University. She has authored or coauthored over 100 peer-reviewed publications and edited three books and is currently Editor-in-Chief of the journal Microbial Ecology. She also serves on the Editorial Boards of BMC Genomics, GigaScience, and the Central European Journal of Biology. She is also a standing member of the NRC Committee on Biodefense, a member of the National Academy of Sciences Board of Life Sciences, and a Fellow of the American Academy of Micro- biology. She was recently appointed an Honorary Professor at the University of the West Indies. vii Contributors Takashi Abe Graduate School of Science and Technology, Niigata University, Niigata, Japan Yutaka Akiyama Department of Computer Science, Tokyo Institute of Technology, Meguro-ku Tokyo, Japan Rudolf Amann Molecular Ecology Group, Max Planck Institute for Marine Microbiology, Bremen, Germany Jaime Henrque Amorim Universidade Estadual de Santa Cruz, Laborato´rio de Biotecnologia Microbiana, Ilheús, BA, Brazil Luke D. Bainard Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada Annalisa Ballarini Laboratory of Microbial Genomics, Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy Navneet Batra Department of Biotechnology, GGDSD College, Chandigarh, India Arvind Behal Department of Biotechnology, GGDSD College, Chandigarh, India Robert G. Beiko Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada Terrence H. Bell Department of Natural Resource Sciences, McGill University, Sainte–Anne–de–Bellevue, QC, Canada Johan Bengtsson-Palme Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Go¨teborg, Sweden Nicholas H. Bergman National Biodefense Analysis and Countermeasures Center, Frederick, MD, USA Sonu Bhatia Department of Biotechnology, GGDSD College, Chandigarh, India Kai Blin Interfakult€ares Institut fur€ Mikrobiologie und Infektionsmedizin Tubingen,€ Mikrobiologie/Biotechnologie, Eberhard-Karls Universit€at, Tubingen,€ Germany ix x Contributors Herve´ M. Blottie`re INRA, AgroParisTech, Jouy en Josas, France MetaGenoPolis, INRA, Jouy en Josas, France Paul L. E. Bodelier Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands Germán Bonilla-Rosso Laboratorio de Evolucioń Molecular y Experimental, Instituto de Ecologıá UNAM, Universidad Nacional Autońoma de Me´xico, Mexico City, Mexico Mark Borodovsky Joint Georgia Tech and Emory Wallace H Coulter Department of Biomedical Engineering, Center for Bioinformatics and Computational Genomics, Atlanta, GA, USA Yan Boucher Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada Jean-Luc Bouchot Department of Mathematics, Drexel University, Philadelphia, PA, USA Rainer Breitling Manchester Institute of Biotechnology, University of Manchester, Manchester, UK Florence Busato Laboratory for Epigenetics and Environment, Centre National de Geńotypage, CEA- Institut de Geńomique, Evry, France Brandi Cantarel Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA Rebecca J. Case Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada Patrick Chain Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA Chon-Kit Kenneth Chan Department of Mechanical Engineering, The University of Melbourne, Melbourne, VIC, Australia Trevor C. Charles Department of Biology, University of Waterloo, Waterloo, ON, Canada Chao Chen Dalian University of Technology, Dalian, China Liangyu Chen Dalian University of Technology, Dalian, China Tsute Chen Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA Francis Y. L. Chin Department of Computer Science, The University of Hong Kong, Hong Kong, China Marco Cosentino Lagomarsino Computational and Quantitative Biology, University Pierre et Marie Curie, Paris, France CNRS, Paris, France Contributors xi Paul Cotter Teagasc Food Research Centre, Moorepark, Fermoy, Co., Cork, Ireland Alimentary Pharmabiotic Centre, University College, Cork, Ireland Pedro Coutinho Centre National de la Recherche Scientifique & Aix- Marseille Universite´, Marseille, France Don Cowan Centre for Microbial Ecology and Genomics (CMEG), Genome Research Institute (GRI), University of Pretoria, Hatfield, Pretoria, South Africa David E. Crowley Enviromental Sciences, University of California, Riverside, Riverside, CA, USA Mulan Dai Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada Rolf Daniel Institute of Microbiology and Genetics, Georg–August– University Go¨ttingen, Go¨ttingen, Germany Colin Davenport Hannover Medical School,

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