Revised road map to the phylum Firmicutes

Starting with the Second Edition of Bergey’s Manual of Systematic Bacteriology, the arrangement of content follows a phylogenetic framework or “road map” based largely on analyses of the nucleotide sequences of the ribosomal small-subunit RNA rather than on phenotypic data (Garrity et al., 2005). Implicit in the use of the road map are the convictions that prokaryotes have a phylogeny and that phylogeny matters. However, the reader should be aware that phylogenies, like other experimentally derived hypotheses, are not static but may change whenever new data and/or improved methods of analysis become available (Ludwig and Klenk, 2005). Thus, the large increases in data since the publication of the taxonomic outlines in the preceding volumes have led to a re-evaluation of the road map. Not surprisingly, the taxonomic hierarchy has been modified or newly interpreted for a number of taxonomic units of the Firmicutes. These changes are described in the following paragraphs. The taxonomic road map proposed in Volume 1 and updated and emended in Volume 2 was derived from phylogenetic and principal-component analyses of comprehensive datasets of smallsubunit rRNA sequences. A similar approach is continued here. Since the introduction of comparative rRNA sequencing (Ludwig and Klenk, 2005; Ludwig and Schleifer, 2005), there has been a continuous debate concerning the justification and power of a single marker molecule for elucidating and establishing the phylogeny and taxonomy of organisms, respectively. Although generally well established in taxonomy, the polyphasic approach cannot be currently applied for sequence-based analyses due to the lack of adequate comprehensive datasets for alternative marker molecules. Even in the age of genomics, the datasets for non-rRNA markers are poor in comparison to more than 300,000 rRNA primary structures available in general and special databases (Cole et al., 2007; Pruesse et al., 2007). Nevertheless, the data provided by the full genome sequencing projects allow defining a small set of genes representing the conserved core of prokaryotic genomes (Cicarelli et al., 2006; Ludwig and Schleifer, 2005). Furthermore, comparative analyses of the core gene sequences globally support the small-subunit rRNA derived view of prokaryotic evolution. Although the tree topologies reconstructed from alternative markers differ in detail, the major groups (and taxa) are verified or at least not disproved (Ludwig and Schleifer, 2005). Consequently, the structuring of this volume is based on updated and curated (http://www.arb-silva.de; Ludwig et al., 2004) databases of processed small-subunit rRNA primary structures.