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PubMed1996

A polyphasic reassessment of the genus Paenibacillus, reclassification of Bacillus lautus (Nakamura 1984) as Paenibacillus lautus comb. nov. and of Bacillus peoriae (Montefusco et al. 1993) as Paenibacillus peoriae comb. nov., and emended descriptions of P. lautus and of P. peoriae.

Seventy-seven strains representing 10 species in the Paenibacillus polymyxa 16S rRNA group and 3 other species that exhibit phenetic relatedness to members of this group, Bacillus lautus, "Bacillus longisporus," and Bacillus peoriae, were characterized genotypically and phenotypically by performing an amplified ribosomal DNA restriction analysis, a randomly amplified polymorphic DNA analysis, a fatty acid methyl ester analysis, sodium dodecyl sulfate-polyacrylamide gel electrophoresis of whole-cell proteins, pyrolysis mass spectrometry, and API and other routine phenotypic tests. These analyses revealed distinct clusters representing Paenibacillus alvei, Paenibacillus amylolyticus, Paenibacillus azotofixans, Paenibacillus durum, Paenibacillus larvae subsp. larvae, Paenibacillus larvae subsp. pulvifaciens, B. lautus, Paenibacillus macerans, Paenibacillus macquariensis, B. peoriae, P. polymyxa, and Paenibacillus validus, which confirmed the distinctness of these species, but appreciable within-species heterogeneity was observed in P. alvei, B. lautus, P. macerans, P. polymyxa, and P. validus. The type strain of Paenibacillus pabuli did not cluster with other strains of this species, and in several analyses a relationship between strains of P. pabuli and "B. longisporus" was observed. As the analyses showed that B. lautus and B. peoriae are closely related to the genus Paenibacillus, these species are reclassified as members of this genus.

Bacillus↗

PubMed1997

Reclassification of Paenibacillus durum (formerly Clostridium durum Smith and Cato 1974) Collins et al. 1994 as a member of the species P. azotofixans (formerly Bacillus azotofixans Seldin et al. 1984) Ash et al. 1994.

Phenotypic studies, as well as the reaction of Paenibacillus durum genomic DNA with a 16S ribosomal DNA (sequence of variable regions V1 to V4)-based Paenibacillus azotofixans-specific PCR system and oligonucleotide probe, the presence of sequences homologous to Klebsiella pneumoniae nifKDH in both P. durum and P. azotofixans, and the results of DNA-DNA hybridization experiments performed with the P. durum and P.azotofixans type strains and one additional P. durum strain, showed that these two species form a homogeneous group. In addition, evidence was found for the presence of nif genes in P. durum, and P. durum was shown to fix atmospheric nitrogen. Therefore, the names P. durum and P. azotofixans should be considered synonyms. As P. durum was capable of fixing nitrogen and fixation without inhibition by nitrate is a major characteristic of the group, we propose that P. durum be included in the species P. azotofixans.

Bacillus↗

PubMed1997

Reclassification of the crenarchael orders and families in accordance with 16S rRNA sequence data.

A phylogenetic analysis of all validly published members of the Crenarchaeota, including several new isolates from our laboratory, suggests three orders within this archaeal kingdom. The Thermoproteales consist of both the rod-shaped, hyperthermophilic, neutrophilic representatives of the Thermoproteaceae and the members of the new family Thermofilaceae. The Sulfolobales harbor all thermoacidophilic, coccoid organisms. The neutrophilic, hyperthermophilic cocci are members of a new order tentatively named "Igneococcales." This order comprises two families, the Desulfurococcaceae, characterized by maximal growth temperature of up to 100 degrees C, and the new family Pyrodictiaceae, for which optimal growth occurs at temperatures above 100 degrees C.

Archaea↗

PubMed1997

Characterization of some Actinomyces-like isolates from human clinical specimens: reclassification of Actinomyces suis (Soltys and Spratling) as Actinobaculum suis comb. nov. and description of Actinobaculum schaalii sp. nov.

