Strain ATCC 9341, currently known as Micrococcus luteus, has been designated as a quality-control strain in a number of applications. It is also cited as the standard culture in several official methods and manuals, as well as the Code of Federal Regulations. Over the years, it has become apparent that ATCC 9341 does not resemble other M. luteus strains; however, its phenotypic characteristics alone were ambiguous. Recently, a polyphasic study was performed in which molecular data were combined with cytochemical properties and physiological characteristics. The results clearly indicate that ATCC 9341 is a member of the genus Kocuria. Thus, it is proposed to reclassify ATCC 9341 as Kocuria rhizophila and to alert users worldwide of this name change.
Previous studies using the nuclear SSU rDNA have indicated that the photosynthetic euglenoids are a monophyletic group; however, some of the genera within the photosynthetic lineage are not monophyletic. To test these results further, evolutionary relationships among the photosynthetic genera were investigated by obtaining partial LSU nuclear rDNA sequences. Taxa from each of the external clades of the SSU rDNA-based phylogeny were chosen to create a combined dataset and to compare the individual LSU and SSU rDNA datasets. Conserved areas of the aligned sequences for both the LSU and SSU rDNA were used to generate parsimony, log-det, maximum-likelihood and Bayesian trees. The SSU and LSU rDNA consistently generated the same seven terminal clades; however, the relationship among those clades varied depending on the type of analysis and the dataset used. The combined dataset generated a more robust phylogeny, but the relationships among clades still varied. The addition of the LSU rDNA dataset to the euglenophyte phylogeny supports the view that the genera Euglena, Lepocinclis and Phacus are not monophyletic and substantiates the existence of several well-supported clades. A secondary structural model for the D2 region of the LSU rDNA was proposed on the basis of compensatory base changes found in the alignment.
A representative selection of Prototheca zopfii strains isolated from different environmental habitats or clinical cases was characterized in a polyphasic approach in order to assess their intraspecies taxonomic position. Recently, the recognition of distinct phenotypic clusters has been reported as the assignment of ‘variants’. In the present study, 11 strains were compared by a number of phenotypic and genetic criteria, including growth characteristics, biochemical reactions and serotyping results. Based on emended standards for biotype identification, P. zopfii strains showed auxanographic differences and distinct assimilation patterns with respect to utilization of amino acids and glycerol. Serotyping by means of immunoblotting revealed that all isolates of variant II obtained from clinical cases, i.e. isolates from bovine mastitis or from human enteropathia, showed specific antigen patterns. They were found to be different from strains assigned to the other two variants with respect to their immunogenic antigens. Furthermore, comparison of partial 18S rDNA sequences confirmed distinct differences between the former variants. Based on these results, it is proposed that P. zopfii merits classification as a species comprising three biotypes.