- Volume 48, Issue 4, 1998

A new anaerobic, proteolytic, moderately thermophilic bacterium, strain 3RT, was isolated from a methanogenic mesophilic reactor treating protein-rich wastewater. The cells were Gram-negative, non-spore-forming, non-motile rods. The DNA base composition was 43 mol% G+C. The optimum pH and temperature for growth were 7·0 and 55 °C respectively. The bacterium fermented gelatin, casein, bovine albumin, peptone and yeast extract. Glucose, fructose, sucrose, maltose and starch were poorly fermented. The major fermentation products from glucose were acetate, CO2 and H2 and, from gelatin, propionate was also detected. Growth on glucose was stimulated by thiosulfate, which was reduced to sulfide. Sulfate and nitrate were not reduced. 16S rRNA gene analysis revealed that the isolated bacterial strain was phylogenetically related to Coprothermobacter proteolyticus (96·3% sequence similarity), the only known species within the genus. DNA-DNA hybridization analysis demonstrated a very low level of homology, indicating that the isolated strain and C. proteolyticus were not related at species level. Therefore, it is proposed to classify the described strain in the genus Coprothermobacter as a new species, Coprothermobacter platensis. The type strain of C. platensis is strain 3RT (= DSM 11748T).

A novel extremely halophilic archaeon was isolated from the solar salterns of Cabo Rojo, Puerto Rico. The organism is very pleomorphic motile and requires at least 8% (w/v) NaCI to grow. Polar lipid composition revealed the presence of a novel non-sulfate-containing glycolipid and the absence of the glycerol diether analogue of phosphatidylglycerosulfate. The G+C content of the DNA is 59 mol%. On the basis of 16S rRNA sequence data, the new isolate cannot be classified in one of the recognized genera, but occupies a position that is distantly related to the genus Haloferax. All these features justify the creation of a new genus and a new species for the family Halobacteriaceae, order Halobacteriales. The name Halogeometricum borinquense gen. nov., sp. nov. is proposed. The type strain is ATCC 700274T.

A new genus, Methylopila, and one new species are described for a group of seven strains of facultatively methylotrophic bacteria with the serine pathway of C1 assimilation. These bacteria are aerobic. Gram-negative, non-spore-forming, motile, colourless rods that multiply by binary fission. Their DNA base content ranges from 66 to 70 mol % G+C. Their cellular fatty acid profile consists primarily of C18:1ω7 cis-vaccenic and C19:0 cyclopropane acids. The major hydroxy acid is 3-OH C14:0. The main ubiquinone is Q-10. The dominant cellular phospholipids are phosphatidylethanolamine and phosphatidylcholine. The new isolates have a low level of DNA-DNA homology (5–10%) with the type strains of the serine pathway methylobacteria belonging to the genera Methylobacterium, Aminobacter, Hyphomicrobium and Methylorhabdus. Another approach, involving 16S rRNA gene sequence analysis of strain IM1T, has shown that the new isolates represent a separate branch within the a-2 subclass of the Proteobacteria. The type species of the new genus is Methylopila capsulata sp. nov., with the type strain IM1T (= VKM B-1606T).

Sequencing of mba gene fragments of reference strains of Ureaplasma urealyticum serovars 1, 3, 6, 14 and 8, in addition to 33 clinical U. urealyticum isolates is reported. A phylogenetic tree deduced from alignment of these sequences clearly demonstrates two major clusters (confidence limit 100%), which equate to the parvo and T960 biovars, and five types, which have been designated mba 1, 3, 6, 8 and X. These relationships are supported by bootstrap analysis. Polymorphisms within the mba fragment of types mba 1, 3 and 6 were used to define nine subtypes (mba 1a, 1b, 3a, 3b, 3c, 3d, 3e, 6a and 6b), thus facilitating high resolution typing of U. urealyticum. Inclusion of reference strains for serovars 1, 3, 6 and 8 in the mba typing scheme showed that the results of this analysis are broadly consistent with currently accepted serotyping. In addition, a ure gene fragment from nine of the clinical isolates was amplified and sequenced. Comparisons of the sequences clearly distinguished the two biovars of U. urealyticum; however, this fragment was invariant within the parvo biovar. This study has shown that the mba sequence can reveal the fine details of the relationships between U. urealyticum isolates and also supports the significant evolutionary gap between the two biovars.

