ADVERTISEMENTS:
In this article we will discuss about:- 1. Definition of Meta-Genomics 2. Study of Meta-Genomics 3. Applications.
Definition of Meta-Genomics:
The meta-genomics refers to the collection of genes sequenced from the environmental samples. Due to advancement in molecular biology, meta-genomics is described as sequencing of genetic material from environment i.e. uncultured samples.
Kevin Chen and Lior Pachter (U.S.A) defined meta-genomics as ‘the application of modem genomics techniques to the study of communities of microbe’s directly in their natural environments’. This does not include isolation and cultivation of microorganisms on culture media.
ADVERTISEMENTS:
Out of the microorganisms present in various environments, only 1.8% of all bacteria are known, while rest of 98.2% bacteria have not been cultured because they need specific growth requirement or they are obligate ones. We know about culture-dependent microorganisms. Therefore, meta-genomics has been developed for un-culturable bacteria.
Study of Meta-Genomics:
The study of meta-genome is mainly confined to those microorganisms which are non-culturable and thus cannot be sequenced. Their sequencing is mainly based on 16S ribosomal RNA sequences which are relatively short, often conserved and generally different from species to species. N.R. Pace (1985) used PCR to explore the diversity of ribosomal RNA sequencing. In 1991, he proposed the idea of cloning DNA directly from environmental samples.
Due to their long sequences, it is now possible to construct gene libraries by using bacterial artificial chromosomes (BACs) as vector for molecular cloning. Culture-independent studies which is mostly based on 16S rRNA gene sequencing have made it apparent that a large proportion of these ‘yet to be cultivated’ bacteria belong to new genotypes, classes and divisions in the domains eubacteria and archaea.
These studies have revealed that the presence of newer bacteria even in samples thought to be most well characterized like dental plaques, sea water and garden soil. Molecular analysis of bacterial diversity has already resulted in identification of 40 divisions in eubacteria, including 13 candidate divisions which are not represented by any cultured member. These studies cleared the old belief that archaea present only in extreme environments, are also present in soil, sea water, etc.
ADVERTISEMENTS:
The study on culture-independent molecular microbial diversity not only reveals the vast unexplored bacterial diversity but also has helped in development of techniques suitable for isolation of high purity microbial community DNA i.e. meta-genome from various environmental samples. The meta-genomic DNA helped molecular biologists a chance to peek into the genomes of un-culturable bacteria, circumventing the need to culture them in vitro.
The meta-genomes from many habitats are explored for isolation of novel genes by PGR amplification using primers against the conserved domain of meta-genomic libraries containing small inserts of 2-15 kb in plasmid vectors or large inserts of 40-130 kb in cosmid, fosmid or bacterial artificial chromosome (BAG) vector (Fig. 2.2).
ADVERTISEMENTS:
The methods used for study of meta-genomics are given as below:
(i) Shotgun Meta-genomics:
Shotgun meta-genomics is an ideal method for analysis of DNA sequences of uncultured microbes. Similar shotgun methodology has also been helpful to: sequence genomes of many culturable microbes, randomly shear DNA, sequence many short sequences, and reconstruct them into a consensus sequence.
Breithart Mya (2002) analysed sea water for viral particles isolation by using shotgun sequencing technique. Further, about 1000 viral specimens have been reported from human stool. A majority of them proved new species. A study in the year 2004, on Sargasso sea water samples revealed 2000 different species including 148 types of bacteria which proved new to microbial world.
ADVERTISEMENTS:
A complete genome of some non-culturable bacteria was archaea has gave rise to a new kingdom, Korarchaeota to the domain of microorganisms. Roberts Edwards (2006) published the chip-based pyro-sequencing of meta-genome. This technique does not require cloning the DNA before sequencing, removing one of the main bases in meta-genomics.
(ii) Bioinformatics Tools:
A few bioinformatics tools have been discovered. Daniel Huson and Stephan Schuster (2007) developed a software named MEGAN to analyse a meta-genomic shotgun dataset.
In the same year, Folder Meyer and Roberts Edwards released the meta-genomics RAST server (MG-RAST), a community resource for meta-genome data set analysis. The SEED based free public resource contains 158 public meta-genome for the analysis of several hundred meta-genome data sets.
Applications of Meta-Genomics:
ADVERTISEMENTS:
Meta-genomics is applied in various areas as given below:
(a) Since, the meta-genome gives information about DNA of entire communities of microbes; it gives greater opportunity to explore many commercially important products. This may give insight to new and modem microbiology.
It is the need of hours that besides gene sequence, data base, and information on the method of sampling, DNA extraction techniques as well as computational and algorithmic methods may also be added to the database.
(b) Development of new culture techniques and more innovative tools in molecular biology related to genomic library construction in culturable members of various bacterial groups are expected to revolutionize the field of biocatalysts and drug discovery.
ADVERTISEMENTS:
(c) Further, decrease in cost of sequencing is expected to increase efforts for microbial community structure and ecosystem function.
(d) Availability of community genome sequences will help in development of gene expression profiles and physiological studies providing a comprehensive approach to environmental biology.
