- Volume 44, Issue 4, 1994

The genus Gordona was proposed by Tsukamura in 1971 (M. Tsukamura, J. Gen. Microbiol. 68:15-24,1971) and was revived in 1988 by Stackebrandt et al. (E. Stackebrandt, J. Smida, and M. D. Collins, J. Gen. Appl. Microbiol. 34:341-348, 1988) to accommodate Rhodococcus species containing mycolic acids with 48 to 66 carbon atoms and MK-9(H2) as the predominant menaquinone type. On the basis of mycolic acid composition as determined by high-performance liquid chromatography, DNA-DNA similarity data (S1 nuclease procedure), and the rRNA gene restriction patterns of the type strains, we propose that Rhodococcus chubuensis Tsukamura 1982 is a subjective synonym of Gordona sputi (Tsukamura 1978) Stackebrandt 1989 comb. nov. We found that R. chubuensis type strain ATCC 33609, and G. sputi type strain ATCC 29627 exhibit identical mycolic acid profiles, 97% DNA relatedness (difference in thermal denaturation midpoints, 1.0°C), and similar ribotypes after PvuII endonuclease digestion. Thus, as defined by the type strains and considering the priority of the name G. sputi, these two species should be regarded as a single species named Gordona sputi; an emended description of this taxon is given.

We investigated the taxonomic status of Rhodococcus aichiensis DSM 43978T (T = type strain) and Nocardia amarae DSM 43392T by using both chemotaxonomic and genetic methods. The occurrence of MK-9(H2) as the predominant menaquinone, the presence of relatively long-chain mycolic acids (48 to 62 carbon atoms), and the phylogenetic position as determined by a 16S ribosomal DNA sequence analysis provide strong evidence that both R. aichiensis and N. amarae should be transferred to the genus Gordona as Gordona aichiensis and Gordona amarae, respectively.

A novel extremely halophilic archaeon (archaebacterium) was isolated from rock salt obtained from an Austrian salt mine. The deposition of the salt is thought to have occurred during the Permian period (225 × 106 to 280 × 106 years ago). This organism grew over a pH range of 6.8 to 9.5. Electron microscopy revealed cocci in tetrads or larger clusters. The partial 16S rRNA sequences, polar lipid composition, and menaquinone content suggested that this organism was related to members of the genus Halococcus, while the whole-cell protein patterns, the presence of several unknown lipids, and the presence of pink pigmentation indicated that it was different from previously described coccoid halophiles. We propose that this isolate should be recognized as a new species and should be named Halococcus salifodinae. The type strain is Blp (= ATCC 51437 = DSM 8989). A chemotaxonomically similar microorganism was isolated from a British salt mine.

The genetic relationships among Eubacterium species were assessed by using DNAs from American Type Culture Collection type strains of 10 species and two subspecies of the genus Eubacterium, i.e., Eubacterium aerofaciens, E. alactolyticum, E. brachy, E. lentum, E. limosum, E. nodatum, E. rectale, E. saburreum, E. timidum, E. yurii subsp. yurii, and E. yurii subsp. margaretiae. The DNA base compositions (determined by high-performance liquid chromatography) of these species varied widely, from 38 to 62 mol% G+C. Seven Eubacterium species showed significant differences (nearly 10%) in G+C content compared with E. limosum, the type species of the genus. DNA-DNA hybridization (by the membrane filter method) showed that two subspecies, E. yurii subsp. yurii and E. yurii subsp. margaretiae, and two strains of E. timidum exhibited high levels of DNA relatedness. However, the DNA reassociations among the 10 Eubacterium species studied were 1 to 16%. None of the species examined shared a high level of DNA reassociation with the type species of the genus Eubacterium. The protein profile patterns (determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis) of whole bacterial cells from these Eubacterium species were distinct, and no major peptide bands were shared among the 10 Eubacterium species. Therefore, the Eubacterium species we tested must be considered genetically distinct from each other.

The eubacterial genus Rickettsia belongs to the α subgroup of the phylum Proteobacteria. This genus is usually divided into three biotypes on the basis of vector host and antigenic cross-reactivity characteristics. However, the species Rickettsia bellii does not fit into this classification scheme; this organism has characteristics common to both the spotted fever group and the typhus group biotypes and also exhibits some unique features. Sequences of the 16S rRNA and 23S rRNA genes from Rickettsia rickettsii (spotted fever group), Rickettsia prowazekii (typhus group), and R. bellii were studied to determine the position of R. bellii in the rickettsial classification scheme. The 23S rRNA gene sequences described in this paper are the first 23S rRNA sequences reported for any member of the Rickettsiaceae. The 23S rRNA gene contains substantially more phylogenetic information than is contained in the 16S rRNA sequences, and the 23S rRNA gene sequence has diverged about 1.9 times faster in the three Rickettsia species which we studied. Taken together, the molecular data obtained from the two genes indicate that R. bellii is not a member of either the spotted fever group or the typhus group; rather, this organism appears to be the product of a divergence which predates the separation of the genus into the spotted fever group and the typhus group. Consequently, different combinations of the ancestral characteristics retained by R. bellii have been retained in the more derived lineages of the genus. A comparison of the 16S rRNA and 23S rRNA gene sequences of Rickettsia strains with other proteobacterial sequences confirmed that the genus Rickettsia is a unique deeply branching member of the α subgroup of the Proteobacteria and that the Rickettsia species form a monophyletic cluster. While divergence of the contemporary members of the genus Rickettsia occurred recently, the unique evolutionary line represented by this genus appears to be very old.

