Metagenomics is the genomic analysis of microbial communities directly from environmental samples. While regular microbial genome analysis requires cultivation of the cultures in the lab, metagenomics does not. This type of analysis is initiated by the isolation of DNA from environmental samples. It also generates very useful information about previously unknown genes. There are several strains of bacteria that are capable of degradation of xenobiotic compounds distributed in the nature. They breakdown a variety of compounds and hence keep evolving. This makes environmental samples critical bioremediation agents.
When the environmental sample is from some contaminated site, then it is quite possible that the microbes present in it are capable of utilizing those materials. This makes it rather easy to study the gene involved in this process. But, before the samples can be analyzed, the amount of genes present in it has to be concentrated. For this, the samples can be enriched with those same compounds. This allows much better expression of the genes and hence makes analysis easy.
The current interest in metagenomics arises from the realization that the presence of a majority of the microbial community in the environment was not known. rRNA based studies have found that less that 1% of the microbial population present in the environment are cultured in the laboratories. By studying the metagenome, suddenly there is access to a huge variety of the genes present in the environment. The available genetic information is present in both culturable as well as unculturable bacteria. It is possible that the unculturable bacteria have more potential for degradation and metagenomic techniques give access to these metabolic processes that are as yet unexplored.
It has the capacity to sequence almost the whole genome from the environment. While directly collecting DNA from such sources, the species and number of colonies are not monitored and hence, the least populous strains are the most under-represented in the final sequencing results. To avoid this problem, a large amount of the sample would be required so that even the most underrepresented colonies can be included. Also shotgun sequencing techniques may be employed to include almost all the organisms and strains present.
Cloning libraries can be built and analysed to indicate what genes are available in the sample. This also provides information on what organisms are present in the sample and what metabolic processes they may be associated with. Metagenomic studies can be utilized to develop ideas for reducing the effect of pollutants on the environment and also to aid in cleaning up the polluted ecosystems. Increased knowledge of the interaction of microbes with pollutants and xenobiotics is aiding in the assessment of their ability to help degrade these chemicals and improve the chances of the contaminated sites to recuperate from the pollution.
Studying these microbes and new genomes and their effect on the human body can help diagnose illnesses and also give an unexpected boost to medical research, treatment and prevention studies. Since these microbes may have been unculturable, their role in certain diseases may not be known. Metagenomics can help solve these puzzles. These microbes can function as efficient tools in bioremediation efforts like cleaning up of oil spills, sewage, waste water, nuclear waste etc without producing harmful by products and help clean up the environment. Studying the microbes that live and function in close association with plants and especially, crops, can help prevent crop diseases and even aid in improving the known and previously unknown symbiotic relations between these plants and microbes. Microbial living processes and metabolic pathways can be harnessed to generate renewable forms of energy, at low costs. Learning how microbes affect the air, environmental conditions, soil and oceans may help predict global changes and probably even prevent them. Also study of these new genomes may solve some evolutionary blanks that have been left unfilled due to the unculturable nature of these microbes. Studying potential dangerous pathogens may even help prevent bio-terror attacks and threats in the future.
Also, metagenomic analysis has unearthed a rich pool of previously unknown genes, proteins and other biological compounds. This can favorably impact almost every field- pharmaceuticals industry, medical research, agricultural, environmental, remediation efforts and chemicals manufacturing- all over the world. The possibilities are endless.
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