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PubMed2001

Genetic reclassification of porcine enteroviruses.

The genetic diversity of porcine teschoviruses (PTVs; previously named porcine enterovirus 1) and most serotypes of porcine enteroviruses (PEVs) was studied. Following the determination of the major portion of the genomic sequence of PTV reference strain Talfan, the nucleotide and derived amino acid sequences of the RNA-dependent RNA polymerase (RdRp) region, the capsid VP2 region and the 3' non-translated region (3'-NTR) were compared among PTVs and PEVs and with other picornaviruses. The sequences were obtained by RT-PCR and 3'-RACE with primers based on the sequences of Talfan and available PEV strains. Phylogenetic analysis of RdRp/VP2 and analysis of the predicted RNA secondary structure of the 3'-NTR indicated that PEVs should be reclassified genetically into at least three groups, one that should be assigned to PTVs and two PEV subspecies represented by strain PEV-8 V13 and strain PEV-9 UKG410/73.

Animals↗
PubMed1982

Reclassification of Corynebacterium pyogenes (Glage) in the genus Actinomyces, as Actinomyces pyogenes comb.nov.

Corynebacterium pyogenes (Glage) differs to such an extent from the type species of Corynebacterium, Corynebacterium diphtheriae (Lehmann and Neumann), that it cannot be retained in this genus. Numerical phenetic and chemical data indicate a close relationship between Corynebacterium pyogenes and the species Actinomyces bovis (Harz). It is proposed that Corynebacterium pyogenes be reclassified in the genus Actinomyces, as Actinomyces pyogenes (Glage) comb.nov.

Actinomyces↗
PubMed1982

Reclassification of 'Corynebacterium haemolyticum' (MacLean, Liebow & Rosenberg) in the genus Arcanobacterium gen.nov. as Arcanobacterium haemolyticum nom.rev., comb.nov.

'Corynebacterium haemolyticum' (MacLean, Liebow & Rosenberg) differs to such an extent from the type species of Corynebacterium, C. diphtheriae (Lehmann & Neumann), that it should be removed from this genus. Chemical and numerical phenetic data indicate that 'C. haemolyticum' is a distinct taxon worthy of generic status. A new genus, Arcanobacterium, is described for the species A. haemolyticum (MacLean, Liebow & Rosenberg) nov.rev., comb.nov. The genus is tentatively placed within the 'coryneform group of bacteria'. The type species of the genus is Arcanobacterium haemolyticum and the type strain is ATCC 9345.

Corynebacterium↗
PubMed1998

Psychroflexus torquis gen. nov., sp. nov., a psychrophilic species from Antarctic sea ice, and reclassification of Flavobacterium gondwanense (Dobson et al. 1993) as Psychroflexus gondwanense gen. nov., comb. nov.

A group of sea-ice-derived psychrophilic bacterial strains possessing the unusual ability to synthesize the polyunsaturated fatty acids eicosapentaenoic acid (20:5 omega 3) and arachidonic acid (20:4 omega 6) belong to the Family Flavobacteriaceae (Flexibacter-Bacteroides-Flavobacterium phylum), according to 16S rRNA sequence analysis. Surprisingly, the isolates were also found to cluster closely to the moderately halophilic and psychrotrophic species [Flavobacterium] gondwanense (sequence similarity 97.8-98.1%). The whole-cell fatty acid profiles of this group and [Flavobacterium] gondwanense were very similar and distinct from other related flavobacteria. The sea ice strains and [Flavobacterium] gondwanense differed substantially in terms of ecophysiology, possibly representing divergent adaptations to sympagic and planktonic marine habitats, respectively. Evidence based on phylogeny and fatty acid profiles supports the conclusion that the taxa are close relatives distinct from other bacterial groups. It is thus proposed that the sea ice strains represent a novel taxon designated Psychroflexus torquis gen. nov., sp. nov. (type strain ACAM 623T) while [Flavobacterium] gondwanense becomes Psychroflexus gondwanense gen. nov., comb. nov.