Two Bartonella strains from blood of two wild rats (Rattus norvegicus) living in a rural environment were isolated. These strains were distinct from all previously known Bartonella species based on phenotypic and genotypic characteristics. This new species is distinguished by its trypsin-like activity, the absence of the ability to hydrolyse proline and tributyrin, its 16S rRNA and citrate synthase gene sequences and by whole-DNA hybridization data. This new species, for which the name Bartonella tribocorum sp. nov. is proposed, seems to be genetically related to Bartonella elizabethae, an agent isolated in a case of human endocarditis. The type strain of Bartonella tribocorum sp. nov. is IBS 506T (CIP 105476T).

Two strains of helical, halophilic, Gram-negative, heterotrophic bacteria were isolated from kusaya gravy which is a traditional Japanese fermented brine. These strains were motile by means of a single polar or bipolar tuft flagellum. They had a large cell size, were helical, formed coccoid bodies, were microaerophilic and had quinone type Q-8. The DNA G+C content of the strains was 44–45 mol%. A detailed investigation of the phenotypic, chemotaxonomic and phylogenetic characteristics of the strains revealed that they represent a new species of halophilic helical bacteria. The sequence of the 16S rRNA gene of strain H7T, designated the type strain of the new isolates, and all of the Oceanospirillum species except for Oceanospirillum linum were determined. Phylogenetic analysis indicated that these strains were closely related to Oceanospirillum minutulum, with enough distance to separate the O. minutulum/new isolate H7Tcluster from Oceanospirillum sensu stricto on the genus level. It is proposed that a new genus, Marinospirillum, be created; this genus should include Marinospirillum minutulum ATCC 19193T(formerly Oceanospirillum minutulum) as the type species, as well as Marinospirillum megaterium JCM 10129T(=H7T).

A new, slow-growing, scotochromogenic mycobacterium was isolated from sputum of a 53-year-old patient with Down’s syndrome suffering from tuberculosis. Growth occurred at temperatures between 25 and 40°C with an optimum at 37°C. This strain had surprisingly few enzymic activities (only positive for 68°C heat-stable catalase and weakly positive for urease) and was sensitive to prothionamide, cycloserine, clarithromycin, gentamicin and amikacin but showed resistance to isoniazid, streptomycin, ethambutol, rifampin and ciprofloxacin. These characteristics assign this organism to a novel mycobacterial species characterized by a unique 16S rDNA nucleotide sequence. The name Mycobacterium bohemicum sp. nov. is proposed for this new, slow-growing, scotochromogenic mycobacterium. The type strain is DSM 44277T.

A psychrophilic bacterium, previously described as Vibrio sp. strain ABE-1T, has been reassigned by phenotypic characterization, chemotaxonomic analysis and 16S rRNA phylogenetic analysis. The organism was curved rods and it could reduce nitrate to nitrite and hydrolyse gelatin and DNA, but not chitin. NaCl was required for growth. This strain was susceptible to the vibriostatic compound 0/129. The major isoprenoid quinone was ubiquinone-8 and the DNA G+C content was 39·4 mol%. The whole-cell fatty acids comprised saturated and monounsaturated fatty acids with 10–18 C atoms; saturated and monounsaturated C16 fatty acids were predominant. Strain ABE-1T contained the unique trans-unsaturated fatty acid, 9-trans-hexadecenoic acid. Although strain ABE-1T has been identified as a Vibrio species, the strain did not ferment glucose. Phylogenetic analysis based on 16S rRNA sequencing indicated that strain ABE-1T was more closely related to Colwellia species than to Vibrio species. However, strain ABE-1T differed from other reported Colwellia species in terms of phylogenetic position, some phenotypic characteristics, chemotaxonomic analysis and relatedness by DNA–DNA hybridization. Accordingly, the name Colwellia maris is proposed. The type strain is ABE-1T ( = JCM 10085T).

