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PubMed2004

Reclassification of Amycolatopsis mediterranei DSM 46095 as Amycolatopsis rifamycinica sp. nov.

Previous experiments have suggested that the rifamycin-producing strain DSM 46095 might not belong to Amycolatopsis mediterranei. Analysis of its 16S rRNA gene sequence and construction of a phylogenetic tree showed most similarity to Amycolatopsis kentuckyensis NRRL B-24129T, Amycolatopsis lexingtonensis NRRL B-24129T and Amycolatopsis pretoriensis NRRL B-24133T, but the strain was probably not a member of any of these species. Results from DNA-DNA hybridization experiments and comparison of DNA profiling patterns using pulsed-field gel electrophoresis also supported the assignment of strain DSM 46095 to a novel species. Analyses of phospholipids, fatty acid methyl esters and physiological characteristics also showed that the differences between different isolates of A. mediterranei and A. mediterranei DSM 46095 were as large as those between Amycolatopsis species. Strain DSM 46095 represents a novel species of the genus Amycolatopsis for which the name Amycolatopsis rifamycinica sp. nov. is proposed, with the type strain NT 19T (=DSM 46095T=ATCC 27643T).

Actinomycetales↗
PubMed2004

Reclassification of Mesoplasma pleciae as Acholeplasma pleciae comb. nov. on the basis of 16S rRNA and gyrB gene sequence data.

Genomic DNA sequence data for the 16S rRNA gene and the gyrB gene of Mesoplasma pleciae PS-1(T) (=ATCC 49582(T)=NBRC 100476(T)) demonstrate a much closer relationship to Acholeplasma laidlawii and Acholeplasma oculi than to other species in the order Entomoplasmatales. In addition, the preferred use of UGG rather than UGA as the codon for tryptophan in the gyrB sequence probably places the organism outside the order Entomoplasmatales. It is proposed that M. pleciae be reclassified in the genus Acholeplasma, as Acholeplasma pleciae comb. nov.

Acholeplasma↗
PubMed2004

Reclassification of Brevibacillus brevis strains NCIMB 13288 and DSM 6472 (=NRRL NRS-887) as Aneurinibacillus danicus sp. nov. and Brevibacillus limnophilus sp. nov.

Comparison of the hypervariable region (269-279 bases in length) at the 5' end of the 16S rDNA sequences of 29 bacterial strains that were identified previously as Brevibacillus brevis showed that 13 strains clustered with Aneurinibacillus species, eight strains clustered with Bacillus species and eight strains clustered with Brevibacillus species. Based on DNA-DNA hybridization results, 27 strains, not including [Brevibacillus brevis] NCIMB 13288 and [Brevibacillus brevis] DSM 6472, were reidentified as Aneurinibacillus migulanus, Aneurinibacillus thermoaerophilus, Bacillus methanolicus, Bacillus oleronius, Brevibacillus agri, Brevibacillus brevis and Brevibacillus parabrevis. [Brevibacillus brevis] NCIMB 13288, which was located in the Aneurinibacillus cluster, showed low DNA-DNA relatedness (<14 %) and low 16S rDNA sequence similarity (96.8-97.9 %) to other Aneurinibacillus species. [Brevibacillus brevis] DSM 6472, which was located in the Brevibacillus cluster, also showed low DNA-DNA relatedness (<12 %) and low 16S rDNA sequence similarity (95.4-98.8 %) to other Brevibacillus species. These genotypic and phylogenetic data, plus phenotypic and chemotaxonomic characteristics, suggest that [Brevibacillus brevis] NCIMB 13288 (=IAM 15048) and [Brevibacillus brevis] DSM 6472 (=NRRL NRS-887) represent novel species of the genera Aneurinibacillus and Brevibacillus, respectively, for which the names Aneurinibacillus danicus sp. nov. and Brevibacillus limnophilus sp. nov. are proposed.

Bacillaceae↗
PubMed2004

Reclassification of Lactobacillus kefirgranum Takizawa et al. 1994 as Lactobacillus kefiranofaciens subsp. kefirgranum subsp. nov. and emended description of L. kefiranofaciens Fujisawa et al. 1988.

