- Volume 45, Issue 3, 1995

The phylogenetic position and physiology of strain KoTa2T (T = type strain), which was previously classified as a Ruminococcus pasteurii strain, were studied. A determination of the 16S ribosomal DNA sequence of this taxon revealed its position within the radiation of the gram-positive lactic acid bacteria having low DNA G+C contents and that it is closely related to the genus Carnobacterium. l-Lactic acid was produced from glucose by a fructose-1,6-bisphosphate-activated lactate dehydrogenase, and oxygen tolerance was observed, characteristics which are consistent with assignment to this group. On the basis of its phenotypic characteristics and unique signature nucleotides, we propose that strain KoTa2 (= DSM 2381 = ATCC 35945) should be transferred to a new genus, Lactosphaera gen. nov., as the type strain of the species Lactosphaera pasteurii comb. nov.

The 16S rRNA gene sequence of the type strain of Ruminococcus flavefaciens, the type species of the genus Ruminococcus, was determined by PCR direct sequencing. A comparative sequence analysis showed that R. flavefaciens is phylogenetically related to a small cluster (cluster IV of Collins et al. [M. D. Collins, P. A. Lawson, A. Willems, J. J. Cordoba, J. Fernandez-Garayzabal, P. Garcia, J. Cai, H. Hippe, and J. A. E. Farrow, Int. J. Syst. Bacteriol. 44:812-826, 1994]) of organisms which includes several Clostridium and Eubacterium species. R. flavefaciens was found to be phylogenetically only remotely related to Ruminococcus gnavus, Ruminococcus torques, Peptostreptococcus productus, and Streptococcus hansenii. These findings demonstrate that the genus Ruminococcus is not a monophyletic group, and the proposed transfer of P. productus and S. hansenii to this genus (T. Ezaki, N. Li, Y. Hashimoto, H. Miura, and H. Yamamoto, Int. J. Syst. Bacteriol. 44:130-136, 1994) is not supported.

The type strain of Arthrobacter picolinophilus, strain DSM 20665 (= ATCC 27854), was found to be so closely related to strains of Rhodococcus erythropolis that we propose that this misclassified taxon should be removed from the genus Arthrobacter and reclassified as a strain of R. erythropolis. Our conclusion is based on the results of a comparative analysis of the chemotaxonomic properties of the organism, including the amino acid composition of the peptidoglycan, the mycolic acid composition, and the fatty acid composition, the very similar physiological properties and 16S ribosomal DNA sequences, and the results of DNA-DNA reassociation experiments performed by the renaturation rate method.

A partial 16S rRNA gene sequence of the type strain of Oribaculum catoniae was determined by using PCR direct sequencing. A comparative sequence analysis demonstrated that this species, although saccharolytic, is phylogenetically a member of the genus Porphyromonas. On the basis of the phylogenetic and phenotypic distinctiveness of O. catoniae, we formally propose that this species should be reclassified in the genus Porphyromonas, as Porphyromonas catoniae comb. nov. An emended description of the genus Porphyromonas is presented.

Facultatively alkaliphilic Bacillus sp. strain C-125 grew at temperatures of more than 50°C, did not reduce nitrate to nitrite, and did not deaminate phenylalanine. The guanine-plus-cytosine content of the chromosomal DNA of this organism was 42 mol%. These characteristics indicate that strain C-125 is related to Bacillus lentus group 3.

The genus Bacteroides was recently redefined to include only the type species Baeteroides fragilis and closely related taxa. Most other species that were previously designated Bacteroides have been reclassified in new genera. The taxonomic position of Bacteroides levii (Holdeman, Cato, and Moore) has remained incertae sedis. On the basis of biochemical, chemical and comparative 16S rRNA sequence analyses, this species shares a high degree of similarity with members of the genus Porphyromonas. We therefore formally propose that Bacteroides levii (Holdeman, Cato, and Moore) be reclassified in the genus Porphyromonas, as Porphyromonas levii comb. nov.

Recent studies of Rickettsia tsutsugamushi have demonstrated clearly the phenotypic and genotypic differences between this microorganism and other species belonging to the genus Rickettsia. Therefore, classification of R. tsutsugamushi in a new genus, Orientia gen. nov., is proposed.

A 1.9-kb plasmid DNA fragment from the type strain of Campylobacter coli, CIP 70.80, was used as a probe to characterize this type strain, other C. coli type strains obtained from several culture collections, and other C. coli strains. A specific hybridization pattern was obtained, and this pattern can be used to identify, characterize, and follow up C. coli type strains in culture collections.

Small-subunit rRNA (SSU rRNA) sequencing is a powerful tool to detect, identify, and classify prokaryotic organisms, and there is currently an explosion of SSU rRNA sequencing in the microbiology community. We report unexpectedly high levels of intraspecific variation (within and between strains) of prokaryote SSU rRNA sequences deposited in GenBank. A total of 82% of the prokaryote species with two published SSU rRNA sequences had more variable positions than a 0.1% random sequencing error would predict, and 48% of these sequence pairs had more variable positions than predicted by a 1.0% random sequencing error. Other sources of sequence variability must account for some of this intraspecific variation. Given these results, phylogenetic studies and biodiversity estimates obtained by using prokaryotic SSU rRNA sequences cannot proceed under the assumption that rRNA sequences of single operons from single isolates adequately represent their taxa. Sequencing SSU rRNA molecules from multiple operons and multiple isolates is highly recommended to obtain meaningful phylogenetic hypotheses, as is careful attention to accurate strain identification.

Pseudomonas cocovenenans, the producer of bongkrekic acid and toxoflavin, has been described previously by us (N.-X. Zhao, M.-S. Ma, Y.-P. Zhang, and D.-C. Xu, Int. J. Syst. Bacteriol. 40:452-455,1990) in terms of more than 180 phenotypic traits, G+C content, and DNA relatedness. The bacterium conformed to section II of the genus Pseudomonas. Here, its partial 16S rRNA gene sequence was compared with those of Burkholderia spp., and the results verified that P. cocovenenans is a Burkholderia species. On the basis of the phenotypic and genetic characteristics, P. cocovenenans is transferred to the genus Burkholderia as Burkholderia cocovenenans comb. nov.

In this paper the Subcommittee on the Taxonomy of Mollicutes proposes minimum standards for descriptions of new cultivable species of the class Mollicutes (trivial term, mollicutes) to replace the proposals published in 1972 and 1979. The major class characteristics of these organisms are the lack of a cell wall, the tendency to form fried-egg-type colonies on solid media, the passage of cells through 450- and 220-nm-pore-size membrane filters, the presence of small A-T-rich genomes, and the failure of the wall-less strains to revert to walled bacteria under appropriate conditions. Placement in orders, families, and genera is based on morphology, host origin, optimum growth temperature, and cultural and biochemical properties. Demonstration that an organism differs from previously described species requires a detailed serological analysis and further definition of some cultural and biochemical characteristics. The precautions that need to be taken in the application of these tests are defined. The subcommittee recommends the following basic requirements, most of which are derived from the International Code of Nomenclature of Bacteria, for naming a new species: (i) designation of a type strain; (ii) assignment to an order, a family, and a genus in the class, with selection of an appropriate specific epithet; (iii) demonstration that the type strain and related strains differ significantly from members of all previously named species; and (iv) deposition of the type strain in a recognized culture collection, such as the American Type Culture Collection or the National Collection of Type Cultures. The publication of the description should appear in a journal having wide circulation. If the journal is not the International Journal of Systematic Bacteriology, a reprint must be submitted to that journal so that the name may be considered for inclusion in a validation list as required by the International Code of Nomenclature of Bacteria.