Dissection of the genus Actinobaculum: Reclassification of Actinobaculum schaalii Lawson et al. 1997 and Actinobaculum urinale Hall et al. 2003 as Actinotignum schaalii gen. nov., comb. nov. and Actinotignum urinale comb. nov., description of Actinotignum sanguinis sp. nov. and emended descriptions of the genus Actinobaculum and Actinobaculum suis; and re-examination of the culture deposited as Actinobaculum massiliense CCUG 47753T ( = DSM 19118T), revealing that it does not represent a strain of this species.

The remarkable host specificity of the species of the genus Actinobaculum led us to recharacterize these species by a polyphasic approach. A comparative chemotaxonomic study including analysis of whole-cell sugars, amino acid composition of the peptidoglycan, fatty acid methyl esters, respiratory quinones and polar lipids revealed significant differences that, in combination with molecular data, support a dissection of the genus Actinobaculum. The proposals of this study include the reclassification of Actinobaculum schaalii and Actinobaculum urinale as Actinotignum schaalii gen. nov., comb. nov. (type strain DSM 15541(T) = CCUG 27420(T)) and Actinotignum urinale comb. nov. (type strain DSM 15805(T) = CCUG 46093(T)), respectively. Emended descriptions of the genus Actinobaculum and Actinomyces suis are also provided. The results of 16S rRNA gene sequence analysis and DNA-DNA hybridization also indicated that the type strain of Actinobaculum massiliense deposited as CCUG 47753(T) ( = DSM 19118(T)) should in fact be considered a member of the species Actinobaculum schaalii. In addition, comparative 16S rRNA gene sequencing and DNA-DNA relatedness studies of four strains recovered from clinical materials demonstrated that three of the isolates belonged to Actinotignum schaalii; the remaining strain represents a novel species, for which the name Actinotignum sanguinis sp. nov. is proposed. The type strain is IMMIB L-2199(T) ( = DSM 26039(T) = CCUG 64068(T)).

The status of the species Actinobaculum massiliense (Greub and Raoult 2006). Request for an Opinion.

A recent study on members of the genus Actinobaculum revealed that cultures of the species Actinobaculum massiliense CCUG 47753(T) ( = DSM 19118(T)) currently being distributed do not conform to the properties of the type strain of A. massiliense CIP 107404(T) given by Greub & Raoult [Greub, G. & Raoult, D. (2002). J Clin Microbiol 40, 3938-3941]. The original strain, CIP 107404(T) is no longer available from the Biological Resource Center of Institut Pasteur, Paris. Based on data currently available, the organism currently deposited as CCUG 47753(T) and DSM 19118(T) is a member of the species Actinobaculum schaalii. Clearly, the organism deposited as CCUG 47753(T) and DSM 19118(T) as the type strain of the species Actinobaculum massiliense does not have the properties given by Greub & Raoult. Based on the absence of an authentic type strain, the Judicial Commission is requested to examine the status of the name Actinobaculum massiliense Greub and Raoult 2006 and to issue an Opinion.

Canibacter oris gen. nov., sp. nov., isolated from an infected human wound.

A facultatively anaerobic, Gram-reaction-positive, catalase- and oxidase-negative, rod-shaped bacterium isolated from an infected human wound caused by a dog bite was characterized by phenotypic and molecular genetic methods. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IMMIB Q2029717T was a member of the order Micrococcales of the class Actinobacteria, displaying 91.6% to 96% sequence similarity with members of the family Microbacteriaceae. Phylogentic trees generated by different algorithms indicated that the strain forms an independent phylogenetic line of descent that consistently clustered proximal to the base of the genus Leucobacter. Chemical studies revealed the presence of a cell-wall murein based on L-lysine (type B1α), major menaquinone (MK-10) and a DNA G+C content of 56.9 mol%. The distinct phylogenetic position, ribotyping and matrix-assisted laser desorption/ionization time-of-flight MS profiles and the significant phenotypic differences clearly separate strain IMMIB Q2029717T from its nearest phylogenetic neighbour and support its classification as a representative of a novel genus and species, with the suggested name Canibacter oris gen. nov., sp. nov. The type strain is IMMIB Q2029717T (=DSM 27064T=CCUG 64069T).

