Subdoligranulum variabile gen. nov., sp nov from human feces

During studies on the microflora of human feces we have isolated a strictly anaerobic, non-spore-forming, Gram-negative staining organism which exhibits a somewhat variable coccus-shaped morphology. Comparative 16S ribosomal RNA gene sequencing studies show the unidentified organism is phylogenetically a member of the Clostridium leptum supra-generic rRNA cluster and displays a close affinity to some rDNA clones derived from human and pig feces. The nearest named relatives of the unidentified isolate corresponded to Faecalibacterium prausnitzii (formerly Fusobacterium prausnitzii) displaying a 16S rRNA sequence divergence of approximately 9%, with Anaerofilum agile and A. pentosovorans the next closest relatives of the unidentified bacterium (sequence divergence approximately 10%). Based on phenotypic and phylogenetic considerations, it is proposed that the unusual coccoid-shaped organism be classified as a new genus and species, Subdoligranulum variabile. The type strain of S. variabile is BI 114(T) (= CCUG 47106(T) = DSM 15176(T)). (C) 2004 Elsevier Ltd. All rights reserved.

Characterization of some Actinomyces-like isolates from human clinical sources: description of Varibaculum cambriensis gen. nov., sp nov

Fifteen strains of an anaerobic, catalase-negative, gram-positive diphtheroid-shaped bacterium recovered from human sources were characterized by phenotypic and molecular chemical and molecular genetic methods. The unidentified bacterium showed some resemblance to Actinomyces species and related taxa, but biochemical testing, polyacrylamide gel electrophoresis analysis of whole-cell proteins, and amplified 16S ribosomal DNA restriction analysis indicated the strains were distinct from all currently named Actinomyces species and related taxa. Comparative 16S rRNA gene sequencing studies showed that the bacterium represents a hitherto-unknown phylogenetic line that is related to but distinct from Actinomyces, Actinobaculum, Arcanobacterium, and Mobiluncus. We propose, on the basis of phenotypic and phylogenetic evidence, that the unknown bacterium from human clinical specimens should be classified as a new genus and species, Varibaculum cambriensis gen. nov., sp. nov. The type strain of Varibaculum cambriensis sp. nov. is CCUG 44998(T) = CIP 107344(T).

Actinomyces dentalis sp nov., from a human dental abscess

A previously undescribed filamentous, beaded, Gram-positive, rod-shaped bacterium was isolated from pus of a human dental abscess. Based on its cellular morphology end the results of biochemical testing the organism was tentatively identified as a member of the genus Actinomyces, but it did not correspond to any currently recognized species of this genus. Comparative 16S rRNA gene sequencing studies showed the bacterium represents a distinct subline within the genus Actinomyces, clustering within a group of species that includes Actinomyces bovis, the type species of the genus. Sequence divergence values of >8% with other recognized species within this phylogenetic group clearly demonstrated that the organism represents a hitherto unknown species. Based on biochemical and molecular phylogenetic evidence, it is proposed that the unidentified organism recovered from a dental abscess be classified as a novel species, Actinomyces dentalis sp. nov. The type strain is R18165(T) (= CCUG 48064(T) = CIP 108337(T)).

Actinomyces nasicola sp. nov., isolated from a human nose

A previously undescribed facultatively anaerobic, catalase-negative, Actinomyces-like bacterium was isolated from the nose of a human. On the basis of its cellular morphology and the results of biochemical testing, the micro-organism was tentatively identified as a member of the genus Actinomyces, but it did not correspond to any currently recognized species. Comparative 16S rRNA gene sequencing studies showed the bacterium to be a hitherto unknown subline within the genus Actinomyces, displaying sequence divergence values of more than 6% with respect to recognized species of the genus. On the basis of biochemical, molecular chemical and molecular phylogenetic evidence, it is proposed that the unknown organism, strain R2014(T) (=CCUG 46092(T)=CIP 107668(T)), be classified as the type strain of a novel species, Actinomyces nasicola sp. nov.

Corynebacterium atypicum sp. nov., from a human clinical source, does not contain corynomycolic acids

An unusual Gram-positive, facultatively anaerobic, catalase-positive, diphtheroid-shaped organism originating from an unknown human clinical source was characterized by biochemical, molecular chemical and molecular phylogenetic methods. Based on its morphological and biochemical characteristics and the presence of a murein based on meso-diaminopimelic acid, the unidentified organism was tentatively assigned to the genus Corynebacterium. However, the unknown organism was found to lack the distinctive, short-chain corynomycolic acids that are considered to be characteristic of this genus. Despite the absence of these characteristic lipids, comparative 16S rRNA gene sequencing showed that the unknown bacterium was phylogenetically a member of the genus Corynebacterium and was distinct from all currently known species. Based on both phenotypic and 16S rRNA sequence considerations, it is proposed that the unknown organism be classified as a novel species, Corynebacterium atypicum sp. nov. The type strain of C. atypicum is strain R2070(T) (= CCUG 45804(T) = CIP 107431(T)).

