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Poll: Did you understand what is Metagenomics ?
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Metagenomics- exploring the microbes in their habitat.
This is post no. 1 under the main topic.
Metagenomics- exploring the microbes in their habitat.

The earth is comprised of large varieties of microorganisms.  This variety of microorganisms plays various functions for sustaining life on earth. They provide many necessary functions which are important for other lives to exist in earth.  Every process in the biosphere is touched by these microbes owing to their ability to transform the world around them. They play major roles in the chemical cycles of all the key elements of life like carbon, nitrogen, oxygen, sulfur and thus making them biologically accessible for the other microorganisms. So, it can be said that microbes helps in sustaining life on earth.   All plant and animals are closely associated with microbial communities which provide nutrients, metals ions and vitamins to their hosts. Even human body which comprises of approx 3 trillion cells also acts as a host of billions microbes associated with them which help us to lead a healthy life. Nowadays microbes also help human beings in production of drugs, biofuel, biopols and fermenting food.

Microbes were discovered during the time of late 18th century when microscope was invented. It makes us aware of microorganisms by making it visible to us. By then to today we know many things about microbes by culturing them in laboratories.  Microbes were studied by focusing on a pure culture which consists of only one species. This enable the scientists to study microbes, however it isn’t natural as microbes are grown on artificial media without having ecological contacts. All most, all the information about the microbes is laboratory knowledge gained by growing them in unnatural environment. In the community, microbes compete for nutrients and space. Also there are several functions which cannot be done by a species alone. Culturing microbes in artificial media is a very old process for getting information from microbes. From pure cultures, there is very little knowledge obtained about some microbes which cannot be grown without community.  The science of Metagenomics empowers us to study the microbes in their natural environment i.e. the complex community in which they normally live.

Defining Metagenomics:

The word Meta is a Greek word for transcendence and term genomics means the total hereditary contain of an organism. This field of biology helps us to understand the biology as a whole.  It takes a community of microbes from natural environment and focuses on the genes and their role in the community. This provides us with the information that how genes can influence each other activity and serve functions collectively as a whole.  Metagenomics consist of extracting DNAs directly from the environment, these DNA are known as metagenomes. DNAs are extracted from the microbes in their native places. For example all microbes from sea water, soil, and human gut etc.

Methods in Metagenomics:

The steps in this process consist of extraction of DNA from samples which are collected from the environment under observation. The samples contain verity of different kinds of organism, the cells of which may be broken by chemical methods such as alkaline condition or by physical methods like sonication.  Then the DNA is isolated from rest of the sample using its chemical and physical properties. Some methods of DNA isolation include density centrifugation, affinity binding and solubility precipitation.  Metagenomic genome is complex since it is mixture of many DNA from a pool of microorganisms making its study more challenging. These DNA can be integrated in to E.coli genome for future study. This creates a library of genomes of microbes which are found in that particular environment. The library contains a large number of clones each containing a random part of DNA, which can be analyzed by sequence methods or function methods i.e. by sequencing the nucleotide sequence of clone DNA or by studying the expression of clones DNA into its protein.

[Image: metagenomic[1].jpg]

Sequence driven method comprises of sequencing the clone DNA which was collected from natural environment and then put it for computational analysis using bioinformatics tools. Sequences are compared with the sequences that are already present in the DNA data banks. Then genes are grouped into similar predictable functions and types of the proteins that conduct those functions and coded by the sequences can be assed.

• In function driven method the DNA is collected from the habitat and is implanted into a surrogate host, instead of its sequencing then the scientists go for studying their functions. For studying the functions firstly it is ensured that the function is absent in the subrogate hosts so, that the resulted function can be interpreted as the function of the Meta DNA.  Genotypic analysis is generally performed after phenotypic analysis. A typical metagenomic analysis consists of several rounds of the procedure to ensure the isolation of the targeted genes from the environment samples and to successfully characterize the function encoded by the gene.

