- Volume 39, Issue 4, 1989

The name Mesophilobacter marinus gen. nov., sp. nov. is proposed for 11 strains of aerobic, mesophilic, nonmotile, oxidase-positive, penicillin-resistant, moderately halophilic, gram-negative coccobacilli that were isolated from seawater. The genus Mesophilobacter is closely related to the genera Acinetobacter, Moraxella, and Psychrobacter, but the levels of deoxyribonucleic acid relatedness to members of these genera are low. The mesophilobacters have optimal growth temperatures of 33 to 37°C and can grow in broth containing 7% sodium chloride. The ubiquinone system is Q-8, and the major cellular fatty acids are C16:1, C18:1, and C16:0 acids. The guanine-plus-cytosine contents of the deoxyribonucleic acids are 44.0 to 46.9 mol%. The type strain of this species is strain 14S-4 (= IAM 13185).

Phenotypic and chemotaxonomic characteristics of seven moderately halophilic isolates from a mediterranean saltern showed that they were very closely related to "Chromobacterium marismortui" This species, which was originally described on the basis of strains isolated from the Dead Sea, was not included on the Approved Lists of Bacterial Names and is not accepted as a member of the genus Chromobacterium since it produces a pigment that is not violacein, does not possess the characteristic flagellar arrangement, and is not genotypically related to this genus as determined by deoxyribonucleic acid-ribosomal ribonucleic acid hybridization experiments. On the basis of the special features of these strains, we propose that they should be placed in a new genus, Chromohalobacter, which includes a single species, Chromohalobacter marismortui comb, nov., nom. rev. The deoxyribonucleic acid base composition is 62.1 to 64.9 mol% guanine plus cytosine. The type strain is strain ATCC 17056 (= CCM 3518).

Revival of the name Streptomyces scabies is proposed for the predominant species causing common scab of potato. Common scab strains from the northeastern United States, Atlantic Canada, and Hungary were differentiated by a phenotypic analysis of 42 criteria from six atypical pathogen strains, three saprophytic streptomycetes isolated from scab lesions, and reference strains of Streptomyces griseus and Streptomyces tendae. The 12 S. scabies strains formed a homogeneous group characterized by smooth grey spores borne in spiral chains, melanin production, and usage of all International Streptomyces Project sugars. Most S. scabies isolates did not degrade xanthine and were susceptible to 25 µg of oleandomycin per ml, 10 IU of penicillin G per ml, 20 µg of streptomycin per ml, 10 µg of thallous acetate per ml, and 0.5 µg of crystal violet per ml. The type strain of S. scabies is strain RL-34 (= ATCC 49173).

A new bacterial species is described, for which we propose the name Streptomyces acidiscabies. This organism causes a scab disease of potatoes (Solanum tuberosum) which may occur in soils with pH values below 5.2. The acid scab symptoms caused by this organism are indistinguishable from the symptoms of commn scab caused by Streptomyces scabies. In culture, S. acidiscabies is distinct from S. scabies, having flexuous spore chains, a growth medium-dependent spore mass color ranging from white to organish red, and a red or yellow, pH-sensitive diffusible pigment rather than melanin. S. acidiscabies grows on agar media at pH 4.0 (versus pH 5.0 for S. scabies), does not use raffinose as a carbon source, and tolerates higher concentrations of crystal violet (0.5 μg/ml), thallium acetate (10 μg/ml), streptomycin (20 μg/ml), oleandomycin (25 μg/ml), and penicillin G (10 IU/ml) than S. scabies. The type strain of S. acidiscabies is strain RL-110 (= ATCC 49003).

Different types of studies have shown that Campylobacter pylori does not belong in the genus Campylobacter. Ribonucleic acid sequencing has indicated that C. pylori might belong in the genus Wolinella, but we describe five major groups of taxonomic features of the genus Wolinella that differ markedly from those of C. pylori, including ultrastructure and morphology, cellular fatty acids, menaquinones, growth characteristics, and enzyme capabilities, indicating that C. pylori should not be included in the genus Wolinella. Thus, we propose the establishment of a new genus, Helicobacter, C. pylori should be transferred to this genus as Helicobacter pylori comb, nov., and H. pylori NCTC 11637 (= ATCC 43504) is the type strain. The gastric spiral organism from ferrets has been elevated recently from Campylobacter pylori subsp. mustelae to Campylobacter mustelae. We describe the similarities and differences between C. mustelae and C. pylori compared with other campylobacters, and we propose that C. mustelae should be included in the new genus Helicobacter as Helicobacter mustelae comb. nov. (type strain, ATCC 43772).

