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At least 253 records · Page 14Linked to original sources
PubMed1999

Catenuloplanes crispus (Petrolini et al. 1993) comb. nov.: incorporation of the genus Planopolyspora Petrolini 1993 into the genus Catenuloplanes Yokota et al. 1993 with an amended description of the genus Catenuloplanes.

The taxonomic position of the genus Planopolyspora comprising a single species, Planopolyspora crispa, was reviewed. This genus was originally characterized by formation of long, curly and sometimes branching sporangia containing numerous zoospores arranged in a single row and by the presence of meso-diaminopimelic acid and madurose (3-O-methyl-D-galactose) in whole-cell hydrolysates. However, our chemotaxonomic analyses of the type strain of P. crispa did not agree with the original description. The peptidoglycan contained L-lysine but not meso-diaminopimelic acid, and the whole-cell hydrolysate contained xylose as the characteristic sugar but not madurose. These characteristics and other chemotaxonomic profiles (e.g. menaquinone, phospholipid and cellular fatty acid compositions) of the genus Planopolyspora coincided with those of the genus Catenuloplanes. These two genera also had very similar morphological characteristics, but in the original description of the genus Catenuloplanes the presence of sporangia was not referred to. This difference is considered to originate from a divergence of views owing to the ambiguity of the definition of the term 'sporangium' in actinomycete morphology. Phylogenetic analysis based on 16S rDNA sequences also supported the proposal that the genera Planopolyspora and Catenuloplanes should be combined into one genus. Levels of DNA relatedness among the type strains of P. crispa and six Catenuloplanes species and their cultural, physiological and biochemical characteristics indicated that P. crispa should be classified as an independent species of the genus Catenuloplanes, which has priority over the genus Planopolyspora. Therefore, it is proposed that Planopolyspora crispa be transferred to the genus Catenuloplanes as Catenuloplanes crispus comb. nov.

Bacterial Typing Techniques↗
PubMed2000

Polyphasic evidence for the reclassification of Rhodothermus obamensis Sako et al. 1996 as a member of the species Rhodothermus marinus Alfredsson et al. 1988.

DNA-DNA reassociation studies, 16S rRNA gene sequence comparisons and fatty acid analysis were used to reassess the taxonomic status of the type strain of Rhodothermus obamensis and several strains of the genus Rhodothermus isolated from widely distributed shallow marine hot springs. The results show that the type strain of R. obamensis, JCM 9785T, has a DNA-DNA reassociation value of 78% with the type strain of R. marinus, DSM 4252T. The other strains examined had DNA-DNA reassociation values that varied between about 68 and 94% with R. marinus. The 165 rRNA gene sequence was determined for the type strain of R. obamensis and found to share 99.5% similarity with the type strain of R. marinus. The fatty acid composition of R. obamensis was slightly different from that of the other strains examined, but indicated that this strain is very closely related to the other strains examined in this study. On the basis of DNA-DNA reassociation values, 16S rRNA gene sequence comparison and fatty acid profiles, it was concluded that R. obamensis and R. marinus represent the same species and that the name Rhodothermus obamensis should be regarded as a junior synonym of Rhodothermus marinus.

Cloning, Molecular↗
PubMed2001

Planomicrobium koreense gen. nov., sp. nov., a bacterium isolated from the Korean traditional fermented seafood jeotgal, and transfer of Planococcus okeanokoites (Nakagawa et al. 1996) and Planococcus mcmeekinii (Junge et al. 1998) to the genus Planomicrobium.

A bacterial strain, JG07T, isolated from the Korean traditional fermented seafood jeotgal, was subjected to a polyphasic taxonomic study. Cells of strain JG07T are cocci or short rods in the early growth phase but change to rods as the cultures age. The peptidoglycan type is A4alpha, based on L-Lys-D-Glu. The menaquinone profile is characterized by the predominance of MK-8 followed by MK-7 and MK-6. The cellular fatty acid profile contains major amounts of saturated, unsaturated and branched fatty acids. The cellular phospholipids are phosphatidylethanolamine, phosphatidylglycerol and bisphosphatidylglycerol. The G+C content of the DNA is 47 mol%. Phylogenetic analysis showed that strain JG07T forms a cluster with Planococcus okeanokoites and Planococcus mcmeekinii, and the relationship between this cluster and two other Planococcus species described previously is supported by bootstrap analysis at a confidence level of 100%. The 16S-23S internally transcribed spacer (ITS) sequence similarity and DNA-DNA relatedness values between strain JG07T and the type strains of other Planococcus species are in the range 74.6-83.2% and 10.4-20.5%, respectively. On the basis of the phenotypic and phylogenetic data and the genomic distinctiveness, strain JG07T is considered to represent a new genus and a new species, for which the name Planomicrobium koreense gen. nov., sp. nov. is proposed. It is also proposed that Planococcus okeanokoites and Planococcus mcmeekinii be transferred to the new genus Planomicrobium as Planomicrobium okeanokoites and Planomicrobium mcmeekinii, respectively.

