Journal of Chemical Technology and Biotechnology J Chem Technol Biotechnol 82:421–423 (2007) Perspective Microbial metagenomes: moving forward industrial biotechnology Manuel Ferrer, 1* Ana Beloqui 1 and Peter N Golyshin 2,3 1 CSIC, Institute of Catalysis, Cantoblanco, Madrid 28049, Spain 2 Department of Environmental Microbiology, HZI-Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany 3 Institute of Microbiology, Carolo-Wilhelmina Technical University of Braunschweig, 38106 Braunschweig, Germany Abstract: Biotechnology, in terms of exploitation of catalytic activities for industrial applications, is increasingly recognized as one of the pillars of the knowledge-based economy that we are heading for. Comprehensive knowledge of enzymology should be of practical importance for effective intervention on whole cell processes and enzymatic networks. Over the last decade metagenome-based technologies have been developed to take us farther and deeper into the enzyme universe from uncultivable microbes. This sophisticated platform, which identifies new enzymes from vast genetic pools available, and assesses their potential for novel chemical applications, should be increasingly important in the discovery of advanced biotechnological resources.  2007 Society of Chemical Industry Keywords: biotransformation; chemical diversity; biodiversity; metagenome METAGENOMES EXPAND THE POSSIBILITIES OF BIOTECHNOLOGY It is widely accepted that ongoing enzyme discovery will enhance the potential of biotechnology towards synthetic industrial conversions and ultimately con- tribute to sustainable and environmentally friendly practices. 1 Microorganisms, comprising the largest fraction of all organisms in the Earth in any respect (total cell numbers, total number of species and total biomass), should play an important role in this regard. However, the majority of these microbial species are either not amenable to culturing (up to 5000 species have been validly described taxonomically and are deposited in public strain collections) or have not had an attempt made. For example, up to 25 000 different microbial genotypes were found in just one millilitre of seawater sample from a marine ecosystem. 2 In fact, to access this great genetic and metabolic diversity the new ‘‘metagenomic’’ approach is currently used. 3–5 This approach involves harvesting bulk DNA from environmental samples (or from enrichment cultures), archiving it in libraries with appropriate heterologous hosts and either consequent screening of these libraries for a gene of interest with a gene probe, or expression of the DNA and screening for enzymatic activities of interest. Alternatively, these libraries may be sub- jected to high throughput shotgun sequencing and automated annotation. The latter approach, applied to a variety of environmental DNAs such as those from the Sargasso Sea, 6 worm and human gut, 7,8 and coastal virus, 9 yielded thousands of billions of base pairs derived from thousands of genomic species and deduced more than five million previously unknown genes. A significant part of these coded for peptides with low sequence similarity to known proteins, and thus these peptides do most likely possess new struc- tures and new catalytic properties. This type of work, however, often faces difficulties with genome assem- bly and other challenges in interpretation of large data sets. 10 Nevertheless, these efforts have led to the situation that the majority of protein sequences in electronic databases are predicted in silico from the shotgun sequences of yet uncultured microbes, with up to 40% being genes coding for proteins with yet unknown function. By using the molecular and high-throughput facilities actually available, the efficiency has been demonstrated of mining the metagenome libraries to search for novel activities, 11 and microbial bioactives (anticancer drugs, antibiotics, secondary metabolites and the genes responsible for them). 12 These may provide a good basis for further engineering, aiming at specific industrial processes. However, even though ongoing efforts have revealed a whole arsenal of enzymes whose physiological roles and biotechnological potential were well established in the laboratory and in industry, we strongly believe that the experimental enzymology is a bottleneck in enzyme * Correspondence to: Manuel Ferrer, CSIC, Institute of Catalysis, Cantoblanco, Madrid 28049, Spain E-mail: mferrer@icp.csic.es (Received 16 January 2007; accepted 27 February 2007) Published online 20 April 2007; DOI: 10.1002/jctb.1695  2007 Society of Chemical Industry. J Chem Technol Biotechnol 0268–2575/2007/$30.00