Cell-free extracts from 10 strains of Spiroplasma species were examined for 67 enzyme activities of the Embden-Meyerhof-Parnas pathway, pentose phosphate shunt, tricarboxylic acid cycle, and purine and pyrimidine pathways. The spiroplasmas were fermentative, possessing enzyme activities that converted glucose 6-phosphate to pyruvate and lactate by the Embden-Meyerhof-Parnas pathway. Substrate phosphorylation was found in all strains. A modified pentose phosphate shunt was present, which was characterized by a lack of detectable glucose 6-phosphate and 6-phosphogluconate dehydrogenase activities. Spiroplasmas could synthesize purine mononucleotides by using pyrophosphate (PPi) as the orthophosphate donor. All spiroplasmas except Spiroplasma floricola used adenosine triphosphate (ATP) to phosphorylate deoxyguanosine; no other nucleoside could be phosphorylated with ATP by any spiroplasma tested. These results contrast with those reported for other mollicutes, in which PPi serves as the orthophosphate donor in the nucleoside kinase reaction. The participation of ATP rather than PPi in this reaction is unknown in other mollicutes regardless of the nucleoside reactant. Deoxypyrimidine enzyme activities were similar but varied in the reactions involving deamination of deoxycytidine triphosphate and deoxycytidine. All Spiroplasma spp. strains had deoxyuridine triphosphatase activity. Uridine phosphorylase activity varied among strains and is possibly group dependent. As in all other mollicutes, a tricarboxylic acid cycle is apparently absent in Spiroplasma spp. Reduced nicotinamide adenine dinucleotide oxidase activity was localized in the cytoplasmic fraction of all Spiroplasma species tested. Our assays indicate that the members of the Spiroplasmataceae are essentially metabolically homogeneous in the highly conserved pathways which we studied, but differ from other mollicutes in several important respects. These differences are of probable phylogenetic significance and may provide tools for recognition of higher taxonomic levels of mollicutes.

Some of the wall-less bacteria of the class Mollicutes (mycoplasmas) have pyrophosphate (PPi)-dependent enzymic activities, including PPi-dependent phosphofructokinase (PPi-PFK), PPi-dependent nucleoside kinase, and pyruvate, orthophosphate dikinase (PPDK) activities. In most other bacteria, adenosine 5′-triphosphate (ATP), not PPi, is the cofactor of analogous enzymic reactions. Because PPi-dependent enzymes are more common among mollicutes than other bacteria, we describe here an examination of the six walled bacteria that have been reported to be phylogenetically related to the mollicutes (Clostridium innocuum, Clostridium ramosum, Erysipelothrix rhusiopathiae, Lactobacillus catenaformis, Lactobacillus vitulinus, and Streptococcus pleomorphus) for PPi-PFK, ATP-dependent PFK, phosphoenolpyruvate car boxy transphosphorylase, PPDK, and PPi- and ATP-dependent acetate kinases. Two anaerobic mollicutes, Anaeroplasma intermedium and Asteroleplasma anaerobium, were also tested. C. innocuum, E. rhusiopathiae, S. pleomorphus, and Anaeroplasma intermedium had PPi-PFK activities, whereas C. ramosum, the two lactobacilli, and Asteroleplasma anaerobium had only ATP-dependent PFK activities. Asteroleplasma anaerobium and all of the walled bacteria except E. rhusiopathiae had PPDK activities. All of the species except Asteroleplasma anaerobium and E. rhusiopathiae also had pyruvate kinase activities; the effects of allosteric activators were tested. Phosphoenolpyruvate carboxytransphosphorylase was detected by using two methods in C. innocuum, C. ramosum, and S. pleomorphus. All of the species tested had ATP-dependent acetate kinase activities, but none had detectable PPi-dependent acetate kinase activity. The occurrence of one or more PPi-dependent enzymes in the mollicutes and their walled relatives is a phenotypic indicator of the phylogenetic relatedness of these organisms. The distribution of these enzymes among members of this group substantiates the subgroups proposed by other workers who used 16S ribosomal ribonucleic acid analysis.