Bacillaceae↗
PubMed2002

Proposal of Ureaplasma parvum sp. nov. and emended description of Ureaplasma urealyticum (Shepard et al. 1974) Robertson et al. 2001.

The phenotypic and genotypic properties of Ureaplasma urealyticum (family Mycoplasmataceae, order Mycoplasmatales, class Mollicutes) are reviewed here. The 14 recognized serovar standard strains found in humans exhibit no serological cross-reactivity with ureaplasmas from other hosts and uniquely express human immuoglobulin A1 protease activity. However, they exhibit many characteristics which place them in two distinct clusters known as the parvo biovar (or biovar 1 or B) and the T960T biovar (or biovar 2 or A). Established phenotypic markers of the biovars include clustering of antigenic types, polypeptide patterns of whole-cell preparations, differential inhibition by manganese, and polymorphism among their ureases, pyrophosphatases and diaphorases. Established genotypic markers of the biovars are DNA-DNA hybridization of 60% between biovars, and distinctive RFLP patterns and genome sizes. Divergent nucleotide sequences of several highly conserved genes attest to the phylogenetic distinctiveness of the two biovars. PCRs founded upon the sequences for 16S rRNA, the 16S-23S rRNA intergenic regions, the genus-defining urease, the serovar-defining, multiple-banded antigen genes or randomly amplified polymorphic DNA tests differentiate the biovars unambiguously. With the availability of rapid, reliable and economical tests for biovar determination, it is now appropriate to propose that the taxonomic status of U. urealyticum be emended. Serovar standard strains exhibiting traits of biovar parvo (serovars 1, 3, 6 and 14) will be designated as a separate species, Ureaplasma parvum sp. nov., as befits its smaller genome size. The serovar 3 standard (strain 27T) will be the type strain of U. parvum and is represented by ATCC 27815T and NCTC 11736T. Serovar standard strains exhibiting traits of biovar T960T (2, 4, 5, 7, 8T, 9, 10, 11, 12 and 13) will retain the U. urealyticum designation and type strain, the serovar 8 standard (strain T960T), represented by ATCC 27618T and NCTC 10177T.

Genotype↗
PubMed2002

Chelatobacter heintzii (Auling et al. 1993) is a later subjective synonym of Aminobacter aminovorans (Urakami et al. 1992).

Chelatobacter heintzii, which was described as a nitrilotriacetate-utilizing organism, was re-investigated in order to clarify its taxonomic position. On the basis of 16S rDNA sequence comparisons, it is obvious that this species clusters phylogenetically with species of the genus Aminobacter. The results of investigations of the fatty acid patterns, polar lipid profiles, polyamine patterns and quinone system supported this placement. The substrate-utilization profiles and fatty acid patterns of four strains (belonging to two different genomovars) revealed homogeneous results and showed high levels of similarity to Aminobacter aminovorans. DNA-DNA similarity studies confirmed that both genomovars of Chelatobacter heintzii belong to Aminobacter aminovorans. It could be shown that all species of this group are highly interrelated. On the basis of these data and previously published results, it is obvious that Chelatobacter heintzii is a later subjective synonym of Aminobacter aminovorans.

Alphaproteobacteria↗
PubMed2002

Vibrio trachuri Iwamoto et al. 1995 is a junior synonym of Vibrio harveyi (Johnson and Shunk 1936) Baumann et al. 1981.

The taxonomic position of Vibrio trachuri was examined through a polyphasic approach using 16S rDNA sequencing, fluorescent amplified fragment length polymorphisms (FAFLP), DNA-DNA hybridization experiments, G+C content of DNA and phenotypical tests. Phylogenetic analysis showed that Vibrio harveyi is the closest neighbour of V. trachuri, sharing about 98.8% similarity in the 16S rDNA gene. Moreover, numerical analysis of the FAFLP patterns revealed that both species have highly related genomes, sharing 55% pattern similarity. DNA-DNA hybridization experiments and G+C content measurements reinforced these results, since V. trachuri and V. harveyi had at least 74% DNA similarity and 44.5-45.2 mol % G+C. Phenotypical features of both species were also very similar, except that V. trachuri utilized itaconic acid, whereas V. harveyi did not. Therefore, it is proposed that the species V. trachuri should be reclassified as V. harveyi.

Animals↗
PubMed2003

Reclassification of Lactobacillus maltaromicus (Miller et al. 1974) DSM 20342(T) and DSM 20344 and Carnobacterium piscicola (Collins et al. 1987) DSM 20730(T) and DSM 20722 as Carnobacterium maltaromaticum comb. nov.