Cruoricaptor ignavus gen. nov., sp. nov., a novel bacterium of the family Flavobacteriaceae isolated from blood culture of a man with bacteraemia.

A Gram-reaction-negative bacterium, strain IMMIB L-12475(T), was isolated from blood cultures of a human with septicaemia. The yellowish orange pigmented strain contained flexirubin pigment. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain IMMIB L-12475(T) belonged to the family Flavobacteriaceae, forming a distinct phyletic line that is distantly related (79.1-89.4% sequence similarity) to described genera of this family. Membership to the family was confirmed by a fatty acid profile consisting of branched-chain and 3-hydroxy fatty acids with major amounts of iso-C(17:0) 3-OH and iso-C(15:0), by the presence of menaquinone MK-6 as the only respiratory quinone and a polyamine pattern that contained sym-homospermidine as major component. The phospholipids consisted of phosphatidylethanolamine and an unknown phospholipid. The genomic DNA mol% G+C content was 45.6%. The distant phylogenetic position as compared to other representative of the family and the significant phenotypic properties such as pigment composition, morphology, and physiology support the proposal of a novel genus and species Cruoricaptor ignavus gen. nov., sp. nov. The type strain is IMMIB L-12475(T) (=DSM 25479(T)=CCUG 62025(T)).

Corynebacterium aquatimens sp. nov., a lipophilic Corynebacterium isolated from blood cultures of a patient with bacteremia.

An unknown lipophilic coryneform bacterium isolated from the blood cultures of a patient with bacteremia was characterized by phenotypic and molecular genetic methods. Chemical analysis revealed the presence of short chain mycolic acids consistent with the genus Corynebacterium. The DNA G+C content was 60.8 mol%. Comparative 16S rRNA gene sequence analysis demonstrated that the isolate represents a new subline within the genus Corynebacterium. The closely phylogenetic relative of the unknown bacterium was found to be C. tuscaniense (97.8% sequence similarity). Partial rpoB gene sequence revealed that strain IMMIB L-2475(T) exhibited 13.5% sequence divergence with C. tuscaniense. The unknown bacterium was distinguished from C. tuscaniense by, DNA-DNA hybridization, cellular fatty acid profiles, MALDI-TOF analyses of cell extracts and biochemical tests. Based on the phylogenetic and phenotypic criteria, it is proposed that this bacterium be classified as new species, Corynebacterium aquatimens sp. nov., and is represented by strain IMMIB L-2475(T) (=DSM 45632(T)=CCUG 61574(T)).

Comparative chemotaxonomic and phylogenetic studies on the genus Arcanobacterium Collins et al. 1982 emend. Lehnen et al. 2006: proposal for Trueperella gen. nov. and emended description of the genus Arcanobacterium.

The results of a study comparing the chemotaxonomic characteristics and phylogenetic positions of members of the genus Arcanobacterium indicated that the genus was not monophyletic and, therefore, was in need of taxonomic revision. Phylogenetically, the genus Arcanobacterium consisted of two distinct lines; a group comprising the species Arcanobacterium haemolyticum (the type species of the genus), A. hippocoleae, A. phocae and A. pluranimalium and a robust group consisting of the species A. abortisuis, A. bernardiae, A. bialowiezense, A. bonasi and A. pyogenes. On the basis of 16S rRNA signature nucleotide comparisons and menaquinone and phospholipid compositions, it is proposed that of these nine species only four, A. haemolyticum, A. hippocoleae, A. phocae and A. pluranimalium, should be affiliated with the genus Arcanobacterium and the species A. abortisuis, A. bernardiae, A. bialowiezense, A. bonasi and A. pyogenes should be reclassified as members of a new genus, Trueperella, as Trueperella abortisuis comb. nov., Trueperella bernardiae comb. nov., Trueperella bialowiezensis comb. nov., Trueperella bonasi comb. nov. and Trueperella pyogenes comb. nov. Positive results in Christie-Atkins-Munch-Petersen (CAMP) tests on A. haemolyticum, A. hippocoleae, A. phocae and A. pluranimalium also supported the rearrangement of the nine species in to separate genera. As such, an emended description of the genus Arcanobacterium is provided.

