- Volume 45, Issue 1, 1995

DNA relatedness experiments were performed with 38 clinical isolates and 13 reference strains of coryneform taxa exhibiting a lipid requirement for optimal growth. Forty-five of these strains split into five genomic groups at the species level, whereas six other strains remained unclustered. Genomospecies II fits Corynebacterium accolens, but the other genomospecies were not genetically related to any of the defined Corynebacterium species. Phylogenetic analyses of genes coding for small-subunit rRNA sequences revealed that two genomospecies (I and III) and C. accolens form a tight cluster within the robust branch that groups all Corynebacterium species presently sequenced. Reference strains of biotypes C-1, C-2, and C-3 of “Corynebacterium pseudogenitalium” were found to fall into genomospecies I, as well as “Corynebacterium tuberculostearicum” center for Disease Control and Prevention (CDC) coryneform group G-1, and CDC coryneform group G-2 reference strains. Biochemical tests allowed differentiation between genomospecies except between genomospecies IV and V and between six unclustered strains and genomospecies I. We propose a new classification for these lipid-requiring diphtheroids within the genus Corynebacterium with the delineation of some CDC coryneform group G-1 strains (genomospecies III) as a new species for which the name Corynebacterium macginleyi is proposed. The type strain is strain JCL-2 (CIP 104099), isolated from a human corneal ulcer.

Six similar strains which were isolated as pathogens of cultured kuruma prawns (Penaeus japonicus) in Japan had characteristics of the genus Vibrio. These organisms were distinguished from previously described Vibrio species by their positive results in tests for gelatinase and lipase activities and their negative reactions in tests for arginine dihydrolase and lysine and ornithine decarboxylase activities, growth in the presence of 6% NaCl and at 35°C, acid production from sucrose, utilization of d-glucuronate and propionate, and luminescence. The G+C contents of the DNAs of these organisms were 46.2 to 47.0 mol%. The levels of DNA relatedness among these six strains were 87 to 99% (as determined by the membrane filter method), while the levels of DNA relatedness between prawn pathogen strain KH-1T (T = type strain) and members of 28 previously described Vibrio species were less than 18%. The name Vibrio penaeicida sp. nov. is proposed for the prawn-pathogenic strains. The type strain is strain KH-1 (= IFO 15640 = JCM 9123).

The taxonomic status of Pasteurella piscicida (strain NCIMB 2058T [T = type strain] and a strain isolated from the environment) was investigated by performing phylogenetic analyses of small-subunit rRNA sequences, DNA-DNA hybridization analyses, and biochemical characterization analyses. The results of the phylogenetic analyses and the levels of DNA-DNA complementarity demonstrated conclusively that Pasteurella piscicida is extremely closely related to Photobacterium damsela ATCC 33539T. Since the two taxa exhibited a level of DNA-DNA relatedness of 80%, they are members of the same species. The high level of DNA relatedness and the presence of specific morphological and biochemical characteristics support the hypothesis that two subspecies should be recognized. On the basis of its phylogenetic position, we concluded that Pasteurella piscicida should be renamed Photobacterium damsela subsp. piscicida comb. nov.

The cellular fatty acids, respiratory quinones, and proteins of the generically misnamed taxa Bacteroides gracilis and Bacteroides ureolyticus were analyzed and compared with the corresponding chemotaxonomic features of their closest relatives, the campylobacters. Our results and previously published data for genotypic and phenotypic characteristics were used in a polyphasic approach to reconsider the classification of these organisms. We transfer B. gracilis to the genus Campylobacter as Campylobacter gracilis comb. nov. B. ureolyticus can be considered a campylobacter on genotypic grounds; in contrast, the proteolytic metabolism and fatty acid components of this taxon exclude it from the genus Campylobacter. We prefer to consider this taxon a species incertae sedis pending the isolation and characterization of additional B. ureolyticus-like bacteria.

