Description of Auricoccus indicus gen. nov., sp. nov., isolated from skin of human ear.

A Gram-stain-positive, non-motile, non-spore-forming, small spherical bacterium, strain S31T, was isolated from skin surface (external ear lobe) of a healthy human subject and characterized using a polyphasic approach. On the basis of 1507 bp 16S rRNA gene sequence comparison, S31T showed highest (92.8 %, AY119686) sequence similarity with Macrococcus brunensis CCUG 47200T followed by Macrococcus caseolyticus DSM 20597T (92.7 % AP009484) and formed a separate clade with 65 % bootstrap support. The DNA G+C content was found to be 34 mol%. Anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0 are the predominant fatty acids in fatty acid methyl ester (FAME) profile of strain S31T. It contained A3α type peptidoglycan with l-Lys-Gly3-l-Ala peptide. Comparative study of morphological and physiological traits indicated that S31T has phenetically diverged from its closest relatives. On the basis of morphological, chemotaxonomic and genotypic data, S31T showed marked distinctions from its closest relatives of the family Staphylococcaceae and is proposed to represent a novel genus Auricoccus with Auricoccus indicus as type species of the genus. S31T (CCUG 69858T=KCTC 33611T=MCC 3027T) is the type strain of the species.

Gelatiniphilus marinus gen. nov., sp. nov., a bacterium from the culture broth of a microalga, Picochlorum sp. 122, and emended description of the genus Hwangdonia.

A Gram-stain-negative, non-motile, non-spore-forming, rod-shaped bacterium, designated strain GYP-24T, was isolated from the culture broth of a marine microalga, Picochlorum sp. 122. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain GYP-24T forms a robust cluster with H.wangdoniaseohaensis KCTC 32177T (95.8 % sequence similarity) in the family Flavobacteriaceae. Growth of strain GYP-24T was observed at 15, 22, 28, 30, 33 and 37 °C (optimal 30-33 °C), pH 6.0-10.0 (optimal pH 7.0-8.0) and in the presence of 0.5-4 % (w/v) NaCl (optimal 2-3 %). The only menaquinone of strain GYP-24T was MK-6, and the G+C content of the genomic DNA was 36.9 mol%. The major fatty acid profile comprised iso-C17 : 0 3-OH, summed feature 3 (C16 : 1 ω7c/ω6c), iso-C15 : 1 G and iso-C15 : 0. The major polar lipids of strain GYP-24T were phosphatidylethanolamine, one unidentified phospholipid, three unidentified aminolipids and three unidentified lipids. Comprehensive analyses based on polyphasic characterization of GYP-24T indicated that it represents a novel species of a new genus, for which the name Gelatiniphilus marinus gen. nov., sp. nov. is proposed. The type strain is GYP-24T (=KCTC 42903T=MCCC 1K01730T). An emended description of the genus Hwangdonia is also given.

Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov., obligately anaerobic bacteria from the human oral cavity, and emended description of the genus Oribacterium.

Three strictly anaerobic, Gram-positive, non-spore-forming, rod-shaped, motile bacteria, designated strains ACB1(T), ACB7(T) and ACB8, were isolated from human subgingival dental plaque. All strains required yeast extract for growth. Strains ACB1(T) and ACB8 were able to grow on glucose, lactose, maltose, maltodextrin and raffinose; strain ACB7(T) grew weakly on sucrose only. The growth temperature range was 30-42 °C with optimum growth at 37 °C. Major metabolic fermentation end products of strain ACB1(T) were acetate and lactate; the only product of strains ACB7(T) and ACB8 was acetate. Major fatty acids of strain ACB1(T) were C(14 : 0), C(16 : 0), C(16 : 1)ω7c dimethyl aldehyde (DMA) and C(18 : 1)ω7c DMA. Major fatty acids of strain ACB7(T) were C(12 : 0), C(14 : 0), C(16 : 0), C(16 : 1)ω7c and C(16 : 1)ω7c DMA. The hydrolysate of the peptidoglycan contained meso-diaminopimelic acid, indicating peptidoglycan type A1γ. Genomic DNA G+C content varied from 42 to 43.3% between strains. According to 16S rRNA gene sequence phylogeny, strains ACB1(T), ACB8 and ACB7(T) formed two separate branches within the genus Oribacterium, with 98.1-98.6% sequence similarity to the type strain of the type species, Oribacterium sinus. Predicted DNA-DNA hybridization values between strains ACB1(T), ACB8, ACB7(T) and O. sinus F0268 were <70%. Based on distinct genotypic and phenotypic characteristics, strains ACB1(T) and ACB8, and strain ACB7(T) are considered to represent two distinct species of the genus Oribacterium, for which the names Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov. are proposed. The type strains are ACB1(T) ( = DSM 24637(T) = HM-481(T) = ATCC BAA-2638(T)) and ACB7(T) ( = DSM 24638(T) = HM-482(T) = ATCC BAA-2639(T)), respectively.

