Akiko Kageyama

Phylogenetic evidence for the transfer of Eubacterium lentum to the genus Eggerthella as Eggerthella lenta gen. nov., comb. nov.

Eubacterium lentum has unique phenotypic characters within the genus Eubacterium. The 16S rRNA sequence of Eubacterium lentum was determined and its phylogenetic position was defined. This micro-organism is a member of the genus Eubacterium but it is not closely related to Eubacterium limosum, the type species of the genus Eubacterium, and is nearer to Collinsella aerofaciens and Coriobacterium glomerans. A PCR-based identification system using species-specific primers designed on the basis of DNA sequences encoding the 16S rRNA of strains of Eubacterium lentum, Collinsella aerofaciens and Coriobacterium glomerans is described. A species-specific primer set can distinguish Eubacterium lentum from Eubacterium limosum or closely related species including Collinsella aerofaciens, Coriobacterium glomerans and Atopobium species. This species-specific PCR method can be used to identify Eubacterium lentum-like species isolated from human faeces. On the basis of the 16S rRNA sequence divergence from Collinsella aerofaciens and Coriobacterium glomerans and the presence of unique phenotypic characters, a new genus, Eggerthella gen. nov., is proposed for Eubacterium lentum, with one species, Eggerthella lenta comb. nov. The type strain of Eggerthella lenta is JCM 9979T.

Phylogenetic and phenotypic evidence for the transfer of Eubacterium aerofaciens to the genus Collinsella as Collinsella aerofaciens gen. nov., comb. nov.

Three strains of Eubacterium aerofacien, JCM 10188T, JCM 7790 and JCM 7791, and 178 freshly isolated strains of the Eubacterium aerofaciens group from human faeces were characterized by biochemical tests, cell wall peptidoglycan type and 16S rRNA analysis. The Eubacterium aerofaciens group was divided into four groups by fermentation patterns of sucrose and cellobiose, and were further divided into 16 sub-groups by fermentation patterns of aesculin, salicin and amygdalin. All of the strains of the Eubacterium aerofaciens group were shown to be phylogenetically distantly related to Eubacterium limosum, which is the type species of genus Eubacterium. Eubacterium aerofaciens was shown to have a specific phylogenetic association with Coriobacterium glomerans. All the strains belonging to Eubacterium aerofaciens resembled Coriobacterium glomerans in possessing a high G + C content (60 mol%). Cell wall analysis, however, revealed the presence of different A4 beta (L-Ala)-D-Glu-L-Orn-L-Asp peptidoglycan types. Based on a 16S rRNA sequence divergence of greater than 9% with Coriobacterium glomerans and the presence of a unique peptidoglycan type, a new genus, Collinsella, is proposed for Eubacterium aerofaciens, with one species, Collinsella aerofaciens. The type strain of Collinsella aerofaciens is JCM 10188T.

Phylogenic and Phenotypic Characterization of Some Eubacterium-Like Isolates from Human Feces: Description of Solobacterium moorei Gen. Nov., Sp. Nov.

Three isolated strains from human feces were characterized by biochemical tests and 16S rDNA analysis. Phylogenetic analysis revealed that these isolated strains were members of the Clostridium subphylum of Gram‐positive bacteria. The phenotypic characters resembled those of the genus Eubacterium, but these strains were shown to be phylogenetically distant from the type species of the genus, Eubacterium limosum. The strains showed a specific phylogenetic association with Holdemania filiformis and Erysipelothrix rhusiopathiae. Based on a 16S rDNA sequence divergence of greater than 12% with H. filiformis and E. rhusiopathiae, a new genus, Solobacterium, is proposed for three strains, with one species, Solobacterium moorei. The type strain of Solobacterium moorei is JCM 10645T.

Catenibacterium mitsuokai gen. nov., sp. nov., a gram-positive anaerobic bacterium isolated from human faeces.

Six strains of Eubacterium-like strains from human faeces were characterized by biochemical tests and analysis of cell wall peptidoglycan type and 16S rRNA. They were members of the Clostridium subphylum and have a specific phylogenetic association with Lactobacillus catenaformis and Lactobacillus vitulinus. These organisms resembled L. vitulinus in possessing the same A1gamma type of murein, but they showed different fermentation end-products. On the basis of a 16S rDNA sequence divergence of greater than 8% from L. vitulinus as well as phenotypic characteristics, a new genus, Catenibacterium, with one species (Catenibacterium mitsuokai), is proposed for six strains. The type strain of C. mitsuokai is JCM 10609T.

Arthrobacter oryzae sp. nov. and Arthrobacter humicola sp. nov.

