Ignavigranum ruoffiae sp. nov., isolated from human clinical specimens

Two strains of a hitherto undescribed Gram-positive catalase-negative, facultatively anaerobic coccus isolated from human sources were characterized by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing studies demonstrated the unknown strains were genealogically identical, and constitute a new line close to, but distinct from, the genera Facklamia and Globicatella. The unknown bacterium was readily distinguished from Facklamia species and Globicatella sanguinus by biochemical tests and electrophoretic analysis of whole-cell proteins. Based on phylogenetic and phenotypic evidence it is proposed that the unknown bacterium be classified as Ignavigranum ruoffiae gen. nov., sp. nov. The type strain of Ignavigranum ruoffiae is CCUG 37658T.

Anaerobic transformation of quercetin-3-glucoside by bacteria from the human intestinal tract

From human feces two phenotypically different types of bacteria were isolated on quercetin-3-glucoside as carbon and energy source. Isolates of one type were identified as strains of Enterococcus casseliflavus. They utilized the sugar moiety of the glycoside, but did not degrade the aglycon further. The sugar moiety (4 mM) was fermented to 5.5 +/- 2.1 mM formate, 2.1 +/- 0.7 mM acetate, 1.6 +/- 0.3 mM l-lactate, and 1.3 +/- 0.4 mM ethanol. The second type of isolate was identified as Eubacterium ramulus. This organism was capable of degrading the aromatic ring system. Growing cultures of Eubacterium ramulus converted 5 mM quercetin-3-glucoside to 1.7 +/- 0.6 mM 3,4-dihydroxyphenylacetic acid, 7.6 +/- 1.0 mM acetate, and 4.0 +/- 0.4 mM butyrate. Molecular hydrogen, 3,4-dihydroxybenzaldehyde, and ethanol were detected in small amounts. Phloroglucinol was a transient intermediate in the breakdown of quercetin-3-glucoside. Eubacterium ramulus did not grow on the aglycon quercetin or the ring-fission intermediate phloroglucinol, but cleaved the flavonoid ring system when glucose was present as a cosubstrate. The most probable number of quercetin-3-glucoside-degrading bacteria determined in nine human fecal samples was 10(7)-10(9)/g dry mass. Isolates from these experiments were all identified as Eubacterium ramulus.

Roseovarius tolerans gen. nov., sp. nov., a budding bacterium with variable bacteriochlorophyll a production from hypersaline Ekho Lake

Eight Gram-negative, aerobic, pointed and budding bacteria were isolated from various depths of the hypersaline, heliothermal and meromictic Ekho Lake (Vestfold Hills, East Antarctica). The cells contained storage granules and daughter cells could be motile. Bacteriochlorophyll a was sometimes produced, but production was repressed by constant dim light. The strains tolerated a wide range of temperature, pH, concentrations of artificial seawater and NaCl, but had an absolute requirement for sodium ions. Glutamate was metabolized with and without an additional source of combined nitrogen. The dominant fatty acid was C18:1; other characteristic fatty acids were C18:2, C12:0 2-OH, C12:1 3-OH, C16:1, C16:0 and C18:0. The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. The DNA G+C base composition was 62-64 mol%. 16S rRNA gene sequence comparisons showed that the isolates were phylogenetically close to the genera Antarctobacter, 'Marinosulfonomonas', Octadecabacter, Sagittula, Sulfitobacter and Roseobacter. Morphological, physiological and genotypic differences to these previously described and distinct genera support the description of a new genus and a new species, Roseovarius tolerans gen. nov., sp. nov. The type strain is EL-172T (= DSM 11457T).

