Metagenomics

Metagenomics (also Environmental Genomics or Community Genomics) is the study of genomes recovered from environmental samples as opposed to from clonal cultures. This relatively new field of genetic research allows the genomic study of organisms that are not easily cultured in a laboratory. Early molecular work prior to the founding of metagenomics was conducted by Norm Pace and colleagues, who used PCR to explore the diversity of 16S sequences from organisms present in uncultured environmental samples by amplifying related sequences. Considerable effort was applied to ensure that these were not PCR false positives and supported the existence of a complex community of unexplored species. Although this methodology was limited to exploring highly conserved, non-protein coding genes, it did support early microbial morphology based observations that diversity was far more complex than was known by culturing methods.

Metagenomics was first conceived and practiced by Jay M. Short, head of research and a founder of Diversa Corporation, at least as early as 1994. Short published articles, and filed and was issued many U.S. patents on the discovery of genes, gene pathways and their products from gene libraries made from communities of uncultured organisms, using a variety of functional and sequence based methods for screening. Following earlier patent filings, one of the earlier publications related to Short’s inventions appeared in SIM News (46:3-8) in 1996 and was titled “The Discovery of New Biocatalysts from Microbial Diversity”. There are over a dozen of publications and patents between 1996 and 2005, one of the latest appearing in 2005 in Science (308:554-557) entitled “Comparative Metagenomics of Microbial Communities”.

The term "metagenomics" was first used by Jo Handelsman and others in the University of Wisconsin Department of Plant Pathology, and appeared in publication in 1998 (see references below). Kevin Chen and Lior Pachter (researchers at the University of California, Berkeley) defined metagenomics as "the application of modern genomics techniques to the study of communities of microbial organisms directly in their natural environments, bypassing the need for isolation and lab cultivation of individual species."

Sequences from environmental samples

Conventional sequencing begins with a culture of identical cells as a source of DNA. However early metagenomic studies revealed that there are probably large groups of microorganisms in many environments that cannot be cultured and thus cannot be sequenced. These early studies focused on 16S ribosomal RNA sequences which are relatively short, often conserved within a species, and generally different between species. Many 16S rRNA sequences have been found which do not belong to any known cultured species, indicating that there are numerous unisolated organisms out there.

Recovery of DNA sequences longer than a few thousand base pairs from environmental samples was very difficult until recent advances in molecular biological techniques, particularly related to constructing libraries in bacterial artificial chromosomes (BACs), provided better vectors for molecular cloning. In addition, advances in bioinformatics, refinements of DNA amplification, and proliferation of computational power have greatly aided the analysis of DNA sequences recovered from environmental samples by metagenomics. A 2004 metagenomic study of the Sargasso Sea found DNA from nearly 2000 different species including 148 types of bacteria never seen before. Another study, also from 2004, revealed the genomes of bacteria and archaea from an acid mine drainage system that had resisted attempts to culture them.

Because the collection of DNA from an environment is largely uncontrolled, large samples, often sometimes prohibitively so, are needed to fully resolve the genomes of underrepresented members of a microbial community. On the other hand, many such underrepresented organisms might never be noticed without metagenomic analysis if they are difficult to isolate using traditional culturing techniques.

Community metabolism

Many bacterial communities show significant division of labor in metabolism. Waste products of some organisms are metabolites for others. Working together they turn raw resources into fully metabolised waste. Using comparative gene studies and expression experiments with microarrays or proteomics researchers can piece together a metabolic network that goes beyond species boundaries. Such studies require detailed knowledge about which versions of which proteins are coded by which species and even by which strains of which species. So, community genomic information is fundamental to the study of how metabolites move through a community to be processed.

References

• Chen K, Pachter L (2005) Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Comp Biol 1(2): e24.
• Handelsman J. (2004). Metagenomics: application of genomics to uncultured microorganisms. Microbiology and Molecular Biology Reviews 68:669-685.
• Tyson et al. (2004). Insights into community structure and metabolism by reconstruction of microbial genomes from the environment. Nature 428:37-43.
• Venter et al. (2004). Environmental Genome Shotgun Sequencing of the Sargasso Sea. Science 304:66-74.
• Rodriguez-Valera. (2004). Environmental genomics, the big picture?. FEMS Microbiology Letters 231:153-158.
• Diversa Corporation (2004). Diversa Scientists First to Link Protein Function to Genetic Sequence Information Derived from Complex Microbial Communities. April 21st Press Release.
• Diversa Corporation (2003). Diversa and Department of Energy’s Joint Genome Institute Announce Large-scale Microbial Sequencing Collaboration. May 5th Press Release.
• Handelsman et al. (1998). Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chemistry Biology 5:R245-R249.
• Short, JM (2001) Sequence Based Screening. U.S. Patent Number 6,455,245.
• Short, JM (1997) Screening Methods for Enzymes and Enzyme Kits. U.S. Patent Number 6,168,919.
• Short, JM (1997) Protein Activity Screening of clones having DNA from Uncultured Microorganisms. U.S. Patent Number 5,958,672.
• Short, JM (1997) Production of Enzymes Having Desired Activities by Mutagenesis. U.S. Patent Number 5,939,250.
• Short, JM (1997) Recombinant Approaches for Accessing Biodiversity. Nature Biotechnology 15:1322-1323