- Volume 47, Issue 4, 1997

A strain isolated from a biopsy sample taken from a slowly spreading skin granulation on a child’s hand was found to have properties consistent with its classification in the genus Mycobacterium. An almost complete gene sequence of the 16S rRNA of the strain was determined following the cloning and sequencing of the amplified gene. The sequence was aligned with those available for mycobacteria, and phylogenetic trees were inferred with four tree-making algorithms. The organism, which formed a distinct phyletic line within the evolutionary radiation occupied by rapidly growing mycobacteria, was readily distinguished from members of validly described species of rapidly growing mycobacteria on the basis of its mycotic acid pattern and a number of other phenotypic features, notably its ability to form yellow pigmented colonies when incubated in the light. The name proposed for this new species is Mycobacterium novocastrense. The type strain is DSM 44203.

Organisms with characteristics typical of mycoplasmas were isolated from the preputial smegma of Afghan picas (Ochotona rufescens rufescens). The results of growth inhibition tests, metabolic inhibition tests, and immunobinding assays showed that the isolated strains were identical and that they were distinct from previously described Mycoplasma, Entomoplasma, Mesoplasma, and Acholeplasma species. These organisms represent a new species, for which the name Mycoplasma lagogenitalium is proposed. M. lagogenitalium ferments glucose, does not hydrolyze arginine or urea, reduces tetrazolium chloride, possesses phosphatase activity, does not digest gelatin or casein, and does not produce films or spots. It lyses sheep erythrocytes and does not adsorb sheep, rabbit, or horse erythrocytes. Cholesterol or serum is required for growth. The growth temperature is 37°C. The guanine-plus-cytosine content of the DNA is 23.0 ± 1.0 mol%. The type strain is M. lagogenitalium 12MS (= ATCC 700289T).

The isolation of a new motile, gram-negative, heterotrophic, sulfur-reducing, microaerophilic, vibrioid bacterium, strain F1F6, from oxidized marine surface sediment (Arcachon Bay, French Atlantic coast) is described. Hydrogen (with acetate as the carbon source), formate (with acetate as the carbon source), pyruvate, lactate, α-ketoglutarate, glutarate, glutamate, and yeast extract supported growth with elemental sulfur under anaerobic conditions. Apart from H2 and formate, the oxidation of the substrates was incomplete. Microaerophilic growth was supported with hydrogen (acetate as the carbon source), formate (acetate as the carbon source), acetate, propionate, pyruvate, lactate, α-ketoglutarate, glutamate, yeast extract, fumarate, succinate, malate, citrate, and alanine. The isolate grew fermentatively with fumarate, succinate being the only organic product. Elemental sulfur and oxygen were the only electron acceptors used. Vitamins or amino acids were not required. The isolate was oxidase, catalase, and urease positive. Comparative 16S rDNA sequence analysis revealed a tight cluster consisting of the validly described species Sulfurospirillum deleyianum and the strains SES-3 and CCUG 13942 as the closest relatives of strain F1F6 (level of sequence similarity, 91.7 to 92.4%). Together with strain F1F6, these organisms form a novel lineage within the epsilon subclass of proteobacteria clearly separated from the described species of the genera Arcobacter, Campylobacter, Wolinella, and Helicobacter. Due to the phenotypic characteristics shared by strain F1F6 and S. deleyianum and considering their phylogenetic relationship, we propose the inclusion of strain F1F6 in the genus Sulfurospirillum, namely, as S. arcachonense sp. nov. Based on the results of this study, an emended description of the genus Sulfurospirillum is given.

A gram-positive, aerobic actinomycete was isolated from soil. Spherical cells of this organism occur singly or form packets, which may cluster. The diagnostic diamino acid of the cell wall peptidoglycan is LL-diaminopimelic acid. The predominate menaquinone is MK-8 (H4), and the main fatty acids are 13-methyl tetradecanoic acid and 12-methyl tetradecanoic acid. The diagnostic polar lipids are phosphatidylethanolamine and phosphatidylinositol. The DNA base composition is 73 mol% G+C. Comparison of 16S ribosomal DNA sequences showed that this isolate is a phylogenetic neighbor of Terrabacter tumescens and Intrasporangium calvum. Genotypic, chemotaxonomic, morphological, and physiological characteristics are used to describe a new genus and species, Terracoccus luteus gen. nov., sp. nov. The type strain is strain IMET 7848 (= DSM 44267).