Zygosaccharomyces lentus sp. nov., a new member of the yeast genus Zygosaccharomyces Barker

Unusual growth characteristics of a spoilage yeast, originally isolated from spoiled whole-orange drink and previously identified as Zygosaccharomyces bailii, prompted careful re-examination of its taxonomic position. Small-subunit rRNA gene sequences were determined for this strain and for four other strains also originally described as Z. bailii but which, in contrast to other strains of this species, grew poorly or not at all under aerobic conditions with agitation, failed to grow in the presence of 1% acetic acid and failed to grow at 30 degrees C. Comparative sequence analysis revealed that these strains represented a phylogenetically distinct taxon closely related to, but distinct from, Z. bailii and Zygosaccharomyces bisporus. Furthermore, sequence analysis of the internal transcribed spacer (ITS) region showed that, while all five strains had identical ITS2 sequences, they could be subdivided into two groups based on ITS1 sequences. Despite such minor inter-strain sequence variation, these yeasts could readily be distinguished from all other currently described Zygosaccharomyces species by using ITS sequences. On the basis of the phylogenetic results presented, a new species comprising the five strains, Zygosaccharomyces lentus sp. nov., is described and supporting physiological data are discussed, including a demonstration that growth of this species is particularly sensitive to the presence of oxygen. The type strain of Z. lentus is NCYC D2627T.

Characterization of the genes encoding the botulinum neurotoxin complex in a strain of Clostridium botulinum producing type B and F neurotoxins

The organization of the clusters of genes encoding proteins of the botulinum neurotoxin (BoNT) progenitor complex was elucidated in a strain of Clostridium botulinum producing type B and F neurotoxins. With PCR and sequencing strategies, the type B BoNT-gene cluster was found to be composed of genes encoding BoNT/B, nontoxic nonhemagglutinin component (NTNH), P-21, and the hemagglutinins HA-33, HA-17, and HA-70, whereas the type F BoNT-gene cluster has genes encoding BoNT/F, NTNH, P-47, and P-21. Comparative sequence analysis showed that BoNT/F in type BF strain 3281 shares highest homology with BoNT/F of non-proteolytic (group II) C. botulinum whereas NTNH and P-21 in the type F cluster of strain 3281 are more similar to the corresponding proteins in proteolytic (group I) type F C. botulinum. These findings indicate diverse evolutionary origins for genes encoding BoNT/F and its associated non-toxic proteins, although the genes are contiguous. By contrast, sequence comparisons indicate that genes encoding BoNT/B and associated non-toxic proteins in strain 3281 possess a similar evolutionary origin. It was demonstrated that the genes present in the BoNT/B gene cluster of this type BF strain show exceptionally high homology with the equivalent genes in the silent BoNT/B gene cluster of C. botulinum type A(B), possibly indicating their common ancestry.

Description of Gemella sanguinis sp. nov., isolated from human clinical specimens

Six strains of a hitherto undescribed gram-positive, catalase-negative, facultatively anaerobic coccus isolated from human sources were characterized by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing studies demonstrated that the unknown strains were genealogically identical and constitute a new subline within the genus Gemella. The unknown bacterium was readily distinguished from Gemella haemolysans, Gemella bergeriae, and Gemella morbillorum by biochemical tests and electrophoretic analysis of whole-cell proteins. Based on phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified as Gemella sanguinis sp. nov. The type strain is CCUG 37820(T).

Corynebacterium kroppenstedtii sp. nov., a novel corynebacterium that does not contain mycolic acids

A strain of a hitherto undescribed coryneform bacterium from human clinical material was characterized by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequence analysis demonstrated the strain represents a novel and deep lineage within the genus Corynebacterium sensu stricto. Chemical analyses revealed the unidentified strain was unusual in that it lacked mycolic acids. Based on the phylogenetic and phenotypic distinctiveness of the unknown isolate, it is proposed that the bacterium be classified as a new Corynebacterium species, for which the name Corynebacterium kroppenstedtii sp. nov. is proposed. The type strain is CCUG 35717T.

Analysis of the botulinum neurotoxin type F gene clusters in proteolytic and nonproteolytic Clostridium botulinum and Clostridium barati

Comparison of genes encoding type F botulinum neurotoxin progenitor complex in strains of proteolytic Clostridium botulinum strain Langeland, nonproteolytic Clostridium botulinum strain 202F, and Clostridium barati strain ATCC 43256 reveals an identical organization of genes encoding a protein of molecular mass of approx. 47 kDa (P-47), nontoxic-nonhemagglutinin (NTNH) and botulinum toxin (BoNT). Although homology between the protein components of the complexes encoded by these different species all producing botulinum neurotoxin type F is considerable (approx. 69-88% identity), exceptionally high homology is observed between the C-termini of the P-47s (approx. 96% identity) and the NTNHs (approx. 94% identity) encoded by Clostridium botulinum type F strain Langeland and Clostridium botulinum type A strain Kyoto. Such a region of extremely high sequence identity is strongly indicative of recombination in these strains synthesizing botulinum neurotoxins of different antigenic types.