Antarctic Regions↗
PubMed1996

Reclassification of the Penicillium roqueforti group into three species on the basis of molecular genetic and biochemical profiles.

Penicillium roqueforti is currently divided into two varieties, one used for cheese starter cultures, P. roqueforti var. roqueforti, and one ubiquitous patulin-producing variety, P. roqueforti var. carneum. The ribosomal regions comprising the 5.8S gene and the internal transcribed spacers, ITS I and ITS II, have been analysed from 10 isolates belonging to each variety. The 10 P. roqueforti var. carneum isolates were separated into two groups of five on the basis of 12 base-pair differences in the ITS regions. One of the groups of P. roqueforti var. carneum, in the following designated P. carneum, differed from P. roqueforti var. roqueforti, here designated P. roqueforti, in just two positions, while the other group, here called P. paneum, differed from P. roqueforti in 12 positions. Random Amplified Polymorphic DNA (RAPD) analysis substantiated these findings, and a comparison of secondary metabolites produced by the three groups showed that the P. roqueforti isolates all produce Penicillium Roqueforti (PR) toxin, marcfortines and fumigaclavine A, while the P. carneum isolates produce patulin, penitrem A and mycophenolic acid, as well as unidentified metabolites. P. paneum produces secondary metabolites in five chromophore families including the known mycotoxins patulin and botryodiploidin. On the basis of these findings it is proposed that P. roqueforti is reclassified into three species named P. roqueforti, P. carneum and P. paneum.

Base Sequence↗
PubMed2003

Description of Alcanivorax venustensis sp. nov. and reclassification of Fundibacter jadensis DSM 1 21 78T (Bruns and Berthe-Corti 1999) as Alcanivorax jadensis comb. nov., members of the emended genus Alcanivorax.

Two strains of a novel bacterium were isolated independently of each other, from different depths in the Mediterranean Sea, within a time period of 7 months, using two different isolation approaches that were focused on different objectives. Both strains, designated ISO1 and ISO4T, were halophilic, Gram-negative, strictly aerobic, straight rods that were oxidase- and catalase-positive. Both strains produced mucoid colonies in some defined minimal media and were able to grow with organic acids and some alkanes; they were also able to accumulate intracellular poly-beta-hydroxybutyrate granules. The G + C content of the DNA of strain ISO4T was 66 mol%. Comparative analysis of 16S rRNA gene sequences showed that the closest described species to the novel strains were Alcanivorax borkumensis and Fundibacter jadensis, both of the gamma-Proteobacteria. Both of these recognized species were originally isolated from North Sea waters and are able to degrade aliphatic compounds, a property shared with strains ISO1 and ISO4T. However, strains ISO1 and ISO4T were different from A. borkumensis and F. jadensis, not only in their 16S rDNA sequences but also in the motility of their cells (by polar flagella) and by the presence of C19:Ocyclo in their cellular fatty acids, among other differential features. On the basis of biochemical and molecular data, it is suggested that strains ISO1 and ISO4T be recognized as a novel species of the genus Alcanivorax, for which the name Alcanivorax venustensis (ISO4T =DSM 13974T =CECT 5388T) is proposed. On the basis of its high phenotypic similarity and close phylogenetic relatedness to A. borkumensis, it is also proposed that F. jadensis (DSM 12178T) be reclassified as Alcanivorax jadensis in the genus Alcanivorax, and that the description of the genus Alcanivorax be emended.

Base Composition↗
PubMed2003

Reclassification of 'Blastobacter viscosus' 7d and 'Blastobacter aminooxidans' 14a as Xanthobacter viscosus sp. nov. and Xanthobacter aminoxidans sp. nov.

On the basis of morphological, physiological and genotypic properties 'Blastobacter viscosus' 7d and 'Blastobacter aminooxidans' 14a are proposed as new species of the genus Xanthobacter, Xanthobacter viscosus (type strain 7dT =VKM B-2253T =ATCC BAA-298T) and Xanthobacter aminoxidans corrig. (type strain 14aT =VKM B-2254T =ATCC BAA-299T).

