Metagenomics and Ecosystems Biology: Conceptual Frameworks, Tools, and Methods
from: Metagenomics: Theory, Methods and Applications (Edited by: Diana Marco). Caister Academic Press, U.K. (2010)
Metagenomic analyses of natural biological communities are revolutionizing our understanding of the diversity, function, and inter-relationships among organisms in diverse ecological niches. The rapid advancements in metagenomics are largely due to the technical and analytical methods developed from high throughput platforms for cloning, DNA sequencing, robotics, high-density microarrays, 2D-gel electrophoresis, and mass spectrometry as well as associated bioinformatics softwares. In this chapter, I summarize a general framework of broad-sense metagenomics. The specific areas as well as the tools used are highlighted for identifying diversity, searching for novel genes and gene products, and investigating relationships among genes, mRNAs, and proteins in microbial communities. Of special notes are the recent developments in single cell isolation, whole-genome amplification, pyrosequencing, and database warehousing and the potential impact of these developments on our future understandings of microbial communities in nature. These exciting developments are bringing the dawn of a new era in biology, that of ecosystems biology read more ...