Corynebacterium confusum sp. nov., isolated from human clinical specimens

Three strains of a previously unknown coryneform bacterium were isolated from two patients with foot infections and from a blood culture of a third patient. The three non-lipophilic strains exhibited very slow fermentative acid production from glucose but not from maltose or sucrose, nitrate reductase activity, no tyrosinase activity and the presence of small amounts of tuberculostearic acid as the most significant phenotypic features. Differentiation of these strains from all other presently defined coryneform bacteria was readily achieved. Chemotaxonomic investigations revealed that the three strains unambiguously belonged to the genus Corynebacterium. Comparative 16S rRNA gene sequence analysis demonstrated that the isolates were almost identical and represented a new subline within the genus Corynebacterium, for which the designation Corynebacterium confusum sp. nov. is proposed. The type strain of Corynebacterium confusum is CCUG 38267T.

Allorhizobium undicola gen. nov., sp. nov., nitrogen-fixing bacteria that efficiently nodulate Neptunia natans in Senegal

A group of nodule isolates from Neptunia natans, an indigenous stemnodulated tropical legume found in waterlogged areas of Senegal, was studied. Polyphasic taxonomy was performed, including SDS-PAGE of total proteins, auxanography using API galleries, host-plant specificity, PCR-RFLP of the internal transcribed spacer region between the 16S and the 23S rRNA coding genes, 16S rRNA gene sequencing and DNA-DNA hybridization. It was demonstrated that this group is phenotypically and phylogenetically separate from the known species of Rhizobium, Sinorhizobium, Mesorhizobium, Agrobacterium, Bradyrhizobium and Azorhizobium. Its closest phylogenetic neighbour, as deduced by 16S rRNA gene sequencing, is Agrobacterium vitis (96.2% sequence homology). The name Allorhizobium undicola gen. nov., sp. nov., is proposed for this group of bacteria, which are capable of efficient nitrogen-fixing symbiosis with Neptunia natans, and the type strain is ORS 992T (= LMG 11875T).

Antarctobacter heliothermus gen. nov., sp. nov., a budding bacterium from hypersaline and heliothermal Ekho Lake

Four Gram-negative, aerobic, pointed and budding bacteria were isolated from various depths of the hypersaline, heliothermal and meromictic Ekho Lake (Vestfold Hills, East Antarctica). The cells contained storage granules and formed rosettes. Daughter cells may be motile. Growth required sodium ions. Nitrate was reduced to nitrite, and dissimilatory reduction of nitrite was possible. DNase and gelatinase were produced. Glutamate was metabolized with and without an additional source of combined nitrogen. The most abundant fatty acid was C18:1; other fatty acids present in lower concentrations were C12:1 3-OH, C16:1, C16:0, C18:0 and C19:0 cyc. The main polar lipids were phosphatidylglycerol and phosphatidylcholine. The DNA base composition was 62.3-62.8 mol% G + C. 16S rDNA sequence comparisons showed the isolates to be phylogenetically related to the genera Sagittula and Roseobacter. Morphological, physiological and genotypic differences to these and distinct characteristics supported the description of a new genus and a new species, Antarctobacter heliothermus gen. nov., sp. nov. The type strain is EL-219T (= DSM 11445T).

