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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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

Comparison of plastid 16S rRNA (rrn16) genes from Helicosporidium spp.: evidence supporting the reclassification of Helicosporidia as green algae (Chlorophyta).

The Helicosporidia are invertebrate pathogens that have recently been identified as non-photosynthetic green algae (Chlorophyta). In order to confirm the algal nature of the genus Helicosporidium, the presence of a retained chloroplast genome in Helicosporidia cells was investigated. Fragments homologous to plastid 16S rRNA (rrn16) genes were amplified successfully from cellular DNA extracted from two different Helicosporidium isolates. The fragment sequences are 1269 and 1266 bp long, are very AT-rich (60.7 %) and are similar to homologous genes sequenced from non-photosynthetic green algae. Maximum-parsimony, maximum-likelihood and neighbour-joining methods were used to infer phylogenetic trees from an rrn16 sequence alignment. All trees depicted the Helicosporidia as sister taxa to the non-photosynthetic, pathogenic alga Prototheca zopfii. Moreover, the trees identified Helicosporidium spp. as members of a clade that included the heterotrophic species Prototheca spp. and the mesotrophic species Chlorella protothecoides. The clade is always strongly supported by bootstrap values, suggesting that all these organisms share a most recent common ancestor. Phylogenetic analyses inferred from plastid 16S rRNA genes confirmed that the Helicosporidia are non-photosynthetic green algae, close relatives of the genus Prototheca (Chlorophyta, Trebouxiophyceae). Such phylogenetic affinities suggest that Helicosporidium spp. are likely to possess Prototheca-like organelles and organelle genomes.

Chlorella↗

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↗

Kerstersia gyiorum gen. nov., sp. nov., a novel Alcaligenes faecalis-like organism isolated from human clinical samples, and reclassification of Alcaligenes denitrificans Rüger and Tan 1983 as Achromobacter denitrificans comb. nov.

A polyphasic taxonomic study was performed on nine isolates recovered from various human clinical samples. Phenotypically, these isolates resembled Alcaligenes faecalis. Whole-cell protein analysis distinguished two different species, and this was confirmed by DNA-DNA hybridizations. Cellular fatty acid analysis and 16S rDNA sequence analysis indicated that these isolates were related to the genera Alcaligenes, Bordetella, Achromobacter and Pigmentiphaga and belonged to the family Alcaligenaceae. On the basis of the results of this study, the organisms were classified in a novel genus, Kerstersia gen. nov. This genus comprises one species, Kerstersia gyiorum sp. nov. (type strain LMG 5906(T)=API 184-2-84(T)=CCUG 47000(T)), and several unnamed isolates. The DNA G+C content of members of the genus Kerstersia is between 61.5 and 62.9 mol%. On the basis of previously published DNA-DNA hybridization results and data from chemotaxonomic studies, it is proposed that Alcaligenes denitrificans Rüger and Tan 1983 be reclassified as Achromobacter denitrificans comb. nov.

Achromobacter↗

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↗

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↗

Reclassification of Bisgaard taxon 33, with proposal of Volucribacter psittacicida gen. nov., sp. nov. and Volucribacter amazonae sp. nov. as new members of the Pasteurellaceae.

A total of 25 strains isolated from parrots, budgerigars, parakeets (Psittaciformes) and a chicken, mostly associated with respiratory disease or septicaemia, were classified as a new genus, Volucribacter gen. nov., within the family Pasteurellaceae, on the basis on unique phenotypic characteristics and clear monophyly as determined by 16S rRNA gene sequence comparison. Comparison of 16S rRNA gene sequences from six strains showed at least 98.8 % similarity and the closest similarity outside the genus was found to Bisgaard taxon 34 and to Pasteurella avium, at 94.6 and 94.5 %, respectively. Phenotypes that separate the new genus from other genera of the Pasteurellaceae included at least two characters. The genus includes two species, Volucribacter psittacicida sp. nov. and Volucribacter amazonae sp. nov., corresponding to the two biovars previously outlined, underlining that most isolates have been obtained from psittacine birds. The two species can be separated by fermentation of meso-inositol, (-)-L-fucose, maltose and dextrin and a positive ONPG test. The type strains for Volucribacter psittacicida and Volucribacter amazonae are respectively Gerl. 236/81(T) (=CCUG 47536(T)=DSM 15534(T)) and 146/S8/89(T) (=CCUG 47537(T)=DSM 15535(T)).

Animals↗

Reclassification of Cellulosimicrobium variabile Bakalidou et al. 2002 as Isoptericola variabilis gen. nov., comb. nov.

As already depicted in the original publication, the type strain of the species Cellulosimicrobium variabile Bakalidou et al. 2002, DSM 10177(T), does not cluster unambiguously with the type species, Cellulosimicrobium cellulans DSM 43879(T), in phylogenetic analysis. Strain DSM 10177(T) is moderately related to the recently described species Xylanimonas cellulosilytica, Promicromonospora pachnodae and Xylanibacterium ulmi, forming a lineage that branches between C. cellulans and members of the genus Promicromonospora in most dendrograms generated on the basis of different algorithms and reference strains. The type strains of the two Cellulosimicrobium species resemble each other in morphology, composition of fatty acids, DNA G+C content, phospholipids and the presence of lysine in position 3 of the peptide subunit of peptidoglycan. However, the two strains differ from each other in cell-wall sugars and in the amino acid composition of the A4alpha-type peptidoglycan, which contains serine and aspartic acid in C. cellulans, whereas only aspartic acid is present in the interpeptide bridge of C. variabile. This type is also present in Xylanimonas cellulosilytica XIL07(T), but not in the neighbouring species P. pachnodae DSM 12657(T), which exhibits the L-lys-L-ser-D-Glu type. On the basis of distinct phylogenetic position and the amino acid composition of peptidoglycan, a novel genus and combination for C. variabile, Isoptericola variabilis gen. nov., comb. nov., is proposed.

Actinomycetales↗