Base Sequence↗
PubMed2003

Reclassification of 'Pseudomonas fluorescens subsp. cellulosa' NCIMB 10462 (Ueda et al. 1952) as Cellvibrio japonicus sp. nov. and revival of Cellvibrio vulgaris sp. nov., nom. rev. and Cellvibrio fulvus sp. nov., nom. rev.

'Pseudomonas fluorescens subsp. cellulosa' NCIMB 10462 has been demonstrated by a polyphasic taxonomic approach to be a member of the genus Cellvibrio. 16S rDNA sequence analysis suggests that this is the only genus that could accept this specimen. The sequence is 95.5% similar to that of Cellvibrio mixtus subsp. mixtus ACM 2601T (the type strain of the type species of the genus), which is its closest relation. The genomic DNA G + C content was determined to be 53.3 mol%, which is similar to the values obtained for the validly described Cellvibrio species. DNA-DNA hybridization experiments have shown that strain NCIMB 10462T (= NCDO 2697T) represents a novel species; therefore, it is proposed that it be designated as the type strain of the novel species Cellvibrio japonicus sp. nov. This study also used 16S rDNA analysis, DNA-DNA hybridization experiments and phenotypic testing to revive the species Cellvibrio vulgaris sp. nov., nom. rev. and Cellvibrio fulvus sp. nov., nom. rev. C. vulgaris NCIMB 8633T (=LMG 2848T) and C. fulvus NCIMB 8634T (=LMG 2847T) are the proposed type strains.

Base Composition↗
PubMed2003

Reclassification of ATCC 9341 from Micrococcus luteus to Kocuria rhizophila.

Strain ATCC 9341, currently known as Micrococcus luteus, has been designated as a quality-control strain in a number of applications. It is also cited as the standard culture in several official methods and manuals, as well as the Code of Federal Regulations. Over the years, it has become apparent that ATCC 9341 does not resemble other M. luteus strains; however, its phenotypic characteristics alone were ambiguous. Recently, a polyphasic study was performed in which molecular data were combined with cytochemical properties and physiological characteristics. The results clearly indicate that ATCC 9341 is a member of the genus Kocuria. Thus, it is proposed to reclassify ATCC 9341 as Kocuria rhizophila and to alert users worldwide of this name change.

DNA, Bacterial↗
PubMed2003

Reclassification of Desulfotomaculum auripigmentum as Desulfosporosinus auripigmenti corrig., comb. nov.

The species Desulfotomaculum auripigmentum is reclassified as Desulfosporosinus auripigmenti corrig., comb. nov. on the basis of morphological and physiological traits, phylogenetic position and chemotaxonomic properties. Characteristics supplementary to those provided in the original description reveal that the type strain, DSM 13351(T) (=ATCC 700205(T)), forms oval, subterminal to terminal spores, possesses LL-diaminopimelic acid and contains MK-7 as the predominant menaquinone, while the whole-cell methanolysate contains even-carbon, straight-chain saturated and mono-unsaturated fatty acids and 1,1-dimethylacetals as major components. DNA-DNA reassociation values below 30 % for Desulfosporosinus orientis DSM 765(T) and Desulfosporosinus meridiei DSM 13257(T) demonstrate that strain DSM 13351(T) shows sufficient genomic differences to maintain its species status. Lack of motility, a smaller cell diameter and the ability to use malate and glycerol as electron donors and fumarate and arsenate as electron acceptors are the main properties that differentiate Desulfosporosinus auripigmenti from the other two species of the genus.

DNA, Bacterial↗
PubMed2003

Description of Enterococcus canis sp. nov. from dogs and reclassification of Enterococcus porcinus Teixeira et al. 2001 as a junior synonym of Enterococcus villorum Vancanneyt et al 2001.