Identification of a gene encoding a methyl-accepting chemotaxis-like protein form Campylobacter coli and its use in a molecular typing scheme for campylobacters

Using PCR amplification with degenerate primers, a gene (tlpA) form Campylobacter coli encoding a putative 63x0 kDa polypeptide which exhibited significant identity with bacterial methyl-accepting chemotaxis proteins (MCPs) was identified. A mutant containing an inactivated copy of the tlpA A gene showed a wild-type chemotactic response to all of the chemo-attractants tested. A DNA probe based on the Highly Conserved Domain (HCD) of TlpA revealed the presence of multiple copies of genes encoding MCP-like proteins in both Camp. coli and Camp. jejuni. The arrangement of restriction sites within, and proximal to, genes with homology to the HCD probe varied among strains, resulting in a high degree of polymorphism. It is demonstrated here that a DNA probe compromising the HCD region of MCP-like proteins can be used, in Southern hybridization-based assays, to provide novel information which allows the discrimination of individual strains of Camp. coli and Camp. jejuni.

Actinobacillus scotiae sp. nov., a new member of the family Pasteurellaceae Pohl (1979) 1981 isolated from porpoises (Phocoena phocoena)

Phenotypic and phylogenetic studies were performed on a Gram-negative, rod-shaped bacterium isolated from three porpoises. Biochemical and physiological studies indicated that the bacterium was related to the family Pasteurellaceae. Comparative 16S rRNA gene sequencing studies confirmed these findings and demonstrated that the bacterium represents a hitherto unknown subline. The nearest phylogenetic relative of the unknown bacterium was Actinobacillus delphinicola, an organism also originating from sea mammals, although a sequence divergence of 3% demonstrated that the newly isolated bacterium is a distinct species. On the basis of the results of the phylogenetic analysis and phenotypic criteria, it is proposed that the bacterium should be classified as a new species, Actinobacillus scotiae sp. nov. The type strain of Actinobacillus scotiae sp. nov. is NCTC 12922T (= M2000/95/1T).

Tissierella creatinophila sp. nov., a gram-positive, anaerobic, non-spore-forming, creatinine-fermenting organism

A strictly anaerobic, Gram-positive, non-spore-forming bacterium was isolated from sewage sludge which grew on creatinine as sole source of carbon and energy. This new isolate, designated strain KRE 4T, totally degraded creatinine via creatine, sarcosine and glycine to the products acetate, monomethylamine, ammonia and carbon dioxide. Growth on creatinine or creatine was selenium-dependent and stimulated by formate, indicating the involvement of a creatine reductase, sarcosine reductase and/or glycine reductase. This was substantiated by the fact that creatine, sarcosine and glycine were reduced by cell-free extracts. Growth on creatinine or creatine was also possible in the absence of formate, but with an increase in doubling time. The new bacterium occurred as rod-shaped cells, which exhibited an angular form (2-6 microns long and 0.7-1.1 microns wide) and showed motility by means of peritrichous flagella. The G+C content of the DNA was 30 mol %. Comparative 16S rRNA sequence analysis demonstrated that strain KRE 4T represents a new subline within the genus Tissierella. Due to its very restricted substrate spectrum and the inability of whole cells to utilize sarcosine and glycine as intermediates of creatine breakdown, this organism can be readily separated from currently described species of Tissierella. Therefore, based on the phenotypic and phylogenetic distinctiveness of the new isolate, it si proposed that the bacterium be classified as a new species of the genus Tissierella, Tissierella creatinophila sp. nov. The type strain is KRE 4 (= DSM 6911T).

Facklamia ignava sp. nov., isolated from human clinical specimens

Two strains of a hitherto-undescribed gram-positive, catalase-negative coccus isolated from human sources were characterized by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing studies demonstrated that the unknown strains are genealogically identical and constitute a new line close to, but distinct from, Facklamia hominis. The unknown bacterium was readily distinguished from F. hominis by biochemical tests and electrophoretic analysis of whole-cell proteins. On the basis of phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified as Facklamia ignava sp. nov. The type strain of Facklamia ignava is CCUG 37419.

Gemella bergeriae sp. nov., isolated from human clinical specimens

Six strains of a hitherto-undescribed gram-positive, catalase-negative, facultatively anaerobic coccus from human sources were characterized by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing studies demonstrated that the unknown strains are genealogically homogeneous and constitute a new subline within the genus Gemella. The unknown bacterium was readily distinguished from Gemella haemolysans, the type species of the genus Gemella, and from Gemella morbillorum by biochemical tests and electrophoretic analysis of whole-cell proteins. On the basis of phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium from clinical specimens be classified as Gemella bergeriae sp. nov. The type strain of G. bergeriae is CCUG 37817 (= strain 617-93).