Strains of Meiothermus cerbereus sp. nov. were isolated from the hot springs within the Geysir geothermal area of Iceland. The strains of Meiothermus cerbereus produce red-orange-pigmented colonies, have an optimum growth temperature of about 55°C, and have higher levels of 3-OH fatty acids than the strains of the other species of the genus Meiothermus. These strains, unlike all other strains of the species of the genus Meiothermus examined previously, require cysteine, thiosulfate, or thioglycolate for growth in liquid Thermus medium, but not in the corresponding medium solidified with agar. Several strains belonging to Meiothermus silvanus, isolated from Geysir, also required reduced sulfur compounds for growth in liquid medium, leading to the hypothesis that this requirement is not a taxonomic characteristic of the new species. The new species represented by strains GY-1T and GY-5 can be distinguished from the other species of the genus Meiothermus by biochemical characteristics, fatty acid composition, DNA-DNA reassociation values, and 16S ribosomal DNA sequence. The type strain for Meiothermus cerbereus is GY-1 (= DSM 11376).

A phenotypic study has been carried out on six moderately halophilic gram-positive nonmotile cocci isolated from ponds of a saltern located in Huelva, Spain. These strains were examined for 150 morphological, physiological, biochemical, and nutritional traits and showed phenotypic characteristics similar to those of Nesterenkonia halobia (formerly Micrococcus halobius). The guanine-plus-cytosine (G+C) content of their DNA ranged between 70 and 72 mol%, values quite similar to those described for N. halobia (71.5 mol%). The 16S rDNA sequence analysis of one representative isolate showed that it is phylogenetically quite close to N. halobia, within the high-G+C-content gram-positive branch. DNA-DNA hybridization experiments showed a high degree of homology (72 to 100%) among the six isolates and the type strain N. halobia ATCC 21727. All data demonstrate quite clearly that the six isolates are members of the species N. halobia. Since this species was described on the basis of a single strain isolated from unrefined solar salt, and its description is not complete (especially in the utilization of different compounds), our study contributes to a better description of the moderate halophile N. halobia.

In an attempt to characterize an unusual mycobacterial strain isolated from a 2-year-old Somali patient with lymphadenitis, we applied various molecular methods not previously used for the taxonomic classification of mycobacteria. This isolate, designated So93, did not differ from Mycobacterium tuberculosis in the biochemical tests and in its 16S rRNA sequence, but produced smooth and glossy colonies, which is highly exceptional for this species. This smooth phenotype was unstable and switched nonreversibly to a rough colony morphology with a low frequency. The two colony types were equally virulent for the guinea pig, exhibiting characteristic tuberculous disease. Both morphotypes had shorter generation times than the M. tuberculosis reference laboratory strain H37Rv and clinical isolates of M. tuberculosis and Mycobacterium bovis. Furthermore, the So93 isolate differed from all M. tuberculosis complex strains described thus far by having only a single copy of insertion sequence IS1081, an unusual composition of the direct repeat cluster, and a characteristic phenolic glycolipid and lipooligosaccharide. This glycolipid had previously been observed only in a smooth isolate of M. tuberculosis obtained in 1969 by Canetti in France. Analysis of the Canetti strain showed that it shared virtually all genetic properties characteristic of So93, distinguishing these two strains from the known M. tuberculosis complex taxa, M. tuberculosis, Mycobacterium africanum, M. bovis, and Mycobacterium microti. The natural reservoir, host range, and mode of transmission of the group of bacteria described in this paper are presently unknown. This study, partly based on not previously used molecular criteria, supports the idea that the established members within the M. tuberculosis complex and the newly described Canetti grouping should be regarded as a single species, which likely will be designated “M. tuberculosis”.

The restriction enzyme profiles of 16S ribosomal DNAs (rDNAs) amplified by PCR from thermophilic heterotrophic bacterial strains isolated from composts were compared with those of reference strains. This allowed us to assign all but 1 of 16 strains to four different Bacillus species (namely, Bacillus stearothermophilus, Bacillus pallidus, Bacillus thermoglucosidasius, and “Bacillus thermodenitrificans”). This study showed that PCR restriction analysis of 16S rDNA contributes to rapid and reliable identification of newly isolated strains belonging to recognized species.