Arthrobacter equi sp. nov., isolated from veterinary clinical material.

A Gram-positive-staining, catalase-positive, non-spore-forming, rod-shaped bacterium, strain IMMIB L-1606(T), isolated from genital swabs of a horse, was characterized using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that the organism was related to members of the genus Arthrobacter, displaying sequence similarities of 93.5-99.1 % with the type strains of recognized species of the genus. Cell-wall analysis revealed peptidoglycan type A3α L-Lys-L-Ser-L-Thr-L-Ala. DNA-DNA hybridization data and biochemical characterization of strain IMMIB L-1606(T) enabled the isolate to be differentiated genotypically and phenotypically from phylogenetically closely related species of the genus Arthrobacter. Therefore, it is concluded that strain IMMIB L-1606(T) represents a novel species of the genus Arthrobacter, for which the name Arthrobacter equi sp. nov. is proposed. The type strain of Arthrobacter equi sp. nov. is IMMIB L-1606(T) ( = DSM 23395(T) = CCUG 59597(T)).

Auritidibacter ignavus gen. nov., sp. nov., of the family Micrococcaceae isolated from an ear swab of a man with otitis externa, transfer of the members of the family Yaniellaceae Li et al. 2008 to the family Micrococcaceae and emended description of the suborder Micrococcineae.

A Gram-reaction-positive, aerobic, catalase-positive, non-spore-forming, rod-shaped bacterium designated IMMIB L-1656(T) was isolated from an ear swab of a man and characterized using a polyphasic approach. 16S rRNA gene sequence analysis indicated that strain IMMIB L-1656(T) is related to members of the family Micrococcaceae (<95.1 % sequence similarity). Anaylsis using different phylogenetic algorithms consistently grouped strain IMMIB L-1656(T) with members of the genus Yaniella. The organism posessed a cell-wall murein based on L-lysine (variation A4α, type L-Lys-Gly-L-Glu), MK-10 as the predominant menaquinone and long-chain cellular fatty acids of straight-chain and branched-chain saturated types (with iso-C(15 : 0) and anteiso-C(17 : 0) predominating). The polar lipids included diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol in addition to unknown glycolipids. The DNA G+C content was 59.7 mol%. Based on its distinctive genotypic and phenotypic characteristics, strain IMMIB L-1656(T) represents a novel species in a novel genus, for which the name Auritidibacter ignavus gen. nov., sp. nov. is proposed. We also propose that members of the family Yaniellaceae be transferred to the family Micrococcaceae with amendments to the description of the suborder Micrococcineae. The type strain of Auritidibacter ignavus is IMMIB L-1656(T) (=DSM 45359(T) =CCUG 57943(T)).

Clinical characteristics of viral intestinal infection in preterm and term neonates.

The clinical presentation of the viral enteric pathogens in newborn infants has not been adequately examined. The aim of this study was to evaluate the clinical characteristics of viral intestinal infections in newborn infants. Clinical data of all term and preterm infants admitted to our tertiary neonatal intensive care unit from 1998 to 2007 with clinical signs of gastroenteritis (GE) or necrotizing enterocolitis (NEC) were retrospectively reviewed and compared between infants with different viral enteric pathogens in stool specimens. In 34 infants with signs of GE or NEC, enteropathogenic viruses were found in stool specimens. Rotavirus was detected in 12 cases, of which two infants had NEC. Compared with infants with rotavirus or norovirus, infants with astrovirus more frequently suffered from NEC (p<0.05). In addition, an acute systemic inflammatory response was significantly more common in patients with astrovirus infection (astrovirus vs. rotavirus and astrovirus vs. norovirus, p < 0.01 and p < 0.05, respectively). Of eight children infected with norovirus, one infant had a systemic acute inflammatory response and NEC. This study demonstrates that in newborn infants, intestinal rotavirus, norovirus, and astrovirus infections may be associated with severe illness such as hemorrhagic enteritis resulting in bloody diarrhea or even NEC.