Two novel bacterial strains were isolated from a paddy soil sample collected in Japan using GPM agar plates supplemented with superoxide dismutase and/or catalase. The strains were Gram-positive, catalase-positive and motile, with lysine as the peptidoglycan diagnostic diamino acid and acetyl as the peptidoglycan acyl type. The major menaquinone was MK-9(H(2)). Mycolic acids were not detected. The G+C content of the DNA was 66-68 mol%. On the basis of phenotypic analysis, 16S rRNA gene sequence comparisons and DNA-DNA hybridization data, it is proposed that these strains represent two novel species, Arthrobacter oryzae sp. nov. (type strain is KV-651(T)=NRRL B-24478(T)=NBRC 102055(T)) and Arthrobacter humicola sp. nov. (type strain is KV-653(T)=NRRL B-24479(T)=NBRC 102056(T)), respectively.

Coprobacillus catenaformis Gen. Nov., Sp. Nov., a New Genus and Species Isolated from Human Feces

Three strains of Eubacterium‐like isolates from human feces were characterized by biochemical tests and 16S rDNA analysis. The phenotypic characteristics of the three strains resembled those of the genus Collinsella transferred from the genus Eubacterium recently. However, Eubacterium‐like strains were phylogenetically members of the Clostridium subphylum of Gram‐positive bacteria, and these showed a specific phylogenetic association with Clostridium ramosum and C. spiroforme. C. ramosum and C. spiroforme are Gram‐positive, anaerobic, spore‐forming bacteria that belong to the genus Clostridium, and the G + C contents are 26.0 and 27.4 mol%, respectively. However, the three Eubacterium‐like strains had G + C contents of 32.1 to 33.1 mol% and were non‐spore‐forming rods. Based on phenotypic characteristics, we can differentiate these species, and furthermore, a 16S rDNA sequence divergence of greater than 9% with a new related genus, Coprobacillus, is proposed for the three strains, with one species, Coprobacillus catenaformis. The type strain of C. catenaformis is JCM 10604T.

Emendation of genus Collinsella and proposal of Collinsella stercoris sp. nov. and Collinsella intestinalis sp. nov.

Collinsella aerofaciens-like strains isolated from human faeces were characterized by biochemical tests, cell wall murein analysis and 16S rDNA analysis. The results indicated that these strains are phylogenetically a member of the family Coriobacteriaceae and close to the genus Collinsella. Their phenotypic characters resembled those of Collinsella aerofaciens. Determination of DNA-DNA relatedness showed that these strains could be divided into two groups (groups 1 and 2). Collinsella aerofaciens and both new groups have A4-type cell wall murein. Based on their phenotypic and phylogenetic characters, two new species of the genus Collinsella are proposed for the isolated strains: Collinsella stercoris for group 1 and Collinsella intestinalis for group 2. Species-specific PCR primer sets for these two species were also constructed. Using these primer sets, Collinsella stercoris and Collinsella intestinalis can be identified easily and rapidly.

Rapid Detection of Human Fecal Eubacterium Species and Related Genera by Nested PCR Method

PCR procedures based on 16S rDNA gene sequence specific for seven Eubacterium spp. and Eggerthella lenta that predominate in the human intestinal tract were developed, and used for direct detection of these species in seven human feces samples. Three species of Eggerthella lenta, Eubacterium rectale, and Eubacterium eligens were detected from seven fecal samples. Eubacterium biforme was detected from six samples. It was reported that E. rectale, E. eligens, and E. biforme were difficult to detect by traditional culture method, but the nested PCR method is available for the detection of these species. This result shows that the nested PCR method utilizing a universal primer pair, followed by amplification with species‐specific primers, would allow rapid detection of Eubacterium species in human feces.

Phylogenic and Phenotypic Evidence for the Transfer of Eubacterium fossor to the Genus Atopobium as Atopobium fossor Comb.Nov.

The 16S rRNA primary structure of Eubacterium fossor was determined by sequencing in vitro amplified rDNA. Sequence comparisons indicated that E. fossor has a specific phylogenetic association with the Atopobium species and is far from E. limosum, the type species of the genus Eubacterium. Phenotypic characters of E. fossor resemble those of the genus Atopobium. Therefore, we propose that E. fossor should be transferred to the genus Atopobium as Atopobium fossor comb. nov.

Marihabitans asiaticum gen. nov., sp. nov., a meso-diaminopimelic acid-containing member of the family Intrasporangiaceae

Strain HG667(T), isolated from surface seawater collected at the Kesennuma ferry port in Miyagi Prefecture, Japan, was found to be a Gram-positive, catalase-positive bacterium comprising irregular short rods and cocci. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major menaquinone was MK-8(H4). Mycolic acids were not detected. The G+C content of the DNA was 70 mol%. Analysis of the 16S rRNA gene sequence revealed that the strain represents a novel lineage within the family Intrasporangiaceae, order Actinomycetales, being associated with the genus Kribbia. On the basis of morphological, biochemical and chemotaxonomic properties of the strain, together with phylogenetic data relating to the 16S rRNA gene sequence, HG667(T) represents a novel genus and species in the family Intrasporangiaceae, for which the name Marihabitans asiaticum gen. nov., sp. nov. is proposed. The type strain of Marihabitans asiaticum is HG667(T) (=MBIC07497(T) =DSM 18935(T)).