Phenotypic and genotypic characterizations of Lactobacillus maltaromicus strains DSM 20342(T) and DSM 20344 provided evidence for the reclassification of this species in the genus Carnobacterium. Moreover, phenotypic and genotypic comparisons made between L. maltaromicus and Carnobacterium piscicola highlighted that these two species should be considered synonyms. For these reasons, the species Carnobacterium maltaromaticum comb. nov. (type strain DSM 20342(T) = ATCC 27865(T) = CCUG 30142(T) = CIP 103135(T) = JCM 1154(T) = LMG 6903(T) = NRRL B-14852(T)) is proposed to accommodate L. maltaromicus and C. piscicola.

Bacterial Typing Techniques↗
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

Aquaspirillum dispar Hylemon et al. 1973 and Microvirgula aerodenitrificans Patureau et al. 1998 are subjective synonyms.

The 16S rDNA sequences of [Aquaspirillum] dispar LMG 4329(T) and Microvirgula aerodenitrificans SGLY2(T) (=LMG 18919(T)) were found to be very similar (>99 %). DNA-DNA hybridizations between the two strains revealed a high level of DNA-DNA binding (84 %), showing that they represent a single species. M. aerodenitrificans and [A.] dispar were also phenotypically very similar. It is concluded that [A.] dispar and M. aerodenitrificans are subjective synonyms. As [A.] dispar was wrongly assigned to the genus Aquaspirillum, we propose that strains of [A.] dispar must be reclassified in the genus MICROVIRGULA: The name Microvirgula aerodenitrificans must be retained for the unified taxon since it is the type of the genus MICROVIRGULA:

DNA, Bacterial↗
PubMed2004

Genetic evidence that Weissella kimchii Choi et al. 2002 is a later heterotypic synonym of Weissella cibaria Björkroth et al. 2002.

The taxonomic positions of Weissella kimchii and Weissella cibaria were examined using phenotypic tests, 16S rRNA gene sequencing and DNA-DNA hybridization. The two species displayed very similar sugar-fermentation patterns and produced the D-form of lactic acid. Phylogenetic analysis showed that W. cibaria is the closest neighbour of W. kimchii, sharing about 99.7 % similarity in the 16S rRNA gene sequence. DNA-DNA hybridization experiments further reinforced these results, demonstrating a 98.2 % reassociation level between W. cibaria LMG 17699(T) and W. kimchii DSM 14295(T). On the other hand, strain RO5, an isolate from paddy rice silage, exhibited 99.4 % 16S rRNA gene sequence similarity and a DNA reassociation level of more than 97 % with both type strains. Therefore, it is proposed that the species W. kimchii should be reclassified as W. cibaria.

Bacillus↗
PubMed2005

Transfer of Pectobacterium chrysanthemi (Burkholder et al. 1953) Brenner et al. 1973 and Brenneria paradisiaca to the genus Dickeya gen. nov. as Dickeya chrysanthemi comb. nov. and Dickeya paradisiaca comb. nov. and delineation of four novel species, Dickeya dadantii sp. nov., Dickeya dianthicola sp. nov., Dickeya dieffenbachiae sp. nov. and Dickeya zeae sp. nov.

A collection of 75 strains of Pectobacterium chrysanthemi (including all biovars and pathovars) and the type strains of Brenneria paradisiaca (CFBP 4178(T)) and Pectobacterium cypripedii (CFBP 3613(T)) were studied by DNA-DNA hybridization, numerical taxonomy of 121 phenotypic characteristics, serology and 16S rRNA gene-based phylogenetic analyses. From analysis of 16S rRNA gene sequences, it was deduced that P. chrysanthemi strains and B. paradisiaca CFBP 4178(T) formed a clade distinct from the genera Pectobacterium and Brenneria; therefore, it is proposed to transfer all the strains to a novel genus, Dickeya gen. nov. By DNA-DNA hybridization, the strains of P. chrysanthemi were distributed among six genomic species: genomospecies 1 harbouring 16 strains of biovar 3 and four strains of biovar 8, genomospecies 2 harbouring 16 strains of biovar 3, genomospecies 3 harbouring two strains of biovar 6 and five strains of biovar 5, genomospecies 4 harbouring five strains of biovar 2, genomospecies 5 harbouring six strains of biovar 1, four strains of biovar 7 and five strains of biovar 9 and genomospecies 6 harbouring five strains of biovar 4 and B. paradisiaca CFBP 4178(T). Two strains of biovar 3 remained unclustered. Biochemical criteria, deduced from a numerical taxonomic study of phenotypic characteristics, and serological reactions allowed discrimination of the strains belonging to the six genomic species. Thus, it is proposed that the strains clustered in these six genomic species be assigned to the species Dickeya zeae sp. nov. (type strain CFBP 2052(T)=NCPPB 2538(T)), Dickeya dadantii sp. nov. (type strain CFBP 1269(T)=NCPPB 898(T)), Dickeya chrysanthemi comb. nov. (subdivided into two biovars, bv. chrysanthemi and bv. parthenii), Dickeya dieffenbachiae sp. nov. (type strain CFBP 2051(T)=NCPPB 2976(T)), Dickeya dianthicola sp. nov. (type strain CFBP 1200(T)=NCPPB 453(T)) and Dickeya paradisiaca comb. nov., respectively.

