Friday, October 31, 2014

Seeing beyond the Scene: Metagenomics Demystified

Our world is diversely inhabited by micro-organisms, they practically thrive everywhere. From the high-altitude mountains, to the subterranean layers, deep oceans, and even extreme environments that were once thought to be free of living organisms – acidic and highly saline waters, and even harsh temperatures of hot springs and subzero regions of the Antarctic. With this massive and highly distributed population, they hold the secrets in transforming the world around them. They are the boss, and if we want to gain more knowledge about biological processes, it is logical to get to know more about them in molecular level.

Since the advent of microbiological cultivation techniques, which started in mid-1800s, we have studied microbes as individual organisms isolated in pure cultures without or with very little inclusion of ecological factors such as presence of other microorganisms, tremendously high temperatures and other biotic and abiotic factors because of laboratory limitations, making our knowledge of them narrow and inadequate.

Metagenomics, one of the emerging neo-sciences, can be a tool for discovering novel genes and enzymes from environmental samples, especially in extreme environments. Extreme environments are interesting source of enzymes or biocatalysts that are active during extreme conditions and that can have biotechnologically valuable properties. An example is the hot and thermal environments like hot springs and mudsprings. One benefit of metagenomic analysis from hot environments is that it can better understand the microbial diversity and composition in hot springs and their relationship with geo-chemical conditions. The features of the microbial community gathered from hot  environments can be documented and analyzed for fu-ture studies. Also, the study of this can lead to the discovery of novel genes and enzymes, species and other features. Examples of novel enzymes harnessed in hot environments through metagenomics are lipases/esterase, Fe-superoxide dismutase and Taq DNA polymerase.

Far from the concept of genomics, metagenomics, traverses the lab-cultured dependent methods of sequencing and analyzing ge-nomes. Only 0.1 to 1.0% of the living bacteria that can be collected in soils can be grown in the laboratory in standard conditions, while most resist being cultured. According to a book published by the National Research Council (US) Committee on Metagenomics, entitled “The Science of Metagenomics: Revealing the Secrets of Our Microbial Planet”, most microorganisms interact with one another as communities, and separating the specimen from the group will alter its normal response to factors that will be induced. If ordinary methods of microbiology apply, organisms that require extreme conditions or community interaction will be difficult or cannot be cultivated, thus sequencing of isolates is not possible, hence no genome analysis and studies about that certain microorganism can be conducted.

On the other hand, metagenomics smites the problem of “unculturability” - the ball and chains of microbiological studies. General methods in metagenomics involves nucleic acid (e.g. DNA) extraction from the microbial community directly obtained from the environment, cloning into a surrogate host, and then analysis by sequencing or screening for expression of activities of interest, bypassing the need for artificial cultivation, therefore more efficient analysis of data. In example, metabolic processes, microbial diversity and relationship with geo-chemical conditions of microorganisms inhabiting aquatic environment near hydrothermal vents, can be better understood their relationship through metagenomics than in the laboratory because of restrictions.#

Metagenomics is also the theme of the 2014 Genetics Week (Harnessing Novel genes in thermal environments through Metagenomics). Started in 1986, the Genetics Week, which is a week-long event that presents recent advancements in the field of Genetics, is an annual event conducted every December of each year. Aside from presenting Genetic concepts, the event also showcases the history, membership and achievements of the organization in celebration of its founding anniversary. The events included in the Genetics week are the opening of the exhibit at the Institute of Biological Sciences Lobby (Wing C), a symposium, the IQlympics, orientation for interested applicants, Open Tambayan and Alumni Homecoming. Following the academic calendar shift which was implemented in AY 2014-2015, the annual Genetics Week was moved to October from its traditional schedule. 

No comments:

Post a Comment