Strains from anal swabs and chronic otitis externa in dogs were shown to be phylogenetically related to the Enterococcus faecium species group. They shared a number of phenotypic characteristics with these species, but they could be easily differentiated by biochemical reactions. In addition, the canine strains were unusual in their nearly complete failure to grow on sodium azide-containing enterococci-selective media and in their Voges-Proskauer reactions (usually negative). By using 16S rRNA sequencing and DNA-DNA hybridization of representative strains, as well as tDNA interspacer gene PCR and SDS-PAGE of whole-cell proteins, the group of canine strains was shown to constitute a novel enterococcal species. The name Enterococcus canis sp. nov. is proposed for this species, with LMG 12316T (= CCUG 46666T) as the type strain. Concurrently, the taxonomic situation and nomenclatural position of Enterococcus porcinus were investigated. As no phenotypic or genotypic differences were found between this species and Enterococcus villorum, the name E. porcinus is considered to be a junior synonym of E. villorum.

Animals↗
PubMed2003

Characterization of novel psychrophilic clostridia from an Antarctic microbial mat: description of Clostridium frigoris sp. nov., Clostridium lacusfryxellense sp. nov., Clostridium bowmanii sp. nov. and Clostridium psychrophilum sp. nov. and reclassification of Clostridium laramiense as Clostridium estertheticum subsp. laramiense subsp. nov.

Taxonomic studies were performed on four strains (D-1/D-an/IIT, C/C-an/B1T, A-1/C-an/C1T and A-1/C-an/IT) of anaerobic, gram-positive, spore-forming bacteria originally isolated from a mat sample retrieved from a shallow, moated area around Lake Fryxell, an Antarctic freshwater lake. Phylogenetic analyses based on 16S rRNA gene sequence data indicated that these strains are affiliated with cluster I clostridia and form a coherent group with Clostridium estertheticum and Clostridium laramiense. Similarity values among 16S rRNA gene sequences within this assemblage ranged between 96.7 and 99.8%. Despite the close phylogenetic relationship, several distinguishing phenotypic traits were found among the novel strains using a polyphasic approach. All strains were psychrophilic, but the temperature optimum for growth differed markedly, ranging from 4 to 16 degrees C. In addition, substrate utilization patterns, fermentation end products, cellular fatty acid profiles and morphological traits enabled a clear differentiation between the strains. DNA-DNA hybridization experiments revealed that each of the four novel strains represents a distinct species, with DNA-DNA similarity values to related strains in the range 16-62%. In contrast, the type strains of C. estertheticum and C. laramiense shared 79% DNA-DNA similarity, indicating a close relationship at the species level. On the basis of genetic and phenotypic properties, it is proposed to designate four novel species of the genus Clostridium to harbour the newly isolated strains: Clostridium frigoris sp. nov. (type strain D-1/D-an/IIT=DSM 14204T=ATCC BMAA-579T), Clostridium lacusfryxellense sp. nov. (type strain C/C-an/B1T=DSM 14205T=ATCC BAA-580T), Clostridium bowmaniisp. nov. (type strain A-1/C-an/C1T=DSM 14206T=ATCC BAA-581T) and Clostridium psychrophilum sp. nov. (type strain A-1/C-an/IT=DSM 14207T=ATCC BAA-582T). It is also proposed to unite C. laramiense and C. estertheticum under C. estertheticum. The subspecies C. estertheticum subsp. laramiense subsp. nov. is established, represented by strain ATCC 51254T (=DSM 14884T). The type strain of C. estertheticum subsp. estertheticum remains NCIMB 12511T (=DSM 8809T).

Antarctic Regions↗
PubMed2003

Reclassification of Desulfobacterium macestii as Desulfomicrobium macestii comb. nov.

Phylogenetic, chemotaxonomic and metabolic data obtained for Desulfobacterium macestii indicate that this species is not a member of the genus Desulfobacterium, but of the genus Desulfomicrobium. Phylogenetically, it is closely related to Desulfomicrobium baculatum and Desulfomicrobium norvegicum, but it can be differentiated from these species by its metabolic properties. It is therefore proposed to reclassify Desulfobacterium macestii as Desulfomicrobium macestii comb. nov.