Genotypic and phenotypic variation among Lysobacter capsici strains isolated from Rhizoctonia suppressive soils.

Four Gram-negative bacterial strains, recovered from clay soils cultivated with different crops in the Netherland, were subjected to a polyphasic taxonomic study in order to clarify their taxonomic status. Comparative analysis of the 16S rRNA gene sequences revealed that they belong to the genus Lysobacter and to be highly related to the type strains of L. antibioticus DSM 2044(T), L. gummosus DSM 6980(T), and L. capsici DSM 19286(T), displaying 99.1-99.3%, 99.2-99.6% and 99.4-100% sequence similarities, respectively, to these species. The results of DNA-DNA hybridization studies unambigiously indicated that the four strains belonged to the species L. capsici. Nevertheless, DNA fingerprinting and phenotypic characterization indicated that there was a considerable diversification and niche differentiation among the strains belonging to L. capsici. The newly identified L. capsici strains strongly inhibit Rhizoctonia solani AG2 and originate from Rhizoctonia-suppressive soils where also populations of L. antibioticus and L. gummosus were present. This is the first report of the presence of combined populations of closely related Lysobacter spp. within agricultural soils.

Corynebacterium pilbarense sp. nov., a non-lipophilic corynebacterium isolated from a human ankle aspirate.

A non-lipophilic coryneform bacterium isolated from an anaerobic Bactec bottle inoculated with an ankle aspirate from a male patient was characterized by phenotypic and molecular taxonomic methods. Chemotaxonomic investigations revealed the presence of short-chain mycolic acids in the cell wall of the bacterium, a feature consistent with members of the genus Corynebacterium. Comparative 16S rRNA gene sequence analysis demonstrated that the isolate displayed 92.0-99.0 % gene sequence similarity with members of the genus Corynebacterium, with Corynebacterium ureicelerivorans as the most closely related phylogenetic species (99.0 % gene sequence similarity). However, the isolate could be genomically separated from C. ureicelerivorans on the basis of DNA-DNA hybridization studies (39.5 % relatedness). Furthermore, the isolate could also be differentiated from C. ureicelerivorans and other species of the genus Corynebacterium on the basis of biochemical properties. Based on both phenotypic and phylogenetic evidence, it is proposed that this isolate be classified as representing a novel species, Corynebacterium pilbarense sp. nov. (type strain IMMIB WACC 658(T)=DSM 45350(T)=CCUG 57942(T)).

Chryseobacterium treverense sp. nov., isolated from a human clinical source.

A yellow-pigmented, Gram-reaction-negative bacterium isolated from a human clinical source was investigated using a polyphasic approach in order to clarify its taxonomic status. Comparative 16S rRNA gene sequence analysis showed that the new isolate constituted a distinct phyletic line within the genus Chryseobacterium, displaying >2.8 % sequence divergence with recognized species of this genus. The generic assignment was confirmed by chemotaxonomic data which revealed a fatty acid profile consisting of straight-chain saturated, monounsaturated and branched-chain fatty acids of iso-/anteiso-types as well as 3-hydroxylated fatty acids; a menaquinone with six isoprene units (MK-6) as the predominant respiratory quinone and sym-homospermidine as the predominant polyamine. The novel isolate could be distinguished from other members of the genus Chryseobacterium by a set of distinct biochemical properties. On the basis of phenotypic and phylogenetic evidence, it is proposed that the new isolate represents a novel species of the genus Chryseobacterium for which the name Chryseobacterium treverense sp. nov. is proposed. The type strain is IMMIB L-1519(T) (=DSM 22251(T)=CCUG 57657(T)).

Actinomadura sputi sp. nov., isolated from the sputum of a patient with pulmonary infection.

The taxonomic position of an actinomycete, strain IMMIB L-889(T), isolated from the sputum of a 64-year-old man, was determined using a polyphasic taxonomic approach. The strain had chemical and morphological properties that were consistent with its classification in the genus Actinomadura. It formed a distinct phyletic line in the 16S rRNA gene tree of Actinomadura and was most closely related to the type strain of Actinomadura hallensis (98.4 % sequence similarity), but could be readily distinguished from the latter species using DNA-DNA relatedness and phenotypic data. The combined genotypic and phenotypic data indicate that strain IMMIB L-889(T) represents a novel species of the genus Actinomadura, for which the name Actinomadura sputi sp. nov. is proposed. The type strain is IMMIB L-889(T) =DSM 45233(T)=CCUG 56589(T). [corrected]

Nocardiopsis potens sp. nov., isolated from household waste.

