Metagenomics

Metagenomics (English metagenomics ) is a research field of life sciences, which tries to capture the entirety of the genome of a biotope with modern molecular biological methods. For this genome mainly include microorganisms, but also viruses are an important element.

The term metagenomics comes from a combination of the concepts of meta-analysis, a process from the statistics, should be made quantitatively comparable for the different results from different studies, and genomics, the analysis of the complete genetic information ( genome) of an organism.

As metagenome is defined as the totality of the genomic information of the micro-organisms of a particular community ( biocenosis ) or a biotope.

It is generally believed that more than 99% of existing microorganisms and thus can not be cultivated by conventional, classical microbiological methods can not also be identified. Metagenomic methods allow the identification of microorganisms irrespective of their culturability. In addition to the first time allowed insights into the complexity of the physiology and ecology of microorganisms pose metagenomic approaches to the analysis of naturally occurring biodiversity also a huge potential for the identification and development of new biotechnological and pharmaceutical products.

The general procedure of a metagenomic analysis includes the following four steps:

Two general types are tracked by metagenomic studies: functional approaches and sequence- based approaches.

Metagenomic methods

• Functional assays
• DNA microarray analyzes
• PCR with degenerate primers
• In situ hybridization
• 16S rRNA analyzes
• Whole Genome Shotgun Sequencing

Functional metagenomic approaches

The functional metagenomic analysis of environmental samples, the identification of clones associated with specific known properties in the foreground. The active in this respect clones are then sequenced and characterized biochemically. In most cases here is the identification of features in the foreground, which have medicinal, agricultural or industrial relevance. Limitations of this approach arise from the sometimes problematic expression of foreign proteins ( heterologous expression ) in the used "guest organism " (usually Escherichia coli ) and by restriction digestion of the genomic DNA prior to cloning ( see above) do not always guaranteed spatial accumulation ( " clustering " ) of all the genes required for the expression of a particular property. You will also need a simple and feasible in large quantities experimental setup for the identification of the desired property, because the frequency of active clones is usually very low.

Sequence -based metagenomic approaches

While methods such as PCR, or in situ hybridization are carried out on the basis of certain of known DNA sequences which direct extraction, cloning and sequencing of genomic DNA has the advantage of potential isolation of all genes in the organisms occur. The isolation is independent of the sequence or the function of genes and thus also allows the identification of hitherto unknown genes with low or complete absence of sequence homology to existing genes. Further, this sequence -based approach also allows the identification of so-called operon thus spatially coherent accumulation on the genomic DNA of genes which are in a functional relationship and, for example, for the components of certain pathways or synthetic routes encode for enzymes such as for the production of antibiotics. Of course, another object of this sequence- based metagenomic approaches is also the elucidation of whole genomes by combining the individual sequence segments to a pan - genomic sequence using bioinformatics.

The possibilities offered by today's molecular biological methods in order, in particular the arrangements established by the sequencing of the human genome by Craig Venter method of " Whole Genome Shotgun Sequencing ", are impressive by the carried out also by Venter et al. 2004 metagenomics project " Sargasso See ", an area near the Bermuda triangle shown. Sargossa the Lake project presented the public databases more than 1.6 Gb (ie 1.6 billion base pairs! ) in 1.045970 individual entries at the DNA level and 1,001,987 entries potentially of translated proteins. with the results from the completed by Venter et al. project the size of the public protein database Venter et al was doubled at a stroke. . identified more than 69,000 new genes with no apparent homology to known genes. This corresponds to a share of 7% based on the total number of annotated genes of Venter. on average, with each new genome sequencing of about 15-20% identified new protein sequences. Looking at Venter's data with regard to biodiversity, so could be distinguished in the investigated samples at least 1,800 species. However, it is assumed that the habitat is still home to many more species.

Other under planning metagenomics projects is to analyze, for example, the goal of the composition of microbial organisms in urban air ( Venter et al. ) Or the composition of the oral microbial community ( National Institute of Dental and Craniofacial Research).

These figures are impressive proof that the dimension of the still unexplored portion of the world of micro-organisms and show that we are just beginning to scratch the surface of the microbial diversity. They affirm that we are still far from a complete understanding of the ecological relationships in the microbial world, which, though indeed not usually detectable, is still the basis for all life and for the essential in the natural organic and inorganic material cycles are essential.