The information gained from the metagenomic procedure includes information regarding structure, expression, evolution and origin of DNA. These informations can be scientifically applicable for benefiting the society and environment. Many microorganisms have ability to degrade waste material, make new drugs for medicine, and make biodegradable plastics and some of the important food we consume regularly. Isolation of this Meta DNA enables us to optimize those processes and adapt them for use in our society. As a result of ineffective laboratory standard technique the potential of organisms in the nature like microbes is relatively unknown and uncharacterized.  Metagenomic is a revolutionary tool for exploring the diversity on organism from their native habitat samples.  Metagenomic effectively involves characterization of function or naturally occurring samples without laboratory culturing technique.

Application of metagenomic in human welfare

Environment sustainability: Metagenomics can give new techniques for monitoring the impact of pollutants on ecosystems and for removing the contaminating agents from environment. Gaining the understanding of how microbial communities cope with pollutants can be use as a scale for measuring the potential of contaminated sites to recover from pollution and increases the chances of bioaugmentation or biostimulation trials to succeed.

Biochemical products: Microbial communities produce a large variety of biologically active chemical agents that are used in competition and communication. Many of the drugs which are in use today were originally discovered in microbes; recent progress in exploring the rich genetic resource of non-culturable microbes has led to the uncovering of new functional genes, enzymes, and natural products. The application of Metagenomics has allowed the development of commodity and fine chemicals, agrochemicals and pharmaceutical products where the benefit of enzyme-catalyzed synthesis of products is increasingly recognized.
Agriculture: Plants grow in soil which is inhabited by a variety of microbial communities, with 1 gram of soil containing around 10^9-10^10 microbial cells which comprises of about 1 gigabase of sequence information. The microbial communities which are living in soils are some of the most complex known to science, and remain not understood despite their industrial importance. Microbes perform a wide variety of ecosystem services which are important for plant growth and development, including fixing atmospheric nitrogen into soil, nutrient cycling, disease suppression, and arranging iron and other metals. Functional Metagenomics methods are being applied to explore the interactions between plants and microorganisms through cultivation-independent study of these communities. By allowing insights into the function of previously uncultivated or community members in nutrient cycling and the promotion of plant growth, metagenomic methods can contribute to improved disease detection in crops and livestock. This will also help in the adaptation of enhanced farming practices which improve crop health by harnessing the relationship between microbes and plants.
Metagenomics can also provide valuable information about the functional ecology of environmental communities. The Metagenomic analysis of the bacterial species found in the defecations of Australian sea lions suggests that nutrient-rich sea lion faeces may be an important nutrient source for coastal ecosystems. This is because the bacteria that are exposed simultaneously with the defecations are adept at breaking down the nutrients present in the faeces into a biologically accessible form that can be taken up into the food chain.

Information from metagenomic libraries has the ability to enrich the development of industries and environmental sustainability. This information can be applied to the human world, in an effort of creating a healthy society that lives with a balance with the environment. DNA sequencing can also be applied more appropriately to identify species present in a body of water, debris filtered from the air, or sample of dirt. This can establish the total range of invasive species and endangered species, and track seasonal populations.  Metagenomics is a new technique of molecular biology that is full of promise and uncertainty. It gives us a window to the world which was unseen ever before. It is uncertain that what will be found but, it will surely help us in understanding the relation between different organism in their natural conditions, and promising us to provide more complete understanding of global cycles that keeps the biosphere bound, discoveries of new anti microbial therapies and also over coming environmental challenges. Metagenomics is just at its initial stages and continuously growing. Advances in Metagenomics can lead us to know the microbial community more appropriately and use them for human welfare and environmental sustainability.
This is post no. 2 under the main topic.
I spend a lot of my time working with researchers in human genomics and metagenomics. The study of the human microbiome is still a new field, and therefore there are very few repositories dedicated to storing metagenomic data, and as a result the data is fragmented across many different repositories.

I thought I would add here some sources of human metagenomic data for those who are interested in working with this data:
- Repositive has indexed ~21,000 datasets from human metagenomic studies
- Many studies that have deposited their data in SRA: a major study within the SRA datasets is the Human Microbiome Project.
- dbGaP also has some restricted access data.
- GigaDB
- EBI Metagenomics

For personal data you can also look at:
- The Personal Genome Project
- Steven Keating's Genome
- The Corpasome

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