Metagenome Analyses

Abstract

Robert Koch’s invention of pure culture techniques at the end of the nineteenth century focused microbiology on the isolation of bacteria for laboratory studies. Even today, in clinical diagnostics and foodstuff biotechnology, cultivation remains the gold standard because full characterisation of metabolic capabilities, resistance and pathogenesis can still only be achieved with pure cultures. “Winds of change” (Olsen et al. 1994) blew in the field of microbiology when the first cultivation-independent investigations reported an immense array of completely unexpected microbial diversity in the environment (Torsvik et al. 1990). Today it is estimated that only 1% of the microbial diversity in the biosphere can be assessed by means of standard cultivation techniques (Amann et al. 1995; Curtis et al. 2002). Although new approaches have recently been introduced to gain access to the “not currently cultureable majority” (Connon and Giovannoni 2002; Rappe et al. 2002; Zengler et al. 2002), they are not keeping pace with the substantial set of molecular tools to address the diversity and structure of microbial communities. Examples of these molecular tools are the powerful PCR-based methods that have been established for direct amplification, cloning and analysis of ribosomal RNA (rRNA) genes from the environment (Pace et al. 1985; Olsen et al. 1986; Giovannoni et al. 1990; Ward et al. 1990). Beyond diversity, the design and application of specific rRNA-targeted oligonucleotide probes allows insights into the structure of microbial communities in situ (Stahl and Amann 1991).