By Kassapa Ellepola
Since the invention of the simple microscope and the first observation of microorganisms in a pond water sample by Antonie Van Leeuwenhoek, after more than three centuries of microbial studies, it would be surprising to know that only around 1% of microorganisms has still been isolated and identified. This fact mainly exists due to the presence of ‘Unculturable Microorganisms’ whose culturing techniques has still not been properly understood. Genomic analyses of these organisms are possible only after the isolation of pure cultures. Lack of knowledge in culturing techniques has been a setback for microbiologists throughout the 20th century, until the discovery in the science of ‘Metagenomics’.
Simply ‘Metagenomics’ (Environmental genomics, Ecogenomics or Community genomics) can be referred to as the study of genetic material recovered directly from the environmental samples, instead of from cultures.
The modern aspects of metagenomics first appeared in publication in 1998 and the term was first used by scientists such as Jo Handelsman, Jon Clardy and Robert M. Goodman.
Genetic Material isolated from environmental samples are investigated, classified and is manipulated in metagenomics. This process can be simply summarized into four main steps (see Figure 1) which consists of
- The isolation of genetic material from the environment
- manipulation of the genetic material isolated,
- library construction, and
- finally the analysis of genetic material in the metagenomic library.
In the first step, a representative sample is collected from the environment. The sample contains many different types of microorganisms. Chemical methods such as alkaline conditions or physical methods such as sonication can be used to brake open the cells to free the DNA. The DNA should be separated from the rest of the sample. Using physical and chemical properties of DNA, isolation can be done using density centrifugation, affinity binding, and solubility/precipitation techniques.
The need for manipulation of the genomic DNA, isolated from the organisms is due to the large size of the DNA which makes it extremely hard to handle, especially when introducing into vectors and model organisms. This is achieved through cutting the DNA into smaller, linear fragments using enzymes called ‘Restriction Endonucleases’. (enzymes that cut DNA at a particular sequence of base pairs). Then these small fragments can be ligated into vectors which are small units of DNA used to insert the DNA fragments into the cells. The DNA is transcribed to produce the mRNA and then is translated to produce the proteins. The vectors are designed with a selectable marker which creates abnormal growth ability (such as resistance to a particular antibiotic) in model organisms. This helps the selection of organisms containing vectors and the ones which do not.
The third step is the transformation of the metagenomic DNA containing vector, into cells of a model organism, typically Escherichia coli. This allows the DNA from organisms that would not grow under laboratory conditions to be grown, expressed, and studied. The insertion of foreign DNA into cells and stable expression of proteins is called ‘Transformation’ and it can be achieved through chemical, electrical, or biological methods.
Differently sized metagenomic DNA fragments may exist which has the same restriction enzyme cutting sequence. Although, the vectors are designed in such a way that only one kind of DNA fragments are incorporated from the sample to each individual cell. Different Restriction Endonucleases can be selected to analyze different locations of the metagenome. The transformed cells are then grown on selective media. Cells carrying vectors can be differentiated with a growing colony consisting cloned cells that originate from one single cell. These samples of cell colonies which contain the metagenomic DNA samples on vectors are called a ‘metagenomic library’. These colonies can be used and preserved for future study of the fragments of DNA isolated from the environmental sample.
The DNA from the metagenomic library is analyzed in the fourth and final step of the procedure. The DNA is the material which expresses the characteristics of organisms. DNA determines the physical and chemical properties of organisms. Hence these properties can be employed for many potential methods of analysis. Phenotypic characteristics, such as an unusual color or shape in the model organism are an example of a character in metagenomic analysis. Although chemical properties are not readily observable, performing chemical assay on products created by the model organism leads the way to identification of chemical properties expressed from metagenomic DNA. A change in chemical properties may be due to the model organism incurring enzymatic function which it previously lacked.
The influence of metagenomics has opened doors for research in a variety of fields including agriculture, medical, environmental, earth science and energy.
Microbial communities which inhabit our bodies from in and outside, affect the human health. Investigating the human microbiome and its metagenome may lead to the discoveries in tools and guidelines to human and animal nutrition, drug discovery and preventative medicine. The metagenome may reveal characters such as digesting indigestible components of the diet and also helping in synthesizing essential vitamins and amino acids. Some of the microflora in the gut has the ability to detoxify potentially harmful chemicals contained in food. Some microbes have the ability to defend the body against pathogens. Metagenomics has the ability to derive a stunning array of biologically active chemicals and has helped researchers to learn more about common diseases like obesity.
Metagenomics has a part to play in Earth Science and global change as well. Bacteria have directly influenced the photosynthesis, chemical balance of the earths’ atmosphere and have played a crucial role in the habitability of the planet. Metagenomics has helped scientists to gain an insight of the genetic bases behind achieving complex chemical transformations of a microbial community in the atmosphere and the ocean. It also broadens the knowledge about the biogeochemical cycles and the change of energy and matter.
In the field of Agriculture, metagenomics offers an opportunity to explore how microbial communities together interact with crops and what their role is, in harnessing soil microbial community to produce healthier and more robust crops. Scientists believe that microbial communities have a crucial role to play in suppressing diseases caused by other microbes and therefore metagenomics will reveal the opportunity to study on microbial community characters on crop enhancement.
Communities of microorganisms take part more effectively than single organisms in bioremediation of natural and Xenobiotic compounds. This can be applied to remediation of environmental contaminations such as ground water contamination from gasoline and oil spills in the sea. Metagenomic analysis will help identify the particular community members and their functions which help achieve the full chemical transformations.
A Microbial community convert common agricultural wastes as corn fiber, corn stalks, wheat straw, and other biomass into potential bioenergy sources such as ethanol, hydrogen, methane, butanol, and even electric current. Scientists are trying to manipulate the amount of nutrient availability and environmental conditions to capture and store the useful by-products of such microbes. Metagenomics will open more opportunities to know about how these microbial communities function which would allow scientists to control and channel the energy sources they produce.
Scientific community remains watchful about this new science, which has opened doors to a tremendous amount of scientific exploration, yet to be discovered.
Reference:
· http://dels-old.nas.edu/metagenomics/
· http://www.scq.ubc.ca/metagenomics-the-science-of-biological-diversity/
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