Metagenomics: Theory, methods, and applications

Metagenomics is a young overarching discipline that seeks to understand population dynamics and interactions among vast microbial worlds that have not been revealed by traditional culture methods in the microbiology laboratory. Metagenomics is emerging as an essential scientific discipline: there are far-reaching implications in understanding ecosystem responses to changes in the natural environment, their adaptation to artificial niches resulting from human activities and their role as a source of human disease. And there are substantial opportunities for beneficial applications of meta-genomics knowledge — for example, in energy production, medicinals and bioremediation. Advances in instrumentation and computational and molecular tools enable high-throughput gathering and analyses of environmental samples at several levels: sequence information for microbial DNA, RNA and protein, and analysis of metabolic intermediates. As a new field of study, metagenomics integrates large-scale data about molecules to describe the biodiversity and relationships of an enormous microbial 'underground' in their natural environment. The impact of such ambitious inquiry, however, cannot be understated. It begins by interrogating the microbial world, but metagenomics has the potential to provide a molecular view of interrelationships among all living organisms. Metagenomics: Theory, Methods, and Applications reviews the field at several levels. Chapter 1 is an overview of how culture-independent metagenomic analysis of environmental DNA sequences of small subunit riboso-mal RNA genes increased knowledge about the diversity of all microbial groups. Multiple strand amplification of microbial DNA using Phi29 DNA polymerase, shotgun sequencing and pyrosequencing enabled high-throughput sequencing of microbial DNA. The development of metagenomic bioinfor-matics tools enabled genome assembly and classification of large-scale sequencing data. These metagenomic approaches have so far expanded bacterial classification into 30 new divisions. Archaea are now represented by 50 distinct phylogenetic groups in both extreme and non-extreme environments. Fungi are now estimated at over one million species, distributed among 49 distinct phylotypes. New eukaryotic microbes in anoxic environments are being identified as well. In addition, metagenomic identification and analyses of environmental viruses is revealing their role in shaping microbial ecosystems. The challenge that follows large-scale classification and genome sequencing of new organisms is to define the composition, structure and temporal connectivity of microbial ecosystems. The combination of several 'omics' approaches and bioinfor-matics should help model microbial communities in the future. Chapter 2 complements Chapter 1, and is an in-depth review of meta'omics approaches that measure active genes in microbial populations at the levels of RNA (metatranscriptomics) and protein (metaproteo-mics) sequences, and their …