Encyclopedia of Metagenomics

1. 123 of Metagenomics

   • Torsten Thomas, Jack Gilbert, Folker Meyer

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

   • Huaiqiu Zhu

3. Ab Initio Gene Identification in Metagenomic Sequences

   • Shiyuyun Tang, Mark Borodovsky

4. AbundanceBin, Metagenomic Sequencing

   • Yuzhen Ye

5. Abyssal Zone, Metagenomics of

   • Federico M. Lauro, Timothy J. Williams

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

   • Fengzhu Sun, Li Charlie Xia

7. Activated Sludge Metagenomics

   • Ke Yu, Tong Zhang

8. All-Species Living Tree Project

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

9. Analysis of Federal Regulatory Framework on Probiotics, Project

   • Diane Hoffmann

10. Animal Diseases, Applications of Metagenomics

    • Richard Isaacson

11. Antarctic Soil Metagenome

    • Pablo Power, Renaud Berlemont

12. Antibiotic Classes and Mechanisms of Resistance

    • Kimberly M. Carlson-Banning, Lynn Zechiedrich

13. Antibiotic-Associated Diarrhea

    • Casey Theriot, Vincent B. Young

14. antiSMASH

    • Eriko Takano, Rainer Breitling, Marnix H. Medema

15. Approaches in Metagenome Research: Progress and Challenges

    • Heiko Nacke, Rolf Daniel

16. Arbuscular Mycorrhizal Fungi Assemblages in Chernozems

    • Chantal Hamel, Luke D. Bainard, Mulan Dai

17. Bacterial Diversity in a Nonsaline Alkaline Environment

    • António Veríssimo, Igor Tiago

18. Bacterial Diversity in Cases of Lung Infection in Cystic Fibrosis Patients

    • European Cystic Fibrosis Society Lung Microbiome Working Group

19. Bacterial Diversity in Tree Canopies of the Atlantic Forest

    • Marcio R. Lambais, David E. Crowley

20. Bacteriocin Mining in Metagenomes

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

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; http://nihroadmap.nih.gov/hmp/) which has become a world-wide effort, and the Global Ocean Sampling (GOS) surveys; http://www.jcvi.org/cms/research/projects/gos/overview/). 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 to collate all this information in a centralized place. By having all the information in an Encyclopedia form, we have an opportunity to receive 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, via colleges, libraries, and just through online access. This format also allows scientists in the developing world to have continued access to this growing field. 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.

• J. Craig Venter Institute (JCVI), Rockville, USA

  Karen E. Nelson

Dr. Nelson is the Director of Human Microbiology and Metagenomics in the Department of Human Genomic Medicine at the JCVI. Dr. Nelson has extensive experience in microbial ecology, genomics and metagenomics as well as in microbial physiology. Since joining the JCVI legacy institutes, Dr. Nelson has led several genomic and metagenomic efforts. She has also been involved in the analysis of the microbiota of the human stomach and gastrointestinal tract, and more recently led a metagenomics study on fecal material derived from three individuals. Additional ongoing studies in her group include metagenomic approaches to study the ecology of the rumen and corals. 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 90 publications, and is currently Editor-in-Chief of the journal Microbial Ecology. She is also a standing member of the NRC Committee on Biodefense, and a member of the American Society for Microbiology Communications Committee.

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