Fourteen homofermentative lactic acid bacteria that were isolated from kefir grains and kefir fermented milks were assigned to either Lactobacillus kefiranofaciens or Lactobacillus kefirgranum, based on their characteristic morphotypes, phenotypic features and SDS-PAGE profiles of whole-cell proteins. Further genotypic analyses on representative strains from both taxa demonstrated that L. kefiranofaciens and L. kefirgranum share 100 % 16S rDNA sequence similarity and belong phylogenetically to the Lactobacillus acidophilus species group. DNA-DNA binding values of >79 % and analogous DNA G+C contents of 37-38 mol% showed that the strains studied belonged to one species: L. kefirgranum is a later synonym of L. kefiranofaciens. An emended description is proposed for L. kefiranofaciens. Due to the specific morphological and biochemical characteristics of these taxa in kefir grain formation, it is proposed that L. kefirgranum should be reclassified as L. kefiranofaciens subsp. kefirgranum subsp. nov.

Animals↗
PubMed2004

Geobacillus gargensis sp. nov., a novel thermophile from a hot spring, and the reclassification of Bacillus vulcani as Geobacillus vulcani comb. nov.

A novel thermophilic spore-forming strain, Ga(T), was isolated from the Garga hot spring located in the northern part of the Transbaikal region (Russia). Strain Ga(T) was found to be an aerobic, Gram-positive, rod-shaped, thermophilic (optimum growth temperature is 60-65 degrees C), chemo-organotrophic bacterium that grows on various sugars, carboxylic acids and hydrocarbons. The G+C content of its DNA is 52.9 mol%. The 16S rRNA gene sequence similarity data show that strain Ga(T) is closely related to members of the genus Geobacillus. Relevant chemotaxonomic data (in particular, the major fatty acid profile of strain Ga(T), which includes iso-C15 : 0, iso-C16 : 0 and iso-C17 : 0 acids) support the assignment of this strain to the genus Geobacillus. The physiological, biochemical and DNA-DNA hybridization studies of strain Ga(T) showed that it differs both genotypically and phenotypically from the recognized Geobacillus species. Based on these data, strain Ga(T) belongs to a novel species, Geobacillus gargensis sp. nov. (type strain, Ga(T)=VKM B-2300(T)=DSM 15378(T)). The analysis of the phenotypic characteristics (additional to those given in the original description) of the type strain of Bacillus vulcani (DSM 13174(T)) showed that they are very similar to the major phenotypic characteristics of the genus Geobacillus. The low DNA-DNA reassociation values of strain DSM 13174(T) with various species of this genus (from 38 to 54 %) clearly demonstrate a sufficient genomic distinction of this strain and its taxonomic status as a species. The physiological characteristics, phylogenetic position and DNA-DNA reassociation values of B. vulcani allow this species to be reclassified as Geobacillus vulcani comb. nov. The main properties that differentiate G. vulcani from the other species of the genus are its ability to produce acids from glycerol, lactose and ribose.

Aerobiosis↗
PubMed2004

Reclassification of Lactobacillus cellobiosus Rogosa et al. 1953 as a later synonym of Lactobacillus fermentum Beijerinck 1901.

The name Lactobacillus cellobiosus is validly published, but the species is often neglected in taxonomic studies, due to its high similarity to Lactobacillus fermentum. In the present paper, literature data concerning the two species were reviewed. Phylogenetic placement of L. cellobiosus was obtained based on 16S rDNA sequences, and genetic similarity was further investigated by comparing partial recA gene sequences for the type strains of L. cellobiosus and L. fermentum. Based on the high identity values for 16S rDNA (99 %) and recA gene (98 %) sequences, the results of DNA-DNA hybridization assays and phenotypic traits available from the literature, it is proposed that L. cellobiosus be reclassified and, as a rule of priority, renamed as L. fermentum, the first described species.

Bacterial Proteins↗
PubMed2004

Proposals of Curvibacter gracilis gen. nov., sp. nov. and Herbaspirillum putei sp. nov. for bacterial strains isolated from well water and reclassification of [Pseudomonas] huttiensis, [Pseudomonas] lanceolata, [Aquaspirillum] delicatum and [Aquaspirillum] autotrophicum as Herbaspirillum huttiense comb. nov., Curvibacter lanceolatus comb. nov., Curvibacter delicatus comb. nov. and Herbaspirillum autotrophicum comb. nov.