Actinomyces oricola sp. nov., from a human dental abscess

A previously undescribed Actinomyces-like bacterium was isolated from a human dental abscess. Based on its cellular morphology and the results of biochemical testing the organism was tentatively identified as a member of the genus Actinomyces, but it did not correspond to any currently recognized species of this genus. Comparative 16S rRNA gene sequencing studies showed the bacterium represents a hitherto unknown subline within the genus Actinomyces, clustering within a group of species, which includes Actinomyces bovis, the type species of the genus. Based on biochemical and molecular phylogenetic evidence, it is proposed that the unknown organism recovered from a dental abscess be classified as a new species, Actinomyces oricola sp. nov. The type strain of Actinomyces oricola is R5292(T) (=CCUG 46090(T)=CIP 107639(T)).

Actinobaculum urinale sp. nov., from human urine

A hitherto undescribed Actinomyces-like bacterium was isolated from human urine. Based on its biochemical characteristics, the unidentified bacterium did not correspond to any currently described Actinomyces species or related taxa. Comparative 16S rRNA gene sequencing showed that the unknown bacterium exhibits a specific phylogenetic association with the genus Actinobaculum, but a sequence divergence of > 5% from the two currently recognized members of this genus, Actinobaculum schaalii and Actinobaculum suis, demonstrates that it represents a distinct species. Based on both phenotypic and 16S rRNA gene sequence considerations, it is proposed that the unknown bacterium from urine should be classified as a novel species, Actinobaculum urinale sp. nov. The type strain of Actinobaculum urinale is CCUG 46093(T) (= CIP 107424(T)).

Actinomyces vaccimaxillae sp. nov., from the jaw of a cow

A previously undescribed Actinomyces-like bacterium was isolated from a lesion in the jaw of a cow. Based on its cellular morphology and the results of biochemical testing, the organism was tentatively identified as a member of the genus Actinomyces. Comparative 16S rRNA gene sequencing studies showed that the bacterium represents a hitherto unknown species within the genus Actinomyces, and is related to a group of species that includes Actinomyces turicensis and its close relatives. It is proposed that the unknown organism be classified as Actinomyces vaccimaxillae sp. nov. (the type strain is CCUG 46091(T)=CIP 107423(T)).

Allobaculum stercoricanis gen. nov., sp nov., isolated from canine feces

Morphological, biochemical, and molecular genetic studies were performed on an unknown anaerobic, catalase-negative, nonspore-forming, rod-shaped bacterium isolated from dog feces. The unknown bacterium was tentatively identified as a Eubacterium species, based on cellular morphological and biochemical tests. 16S rRNA gene sequencing studies, however, revealed that it was phylogenetically distant from Eubacterium limosum, the type species of the genus Eubacterium. Phylogenetically, the unknown species forms a hitherto unknown sub-line proximal to the base of a cluster of organisms (designated rRNA cluster XVI), which includes Clostridium innocuum, Streptococcus pleomorphus, and some Eubacterium species. Based on both phenotypic and phylogenetic criteria, it is proposed that the unknown bacterium be classified as a new genus and species, Allobaculum stercoricanis. Using a specific rRNA-targeted probe designed to identify Allobacultan stercoricanis, in situ hybridisation showed this novel species represents a significant organism in canine feces comprising between 0.1% and 3.7% of total cells stained with DAPI (21 dog fecal samples). The type strain of Allobaculum stereoricanis is DSM 13633(T) = CCUG 45212(T). (C) 2004 Elsevier Ltd. All rights reserved.

Clostridium colicanis sp. nov., from canine faeces

Morphological, biochemical and molecular genetic studies were performed on an unknown, anaerobic, rod-shaped organism isolated from faeces of a canine. The organism was tentatively identified as a member of the genus Clostridium based on its cellular morphology and ability to form endospores but, biochemically, it did not appear to correspond to any recognized species of this genus. Comparative 16S rRNA gene sequence analysis showed that the bacterium represents a previously unrecognized subline within Clostridium rRNA group I (Clostridium sensu stricto), which includes Clostridium butyricum, the type species of the genus. The nearest phylogenetic relatives of the unknown bacterium corresponded to Clostridium absonum, Clostridium baratii, Eubacterium budayi, Eubacterium moniliforme, Eubacterium multiforme and Eubacterium nitritogenes, but 16S rRNA sequence divergence values of > 3% demonstrated that it represents a novel species. Based on the findings presented, a novel species, Clostridium colicanis sp. nov., is described, with the type strain 3WC2(T) (=CCUG 44556(T) =DSM 13634(T)).