Five strains of a hitherto unknown Actinomyces-like bacterium were isolated from human clinical sources, including blood cultures. Biochemical and chemotaxonomic characterization indicated that the strains were distinct from previously described Actinomyces and Arcanobacterium species. A comparative 16S rRNA gene sequence analysis demonstrated that the undescribed strains constitute a new subline within the Actinomyces-Arcanobacterium species complex. The closest known relative of the isolates was found to be Actinomyces suis, although a 16S rRNA sequence divergence value of approximately 6% clearly demonstrated that the unknown bacterium represents a distinct species. Based on the results of the present and earlier phylogenetic investigations, it is proposed that Actinomyces suis should be reclassified in a new genus, the genus Actinobaculum, as Actinobaculum suis comb. nov. In addition, a new species, Actinobaculum schaalii, is proposed for the Actinomyces-like bacterium from human sources. The type strain of Actinobaculum schaalii is CCUG 27420.

Actinomyces↗

PubMed1997

Reclassification of Nocardioides simplex ATCC 13260, ATCC 19565, and ATCC 19566 as Rhodococcus erythropolis.

Our phylogenetic analysis based on 16S ribosomal DNA (rDNA) sequences and chemotaxonomic analyses showed that Nocardioides simplex ATCC 13260, ATCC 19565, and ATCC 19566 are more closely related to the genus Rhodococcus, especially Rhodococcus erythropolis, than to the genus Nocardioides. N. simplex ATCC 13260 and N. simplex ATCC 19565 and ATCC 19566 exhibited levels of 16S rDNA similarity of 99.4 and 100%, respectively, to R. erythropolis DSM 43066T. Strains ATCC 13260, ATCC 19565, and ATCC 19566 had mesodiaminopimelic acid in their peptidoglycan and MK-8(H2) as their predominant menaquinone. These three strains produced cellular fatty acid patterns similar to those of R. erythropolis strains rather than those of Nocardioides species. Therefore, N. simplex ATCC 13260, ATCC 19565, and ATCC 19566 should be reclassified as strains of R. erythropolis Gray and Thornton 1928.

DNA, Bacterial↗

PubMed1998

Reclassification of Shewanella putrefaciens Owen's genomic group II as Shewanella baltica sp. nov.

The taxonomic relationship between several Shewanella putrefaciens isolates from the Baltic Sea and reference strains of this species is presented in this study. Results from DNA-DNA hybridization using a newly developed non-radioactive detection system and from 16S rRNA gene sequencing demonstrated that S. putrefaciens is a heterogeneous species containing more than a single genomic group. The genomic group II was phylogenetically, genotypically and phenotypically distant enough from the species type strain to be classified as a single species within the genus Shewanella. Therefore, we propose to reclassify Owen's genomic group II as Shewanella baltica sp. nov. with the type strain NCTC 10735.

DNA, Bacterial↗

PubMed1998

Polaribacter gen. nov., with three new species, P. irgensii sp. nov., P. franzmannii sp. nov. and P. filamentus sp. nov., gas vacuolate polar marine bacteria of the Cytophaga-Flavobacterium-Bacteroides group and reclassification of 'Flectobacillus glomeratus' as Polaribacter glomeratus comb. nov.

Several psychrophilic, gas vacuolate strains of the Cytophage-Flavobacterium-Bacteroides (CFB) phylogenetic group were isolated from sea ice and water from the Arctic and the Antarctic. The closest taxonomically defined species by 16S rRNA sequence analysis is 'Flectobacillus glomeratus'. However, 'Flc. glomeratus' is phylogenetically distant from the Flectobacillus type species, Flc. major. On the basis of phenotypic, genotypic and 16S rRNA sequence analyses we propose a new genus, Polaribacter, with three new species, Polaribacter irgensii strain 23-P (ATCC 700398), Polaribacter franzmannii strain 301 (ATCC 700399) and Polaribacter filamentus strain 215 (ATCC 700397). P. filamentus is the type species of the genus. None of these species exhibits a cosmopolitan or bipolar distribution. This is the first taxonomic description of gas vacuolate bacteria in the CFB group. Additionally, we propose that 'Flc. glomeratus' be reclassified to the genus Polaribacter as P. glomeratus, comb. nov.

Antarctic Regions↗

PubMed1998

Taxonomic significance of 2,4-diaminobutyric acid isomers in the cell wall peptidoglycan of actinomycetes and reclassification of Clavibacter toxicus as Rathayibacter toxicus comb. nov.