DNA, Bacterial↗
PubMed2003

Reclassification of Vibrio hollisae as Grimontia hollisae gen. nov., comb. nov.

The taxonomic positions of three representative strains of Vibrio hollisae (LMG 17719(T), LMG 21416 and LMG 21538) were investigated by means of 16S rDNA sequences and phenotypic data. V. hollisae strains (GenBank/EMBL accession nos AJ514909-AJ514911) shared 99.5 % 16S rDNA sequence similarity, but had only 94.6 % similarity to their closest phylogenetic neighbour, Enterovibrio norvegicus. 16S rDNA sequence similarity of V. hollisae and Vibrio cholerae was only 91 %. These results suggest that V. hollisae should be placed into a novel genus, for which the name Grimontia gen. nov. is proposed.

DNA, Bacterial↗
PubMed2003

Reclassification of Sulfolobus hakonensis Takayanagi et al. 1996 as Metallosphaera hakonensis comb. nov. based on phylogenetic evidence and DNA G+C content.

The taxonomic status of Sulfolobus hakonensis Takayanagi et al. 1996 was re-evaluated by fresh determinations of the 16S rDNA sequence and G+C content of the genomic DNA of the type strain, HO1-1(T). The 16S rDNA sequence of strain HO1-1(T) showed 98 % similarity to those of two Metallosphaera species and only </=92 % similarity to those of other Sulfolobus species. The DNA G+C content (46.2 mol%) is in accordance with those of Metallosphaera species. In addition, strain HO1-1(T) shares some phenotypic properties with Metallosphaera species; however, it can be differentiated from them by its capacity to utilize FeS and tetrathionate and the absence of flagella. Therefore, it is proposed that Sulfolobus hakonensis should be transferred to the genus Metallosphaera as Metallosphaera hakonensis comb. nov.

Base Composition↗
PubMed1994

Incidence of childhood cancer in Osaka, Japan, 1971-1988: reclassification of registered cases by Birch's scheme using information on clinical diagnosis, histology and primary site.

In 1971-1988, 4,021 malignant tumors occurring among children under 15 years of age were registered in the Osaka Cancer Registry, a population-based registry which covers Osaka Prefecture, Japan. These patients were reclassified into 12 diagnostic groups by Birch's scheme using information on clinical diagnosis, histology and primary site. The annual age-standardized incidence rate for childhood cancer per million children was 130.3 for males and 104.9 for females in 1971-88. Comparing the incidence rates for both sexes in 1981-88 with those in 1971-80 in Osaka, we observed a significant decrease of acute non-lymphocytic leukemia (ANLL) and a significant increase of all cancers, acute lymphocytic leukemia, non-Hodgkin lymphoma, sympathetic nervous system tumors, soft-tissue sarcomas, and gonadal and germ-cell tumors. Age-standardized incidence rates in around 1971-80 of the above-mentioned diagnostic groups were compared among 4 population-based registries; Osaka, Miyagi (Japan), SEER (U.S.), and the National Registry of Childhood Tumors (England and Wales). Rates for ANLL and gonadal and germ-cell tumors were higher and those for other diagnostic groups were lower in Osaka, especially for Hodgkin's disease. Thus, in 1980-88 in Osaka, rates for Hodgkin's disease remained low and rates for gonadal and germ-cell tumors increased, though rates for other cancers appeared to resemble the levels in caucasian populations. The incidence of childhood cancer in Japan was estimated according to the diagnostic groups in Birch's scheme.

Adolescent↗
PubMed1989

Malignant angioendotheliomatosis. Reclassification as an angiotropic lymphoma.

A 70-year-old woman with chronic edema of the lower limbs was diagnosed as having a "malignant angio-endotheliomatosis," because histologic examination showed a strict intravascular location of a malignant proliferation. Immunochemical studies actually disclosed the lymphomatous origin of malignant cells. The recent literature regarding the nosology of this rare condition is reviewed.

Aged↗