Encyclopedia of Metagenomics

1. Front Matter

   Pages i-xxi

   PDF

2. A

   1. A 123 of Metagenomics

      • Torsten Thomas, Jack Gilbert, Folker Meyer

      Pages 1-9

   2. A De Novo Metagenomic Assembly Program for Shotgun DNA Reads

      • Huaiqiu Zhu

      Pages 10-12

   3. Ab Initio Gene Identification in Metagenomic Sequences

      • Shiyuyun Tang, Mark Borodovsky

      Pages 13-19

   4. AbundanceBin, Metagenomic Sequencing

      • Yuzhen Ye

      Pages 19-21

   5. Accurate Genome Relative Abundance Estimation Based on Shotgun Metagenomic Reads

      • Fengzhu Sun, Li Charlie Xia

      Pages 21-25

   6. All-Species Living Tree Project

      • Pablo Yarza, Raul Munoz, Jean Euzéby, Wolfgang Ludwig, Karl-Heinz Schleifer, Rudolf Amann et al.

      Pages 25-33

   7. antiSMASH

      • Eriko Takano, Rainer Breitling, Marnix H. Medema

      Pages 33-38

   8. Approaches in Metagenome Research: Progress and Challenges

      • Heiko Nacke, Rolf Daniel

      Pages 38-43

   9. Arbuscular Mycorrhizal Fungi Assemblages in Chernozems

      • Chantal Hamel, Luke D. Bainard, Mulan Dai

      Pages 43-47

3. B

   1. Bacterial Diversity in Tree Canopies of the Atlantic Forest

      • Marcio R. Lambais, David E. Crowley

      Pages 49-54

   2. Bacteriocin Mining in Metagenomes

      • Orla O’Sullivan, Colin Hill, Paul Ross, Paul Cotter

      Pages 54-60

   3. Binning Sequences Using Very Sparse Labels Within a Metagenome

      • Ching-Hung Tseng, Chon-Kit Kenneth Chan, Arthur L. Hsu, Saman K. Halgamuge, Sen-Lin Tang

      Pages 60-73

   4. Biological Treasure Metagenome

      • Geun-Joong Kim, Ho-Dong Lim

      Pages 73-77

4. C

   1. Carbohydrate-Active Enzymes Database, Metagenomic Expert Resource

      • Brandi Cantarel, Pedro Coutinho, Bernard Henrissat

      Pages 79-84

   2. Challenge of Metagenome Assembly and Possible Standards

      • Matthew B. Scholz, Chien-Chi Lo, Patrick Chain

      Pages 84-93

   3. CLUSEAN, Overview

      • Tilmann Weber, Kai Blin

      Pages 93-95

   4. Computational Approaches for Metagenomic Datasets

      • Colin Davenport

      Pages 95-106

   5. Conserved Regions in 16S Ribosome RNA Sequences and Primer Design for Studies of Environmental Microbes

      • Yong Wang, Pei-Yuan Qian

      Pages 106-110

   6. Culture Collections in the Study of Microbial Diversity, Importance

      • Martin Sievers

      Pages 111-114

Metagenomics has taken off as one of the major cutting-edge fields of research. The field has broad implications for human health and disease, animal production and environmental health. Metagenomics has opened up a wealth of data, tools, technologies and applications that allow us to access the majority of organisms that we still cannot access in pure culture (an estimated 99% of microbial life). Numerous research groups are developing tools, approaches and applications to deal with this new field, as larger data sets from environments including the human body, the oceans and soils are being generated. See for example the human microbiome initiative (HMP) which has become a world-wide effort and the Global Ocean Sampling (GOS) surveys. The number of publications as measured through PubMed that are focused on metagenomics continues to increase. The field of metagenomics continues to evolve with large common datasets available to the scientific community. A concerted effort is needed tocollate all this information in a centralized place. By having all the information in an Encyclopedia form, we have an opportunity to gather seminal contributions from the leaders in the field, and at the same time provide this information to a significant number of junior and senior scientists. It is anticipated that the Encyclopedia will also be used by many other groups including, clinicians, undergraduate and graduate level students, as well as ethical and legal groups associated with or interested in the issues surrounding metagenome science.

• Environmental Health
• Environmental Microbiology
• Genomics
• Host-Microbe Interactions
• Human Microbiome Project

• J. Craig Venter Institute, Rockville, USA

  Karen E. Nelson

Dr. Nelson is the President of the J. Craig Venter Institute (JCVI). Dr. Nelson has extensive experience in microbial ecology, microbial genomics, microbial physiology and metagenomics. Since joining the JCVI legacy institutes, Dr. Nelson has led several genomic and metagenomic efforts and led 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 received her undergraduate degree from the University of the West Indies and her Ph.D. from Cornell University. She has authored or co-authored 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, Giga Science 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 Microbiology.

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