DNA Sequencing and Fragment Analysis

Archive for October, 2012

Metagenomics: A New Field of Genetics that Focuses on the Community Genome

Genetic research has evolved over the past ten years. The development of next generation sequencing has provided researchers with a tool capable of sequencing an entire microbial genome. Epigenetics is a new field in which science investigates external factors that effect cellular histones – the protein complexes that control gene expression. It has led to new developments in cancer research and treatment. Despite these new technologies, research still has limitations. Currently, less than one percent of bacterial species could be isolated into pure cultures under a laboratory setting. The answer to this problem is another new field in genetic studies called Metagenomics. In Metagenomics, the total microbial content of an environmental sample is isolated together to analyze the communal genome.

What is the Source of Metagenomic Samples

Samples used in Metagenomic studies are taken directly from the environment. The environment could be defined as soil, water, hot spring, or even inside the mouth of an animal. Each sample could harbor numerous species of microbes including bacteria, fungi and virus particles. We will primarily focus on bacteria cells.

Once the sample has been acquired, bacteria are isolated together. Different species are not separated into pure cultures. Because the environmental sample is unique in terms of mineral content, moisture, pH and other factors, the species of bacteria are related by their ability to grow in this environment. It is believed that the environment in some way shapes genetic development and expression similarly in different species. Therefore, each bacterial type shares basic genetic patterns.

How Are Environmental Species Analyzed

Once the bacteria have been separated from the environmental sample, the DNA is isolated using common extraction techniques. Once the DNA sample has been isolated and purified, the sample is analyzed using fragment analysis or DNA sequencing techniques. Next generation sequencing has been especially useful in determining the sequence of a communal genome. The figure below provides the basic steps in a Metagenomic study.

What is the Goal of Metagenomics

The entire sequence of a communal genome could be compared to bacteria taken from other environmental samples. A comparison of each communal genome could show how environmental factors have shaped the community. It could aid in determining how pollutants and other chemicals have altered basic gene sequences when compared to a relatively clean environmental sample. Another study could isolate bacteria from different seawater depths to compare genetic changes in the community as a result of pressure and light differences.

Fragment analysis is also a useful technique for examination of Metagenomic samples. It is a targeted approach investigating certain genetic functions. The genetic presence of a particular metabolic pathway such as the ability to metabolize a mineral is a good example.

Metagenomics as a field has provided a new way to look at an abundance of genetic material without the process of isolating separate species into pure cultures. It has helped to further understand environmental influences on genetic development. However, it does not yet show the complete relationship separate species living together may have on each other. An example of this is when one species produces a product utilized by another, thus shaping the genetic expression of both. However, it has led to new discoveries that could eventually impact the medical field.

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