Two strains of curved bacteria, 7-1(T) and 7-2(T), isolated from well water, were phylogenetically examined to determine their taxonomic position. Strain 7-1(T) is a Gram-negative, slightly curved rod. Analysis of the 16S rRNA gene sequence showed that strain 7-1(T) formed a cluster with [Aquaspirillum] delicatum and [Pseudomonas] lanceolata. It has some similar characteristics to [A.] delicatum and [P.] lanceolata, but has sufficient distance to separate it from other genera. DNA-DNA hybridization analysis, as well as chemotaxonomic and morphological studies, demonstrated that strain 7-1(T), [A.] delicatum and [P.] lanceolata belong to a new genus, Curvibacter gen. nov. Strain 7-1(T) (=IAM 15033(T)=ATCC BAA-807(T)) is classified as the type strain of Curvibacter gracilis gen. nov., sp. nov., and [A.] delicatum and [P.] lanceolata are classified as Curvibacter delicatus comb. nov. and Curvibacter lanceolatus comb. nov., respectively. Strain 7-2(T) is a Gram-negative spirillum. Phylogenetic study based on the 16S rRNA gene sequences showed that it formed a cluster with the members of the genus Herbaspirillum, [Pseudomonas] huttiensis and [Aquaspirillum] autotrophicum. The classification is therefore proposed of strain 7-2(T) (=IAM 15032(T)=ATCC BAA-806(T)) as the type strain of Herbaspirillum putei sp. nov., and [P.] huttiensis and [A.] autotrophicum are transferred to the genus Herbaspirillum as Herbaspirillum huttiense comb. nov. and Herbaspirillum autotrophicum comb. nov., respectively.

Bacterial Typing Techniques↗
PubMed2004

Diversity and evolution of Bdellovibrio-and-like organisms (BALOs), reclassification of Bacteriovorax starrii as Peredibacter starrii gen. nov., comb. nov., and description of the Bacteriovorax-Peredibacter clade as Bacteriovoracaceae fam. nov.

A phylogenetic analysis of Bdellovibrio-and-like organisms (BALOs) was performed. It was based on the characterization of 71 strains and on all consequent 16S rRNA gene sequences available in databases, including clones identified by data-mining, totalling 120 strains from very varied biotopes. Amplified rDNA restriction analysis (ARDRA) accurately reflected the diversity and phylogenetic affiliation of BALOs, thereby providing an efficient screening tool. Extensive phylogenetic analysis of the 16S rRNA gene sequences revealed great diversity within the Bdellovibrio (> 14 % divergence) and Bacteriovorax (> 16 %) clades, which comprised nine and eight clusters, respectively, exhibiting more than 3 % intra-cluster divergence. The clades diverged by more than 20 %. The analysis of conserved 16S rRNA secondary structures showed that Bdellovibrio contained motifs atypical of the delta-Proteobacteria, suggesting that it is ancestral to Bacteriovorax. While none of the Bdellovibrio strains were of marine origin, Bacteriovorax included separate soil/freshwater and marine-specific groups. On the basis of their extensive diversity and the large distance separating the groups, it is proposed that Bacteriovorax starrii be placed into a new genus, Peredibacter gen. nov., with Peredibacter starrii A3.12T (= ATCC 15145T = NCCB 72004T) as its type strain. Also proposed is a redefinition of the Bdellovibrio and the Bacteriovorax-Peredibacter lineages as two different families, i.e. 'Bdellovibrionaceae' and a new family, Bacteriovoracaceae. Also, a re-evaluation of oligonucleotides targeting BALOs is presented, and the implications of the large diversity of these organisms and of their distribution in very different environments are discussed.

Bdellovibrio↗
PubMed2006

Reclassification of Arthrobacter duodecadis Lochhead 1958 as Tetrasphaera duodecadis comb. nov. and emended description of the genus Tetrasphaera.