A new halophilic chemoorganotrophic bacterium (strain H150T [T = type strain]) related to Haloincola saccharolytica was isolated from the hypersaline sediments of Retba Lake in Senegal. This organism was a rod-shaped, motile, non-spore-forming, gram-negative obligate anaerobe that grew optimally in the presence of 10% NaCl and at 40°C. The DNA base composition was 31.7 ± 0.3 mol% guanine plus cytosine. The fermentation products from glucose were acetate, H2, and CO2. The fermentable substrates included cellobiose, fructose, glucose, maltose, lactose, glycerol, mannitol, mannose, ribose, raffinose, and sucrose. Penicillin G, cephalosporin C, novobiocin, vancomycin, and chloramphenicol inhibited growth. As determined by DNA-DNA hybridization, strain H150T was 71% related to H. saccharolytica, with ΔTm value of 6.0°C. However, strain H150T exhibited marked phenotypic differences, particularly in the range of substrates used, when it was compared with the type species of the genus Haloincola. For this isolate we propose the name Haloincola saccharolytica subsp. senegalensis subsp. nov.; strain H150 (= DSM 7379) is the type strain of this taxon.

The 16S rRNA gene sequences of 34 named and unnamed clostridial strains were determined by PCR direct sequencing and were compared with more than 80 previously determined clostridial sequences and the previously published sequences of representative species of other low- G+C-content gram-positive genera, thereby providing an almost complete picture of the genealogical interrelationships of the clostridia. The results of our phylogenetic analysis corroborate and extend previous findings in showing that the genus Clostridium is extremely heterogeneous, with many species phylogenetically intermixed with other sporeforming and non-sporeforming genera. The genus Clostridium is clearly in need of major revision, and the rRNA structures defined in this and previous studies may provide a sound basis for future taxonomic restructuring. The problems and different possibilities for restructuring are discussed in light of the phenotypic and phylogenetic data, and a possible hierarchical structure for the clostridia and their close relatives is presented. On the basis of phenotypic criteria and the results of phylogenetic analyses the following five new genera and 11 new combinations are proposed: Caloramator gen. nov., with Caloramator fervidus comb. nov.; Filifactor gen. nov., with Filifactor villosus comb. nov.; Moorella gen. nov., with Moorella thermoacetica comb. nov. and Moorella thermoautotrophica comb. nov.; Oxobacter gen. nov., with Oxobacter pfennigii comb. nov.; Oxalophagus gen. nov., with Oxalophagus oxalicus comb. nov.; Eubacterium barkeri comb. nov.; Paenibacillus durum comb. nov.; Thermoanaerobacter kivui comb. nov.; Thermoanaerobacter thermocopriae comb. nov.; and Thermoanerobacterium thermosaccharolyticum comb. nov.

Our present knowledge concerning the genotypic, chemotaxonomic, and phenotypic characteristics of members of the genus Flavobacterium and some related genera, including the genus Weeksella, was used to revise the classification of these organisms. The generically misclassified organisms Flavobacterium balustinum, Flavobacterium gleum, Flavobacterium indologenes, Flavobacterium indoltheticum, Flavobacterium meningosepticum, and Flavobacterium scophthalmum are included in a new genus, Chryseobacterium, with Chryseobacterium gleum as the type species. The generically misclassified organism Flavobacterium breve is included in the revived genus Empedobacter as Empedobacter brevis, whereas the generically misclassified organism Weeksella zoohelcum is included in the new genus Bergeyella as Bergeyella zoohelcum.

Proliferative ileitis of hamsters is consistently associated with the presence of intracellular bacteria in affected ileal epithelial cells. The 16S rRNA gene sequence of the putative etiologic agent of proliferative ileitis was determined by using cell culture-maintained organisms. The highest level of relatedness (98.4%) was observed with a newly described obligately intracellular bacterium obtained from porcine intestines, and the level of homology with Desulfovibrio desulfuricans was 87.5%.

