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Chapter 87 : The Problem of Complexity
The current trend in publishing new Legionella species is to utilize culture and phenotypic characteristics, serology, cellular fatty acids and isoprenoid quinone profiles, DNA relatedness, and a molecular phylogenetic analysis targeting usually more than one gene. To investigate the greater use of sequence-based phylogenetic analyses in lieu of serology, fatty acid and isoprenoid quinone profiles, and even perhaps DNA relatedness, 56 strains representing 33 potentially novel species were phylogenetically assessed with 6 gene targets. First, following a phylo-genetic analysis based on sequence from the mip gene, 49 strains representing 30 potentially novel species were selected because their genetic distance from recognized species was greater than that between recognized species. Second, DNA studies on two strains indicated that they were novel, even though their mip sequence-derived genetic distance was closer to a recognized species than that between recognized species. Last, the remaining five strains were selected because they were genetically related to either of these latter two strains, based on their macrophage infectivity potentiator (mip) sequence-derived genetic distance. The six gene targets used in this analysis, 16S rRNA gene, the mip gene , the RNA polymerase β-subunit (rpoB), the RNase P RNA gene (rnpB), and the DNA gyrase A subunit (gyrA), together with the zinc metallo-protease (proA, also known as mspA) gene. In the interim, the use of a combined approach using the sequenced- based phylogeny to identify “nearest neighbor” species will greatly simplify the use of total DNA relatedness studies.