Animals↗
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

Reconsideration of Arthrobacter ilicis (Mandel et al. 1961) Collins et al. 1982 as a plant-pathogenic species. Proposal to emend the authority and description of the species. Request for an opinion.

Strains now considered to represent the type strain of Arthrobacter ilicis, described as a pathogen of American holly, are not identical. The designated type strain does not represent this pathogen. However, one of the other strains sourced to the type strain of the pathogen does appear to be authentic, but is not a member of A. ilicis. It is proposed that A. ilicis is an unrelated species, not a pathogen of American holly. The nomenclature of A. ilicis can be rectified by emending the authority and by emending the species description to recognize this species as a novel species that is not a plant pathogen. The pathogen of American holly then becomes a novel pathovar, Curtobacterium flaccumfaciens pv. ilicis. The opinion of the Judicial Commission is sought.

Arthrobacter↗
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

Gordonia nitida Yoon et al. 2000 is a later synonym of Gordonia alkanivorans Kummer et al. 1999.

The name of the species Gordonia nitida is validly published but its type strain DSM 44499(T) shares high similarity based on 16S rRNA gene sequences with Gordonia alkanivorans DSM 44369(T) and Gordonia westfalica DSM 44215(T). These three species obviously build up a distinct cluster within the genus Gordonia. In the present paper, data from the literature concerning the three Gordonia species were reviewed and the genetic similarity of G. nitida DSM 44499(T) and G. alkanivorans DSM 44369(T) was further investigated by DNA-DNA-hybridization experiments, revealing approximately 80 % DNA-DNA relatedness. Even though the two type strains could be differentiated by automated ribotyping, it is proposed that, according to the rules of priority, G. nitida is a later synonym of G. alkanivorans.

DNA, Bacterial↗
PubMed2005

Methanogenium frittonii Harris et al. 1996 is a later synonym of Methanoculleus thermophilus (Rivard and Smith 1982) Maestrojuan et al. 1990.

The 16S rRNA gene sequence of [Methanogenium] frittonii DSM 2832(T) was determined and was found to be 99.9 % similar to the sequence of Methanoculleus thermophilus DSM 2373(T). DNA-DNA hybridizations between both strains revealed 86 % DNA-DNA binding, indicating that both strains belong to the same species. The determination of the DNA G + C content of both type strains, DSM 2832(T) and DSM 2373(T), revealed values of 56.1 and 59.1 mol%, respectively. Based on the phenotypic and genotypic characteristics, it is proposed to unite the species [Methanogenium] frittonii and Methanoculleus thermophilus under the name Methanoculleus thermophilus, which is the earlier synonym and hence has priority. Emended descriptions of the species Methanoculleus thermophilus and the genus Methanogenium are also given.

Acetates↗
PubMed2005

Thalassobacter stenotrophicus Macian et al. 2005 is a later synonym of Jannaschia cystaugens Adachi et al. 2004, with emended description of the genus Thalassobacter.

The type strains of Jannaschia cystaugens (LMG 22015(T)) and Thalassobacter stenotrophicus (CECT 5294(T)) were analysed by means of genomic DNA-DNA hybridization, comparison of 16S rRNA gene sequences and phenotypic properties determined under the same methodological conditions. J. cystaugens LMG 22015(T) showed DNA-DNA relatedness levels of 72% when hybridized with the genomic DNA of T. stenotrophicus CECT 5294(T). Sequence comparisons revealed that the 16S rRNA genes of the two strains had a similarity of 99.8%. The cellular fatty acid and polar lipid compositions of the two strains and their DNA mol% G+C contents were almost identical. Bacteriochlorophyll a (Bchl a) and polyhydroxybutyrate were produced by both strains under the same culture conditions. Their closest phylogenetic neighbours were Jannaschia helgolandensis and Jannaschia rubra; however, the low sequence similarity values (95.7-95.9%) and several important differences in phenotypic traits (ionic requirements, Bchl a production and polar lipids) support the distinction between the genera Thalassobacter and Jannaschia. Thus, we propose the unification of J. cystaugens (LMG 22015(T)) and T. stenotrophicus (CECT 5294(T)) as Thalassobacter stenotrophicus (type strain, CECT 5294(T)=DSM 16310(T)). An emended description of the genus Thalassobacter is also presented.

Bacterial Typing Techniques↗