An HPLC procedure which separates D- and L-amino acid isomers was applied to an analysis of peptidoglycan of 2,4-diaminobutyric acid (DAB)-containing actinomycetes. The cell wall peptidoglycans of species of the genera Agromyces, Clavibacter and Rathayibacter contain DAB and have been differentiated principally by their menaquinone profile. These peptidoglycans are known to be identical in structure, all being of the B2 gamma type, possessing both D- and L-DAB. The type strains of all the subspecies of Clavibacter michiganesis have D- and L-DAB in almost equal proportions in their cell wall peptidoglycan as previously reported. In contrast, the type strains of Clavibacter toxicus and all valid species of the genera Agromyces and Rathayibacter contain the L-isomer of DAB almost exclusively. This characteristic is in good agreement with phylogenetic analyses based on 16S rDNA sequences and menaquinone profiles. On the basis of these data, the transfer of Clavibacter toxicus to the genus Rathayibacter as Rathayibacter toxicus comb. nov. is proposed. The isomer profile of DAB is shown to be a good taxonomic marker to differentiate these genera.

Actinomycetales↗

PubMed1998

Reclassification of Thermomonospora and Microtetraspora.

Almost complete 16S rRNA sequences from seven Thermomonospora strains, Thermomonospora curvata, Thermomonospora formosensis, Thermomonospora fusca, Thermomonospora mesophila, Thermomonospora chromogena, Thermomonospora alba and Thermomonospora mesouviformis (a synonym of Thermomonospora alba) were determined and subjected to phylogenetic analysis together with the sequences from all the representative members of the suborder Streptosporangineae. On the basis of phylogenetic, chemotaxonomic and phenotypic evidence, the transfer is proposed of Thermomonospora formosensis to the genus Actinomadura as Actinomadura formosensis comb. nov., Thermomonospora mesophila to the genus Microbispora as Microbispora mesophila comb. nov., and Thermomonospora fusca and Thermomonospora alba to a new genus, Thermobifida gen. nov., which belongs to the family Nocardiopsaceae, as Thermobifida fusca comb. nov. and Thermobifida alba comb. nov. Thermobifida alba is designated the type species of the genus. The transfer is also proposed of all species of the Microtetraspora pusilla group, which were transferred from Actinomadura, to a new genus, Nonomuria gen. nov., as Nonomuria africana comb. nov., Nonomuria angiospora comb. nov., Nonomuria fastidiosa comb. nov., Nonomuria ferruginea comb. nov., Nonomuria flexuosa comb. nov., Nonomuria helvata comb. nov., Nonomuria polychroma comb. nov., Nonomuria pusilla comb. nov., Nonomuria recticatena comb. nov., Nonomuria roseola comb. nov., Nonomuria roseoviolacea comb. nov., Nonomuria rubra comb. nov., Nonomuria salmonea comb. nov., Nonomuria spiralis comb. nov. and Nonomuria turkmeniaca comb. nov. Nonomuria pusilla is designated the type species of the genus.

Actinomycetales↗

PubMed1998

Characterization and reclassification of an aromatic- and chloroaromatic-degrading Pseudomonas sp., strain HV3, as Sphingomonas sp. HV3.

Phylogenetic analyses of 16S rRNA gene sequences showed that the Gram-negative aromatic- and chloroaromatic-degrading Pseudomonas sp. strain HV3 carrying the mega-plasmid pSKY4 belongs to the genus Sphingomonas. The 16SrRNA sequence is most related to Sphingomonas chlorophenolica strains ATCC 33790(T) (98.5%) and SR3 (98.4%) and Sphingomonas sp. SS86 (98.4%). The G+C content was 64 mol%, and the DNA-DNA hybridization-based relative homology of strain HV3 to the S. chlorophenolica ATCC 33790(T) and S. chlorophenolica RA2 was 59.6% and 35.9%, respectively. The results showed that although strain HV3 is related to S. chlorophenolica it differs in certain characteristics. It is therefore proposed to reclassify Pseudomonas sp. strain HV3 as Sphingomonas sp. HV3.