The description of the genus Saccharothrix is amended to include strains having either a type PII (phosphatidylethanolamine) or a type PIV (phosphatidylethanolamine and glucosamine-containing phospholipids) phospholipid pattern. A new antibiotic-producing species, Saccharothrix espanaensis (type strain, NRRL 15764), is described. Nocardiopsis mutabilis Shearer et al. 1983 is transferred to the amended genus as Saccharothrix mutabilis comb. nov. “Nocardiopsis mutabilis subsp. cryophilis” Takahashi et al. 1986 is described as a new species, Saccharothrix cryophilis, based on its physiological properties and lack of high levels of deoxyribonucleic acid relatedness to the previously described Saccharothrix species.

The diversity among 43 isolates of the genus Frankia was studied by determining levels of deoxyribonucleic acid relatedness (SI nuclease method) and DNA base compositions. The guanine + cytosine contents ranged from 66 to 75 mol%. At least nine genomic species were differentiated, including three genomic species among strains compatible with members of the genus Alnus, five genomic species among strains compatible with members of the family Elaeagnaceae, and one genomic species among strains compatible with members of the genus Casuarina. Genomic species 1, which contained proposed type strain CpI1 and nine strains that were compatible with members of the genus Alnus and were 64 to 97 % related to strain ACoN24d, is Frankia alni. Four genomic species contained single strains that were 0 to 30% related to the other genomic species. Typical strains isolated from members of the genus Casuarina were found to be very homogeneous (69 to 100% related to strain ORS020606) and clearly separated from atypical strains. The nine genomic species delineated in this study cannot be named since no phenotypic tests are available for identification.

A thorough taxonomic study of the genera Saccharopolyspora and Faenia showed that both of these taxa can be included in one genus. We propose that Faenia rectivirgula be transferred to the genus Saccharopolyspora Lacey and Goodfellow 1975 as Saccharopolyspora rectivirgula (Kurup and Agre 1983) comb. nov. A description of the new Saccharopolyspora species is presented. The type strain is strain DSM 43 747 (= ATCC 33 515). In addition, we propose that Saccharopolyspora hirsuta subsp. taberi Labeda 1987 strain NRRL B-16 173T (T = type strain) be given species status as Saccharopolyspora taberi sp. nov.

Numerical taxonomic methods were used to analyze taxonomic data gathered for 229 Vibrio strains isolated from fecal, seawater, and seafood specimens collected in Jakarta, Indonesia. Simple matching and Jaccard coefficients yielded similar results. Most of the clinical isolates were identified as Vibrio parahaemolyticus, V. cholerae, or V. mimicus. Environmental isolates included V. alginolyticus and one strain of V. vulnificus. Clusters of V. parahaemolyticus included both clinical and environmental isolates. Biotypes of V. parahaemolyticus were not associated with a specific source. Reference strains of other Vibrio species did not cluster with any of the isolates examined in this study. Four groups remained initially unidentified and were further subjected to deoxyribonucleic acid hybridization analysis, which enabled their identification as V. parahaemolyticus, V. alginolyticus, or possible new Vibrio spp. Descriptions of Vibrio species already published proved useful in identifying and classifying most of the isolates from a tropical climate.

A total of 113 violet chromogens, 45 of which produced spreading colonies characteristic of Chromobacterium fluviatile, were isolated from fresh water. These isolates and 27 other chromobacteria, 9 duplicates, and 11 reference strains were subjected to 95 characterization tests, and similarities were computed by using the coefficient of Gower. Cluster and principal coordinate analyses showed Janthinobacterium lividum to be a heterogeneous species but Chromobacterium violaceum and C. fluviatile to be well-separated and homogeneous phenons. The new, monospecific genus Iodobacter is proposed to accommodate C. fluviatile, which was originally placed in the genus Chromobacterium, despite its low guanine-plus-cytosine content (50 to 52 mol %, but 65 to 68 mol% for C. violaceum), pending the study of further isolates. The type strain of Iodobacter fluviatile comb. nov. is NCTC 11159.

A new genus and species, Pseudoamycolata halophobica, is proposed for two closely related strains formerly assigned to Amycolata (Nocardia) autotrophica. The following characteristics are important for defining the genus Pseudoamycolata•. a type IV cell wall composition (presence of miso-diaminopimelic acid, arabinose, and galactose); lack of mycolates; phospholipid type PII (presence of phosphatidylethanolamine); menaquinone MK-8(H4) as the major menaquinone; iso- and anteiso-branched fatty acids; and a guanine-plus-cytosine content of 72 mol%. P. halophobica is readily differentiated from morphologically similar members of the genera Amycolata and Amycolatopsis by phospholipid composition and menaquinone composition, respectively. In addition, it can be distinguished from Amycolata and Amycolatopsis species by low levels of deoxyribonucleic acid-deoxyribonucleic acid homology (12 to 15 and 7 to 10%, respectively) and a number of physiological characteristics. The type strain of P. halophobica is strain VKM Ac-1069 (= DSM 43089).