The taxonomic position of a misclassified strain, Zoogloea ramigera IAM 12670T (= ATCC 25925T = P. R. Dugan 115T), was reevaluated. A phylogenetic analysis based on 16S ribosomal rDNA sequences revealed that this organism was located in the beta subclass of the class Proteobacteria with members of the genus Telluria as its closest relatives. On the basis of phenotypic and phylogenetic information, we propose that this organism should be reclassified in a new taxon with the name Duganella zoogloeoides gen. nov., sp. nov.

The 16S rRNA gene sequences of Salmonella typhi and Salmonella typhimurium were amplified by PCR, cloned, and sequenced. These sequences were analyzed by comparison with reference organisms from the family Enterobacteriaceae. Both S. typhi and S. typhimurium belong to the gamma subdivision of the class Proteobacteria.

We determined the 16S rRNA gene sequence of Rickettsiella grylli, an intracellular parasite of Gryllus bimaculatus and related species of crickets. Phylogenetic inferences made from alignment of this sequence with the sequences of other bacteria demonstrated that R. grylli is most closely related to Coxiella burnetii and Legionella species in the γ subclass of the phylum Proteobacteria. R. grylli was previously thought to be related to members of the order Rickettsiales, but the representatives of this order have been shown to be members of the α1 subclass of the Proteobacteria. Our results indicate that R. grylli should be removed from the order Rickettsiales.

A newly described strain of the genus Methanosarcina was isolated from submarine canyon sediments and is shown by comparative sequence analyses of 16S ribosomal DNA and the gene encoding methyl coenzyme M reductase, mcrI, to be a strain of Methanosarcina siciliae. Morphological and physiological characteristics are described. In contrast to the two previously described strains that grow exclusively on methanol, methylamines, and dimethylsulfide, M. siciliae C2J is also capable of growth on and methanogenesis from acetate. We propose that the species description for M. siciliae be amended to include aceticlastic strains.

Strain TT4B, isolated from freshwater sediments contaminated with chlorinated ethylenes, is described as Desulfuromonas chloroethenica sp. nov. This organism grows with acetate or pyruvate as electron donors and tetrachloroethylene, trichloroethylene, fumarate, polysulfide, and Fe(III) nitriloacetate as electron acceptors. D. chloroethenica is unique among the desulfuromonads in using chloroethylenes as electron acceptors. It is phenotypically and phylogenetically most closely related to Desulfuromonas acetexigens and shares many other features with this species.

We propose that the order Prochlorales Florenzano, Balloni, and Materassi 1986 (emend. Burger-Wiersma, Stal, and Mur 1989), the family Prochloraceae Florenzano, Balloni, and Materassi 1986, and the family Prochlorotrichaceae Burger-Wiersma, Stal, and Mur 1989, validly published in the International Journal of Systematic Bacteriology under the rules of the Bacteriological Code, be rejected because of the imperfection of ordinal diagnosis. The oxygenic-phototrophic prokaryotes involved are proposed to be incorporated under their validly published names into the orders Chroococcales and Oscillatoriales of the “Cyanobacteria” group. Correspondingly, the latter is proposed to be upgraded to equal “Oxygenic photosynthetic bacteria” (Section 19 in Bergey’s Manual).

Restriction fragment length polymorphism analysis of PCR-amplified 16S ribosomal DNA (16S rDNA PCR-RFLP) was used to generate restriction profiles of the American Type Culture Collection type strains of the genus Veillonella, i.e., V. atypica, V. caviae, V. criceti, V. dispar, V. parvula, V. ratti, and V. rodentium. Whole-cell protein profiles were obtained by sodium dodecyl sulfate-polyacrylamide gel electrophoresis for comparative purposes. The 16S rRNA genes were amplified by PCR, and RFLP analysis of the 16S rDNA was performed with MnlI and Sau3AI.MnlI produced six RFLP patterns for seven type strains, since the patterns for V. atypica and V. caviae were the same. RFLP patterns with Sau3AI could distinguish between V. atypica and V. caviae. The type strains of Veillonella species were easily distinguished by 16S rDNA PCR-RFLP.