Base Sequence↗

PubMed1998

Reclassification of species of the spiral-shaped phototrophic purple non-sulfur bacteria of the alpha-Proteobacteria: description of the new genera Phaeospirillum gen. nov., Rhodovibrio gen. nov., Rhodothalassium gen. nov. and Roseospira gen. nov. as well as transfer of Rhodospirillum fulvum to Phaeospirillum fulvum comb. nov., of Rhodospirillum molischianum to Phaeospirillum molischianum comb. nov., of Rhodospirillum salinarum to Rhodovibrio salexigens.

The 165 rDNA sequence of Rhodospirillum mediosalinum was determined and compared with corresponding sequences from other spiral-shaped purple non-sulfur bacteria classified as or related to the genus Rhodospirillum in the alpha subclass of the Proteobacteria. Sequence similarities separate the currently recognized Rhodospirillum species into five different groups with no more than 91% sequence similarity, clearly indicating the necessity to recognize these groups as different genera. Major diagnostic properties of these bacteria are compared and new genera Phaeospirillum gen. nov., Roseospira gen. nov., Rhodothalassium gen. nov. and Rhodovibrio gen. nov. are described with the species Phaeospirillum fulvum comb. nov., Phaeospirillum molischianum comb. nov., Rhodovibrio salinarum comb. nov., Rhodovibrio sodomensis comb. nov., Rhodothalassium salexigens comb. nov. and Roseospira mediosalina comb. nov. The genus Rhodospirillum is represented by Rhodospirillum rubrum and Rhodospirillum photometricum and an emended description of this genus is also given.

Base Composition↗

PubMed1999

Reclassification of Brevibacterium oxydans (Chatelain and Second 1966) as Microbacterium oxydans comb. nov.

Phylogenetic and chemotaxonomic analyses indicate that Brevibacterium oxydans is closely related to species of the genus Microbacterium, namely Microbacterium liquefaciens, Microbacterium luteolum and Microbacterium saperdae. DNA-DNA reassociation values of less than 60% between Brevibacterium oxydans and these three Microbacterium species support the distinctness of this misclassified Brevibacterium species, which is reclassified as Microbacterium oxydans comb. nov.

Actinomycetales↗

PubMed1999

Reclassification of Brevibacterium incertum (Breed 1953) as Desemzia incerta gen. nov., comb. nov.

Phylogenetic analysis of 16S rDNA indicates that Brevibacterium incertum is not a member of the genus Brevibacterium but related to species of the genus Carnobacterium. Hence, Brevibacterium incertum is not a member of the class Actinobacteria but belongs to the phylogenetically defined broad Bacillus-Lactobacillus cluster. Based upon properties that taxonomically clearly distinguishes Brevibacterium incertum from species of the phylogenetic sister genus Carnobacterium, Brevibacterium incertum is reclassified as Desemzia incerta gen. nov., comb. nov.

Base Sequence↗

PubMed1999

Phylogeny of marine and freshwater Shewanella: reclassification of Shewanella putrefaciens NCIMB 400 as Shewanella frigidimarina.

Dissimilatory Fe(III) reduction by Shewanella putrefaciens and related species has generated considerable interest in biochemical characterization of the pathways for anaerobic electron transfer in this organism. Two strains, MR-1 and NCIMB 400, have been extensively used, and several respiratory enzymes have been isolated from each. It has become apparent that significant sequence differences exist between homologous proteins from these strains. The 16S rRNA from NCIMB 400 was sequenced and compared to the sequences from MR-1 and other Shewanella strains. The results indicate that NCIMB 400 is significantly more closely related to the newly identified Shewanella frigidimarina than to the S. putrefaciens type strain. It is therefore proposed that NCIMB 400 should be reclassified as S. frigidimarina.

Base Sequence↗

PubMed1999

Reclassification of Methanogenium tationis and Methanogenium liminatans as Methanofollis tationis gen. nov., comb. nov. and Methanofollis liminatans comb. nov. and description of a new strain of Methanofollis liminatans.