We performed a numerical analysis of 148 phenotypic characteristics of 20 strains of root nodule bacteria isolated from an arid saline desert soil in the Xinjiang region of northwestern People’s Republic of China and compared these organisms with 28 Rhizobium and Bradyrhizobium strains obtained from different regions of the People’s Republic of China and from other countries, including nine type strains of different species. All of the strains examined clustered into two groups at a similarity level of more than 63%. Group I included all of the previously described Rhizobium species and was divided into eight subgroups, which corresponded to previously described Rhizobium species, at a similarity level of more than 82%. Group II was divided into the following three subgroups at a similarity level of more than 80% Bradyrhizobium japonicum, a cluster containing 17 moderately and slowly growing strains isolated in the Xinjiang region, and a small subgroup containing three fast-growing strains. The generation times of the moderately and slowly growing strains were 5 to 15 h, and these organisms produced acid in medium containing mannitol. The DNA G+C contents of the members of this group ranged from 59 to 63 mol%. DNA-DNA hybridization experiments revealed that the levels of DNA homology among all of the moderately and slowly growing strains obtained from Xinjiang were more than 70% and that the levels of DNA homology between representative strains of this group and the type strains of all previously described species of root- and stem-nodulating bacteria were low. All of our experimental data indicated that the moderately and slowly growing rhizobia isolated from Xinjiang are members of a new species. Partial 16S rRNA gene sequencing of the type strain. A-1BS (= CCBAU3306), and a comparison of the resulting sequence with the sequences of previously described species revealed that strain A-1BS is closely related to Rhizobium loti, Rhizobium huakuii, and Rhizobium galegae, but not to B. japonicum and Azorhizobium caulinodans. On the basis of our results, we propose that the strains which we studied are members of a new species, Rhizobium tianshanense. The type strain, A-1BS (= CCBAU3306), has been deposited in the Culture Collection of Beijing Agricultural University, Beijing, People’s Republic of China.

On the basis of morphological, physiological, and chemotaxonomic characteristics and DNA-DNA hybridization data, we describe three new Brachybacterium species: Brachybacterium conglomeratum sp. nov., nom. rev. (type strain, IFO 15472); Brachybacterium paraconglomeratum sp. nov. (type strain, IFO 15224); and Brachybacterium rhamnosum sp. nov. (type strain, IFO 15203). These new species include some previously misclassified strains and an isolate obtained from corn steep liquor. Although B. conglomeratum and B. paraconglomeratum are similar in their physiological characteristics, they can be differentiated on the basis of their cellular fatty acid patterns and low levels of DNA-DNA hybridization. B. rhamnosum is characterized by the presence of large amounts of rhamnose in its cell wall.

A new coagulase-negative species of the genus Staphylococcus, Staphylococcus pulvereri, was isolated from human and animal specimens. The complete 16S rRNA sequence of the type strain of S. pulvereri, NT215, was determined and compared with the sequences of 16S rRNAs from the other staphylococci. Strains of S. pulvereri were differentiated from other novobiocin-resistant Staphylococcus species by their biochemical activities, cell wall composition, and levels of genetic relatedness. The type strain of this species is NT215 (=PCM 2443T).

Organisms belonging to the genus Spiroplasma are currently classified into 23 groups, 17 of which have been assigned species epithets. We determined the genome sizes of representatives of 20 groups by using pulsed-field gel electrophoresis. Each genome size was deduced from the mobility of linear nonrestricted DNA, as well as from the sum of the sizes of restriction fragments obtained after digestion with NotI, a restriction endonuclease with a limited number of restriction sites in spiroplasma DNA. The values which we obtained indicated that the genome sizes of members of the genus Spiroplasma range from 940 to 2,220 kbp.

The 16S ribosomal DNA-based phylogenetic positions of various members of the Methylococcaceae (group I methanotrophs) were investigated. The Methylococcaceae as a whole formed a distinct branch in the gamma subdivision of the Proteobacteria, and this branch had five distinct subbranches. On the basis of a number of phenotypic traits, phospholipid fatty acid patterns, and the results of a 16S ribosomal DNA analysis, we determined that the species belonging to one subbranch, Methylobacter albus, Methylobacter agilis, and Methylobacter pelagicus, formed a distinct group that could be differentiated from other members of the genus Methylobacter, which grouped in an adjacent subbranch. We propose that these species belong to a new taxon, Methylomicrobium gen. nov.

Consideration should be given to preserving nonliving bacterial specimens as dried material in herbaria for use in future systematic studies. Nucleic acid sequences can be recovered from such material, and it may be possible to utilize it in other techniques. Dried specimens are cheap to prepare and preserve and would record much bacterial variation without the expense of maintaining living cultures. They would also be useful for uncultivable microorganisms. Some technical suggestions are offered.