Two-by-two sequence alignment revealed that the levels of homology between 16S rRNA gene sequences of strains belonging to the two biovars of Ureaplasma urealyticum (class Mollicutes) ranged from 98.5 to 98.9%. Within the biovars, three serovars of the T960 biovar exhibited levels of homology of ≥99.7%, and the four serovars of the parvo biovar exhibited levels of homology of ≥99.7%. A dendrogram of the Mycoplasma pneumoniae-Ureaplasma clade of the Mollicutes reflected the distinctiveness of the biovars.

The International Committee on Systematic Bacteriology Subcommittee on the Taxonomy of Campylobacter and Related Bacteria has agreed in principle on minimum requirements for the description of new species of the family Campylobacteraceae. These requirements, as well as methods for determining specific characteristics, are proposed as minimal standards for the description of new species. In addition to specified phenotypic characteristics, molecular data are required. The placement of a new species should be consistent with the current view on classification usually based on methods such as nucleic acid sequencing, hybridization, or protein fingerprinting.

The qualitative and quantitative monosaccharide spectra of purified yeast cell walls revealed that there are three phylogenetically distinct lineages of sterigma-forming basidiomycetous yeasts: (i) Kurtzmanomyces and Sterigmatomyces species, which contain high levels of mannose; (ii) Tilletiopsis species, which contain glucose, galactose, and small amounts of mannose; and (iii) Fellomyces, Kockovaella, Sterigmatosporidium, and Tsuchiyaea species, which appear to be closely related on the basis of their high levels of glucose and the presence of xylose. The yeast cell wall neutral sugars of Sporobolomyces antarcticus and Sterigmatomyces aphidis were similar to those of members of the genus Tilletiopsis. However, the possibility that these taxa are conspecific was eliminated by the results of a random amplified polymorphic DNA (RAPD) analysis. The conspecificity of Mrakia frigida and Mrakia nivalis, the conspecificity of Mrakia gelida and Mrakia stokesii, and the conspecificity of Sterigmatomyces halophilus and Sterigmatomyces indicus were confirmed by RAPD analysis results. RAPD analysis was found to be a simple and highly sensitive method which can be used to differentiate species at the DNA level; it can replace nuclear DNA-nuclear DNA hybridization experiments for species identification, characterization, and delimitation.

Several strains of the four sibling species of the genus Saccharomyces (S. bayanus, S. cerevisiae, S. paradoxus, and S. pastorianus) were characterized by using a rapid and simple method of restriction analysis of mitochondrial DNA. Patterns obtained with four-cutter endonucleases (such as AluI, DdeI, HinfI, and RsaI) made it possible to differentiate each species. 5. cerevisiae and S. paradoxus presented a greater number of large fragments than S. pastorianus and S. bayanus with all the assay enzymes. With AluI and DdeI, species-specific bands clearly permitted differentiation between S. pastorianus and S. bayanus. To test the resolution of this method, wild Saccharomyces strains were analyzed. The correct assignment of these strains to a known taxon by this rapid method was confirmed by means of electrophoretic karyotyping.

Partial 26S ribosomal DNA sequences of species assigned to the genera Hanseniaspora, Kloeckera, Dekkera, Brettanomyces, and Eeniella were determined. A phylogenetic analysis of the sequences showed that the genus Eeniella is derived within the genus Brettanomyces and that the genus Hanseniaspora (anamorph Kloeckera) is not closely related to the genus Dekkera (anamorph Brettanomyces). As a consequence, the name Eeniella is reduced to synonymy with the name Brettanomyces. In addition, our data do not support reassignment of certain Hanseniaspora species to the recently revived genus Kloeckeraspora.

A comparative electrophoretic karyotyping study was performed with several certified authentic strains of the four species that could be distinguished by nuclear DNA (nDNA)-nDNA reassociation data within the sensu stricto group of the genus Saccharomyces. A multivariate analysis of the polymorphisms observed in pulsed-fleld gel electrophoretic profiles (numbers and molecular weights of separated units) revealed that the strains could be separated into four clusters that corresponded to the taxa that were distinguished on the basis of nDNA comparisons. Discrepancies between nDNA reassociation data and membership in the corresponding clusters were observed only with two strains of Saccharomyces paradoxus. Blind tests carried out with additional industrial strains confirmed the general validity of the statistical model created for comparison of karyotypes within the species included in Saccharomyces sensu stricto.

Some Candida species which can use methanol as a sole carbon source were studied by performing chemotaxonomic tests; we determined the ubiquinone systems of these organisms, their DNA base compositions, their electrophoretic karyotypes, and their DNA relatedness values. The type strains of Candida methanolophaga and Candida succiphila had similar DNA base compositions and exhibited 90% DNA relatedness. All Candida boidinii and Candida methylica strains had DNA G+C contents of 30.8 to 31.0 mol%, and these organisms exhibited 87 to 101% DNA relatedness to the type strain of C. boidinii. We propose that C. methanolophaga and C. methylica should be synonyms of C. succiphila and C. boidinii, respectively.