Alcaligenes aquamarinus and Alcaligenes faecalis subsp. homari proved to be identical to Deleya aesta in respiratory quinone type, cellular fatty acid profiles, and biochemical and physiological characteristics and as determined by deoxyribonucleic acid-deoxyribonucleic acid relatedness studies. The name Alcaligenes aquamarinus has priority. Therefore, the name Deleya aquamarina comb. nov. is proposed for the type species of the genus Deleya; the type strain should be changed from strain IAM 12551 (= ATCC 27128) (type strain of Deleya aesta) to strain IAM 12550 (= ATCC 14400) (type strain of Alcaligenes aquamarinus).

The electrophoretic mobilities of glutamate dehydrogenase and 2-oxoglutarate reductase were compared for three reference strains and 30 human, oral isolates of Fusobacterium nucleatum. Both enzymes allowed the same strains to be grouped into three electrophoretic clusters, designated groups Fn-1, Fn-2, and Fn-3. Group Fn-1 contained the type strain of F. nucleatum, strain ATCC 25586, and nine clinical isolates. Group Fn-2 comprised 20 strains and appeared to contain the strains of F. nucleatum that are isolated most commonly from oral cavities. Strain NCTC 10953 (formerly “Fusobacterium polymorphum”) was a member of this cluster. Strains of group Fn-3 were rarely isolated; this group contained three isolates and reference strain NCTC 11362, which was listed previously as “Fusobacterium fusiforme.” The deoxyribonucleic acid (DNA) base compositions of all strains were between 25 and 27 mol% guanine plus cytosine. Under optimal conditions of DNA-DNA hybridization, all of the strains exhibited high levels of DNA homology (73 to 99%) to the three reference DNA probes belonging to groups Fn-1, Fn-2, and Fn-3. However, under stringent DNA hybridization conditions there was evidence of more genetic homogeneity within each group.

We examined a collection of 151 strains of the viridans type of streptococci, which were isolated mainly from human oral cavities and included several reference strains, in an attempt to revise and improve the taxonomy of this group of bacteria. Our examinations included determinations of a high number of biochemical and physiological characteristics and serological reactivity. The resulting data revealed several hitherto unrecognized characters of taxonomic significance, and several of the species can now be more accurately defined. A diagnostic key to the taxa is presented. Strains previously identified as Streptococcus sanguis could be divided into two clearly distinct species, Streptococcus sanguis sensu stricto (type strain, ATCC 10556) and a new species, Streptococcus gordonii (type strain, ATCC 10558). Streptococcus mitis was divided into two biovars, consisting of strains possessing group O antigens and strains possessing group K antigen. The group of strains assigned to Streptococcus anginosus was biochemically and serologically heterogeneous, but the data did not allow natural subdivisions. Based on the results of this study, emended descriptions of the species Streptococcus oralis, S. mitis, and S. sanguis are provided. The classification resulting from this study is in complete agreement with previously published genetic data.

We previously reported the isolation of five strains of a thermophilic gliding organism. These strains are described here as a new genus and species, Thermonema lapsum. The isolates can be readily distinguished from other thermophilic gliding bacteria as they are apparently unicellular aerobic filaments that grow optimally at 60°C. Their cell walls are similar in ultrastructure to those of gram-negative cells, but they are susceptible to penicillin G. Our isolates can be grown on a fully defined medium containing amino acids. Oxidation-versus-fermentation tests indicate that deamination takes place. The type strain, strain 23/9, has been deposited with the American Type Culture Collection as strain ATCC 43542.

Campylobacter cinaedi and Campylobacter fennelliae possess sheathed flagella, a feature which, among organisms currently classified as Campylobacters, had been associated previously only with Campylobacter pylori. No other Campylobacter or Wolinella species possesses sheathed flagella. This feature helps to characterize the phylogenetic group that includes C. pylori, C. fennelliae, and C. cinaedi; however, Wolinella succinogenes, the fourth member of this group, does not possess sheathed flagella.

Assessment of methane and methanethiol in the headspace gas from cultures of various strains labeled Clostridium hastiforme or Clostridium subterminale allowed differentiation between these two species. C. hastiforme strains produced significantly more methane and less methanethiol than C. subterminale strains. We confirm that strain DSM 1786 (= ATCC 25772) does not belong to either of these species.