Lactobacillus kunkeei sp. nov.: a spoilage organism associated with grape juice fermentations

A Gram-positive rod was isolated from a commercial grape wine undergoing a sluggish/stuck alcoholic fermentation. The organism produced L-lactic acid from glucose, possessed weak catalase activity, and fermented relatively few carbohydrates, i.e. glucose, fructose, sucrose, raffinose (weakly) and mannitol. The 16S rRNA gene sequence analysis revealed that the isolate was phylogenetically a member of the genus Lactobacillus and formed a distinct subline within the Lact. casei cluster of species. Based on phenotypic and phylogenetic evidence, a new species is proposed, Lact. kunkeei. The type strain of Lact. kunkeei is ATCC 700308.

Characterization of tropical tree rhizobia and description of Mesorhizobium plurifarium sp. nov

A collection of strains isolated from root nodules of Acacia species in Senegal was analysed previously by electrophoresis of total cell protein, auxanographic tests, rRNA-DNA hydridization, 16S rRNA gene sequencing, DNA base composition and DNA-DNA hybridization [de Lajudie, P., Willems, A., Pot, B. & 7 other authors (1994). Int J Syst Bacteriol 44, 715-733]. Strains from Acacia were shown to belong to two groups, Sinorhizobium terangae, and a so-called gel electrophoretic cluster U, which also included some reference strains from Brazil. Further taxonomic characterization of this group using the same techniques plus repetitive extragenic palindromic-PCR and nodulation tests is presented in this paper. Reference strains from Sudan and a number of new rhizobia isolated from nodules of Acacia senegal, Acacia tortilis subsp. raddiana and Prosopis juliflora in Senegal were included. As a result of this polyphasic approach, the creation of a new species, Mesorhizobium plurifarium, is proposed for a genotypically and phenotypically distinct group corresponding to the former cluster U and containing strains isolated from Acacia, Leucaena, Prosopis and Chamaecrista in West Africa (Senegal), East Africa (Sudan) and South America (Brazil). The type strain of Mesorhizobium plurifarium ORS 1032 has been deposited in the LMG collection as LMG 11892.

Gene organization and sequence determination of the two botulinum neurotoxin gene clusters in Clostridium botulinum type A(B) strain NCTC 2916

The gene organization and nucleotide sequence of the type A and B BoNT-gene clusters in Clostridium botulinum strain NCTC 2916 were studied. The aim was to clarify the organization of genes within C. botulinum type A strains possessing an unexpressed BoNT/B gene. The BoNT/A-gene cluster includes genes encoding BoNT, NTNH and a part of P-47 (the gene for this protein was reported in strains of C. botulinum types E and F). Clustered with the silent BoNT/B gene were genes encoding NTNH, P-21 and HA-33. Sequencing analysis of the NTNHs revealed the presence of 471 amino acids identical in the type B and A gene clusters. This gene organization contrasts markedly with the purported organization in strain NCTC 2916 described by Henderson et al. (FEMS Microbiol. Lett. 140, 151-158). In type A(B) strain NCTC 2916, the neurotoxin gene is of type BoNT/A1 within a gene cluster that has identical organization to that found in BoNT/A2 type strains; these observations may be significant in establishing the origin of the BoNT-gene cluster.

Corynebacterium phocae sp. nov., isolated from the common seal (Phoca vitulina)

Phenotypic and phylogenetic studies were performed on four strains of a Gram-positive non-acid-fast coryneform-like organism isolated from the nasal cavities of common seals (Phoca vitulina). Chemotaxonomic investigations revealed the presence of corynomycolic acids in the unidentified isolates, which is consistent with corynebacteria. 16S rRNA gene sequence analysis demonstrated that the strains from seals represent a hitherto unknown subline within the genus Corynebacterium sensu stricto. Based on the results of the phylogenetic analysis and phenotypical criteria, it is proposed that the bacterium should be classified as a new species, Corynebacterium phocae. The type strain of Corynebacterium phocae is CCUG 38205T.