Sequencing of 16S rRNA genes and phylogenetic analysis of Methanogenium tationis DSM 2702T (OCM 43T) (T = type strain) and Methanogenium liminatans GKZPZT (= DSM 4140T) as well as other members of the family Methanomicrobiaceae revealed that both species belong to a separate line of descent within this family. In addition, a new strain of Methanogenium liminatans, strain BM1 (= DSM 10196), was isolated from a butyrate-degrading, fluidized bed reactor and characterized. Cells of both species are mesophilic, highly irregular cocci that use H2/CO2 and formate for growth and methanogenesis. In addition, Methanogenium liminatans strains GKZPZT and BM1 used 2-propanol/CO2, 2-butanol/CO2 and cyclopentanol/CO2. Both species contained diether and tetraether lipids. The polar lipids comprised amino-phosphopentanetetrol derivatives, which appear to be characteristic lipids within the family Methanomicrobiaceae. The pattern of glycolipids, phosphoglycolipids and amino-phosphoglycolipids was consistent with the assignment of these two species to a taxon within the family Methanomicrobiaceae, but also permitted them to be distinguished from other higher taxa within this family. The G+C contents of the DNA of Methanogenium tationis and Methanogenium liminatans were 54 and 60 mol% (Tm and HPLC), respectively. On the basis of the data presented, the transfer of Methanogenium tationis and Methanogenium liminatans to the genus Methanofollis gen. nov. as Methanofollis tationis comb. nov. and Methanofollis liminatans comb. nov., respectively, is proposed, with Methanofollis tationis as the type species.

Base Sequence↗

PubMed1999

Reclassification of non-pigmented Erwinia herbicola strains from trees as Erwinia billingiae sp. nov.

Twenty-two Erwinia-like strains, isolated from trees since the late fifties and belonging to a distinct phenotypic group with resemblance to Pantoea agglomerans, were further characterized by conventional biochemical tests, the BIOLOG metabolic fingerprinting system and fatty acid analysis. Their phylogenetic positions were determined by comparing the 16S rRNA gene sequence of a representative strain to available sequences of Erwinia, Pantoea, Pectobacterium and Brenneria species. The strains were shown to belong to the genus Erwinia, with Erwinia rhapontici and Erwinia persicina as the closest phylogenetic relatives. The name Erwinia billingiae sp. nov. is proposed (type strain LMG 2613T) and a description of the species is given.

Bacterial Typing Techniques↗

PubMed1999

Reclassification of Amycolatopsis rugosa Lechevalier et al. 1986 as Prauserella rugosa gen. nov., comb. nov.

An almost complete sequence of the 16S rDNA of the type strain of Amycolatopsis rugosa was determined following direct sequencing of the amplified gene. The sequence was aligned with those of representatives of the family Pseudonocardiaceae and related actinomycetes and phylogenetic trees were inferred by using three tree-making algorithms. The organism formed a distinct clade within the evolutionary radiation occupied by the family Pseudonocardiaceae. It was also readily distinguished from all of the validly described genera classified in this taxon by using a combination of chemical and morphological markers. On the basis of these genotypic and phenotypic differences, the name Prauserella gen. nov. is proposed for a new genus containing the previously misclassified Amycolatopsis rugosa. The type strain of Prauserella rugosa is DSM 43194T (= ATCC 43014T = NCIMB 8926T).

Actinomycetales↗

PubMed1999

The family Coriobacteriaceae: reclassification of Eubacterium exiguum (Poco et al. 1996) and Peptostreptococcus heliotrinreducens (Lanigan 1976) as Slackia exigua gen. nov., comb. nov. and Slackia heliotrinireducens gen. nov., comb. nov., and Eubacterium lentum (Prevot 1938) as Eggerthella lenta gen. nov., comb. nov.

16S rRNA gene sequences were determined for Eubacterium exiguum and Peptostreptococcus heliotrinreducens. These species were found to be closely related and, together with Eubacterium lentum, to constitute a branch of the Coriobacteriaceae. Two new genera are proposed on the basis of phenotypic characteristics and 16S rRNA gene sequence comparisons: Slackia to include the bile-sensitive species Eubacterium exiguum and P. heliotrinreducens, and Eggerthella to include the bile-resistant Eubacterium lentum. It is proposed that Eubacterium exiguum and Peptostreptococcus heliotrinreducens are transferred to the genus Slackia gen. nov. as Slackia exigua gen. nov., comb. nov. (type strain ATCC 700122T) and Slackia heliotrinireducens gen. nov., comb. nov. (type strain NTCC 11029T), respectively, and Eubacterium lentum is transferred to the genus Eggerthella gen. nov. as Eggerthella lenta gen. nov., comb. nov. with Eggerthella lenta as the type species.

Base Composition↗