Four Gram-negative, aerobic, pointed and budding bacteria were isolated from various depths of the hypersaline, heliothermal and meromictic Ekho Lake (Vestfold Hills, East Antarctica). The cells contained storage granules and formed rosettes. Daughter cells may be motile. Growth required sodium ions. Nitrate was reduced to nitrite, and dissimilatory reduction of nitrite was possible. DNase and gelatinase were produced. Glutamate was metabolized with and without an additional source of combined nitrogen. The most abundant fatty acid was C18:1; other fatty acids present in lower concentrations were C12:1 3-OH, C16:1, C16:0, C18:0 and C19:0 eye. The main polar lipids were phosphatidylglycerol and phosphatidylcholine. The DNA base composition was 62·3–62·8 mol% G+C. 16S rDNA sequence comparisons showed the isolates to be phylogenetically related to the genera Sagittula and Roseobacter. Morphological, physiological and genotypic differences to these and distinct characteristics supported the description of a new genus and a new species, Antarctobacter heliothermus gen. nov., sp. nov. The type strain is EL-219T (= DSM 11445T).

The Bacillus cereus group comprises the four valid species Bacillus cereus, Bacillus mycoides, Bacillus thuringiensis and Bacillus anthracis. Some isolates of B. cereus are known to be psychrotolerant (growth at 7 °C or below). Here, specific sequence differences are described between the 16S rDNA, the 23S rDNA, the 16S–23S rDNA spacer region and the genes of the major cold-shock protein homologue cspA in a variety of psychrotolerant and mesophilic B. cereus and B. mycoides strains. Randomly amplified polymorphic DNA analysis using three different primers clearly separated psychrotolerant strains of both species from the rest of the B. cereus group, as did inverse PCR patterns of the rDNA operons. These data strongly support a hitherto unrecognized fifth sub-group within the B. cereus species group comprising psychrotolerant, but not mesophilic, B. cereus strains. Despite the latter finding, the DNA sequences investigated exhibited a high degree of sequence similarity indicating a close relationship between the species of the B. cereus group. Considering the unusual importance of B. cereus in both food poisoning and food spoilage and to avoid merging all species of the group, a new species, Bacillus weihenstephanensis sp. nov., comprising psychrotolerant ‘cereus’ strains, is proposed. Isolates of the new species grow at 4–7°C but not at 43°C and can be identified rapidly using rDNA or cspA targeted PCR. The type strain is B. weihenstephanensis WSBC 10204T(= DSM 11821T).

A syntrophic propionate-oxidizing bacterium, strain MPOBT, was isolated from a culture enriched from anaerobic granular sludge. It oxidized propionate syntrophically in co-culture with the hydrogen- and formate-utilizing Methanospirillum hungateii, and was able to oxidize propionate and other organic compounds in pure culture with sulfate or fumarate as the electron acceptor. Additionally, it fermented fumarate. 16S rRNA sequence analysis revealed a relationship with Syntrophobacter wolinii and Syntrophobacter pfennigii. The G+C content of its DNA was 60·6 mol %, which is in the same range as that of other Syntrophobacter species. DNA-DNA hybridization studies showed less than 26% hybridization among the different genomes of Syntrophobacter species and strain MPOBT. This justifies the assignment of strain MPOBT to the genus Syntrophobacter as a new species. The name Syntrophobacter fumaroxidans is proposed; strain MPOBT (= DSM 10017T) is the type strain.

Phylogenetic analyses based on 16S rDNA sequences and genomic DNA-DNA relatedness showed that the sulphur-oxidizing facultative chemolithotroph Thiobacillus acidophilus was closely related to members of the genus Acidiphilium, which is a group of strictly aerobic, heterotrophic acidophiles now categorized into aerobic photosynthetic bacteria. Lipophilic pigment analyses revealed that zinc-chelated bacteriochlorophyll a and carotenoids occurred in appreciable amounts in T. acidophilus and all established species of the genus Acidiphilium. PCR experiments showed that T. acidophilus as well as Acidiphilium species contained puf genes, encoding the photosynthetic reaction centre proteins and the core light-harvesting complex of the purple bacteria. There were high similarities between T. acidophilus and Acidiphilium species in the primary structure of their reaction centre proteins deduced from the nucleotide sequence data. The phylogenetic tree of the reaction centre proteins was in agreement with the 16S rDNA sequence-based phylogenetic tree in the relationship between T. acidophilus and Acidiphilium species and between the Acidiphilium cluster and other purple photosynthetic bacteria. Based on these results, together with previous phylogenetic and phenotypic information, it is proposed to reclassify T. acidophilus (Guay and Silver) Harrison 1983 as Acidiphilium acidophilum comb. nov. The type strain is ATCC 27807T(= DSM 700T).