Corynebacterium camporealensis sp. nov., associated with subclinical mastitis in sheep

Four strains of a hitherto-unknown catalase-positive, facultatively anaerobic Corynebacterium species were isolated from the milk of sheep affected by subclinical mastitis. The most characteristic phenotypic reactions of the four strains were their weak fermentative acid production from glucose, their failure to produce acid from mannitol, xylose, sucrose and maltose, and a strong CAMP reaction with Staphylococcus aureus. Chemotaxonomic investigations revealed the presence of a cell wall based on meso-diaminopimelic acid and short-chain mycolic acids, which is consistent with the genus Corynebacterium. A comparative 16S rRNA gene sequence analysis confirmed that the organisms from sheep were members of the genus Corynebacterium, where they formed a distinct subline, exhibiting > 4% sequence divergence with other known Corynebacterium species. Based on both phenotypic and phylogenetic findings, a new species, Corynebacterium camporealensis, is proposed. The type strain of Corynebacterium camporealensis is CECT 4897 (= CRS-51T).

Phylogenetic heterogeneity of the genus Williopsis as revealed by 18S rRNA gene sequences

A phylogenetic investigation of the ascomycetous yeast genus Williopsis was performed by using 18S rRNA gene sequence analysis. Comparative sequence analysis revealed the genus to be phylogenetically heterogeneous. The five varieties of Williopsis saturnus [var. mrakii, var. sargentensis, var. saturnus (type), var. suaveolens and var. subsufficiens] were found to have identical 18S rRNA gene sequences and formed a distinct group, quite separate from all other Williopsis and non-Williopsis species examined. Williopsis mucosa was found to be the closet phylogenetic relative to the Williopsis saturnus group, however a sequence divergence of approximately 2.3% suggests this species may belong to a separate genus. The recently described species Williopsis salicorniae was found to exhibit a relatively close association with Ogataea minuta (identical to Pichia minuta), the type species of the genus Ogataea. The remaining two members of the genus, Williopsis californica and Williopsis pratensis, were found to form distinct lineages, displaying no specific association with any other Williopsis or non-Williopsis species. Based on comparative analysis of 18S rRNA genes it is apparent that the genus Williopsis as presently constituted is not monophyletic, and that the five currently recognized species form separate sublines each potentially worthy of separate generic status. The genus Williopsis should be restricted to the type species Williopsis saturnus and its five varieties. Despite the five varieties of Williopsis saturnus being genealogically indistinguishable at the 18S rRNA gene level, sequence analysis of the Internal transcribed spacer (ITS) region revealed that the five varieties could be differentiated on both their ITS1 and their ITS2 sequences, providing further evidence of the value of ITS sequences for discrimination of yeasts at the subspecies level.

Corynebacterium riegelii sp. nov., an unusual species isolated from female patients with urinary tract infections

Four strains of an unknown coryneform bacterium were isolated in pure culture from females with urinary tract infections. Strong urease activity and the ability to slowly ferment maltose but not glucose were the most significant phenotypic features of this catalase-positive, nonmotile, nonlipophilic, rod-shaped bacterium which served to distinguish it from all other presently defined coryneform bacteria. Chemotaxonomic investigations demonstrated that the unknown bacterium belonged to the genus Corynebacterium. Comparative 16S rRNA gene sequence analysis revealed that the isolates were genealogically identical and represented a new subline within the genus Corynebacterium, for which the designation Corynebacterium riegelii sp. nov. is proposed. The type strain of Corynebacterium riegelii is CCUG 38180 (DSM 44326, CIP 105310).

Aureobacterium resistens sp. nov., exhibiting vancomycin resistance and teicoplanin susceptibility

Two similar strains of a coryneform bacterium were isolated from human clinical material. Both strains were resistant to vancomycin but susceptible to teicoplanin. Detailed biochemical, chemotaxonomical, and molecular genetic investigations revealed that both isolates were members of a hitherto undescribed species of genus Aureobacterium. The name Aureobacterium resistens sp. nov. is proposed for the new bacterium and the type strain is CCUG 38312.