The taxonomic position of an actinomycete, designated strain IMMIB L-21(T), was determined using a polyphasic taxonomic approach. The organism, which had phenotypic properties consistent with its classification in the genus Nocardiopsis, formed a distinct clade in the 16S rRNA gene sequence tree together with the type strain of Nocardiopsis composta, but was readily distinguished from this species using DNA-DNA relatedness and phenotypic data. The genotypic and phenotypic data show that the organism represents a novel species of the genus Nocardiopsis, for which the name Nocardiopsis potens sp. nov. is proposed. The type strain is IMMIB L-21(T) (=DSM 45234(T)=CCUG 56587(T)).

Psychrobacter lutiphocae sp. nov., isolated from the faeces of a seal.

The taxonomic status of a Gram-negative-staining bacterium, isolated from the faeces of a seal, was investigated using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that the novel isolate formed a distinct phyletic line within the genus Psychrobacter, displaying >3.3% sequence divergence with other known Psychrobacter species. The generic assignment was confirmed by chemotaxonomic data, which revealed a fatty acid profile that included straight-chain saturated, unsaturated and 3-hydroxylated fatty acids, with C18:1omega9c as the major fatty acid. A ubiquinone with eight isoprene units (Q-8) was the predominant respiratory quinone and spermidine was the predominant polyamine. The novel isolate was distinguished from other members of the genus Psychrobacter by using a set of phenotypic properties. On the basis of phenotypic and phylogenetic considerations, it is proposed that the new isolate represents a novel species, for which the name Psychrobacter lutiphocae sp. nov. is proposed. Strain IMMIB L-1110T (=DSM 21542T=CCUG 56590T) is the type strain.

Saccharopolyspora rosea sp. nov., isolated from a patient with bronchial carcinoma.

The taxonomic status of a bacterium isolated from a patient with bronchial carcinoma was established using a polyphasic taxonomic approach. The strain had morphological and chemotaxonomic characteristics consistent with those of members of the genus Saccharopolyspora. The generic assignment was confirmed by comparative analysis of the 16S rRNA gene sequence, which showed that the strain constituted a distinct phyletic line, displaying 93.5-96.9 % sequence similarity with respect to members of the genus Saccharopolyspora. The isolate was distinguished from the type strains of recognized members of the genus Saccharopolyspora by means of various biochemical tests. The genotypic and phenotypic data obtained demonstrated that strain IMMIB L-1070(T) represents a novel species of the genus Saccharopolyspora, for which the name Saccharopolyspora rosea sp. nov. is proposed. The type strain is IMMIB L-1070(T) (=DSM 45226(T)=CCUG 56401(T)).

Azospirillum picis sp. nov., isolated from discarded tar.

A polyphasic taxonomic study was performed on a pink-coloured unknown bacterium isolated from discarded road tar. Comparative analysis of the 16S rRNA gene sequence demonstrated that the isolate belongs phylogenetically to the genus Azospirillum with Azospirillum lipoferum, A. melinis and A. rugosum as its closest phylogenetic relatives (96.7, 96.6 and 96.6 % similarity to the respective type strains). The generic assignment was confirmed on the basis of chemotaxonomic data, which revealed a fatty acid profile characteristic for the genus Azospirillum, consisting of straight-chain saturated and unsaturated fatty acids, with C(18 : 1)omega7c as the major unsaturated non-hydroxylated fatty acid, and C(16 : 0) 3-OH as the major hydroxylated fatty acid, and a ubiquinone with ten isoprene units (Q-10) as the predominant respiratory quinone. On the basis of both the phenotypic and molecular genetic evidence, it is proposed that the unknown isolate should be classified within a novel species of the genus Azospirillum, for which the name Azospirillum picis sp. nov. is proposed. The type strain is IMMIB TAR-3(T) (=CCUG 55431(T) =DSM 19922(T)).

