Microbial Metagenomics: Beyond the Genome
- 15 January 2011
- journal article
- review article
- Published by Annual Reviews in Annual Review of Marine Science
- Vol. 3 (1), 347-371
- https://doi.org/10.1146/annurev-marine-120709-142811
Abstract
Metagenomics literally means “beyond the genome.” Marine microbial metagenomic databases presently comprise ∼400 billion base pairs of DNA, only ∼3% of that found in 1 ml of seawater. Very soon a trillion-base-pair sequence run will be feasible, so it is time to reflect on what we have learned from metagenomics. We review the impact of metagenomics on our understanding of marine microbial communities. We consider the studies facilitated by data generated through the Global Ocean Sampling expedition, as well as the revolution wrought at the individual laboratory level through next generation sequencing technologies. We review recent studies and discoveries since 2008, provide a discussion of bioinformatic analyses, including conceptual pipelines and sequence annotation and predict the future of metagenomics, with suggestions of collaborative community studies tailored toward answering some of the fundamental questions in marine microbial ecology.This publication has 137 references indexed in Scilit:
- Predicting protein crystallization propensity from protein sequenceJournal of Structural and Functional Genomics, 2010
- Metabolic streamlining in an open-ocean nitrogen-fixing cyanobacteriumNature, 2010
- A phylogeny-driven genomic encyclopaedia of Bacteria and ArchaeaNature, 2009
- A latitudinal diversity gradient in planktonic marine bacteriaProceedings of the National Academy of Sciences of the United States of America, 2008
- The minimum information about a genome sequence (MIGS) specificationNature Biotechnology, 2008
- Microbial community gene expression in ocean surface watersProceedings of the National Academy of Sciences of the United States of America, 2008
- Quantitative assessment of protein function prediction from metagenomics shotgun sequencesProceedings of the National Academy of Sciences of the United States of America, 2007
- The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciationProceedings of the National Academy of Sciences of the United States of America, 2007
- Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique featuresProceedings of the National Academy of Sciences of the United States of America, 2006
- Microbial biogeography: putting microorganisms on the mapNature Reviews Microbiology, 2006