Phylogenetic analysis based on 16S rRNA gene sequences and chemotaxonomic features of Arthrobacter duodecadis Lochhead 1958 indicated that the bacterium belonged within the genus Tetrasphaera. A. duodecadis IAM 14868(T) could be distinguished from other species by the presence of 3-hydroxy meso-diaminopimelic acid in the peptidoglycan and a series of 10-methyl fatty acids. In addition, DNA-DNA relatedness studies indicated that the strain belonged to a genomic species that could be readily distinguished from its nearest neighbours, the type strains of Tetrasphaera elongata, Tetrasphaera japonica and Tetrasphaera australiensis. These features support our proposal to reclassify A. duodecadis in the genus Tetrasphaera, as Tetrasphaera duodecadis comb. nov. The type strain is IAM 14868(T) (=NBRC 12959(T) = ATCC 13347(T) = NCIMB 9222(T)). An emended description of the genus Tetrasphaera is given.

Actinomycetales↗
PubMed2004

Polyphasic taxonomic analysis of Bifidobacterium animalis and Bifidobacterium lactis reveals relatedness at the subspecies level: reclassification of Bifidobacterium animalis as Bifidobacterium animalis subsp. animalis subsp. nov. and Bifidobacterium lactis as Bifidobacterium animalis subsp. lactis subsp. nov.

The taxonomic standing of Bifidobacterium lactis and Bifidobacterium animalis was investigated using a polyphasic approach. Sixteen representatives of both taxa were found to be phenotypically similar and shared more than 70% DNA-DNA relatedness (76-100%), which reinforces the conclusions of previous studies in which B. lactis and B. animalis were considered to be one single species. However, the results of protein profiling, BOX-PCR fingerprinting, Fluorescent Amplified Fragment Length Polymorphism (FAFLP), and atpD and groEL gene sequence analysis demonstrate that representatives of B. animalis and B. lactis constitute two clearly separated subgroups; this subdivision was also phenotypically supported based on the ability to grow in milk. Given the fact that B. lactis Meile et al. 1997 has to be considered as a junior synonym of B. animalis (Mitsuoka 1969) Scardovi and Trovatelli 1974, our data indicate that the latter species should be split into two new subspecies, i.e. Bifidobacterium animalis subsp. animalis subsp. nov. (type strain R101-8T=LMG 10508T=ATCC 25527T=DSM 20104T=JCM 1190T) and Bifidobacterium animalis subsp. lactis subsp. nov. (type strain UR1T=LMG 18314T=DSM 10140T=JCM 10602T).

Animals↗
PubMed2004

Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description).

Sphaerobacter thermophilus was originally classified as the deepest branching member of the phylum Actinobacteria (high-G+C, Gram-positive bacteria) based on 16S rRNA gene comparative analysis. However, the analysis lacked suitable outgroups, and additional 16S rRNA gene sequences indicate that it is most closely related to Thermomicrobium roseum, which it also resembles phenotypically. Furthermore, both species are reproducibly affiliated with the phylum Chloroflexi (green non-sulfur bacteria), despite T. roseum currently being classified in its own phylum, the Thermomicrobia. Transfer of Sphaerobacter to the class Thermomicrobia, and transfer of the class Thermomicrobia to the phylum Chloroflexi, are proposed. Descriptions for the phylum Chloroflexi and the class Thermomicrobia are emended to reflect the proposed changes in classification.

Actinobacteria↗
PubMed2004

Reclassification of Promicromonospora pachnodae Cazemier et al. 2004 as Xylanimicrobium pachnodae gen. nov., comb. nov.

