All-Species Living Tree Project. Encyclopedia of Metagenomics: Genes, Genomes and Metagenomes

Classification and identification of Bacteria and Archaea came across to a turning point around 35 years ago. It was the time when Carl Woese and co-workers demonstrated that ribosomal markers were appropriate to infer genealogical relationships by means of phylogenetic reconstructions (Fox et al. 1977). Rapidly, comparative analysis of rRNA gene sequences became a standard procedure with mature implications in microbial ecology and taxonomy: culture-independent exploration of ecosystems’ diversity (Amann et al. 1995) and settlement of the phylogenetic backbone (i.e., our current accepted classification of Bacteria and Archaea; Garrity 2001). As a result, the total amount of ribosomal RNA entries in the public DNA databases has grown exponentially since early 1990s, currently comprising at least 3,500,000 small (SSU) and 300,000 large (LSU) ribosomal subunit gene sequence entries. On the other hand, the number of bacterial and archaeal species with validly published names has followed arithmetic trends with a ratio of around 500–700 annual descriptions during the last 7 years (Fig. 1), currently (December 2012) exceeding the total number of 10,300 species and subspecies. A comparative overview of these trends until December 2011 is shown in Fig. 1