New directions and interactions in metagenomics research

Abstract

Metagenomics, which aims to access the genomic potential of an environmental sample directly, is a burgeoning area that is generating enormous amounts of biological information. An examination of recent metagenomics literature reveals the discipline to be heading in new and interesting directions, including the investigation of the normal flora of mammals, analysis of ancient genomes, and exploration of the distribution of novel pathways. In addition, the development of new bioinformatics approaches and tools is allowing innovative mining of both existing and new data. Finally, there are indications that the integration of metagenomics with complementary approaches in microbial ecology is beginning.

Ecology and Diversity of Picoeukaryotes

“…A variety of approaches can be taken to conduct environmental genomic studies, such as shotgun or BAC sequencing (for reviews, see Delong and Karl 2005;Ward 2006;Worden et al 2006). Large environmental genomic datasets, such as one from the Sargasso Sea (Venter et al 2004), that are focused on prokaryotes also contain picoeukaryote sequences, since the size-fractionation step (e.g., ,0.8 mm) only eliminates DNA from larger (or particle-attached) organisms.…”

The magic and menace of metagenomics: prospects for the study of plant growth-promoting rhizobacteria

“…This figure will be used as a framework to describe the metagenomic methodology and illustrate the many variations that have evolved over the past few years. For good overviews on the subject of metagenomics, several recent reviews are available (Daniel 2005;Deutschbauer et al 2006;Green and Keller 2006;Handelsman 2004;Kowalchuk et al 2007;Schloss and Handelsman 2005;Schmeisser et al 2007;Streit and Schmitz 2004;Tringe and Rubin 2005;Ward 2006;Xu 2006). The present article presents an overview of metagenomics that is to some extent biased towards the discussion in the final section about how to capitalize on metagenomics as a tool in the study of PGPR.…”

Metagenomics in animal gastrointestinal ecosystem: a microbiological and biotechnological perspective

“…Only 0.001-0.1% of the total microbes in sea water, 0.25% in freshwater, 0.25% in sediments and only 0.3% soil microorganisms were found to be cultivable [8]. As reviewed recently [9,10], the metagenomic studies have largely progressed due to the construction of effi cient cloning vectors (e.g. bacterial artifi cial chromosomes-BACs, and yeast artifi cial chromosomes, YACs etc.…”