The recently described facultatively anaerobic Promicromonospora pachnodae is phylogenetically only moderately related to authentic members of Promicromonospora. P. pachnodae is closely related to Xylanibacterium ulmi and slightly less closely related to Xylanimonas cellulosilytica and Isoptericola variabilis (basonym Cellulosimicrobium variabile). Members of the different genera of Promicromonosporaceae have similar chemotaxonomic properties; they share the same peptidoglycan type (A4alpha) and have similar profiles of polar lipids, menaquinones, fatty acids and whole cell sugars. However, they differ from each other in the detailed amino acid composition of peptidoglycan, a taxonomically significant character that has previously been used in the delineation of actinobacterial genera. Recognized Promicromonospora species and Xylanibacterium ulmi exhibit the L-Lys-L-Ala-D-Glu type, Xylanimonas cellulosilytica and I. variabilis show the L-Lys-D-Asp type, whereas P. pachnodae has the L-Lys-L-Ser-D-Glu type. This property, together with the distinct phylogenetic position of Promicromonospora pachnodae, suggests a novel genus for the xylanolytic organism Xylanimicrobium pachnodae (Cazemier et al. 2004) gen. nov., comb. nov.

Actinomycetales↗
PubMed2005

Phylogenetic relationships of the genus Kluyvera: transfer of Enterobacter intermedius Izard et al. 1980 to the genus Kluyvera as Kluyvera intermedia comb. nov. and reclassification of Kluyvera cochleae as a later synonym of K. intermedia.

In order to assess the relationship between the genus Kluyvera and other members of the family Enterobacteriaceae, the 16S rRNA genes of type strains of the recognized Kluyvera species, Kluyvera georgiana, Kluyvera cochleae, Kluyvera ascorbata and Kluyvera cryocrescens, were sequenced. A comparative phylogenetic analysis based on these 16S rRNA gene sequences and those available for strains belonging to several genera of the family Enterobacteriaceae showed that members of the genus Kluyvera form a cluster that contains all the known Kluyvera species. However, the type strain of Enterobacter intermedius (ATCC 33110T) was included within this cluster in a very close relationship with the type strain of K. cochleae (ATCC 51609T). In addition to the phylogenetic evidence, biochemical and DNA-DNA hybridization analyses of species within this cluster indicated that the type strain of E. intermedius is in fact a member of the genus Kluyvera and, within it, of the species Kluyvera cochleae. Therefore, following the current rules for bacterial nomenclature and classification, the transfer of E. intermedius to the genus Kluyvera as Kluyvera intermedia comb. nov. is proposed (type strain, ATCC 33110T=CIP 79.27T=LMG 2785T=CCUG 14183T). Biochemical analysis of four E. intermedius strains and one K. cochleae strain independent of the respective type strains further indicated that E. intermedius and K. cochleae represent the same species and are therefore heterotypic synonyms. Nomenclatural priority goes to the oldest legitimate epithet. Consequently, Kluyvera cochleae Muller et al. 1996 is a later synonym of Kluyvera intermedia (Izard et al. 1980) Pavan et al. 2005.

Bacterial Typing Techniques↗
PubMed2004

Reclassification of Staphylococcus pulvereri Zakrzewska-Czerwinska et al. 1995 as a later synonym of Staphylococcus vitulinus Webster et al. 1994.

A polyphasic taxonomic approach was applied to strains of the species Staphylococcus vitulinus and Staphylococcus pulvereri in order to clarify their taxonomic relatedness. Four reference strains, representing both species, and seven strains isolated from human clinical material were characterized by biotyping, ribotyping and SDS-PAGE analysis of whole-cell proteins, and none of the screening approaches allowed the two taxa to be distinguished. DNA-DNA hybridization experiments between four selected representative strains, including the type strains, confirmed that Staphylococcus pulvereri is a later synonym of Staphylococcus vitulinus.

Abscess↗
PubMed2005

Reclassification of Leptospira parva Hovind-Hougen et al. 1982 as Turneriella parva gen. nov., comb. nov.

Analysis of the G+C content, DNA-DNA relatedness to other leptospires and 16S rRNA gene sequence of Leptospira parva showed that this species was not related to other Leptospira species. On the basis of these data, it is proposed that Leptospira parva should be transferred to the genus Turneriella as Turneriella parva gen. nov., comb. nov., with strain H(T) (=NCTC 11395(T)=ATCC BAA-1111(T)) as the type strain.

Bacterial Typing Techniques↗
PubMed2005

Hexachlorocyclohexane-degrading bacterial strains Sphingomonas paucimobilis B90A, UT26 and Sp+, having similar lin genes, represent three distinct species, Sphingobium indicum sp. nov., Sphingobium japonicum sp. nov. and Sphingobium francense sp. nov., and reclassification of [Sphingomonas] chungbukensis as Sphingobium chungbukense comb. nov.

