Metagenomics

Viral metagenomes

In virology, next-generation sequencing has developed into a powerful tool that can be used to detect, identify, and quantify novel viruses in one step. As viruses lack a shared universal phylogenetic marker (as 16S RNA for bacteria and archaea, and 18S RNA for eukarya), the only way to access the genetic diversity of the viral community from an environmental sample is through metagenomics. Viral metagenomes (also called viromes) should thus provide more and more information about viral diversity and evolution.

Human metagenomics

Humans carry ten times more bacterial cells than human cells, and 100 times more bacterial genes than the inherited human genome. The human metagenomics is a strategy to understand the microbial components of the human genetic and metabolic landscape and how they contribute to normal physiology and predisposition to disease. Some subjects of the human metagenomic studies include:

• Antibiotic resistance
• Oral microbiome
• the human gut
• IBD and crohn's disease
• Cystic fibrosis

While the gut microbiome has received much attention, there are an increasing number of studies on other human microbiota, such as vaginal and skin microbiota. The ambitious Human Microbiome Project sampled several different sites on the human body, including nasal passages, oral cavities, skin, gastrointestinal tract, and urogenital tract. The project has increased awareness of the complexity and importance of the metagenome in human health.

Soil metagenomics

The soils in which plants grow are inhabited by microbial communities, with one gram of soil containing around 10^9-10^10 microbial cells which comprise about one gigabase of sequence information. But only a very small portion can be cultured in the laboratory. Microbial ecology continues to lag far behind plant and animal ecology in our ability to resolve large-scale biogeographical patterns in diversity, community composition, and functional attributes. Extensive cross-site sampling coupled with metagenomics will provide a more comprehensive understanding of how soil microbial communities vary across time and space.

Bioremediation

Metagenomics can improve strategies for monitoring the impact of pollutants on ecosystems and for cleaning up contaminated environments. Next-generation sequencing is providing crucial insights into the molecular and biological mechanisms involved in bioremediation of environmental pollutants. These insights will improve microbial bioremediation strategies, monitor their progress, and evaluate their success.

Marine metagenomics

Marine environments, including the subsurface, are believed to contain a total of approximately 3.67 × 1030 microorganisms. With approximately 71% of the earth's surface covered by the ocean, this environment represents 80% of life on earth, and an enormous pool of potential microbial biodiversity and exploitable biotechnology. Marine microbial metagenomic databases presently comprise ∼400 billion base pairs of DNA, only ∼3% of that found in 1 ml of seawater. J Craig Venter Institute (JCVI) is undertaking the global metagenomics of the world’s oceans, they discusses the Global Ocean Sampling expedition and analyses performed on the resulting data.

Biofuels and biocatalysts

A primary focus of the biofuel field is the breakdown of lignocellulosic plant material due to its sheer abundance and low commercial value. Microbial enzymes have many known applications as biocatalysts. However, only a few are currently employed for biocatalysis, even though an annotated collection of more than 190 billion bases is available in metagenome sequence databases.

Reference:

1. Gilbert JA, Dupont CL., Microbial metagenomics: beyond the genome. Ann Rev Mar Sci. 2011;3:347-71.
2. Kristensen, David M., et al. "New dimensions of the virus world discovered through metagenomics." Trends in microbiology 18.1 (2010): 11-19.
3. Foxman B. and Rosenthal M. (2013) Implications of the human microbiome project for epidemiology. Am J Epidemiol 177: 197-201
4. Curtis T. P. and Sloan W. T. (2005) Microbiology. Exploring microbial diversity--a vast below. Science 309: 1331-1333
5. Fierer N., Leff J. W., Adams B. J., Nielsen U. N., Bates S. T., et al. (2012) Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc Natl Acad Sci U S A 109: 21390-21395
6. Desai C., Pathak H. and Madamwar D. (2010) Advances in molecular and "-omics" technologies to gauge microbial communities and bioremediation at xenobiotic/anthropogen contaminated sites. Bioresour Technol 101: 1558-1569
7. ilbert JA, Dupont CL., Microbial metagenomics: beyond the genome. Ann Rev Mar Sci. 2011;3:347-71.
8. Fernandez-Arrojo L., Guazzaroni M. E., Lopez-Cortes N., Beloqui A. and Ferrer M. (2010) Metagenomic era for biocatalyst identification. Curr Opin Biotechnol 21: 725-733