Sutterella sterconcanis sp nov., isolated from canine faeces

Morphological, biochemical and molecular genetic studies were carried out on an unknown non-spore-forming, Gram-negative, rod-shaped bacterium which was isolated from dog faeces. The bacterium grew under anaerobic conditions, was asaccharolytic, resistant to 20% (v/v) bile and was oxidase- and urease-negative. Phylogenetic analysis based on comparative 16S rRNA gene sequencing showed that the unidentified bacterium clustered with Sutterella wadsworthensis, although a sequence divergence of > 5% indicated that the bacterium from dog faeces represented a previously unrecognized subline within the genus. On the basis of the presented findings, a novel species, Sutterella stercoricanis sp. nov., is described. The type strain of Sutterella stercoricanis is 5BAC4(T) ( = CCUG 47620(T) = CIP 108024(T)).

Corynebacterium spheniscorum sp nov., isolated from the cloacae of wild penguins

Twenty unidentified Gram-positive, rod-shaped organisms were recovered from the cloacae of apparently healthy wild penguins (Spheniscus magellanicus) and subjected to a polyphasic taxonomic analysis. On the basis of cellular morphology and biochemical criteria, the isolates were tentatively assigned to the genus Corynebacterium, although the organisms did not appear to correspond to any recognized species. Lipid studies confirmed this generic placement, and comparative 16S rRNA gene sequencing showed that the unidentified organisms represent a hitherto unknown subline, associated with a small subcluster of species that includes Corynebacterium diphtheriae and its close relatives. On the basis of phenotypic and phylogenetic evidence, it is proposed that the unknown isolates from penguins be classified in the genus Corynebacterium, as Corynebacterium spheniscorum sp. nov. The type strain is strain PG 39(T) (=CCUG 45512(T) =CECT 5986(T)).

Corynebacterium sphenisci sp nov., isolated from wild penguins

Six unidentified Gram-positive, rod-shaped organisms recovered from the cloacae of apparently healthy wild penguins were characterized by phenotypic and molecular taxonomic methods. Chemotaxonomic investigations revealed the presence of a cell wall based on meso-diaminopimelic acid and long-chain cellular fatty acids of the straight-chain saturated and monounsaturated types, consistent with the genus Corynebacterium. Corynomycolic acids, which are characteristic of the genus, were also detected, albeit in small amounts. Comparative 16S rRNA gene sequencing studies showed that the unidentified organisms were phylogenetically related to corynebacteria and represent a novel subline associated with a small subcluster of species that includes Corynebacterium xerosis, Corynebacterium amycolatum and Corynebacterium freneyi. The unknown isolates were readily distinguished from their closest phylogenetic relatives and all other Corynebacterium species with validly published names by using a combination of biochemical and chemotaxonomic criteria. Based on both phenotypic and 16S rRNA gene sequence considerations, it is proposed that the unknown isolates recovered from penguins be classified as a novel species in the genus Corynebacterium, Corynebacterium sphenisci sp. nov. The type strain is CECT 5990(T) (= CCUG 46398(T)).

Suttonella ornithocola sp nov., from birds of the tit families, and emended description of the genus Suttonella

Phenotypic and phylogenetic studies were performed on three strains of Gram-negative, rod-shaped organisms recovered from dead birds of the tit families (blue tit, coal tit and long-tailed tit). Morphological, cultural and biochemical studies indicated that the organisms were related to the family Cardiobacteriaceae in the gamma-subclass of the Proteobacteria. Comparative 16S rRNA gene sequencing studies confirmed these findings and demonstrated that the bacterium represents a hitherto unknown subline within this family. The closest phylogenetic relative of the strains isolated from the birds was found to be Suttonella indologenes, although a sequence divergence of approximately 5 % demonstrated that the unknown bacterium represented a novel species. On the basis of the results of the phylogenetic analysis and phenotypic criteria, it is proposed that the bacteria recovered from the diseased birds represent a novel species, Suttonella ornithocola sp. nov., with strain B6/99/2(T) (=CCUG 49457(T)=NCTC 13337(T)) as the type strain.

Campylobacter insulaenigrae sp nov., isolated from marine mammals

Phenotypic and phylogenetic studies were performed on four Campylobacter-like organisms recovered from three seals and a porpoise. Comparative 16S rRNA gene sequencing studies demonstrated that the organisms represent a hitherto unknown subline within the genus Campylobacter, associated with a subcluster containing Campylobacter jejuni, Campylobacter coli and Campylobacter lari. DNA-DNA hybridization studies confirmed that the bacteria belonged to a single species, for which the name Campylobacter insulaenigrae sp. nov. is proposed. The type strain of Campylobacter insulaenigrae sp. nov. is NCTC 12927(T) (= CCUG 48653(T)).