Three strains of Sphingomonas paucimobilis, B90A, UT26 and Sp+, isolated from different geographical locations, were found to degrade hexachlorocyclohexane. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains do not fall in a clade that includes the type strain, Sphingomonas paucimobilis ATCC 29837(T), but form a coherent cluster with [Sphingomonas] chungbukensis IMSNU 11152(T) followed by Sphingobium chlorophenolicum ATCC 33790(T). The three strains showed low DNA-DNA relatedness values with Sphingomonas paucimobilis ATCC 29837(T) (8-25%), [Sphingomonas] chungbukensis IMSNU 11152(T) (10-17%), Sphingobium chlorophenolicum ATCC 33790(T) (23-54%) and Sphingomonas xenophaga DSM 6383(T) (10-28%), indicating that they do not belong to any of these species. Although the three strains were found to be closely related to each other based on 16S rRNA gene sequence similarity (99.1-99.4%), DNA-DNA relatedness (19-59%) and pulsed-field gel electrophoresis (PFGE) patterns indicated that they possibly represent three novel species of the genus Sphingobium. The three strains could also be readily distinguished by biochemical tests. The three strains showed similar polar lipid profiles and contained sphingoglycolipids. The strains differed from each other in fatty acid composition but contained the predominant fatty acids characteristic of other Sphingobium species. A phylogenetic study based on 16S rRNA gene sequences showed that [Sphingomonas] chungbukensis IMSNU 11152(T) formed a cluster with members of the genus Sphingobium. Based on these results, it is proposed that strains B90A, UT26 and Sp+, previously known as Sphingomonas paucimobilis, are the type strains of Sphingobium indicum sp. nov. (=MTCC 6364(T)=CCM 7286(T)), Sphingobium japonicum sp. nov. (=MTCC 6362(T)=CCM 7287(T)) and Sphingobium francense sp. nov. (=MTCC 6363(T)=CCM 7288(T)), respectively. It is also proposed that [Sphingomonas] chungbukensis be transferred to Sphingobium chungbukense comb. nov.

Bacterial Proteins↗
PubMed2006

Reclassification of Gluconacetobacter hansenii strains and proposals of Gluconacetobacter saccharivorans sp. nov. and Gluconacetobacter nataicola sp. nov.

Ten strains previously assigned to Acetobacter hansenii (=Gluconacetobacter hansenii), Acetobacter pasteurianus LMG 1584 and eight reference strains of the genus Gluconacetobacter were reclassified by 16S rRNA gene sequencing, DNA-DNA similarity, DNA base composition and phenotypic characteristics. The A. hansenii strains and A. pasteurianus LMG 1584 were included in the cluster of acetic acid bacteria (family Acetobacteraceae) by 16S rRNA gene sequences. Further, they were separated into seven distinct groups by DNA-DNA similarity. DNA-DNA similarity group I was identified as G. hansenii. DNA-DNA similarity group II was retained as Gluconacetobacter sp., because DNA-DNA similarity between the strain and Gluconacetobacter entanii LTH 4560(T) could not be determined. This was due to a lack of availability of the type strain from any source. DNA-DNA similarity group III was regarded as a novel species, for which the name Gluconacetobacter saccharivorans sp. nov. (type strain, LMG 1582(T)=NRIC 0614(T)) is proposed. DNA-DNA similarity group IV included the type strains of Gluconacetobacter oboediens and Gluconacetobacter intermedius, and three A. hansenii strains. This group was identified as G. oboediens because high values of DNA-DNA similarity were obtained between the type strains and G. oboediens has priority over G. intermedius. DNA-DNA similarity group V was identified as Gluconacetobacter europaeus. DNA-DNA similarity group VI was regarded as a novel species, for which the name Gluconacetobacter nataicola sp. nov. (type strain, LMG 1536(T)=NRIC 0616(T)) is proposed. DNA-DNA similarity group VII was reclassified as Gluconacetobacter xylinus. The description of G. hansenii is emended.

Bacterial Typing Techniques↗