Metagenomics, biotechnology with non-culturable microbes

Appl Microbiol Biotechnol (2007) 75:955–962 DOI 10.1007/s00253-007-0945-5

MINI-REVIEW

Metagenomics, biotechnology with non-culturable microbes
Christel Schmeisser & Helen Steele & Wolfgang R. Streit

Received: 28 January 2007 / Revised: 12 March 2007 / Accepted: 12 March 2007 / Published online: 30 March 2007 # Springer-Verlag 2007

Abstract Metagenomics as a new field of research hasbeen developed over the past decade to elucidate the genomes of the non-cultured microbes with the goal to better understand global microbial ecology on the one side, and on the other side it has been driven by the increasing biotechnological demands for novel enzymes and biomolecules. Since it is well accepted that the majority of all microbes has not yet been cultured, the not-yet-cultivatedmicrobes represent a shear unlimited and intriguing resource for the development of novel genes, enzymes and chemical compounds for use in biotechnology. However, with respect to biotechnology, metagenomics faces now two major challenges. Firstly, it has to identify truly novel biocatalysts to fulfil the needs of industrial processes and green chemistry. Secondly, the already available genes andenzymes need to be implemented in production processes to further prove the value of metagenome-derived sequences. Keywords Metagenomics . Biocatalysis . Non-cultivated microbes . Environmental genomics

Metagenomics, the key to advances in biotechnology It is well known that biotechnology has a continuous demand for novel genes and enzymes and compounds. Natural diversity has so far been the bestsupplier for these novel molecules. This can be explained by the vast richness of soil and other microbial niches. Studies based on 16 S
C. Schmeisser : H. Steele : W. R. Streit (*) Abteilung für Mikrobiologie und Biotechnologie, Biozentrum Klein-Flottbek, Universität Hamburg, Ohnhorststrasse 18, 22609 Hamburg, Germany e-mail: wolfgang.streit@uni-hamburg.de

rDNA/rRNA have extensively redefinedand expanded our knowledge of microbial diversity. Simple calculations of soil microbial diversity place it in the range of between 3,000 and 11,000 genomes per gram of soil with less than 1% being accessible through cultivation techniques (Torsvik and Ovreas 2002; Torsvik et al. 2002; Curtis and Sloan 2004). This is probably very similar for many other microbial niches but it is also clear thatmany other microbial communities are less diverse. Pure culture analysis of soil microorganisms has revealed that they are a rich source of novel therapeutic compounds such as antibiotics (Raaijmakers et al. 1997), anticancer agents (Shen et al. 2001) and immunosuppressants (Skoko et al. 2005), as well as a wide range of biotechnologically valuable products (Ullrich et al. 2004; Inoue et al. 2005).However, the cultivation-dependent approach is limited by the fact that the overwhelming majority of microorganisms present in soil cannot be cultured under laboratory conditions. There is a vast amount of information held within the genomes of uncultured microorganisms, and metagenomics is one of the key technologies used to access and investigate this potential (Handelsman 2004; Pettit 2004;Streit et al. 2004; Streit and Schmitz 2004). Metagenomics concerns the extraction, cloning and analysis of the entire genetic complement of a habitat (Handelsman et al. 1998); it is an approach that allows the investigation of the wide diversity of individual genes and their products as well as analysis of entire operons encoding biosynthetic or degradative pathways. Metagenomics also makes itpossible to answer key ecological questions by enabling scientists to relate potential functions to specific microorganisms within multispecies soil communities. Within this framework, this review describes metagenomic methodologies, their applications in novel drug and enzyme discovery and their potential for biotechnological use.

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Appl Microbiol Biotechnol (2007) 75:955–962

Metagenome...