The name Rickettsia honei, strain RBT, has been proposed for a unique spotted fever group (SFG) agent which is pathogenic for humans. This agent has previously been compared to the other SFG agents and was shown to be distinct in protein structure by SDS-PAGE and by immunoblotting. Genetic comparisons of the 16S rRNA, rompA, gltA and the 17 kDa antigen genes with the other SFG rickettsiae confirmed the phylogenetic distance between R. honei and the previously described species. Genetically, Rickettsia honei is more closely related to the Thai tick typhus (TT-118) rickettsia than to any other member of the SFG. Indeed, it is proposed that TT-118 is a strain of R. honei which was previously isolated in Thailand. These results elucidate the presence of a unique SFG rickettsial species in Australasia.

Four freshwater Antarctic lakes were examined for the presence of β-galactosidase-producing bacteria using mineral medium enrichments and lactose. Enrichments from only one of the lakes produced growth and two strains were isolated that were very similar in phenotype and fatty acid profile, and shared considerable homology in their DNA (DNA–DNA hybridization = 93±7%). The strains were psychrotrophic with theoretical T max, T min and T opt of 30–31, –7 ° and 26 °C, respectively. The β-galactosidase in cell extracts had an optimal activity at 39 C. The strains were Gram-negative rods, showed gliding motility, contained branched and hydroxy fatty acids, and menaquinone 6 as the major respiratory quinone. The strains did not form microcysts and utilized lactose while using ammonium ions as a source of nitrogen, and a range of other sugars. The G+C content of the DNA was 34 mol%. Phylogenetic analysis of one of the strains, by comparison of 16S rDNA sequences, showed that it was most similar, but not identical to, Flavobacterium columnare and ‘[Sporocytophaga] cauliformis’. Both species could be differentiated phenotypically from the Antarctic isolates. DNA–DNA hybridization of the Antarctic isolate with six different members of the Flavobacterium 16S rDNA cluster showed no strain with greater than 18% relatedness. The nearest type species to the Antarctic isolate in the phylogenetic analysis was Flavobacterium aquatile. The name Flavobacterium hibernum is proposed for the Antarctic strains, and the type strain is ATCC 51468T(= ACAM376T).

A combination of genotypic and phenotypic properties (a polyphasic taxonomic approach) was used to determine the relatedness between the type strains of Pseudomonas nautica Bauman et al. 1982 and Marinobacter hydrocarbonoclasticus Gauthier et al. 1992 , which were originally found to be highly related by partial 16S rDNA sequence analysis. Analysis of genotypic properties, such as comparison of the almost complete 16S rDNA sequences, base composition of the total genomic DNA and DNA-DNA hybridization revealed that the two strains were highly similar and should be considered members of the same species. The phenotypic properties, such as the physiology and chemotaxonomic data (i.e. fatty acid composition, polar lipid patterns and respiratory lipoquinone content), confirmed the genotypic evaluation, and has lead to the proposal for a unification of the two species, Pseudomonas nautica (DSM 50418T) and Marinobacter hydrocarbonoclasticus (DSM 8798T) as Marinobacter hydrocarbonoclasticus.

A strain of a hitherto undescribed coryneform bacterium from human clinical material was characterized by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequence analysis demonstrated the strain represents a novel and deep lineage within the genus Corynebacterium sensu stricto. Chemical analyses revealed the unidentified strain was unusual in that it lacked mycotic acids. Based on the phylogenetic and phenotypic distinctiveness of the unknown isolate, it is proposed that the bacterium be classified as a new Corynebacterium species, for which the name Corynebacterium kroppenstedtii sp. nov. is proposed. The type strain is CCUG 35717T.

The name Rickettsia slovaca sp. nov. (type strain is strain B) is proposed for a member of the spotted fever group (SFG) rickettsiae which was isolated from Dermacentor marginatus ticks in Slovakia in 1968, and was recently implicated in human febrile illness. This rickettsia can be phenotypically distinguished from other SFG rickettsiae by microimmunofluorescence serotyping, SDS-PAGE, Western blotting and mAbs. Genotypic differences between R. slovaca and the other SFG representatives can be demonstrated by PCR-RFLP analysis, pulsed-field gel electrophoresis and sequencing of 16S rRNA, gltA and ompA genes.