Desmospora activa gen. nov., sp. nov., a thermoactinomycete isolated from sputum of a patient with suspected pulmonary tuberculosis, and emended description of the family Thermoactinomycetaceae Matsuo et al. 2006.

A novel Gram-positive, aerobic, catalase-positive, filamentous micro-organism, designated strain IMMIB L-1269(T), originating from sputum was characterized using phenotypic and molecular taxonomic methods. It showed cell-wall chemotype III, phospholipid type PII (with phosphatidylethanolamine as the diagnostic phospholipid) and contained an unsaturated menaquinone with seven isoprene units (MK-7) as the predominant isoprenoid quinone. It synthesized long-chain cellular fatty acids of the straight-chain saturated, monounsaturated and iso- and anteiso-branched types (with iso-C(15 : 0), C(16 : 0) and iso-C(17 : 0) predominating) and possessed a DNA G+C content of 49.3 mol%. On the basis of its morphological, biochemical and chemical characteristics, strain IMMIB L-1269(T) did not conform to any presently recognized taxon. Comparative analyses based on 16S rRNA gene sequences confirmed the distinctiveness of the isolate, as it displayed sequence-divergence values greater than 7.7 % with respect to recognized Gram-positive taxa. Phylogenetic treeing analysis served to reinforce the view that strain IMMIB L-1269(T) was distinct from recognized taxa, as it formed a relatively long subline branching within a 16S rRNA gene sequence cluster that encompassed the genera Thermoactinomyces, Laceyella, Mechercharimyces, Thermoflavimicrobium, Planifilum, Seinonella and Shimazuella of the family Thermoactinomycetaceae. On the basis of phenotypic and molecular phylogenetic evidence, strain IMMIB L-1269(T) represents a novel genus and species, for which the name Desmospora activa gen. nov., sp. nov. is proposed. The type strain of Desmospora activa is strain IMMIB L-1269(T) (=DSM 45169(T) =CCUG 55916(T)). An emended description of the family Thermoactinomycetaceae is also given.

Corynebacterium ulceribovis sp. nov., isolated from the skin of the udder of a cow with a profound ulceration.

A coryneform bacterium isolated from a cow with a profound ulceration was characterized by using phenotypic and molecular taxonomic methods. Chemotaxonomic investigations revealed the presence of cell-wall chemotype IV and short-chain mycolic acids consistent with the genus Corynebacterium. Comparative 16S rRNA gene sequencing showed that the organism formed a hitherto unknown subline within the genus Corynebacterium. Sequence divergence values of greater than 3.6 % from recognized Corynebacterium species, together with phenotypic differences, showed that the unidentified bacterium represents a new member of this genus. On the basis of phenotypic and phylogenetic considerations, it is proposed that the novel bacterium be classified as representing a novel species of the genus Corynebacterium, with the name Corynebacterium ulceribovis sp. nov. The type strain is IMMIB L-1395T (=DSM 45146T=CCUG 55727T).

Corynebacterium sputi sp. nov., isolated from the sputum of a patient with pneumonia.

A coryneform bacterium isolated from the sputum of a patient with pneumonia was characterized by phenotypic and molecular taxonomic methods. Chemotaxonomic investigations revealed the presence of cell-wall chemotype IV and short chain mycolic acids consistent with the genus Corynebacterium. Comparative 16S rRNA gene sequencing studies confirmed this assignment, with the organism forming a hitherto unknown subline within the genus associated with a subcluster containing Corynebacterium hansenii, Corynebacterium freneyi, Corynebacterium xerosis, Corynebacterium amycolatum and Corynebacterium sphenisci. Sequence divergence values of >2.7 % from established corynebacterial species suggested that the new isolate represented a novel species. This was also supported by the results of the biochemical tests. On the basis of phenotypic and phylogenetic evidence, it is proposed that the unknown bacterium be classified as a novel species of the genus Corynebacterium, Corynebacterium sputi sp. nov. (type strain IMMIB L-999(T)=DSM 45148(T)=CCUG 55795(T)).