Metagenomics: Concept, methodology, ecological inference and recent advances

Abstract

Microorganisms constitute two third of the Earth's biological diversity. As many as 99% of the microorganisms present in certain environments cannot be cultured by standard techniques. Culture-independent methods are required to understand the genetic diversity, population structure and ecological roles of the majority of organisms. Metagenomics is the genomic analysis of microorganisms by direct extraction and cloning of DNA from their natural environment. Protocols have been developed to capture unexplored microbial diversity to overcome the existing barriers in estimation of diversity. New screening methods have been designed to select specific functional genes within metagenomic libraries to detect novel biocatalysts as well as bioactive molecules applicable to mankind. To study the complete gene or operon clusters, various vectors including cosmid, fosmid or bacterial artificial chromosomes are being developed. Bioinformatics tools and databases have added much to the study of microbial diversity. This review describes the various methodologies and tools developed to understand the biology of uncultured microbes including bacteria, archaea and viruses through metagenomic analysis.

Discovery and characterization of thermophilic limonene‐1,2‐epoxide hydrolases from hot spring metagenomic libraries

“…the direct extraction and cloning of DNA from natural environments without culturing isolated microorganisms to discover novel enzymes, has been widely demonstrated in recent years [19][20][21][22]. Thermostable hydrolases with different activities, such as lipases, proteases and glycosidases, have already been identified from (hyper)thermophiles [23,24]; however, there is still no evidence for naturally thermostable EHs or the occurrence of this enzymatic activity in hot environments.…”

Novel Antibacterial Proteins from the Microbial Communities Associated with the Sponge Cymbastela concentrica and the Green Alga Ulva australis

“…To access the uncultured majority of the microbial world (43), functional metagenomic approaches that allow for the expression of environmental DNA from uncultured organisms in surrogate hosts have been developed (6,22,32,35,36,46). Functional screening of metagenomic libraries has led to the discovery of several novel bioactives and metabolic pathways (5,36,52), but the search for new antibiotics has focused mainly on soil-derived samples.…”

Microbial Outlook for the Bioremediation of Crude Oil Contaminated Environments

“…These strategies, combined with general metagenomic naming, use BAC (bacterial artificial chromosome), cosmid, or fosmid vectors for cloning of different-sized inserts and require the use of different methods for host cell transformation (Yung et al, 2009;Singh et al, 2009). Most libraries constructed in vectors that contain large DNA fragments (40-100 Kb) obtained directly from environmental microbial communities, such as soil, sediment, or sludge, are used to investigate the expression of genes involved in the synthesis or metabolism of certain compounds (Rondon et al, 2000;Singh et al, 2009). …”