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Environmental shotgun sequencing

Part 2. Genomics

2.5. Bacteria and Other Pathogens

Short Specialist Review

  1. Gene W. Tyson1,
  2. Philip Hugenholtz2

Published Online: 15 APR 2005

DOI: 10.1002/047001153X.g205313

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Tyson, G. W. and Hugenholtz, P. 2005. Environmental shotgun sequencing. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 2:2.5:65.

Author Information

  1. 1

    University of California, Berkeley, CA, USA

  2. 2

    Department of Energy Joint Genome Institute, Walnut Creek, CA, USA

Publication History

  1. Published Online: 15 APR 2005

Abstract

Shotgun sequencing of microbial communities is a promising means for delving into community function and interactions, population structure and dynamics, and bypassing the cultivation bottleneck in microbiology. However, this approach is mostly blind to low-abundance species as it effectively samples only the dominant populations in a community. It also faces a number of technical challenges such as the assembly and separation of individual genomes from a mixture of genomic fragments compounded by sampling unevenness and data scalability. Despite these limitations, environmental shotgun sequencing should rapidly advance the fields of microbial ecology and evolution.

Keywords:

  • microbial ecology and evolution;
  • communities;
  • shotgun sequencing;
  • genome assembly