Description of Anaerobacterium chartisolvens gen. nov., sp. nov., an obligately anaerobic bacterium from Clostridium rRNA cluster III isolated from soil of a Japanese rice field, and reclassification of Bacteroides cellulosolvens Murray et al. 1984 as Pseudobacteroides cellulosolvens gen. nov., comb. nov.

An obligately anaerobic bacterial strain designated T-1-35(T) was isolated as a dominant cultivable cellulose-degrading bacterium from soil of a Japanese rice field as an anaerobic filter-paper degrader. Cells of strain T-1-35(T) stained Gram-positive and were non-spore-forming rods with rounded ends, 0.8-1.0×3.5-15.0 µm, and motile by means of two to four polar flagella. Cells of strain T-1-35(T) exhibited pleomorphism: in aged cultures (over 90 days of incubation), almost all cells were irregularly shaped. Although no spore formation was observed, cells tolerated high temperatures, up to 90 °C for 10 min. The temperature range for growth was 15-40 °C, with an optimum at 35 °C. The pH range for growth was 5.5-9.0, with an optimum at pH 8.0-8.5 (slightly alkaliphilic). Strain T-1-35(T) fermented some carbohydrates to produce ethanol and lactate as the major products. Major cellular fatty acids were iso-C16 : 0 and iso-C13 : 0 3-OH. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain T-1-35(T) belonged to Clostridium rRNA cluster III. The closest relative of strain T-1-35(T) was Bacteroides cellulosolvens WM2(T), with 16S rRNA gene sequence similarity of 93.4 %. Phenotypic, physiological and molecular genetic methods demonstrated that strain T-1-35(T) was distinct from its phylogenetic relatives (members of Clostridium rRNA cluster III) because it predominantly produced ethanol, iso-C13 : 0 3-OH was a major cellular fatty acid and it always exhibited pleomorphism. On the basis of the results of a polyphasic taxonomic study, strain T-1-35(T) is considered to represent a novel genus and species, Anaerobacterium chartisolvens gen. nov., sp. nov. The type strain of Anaerobacterium chartisolvens is T-1-35(T) ( = DSM 27016(T) = NBRC 109520(T)). In addition, from the results of our phylogenetic analysis and its phenotypic features, the species Bacteroides cellulosolvens Murray et al. 1984 is proposed to be reclassified in the new genus Pseudobacteroides as Pseudobacteroides cellulosolvens gen. nov., comb. nov., with the type strain WM2(T) ( = ATCC 35603(T) = DSM 2933(T) = NRCC 2944(T)).

Fusicatenibacter saccharivorans gen. nov., sp. nov., isolated from human faeces.

Three Gram-stain-positive, obligately anaerobic, non-motile, non-spore-forming, spindle-shaped bacterial strains (HT03-11(T), KO-38 and TT-111), isolated from human faeces were characterized by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing showed that the strains were highly related to each other genetically (displaying >99 % sequence similarity) and represented a previously unknown subline within the Blautia coccoides rRNA group of organisms (cluster XIVa). The closest phylogenetic neighbours of strain HT03-11(T) were Clostridium bolteae WAL 16351(T) (93.7 % 16S rRNA gene sequence similarity) and Clostridium saccharolyticum WM1(T) (93.7 % similarity). All isolates produced lactic acid, formic acid, acetic acid and succinic acid as fermentation end products from glucose. Their chemotaxonomic properties included lysine as the cell wall diamino acid and C16 : 0, C18 : 1ω7c DMA and C16 : 0 DMA as the major fatty acids. The G+C contents of the genomic DNA were 46.9-47.2 mol% (HPLC). Several phenotypic and chemotaxonomic characteristics could be readily used to differentiate the isolates from phylogenetically related clostridia. Therefore, strains HT03-11(T), KO-38 and TT-111 represent a novel species in a new genus of the family Lachnospiraceae, for which the name Fusicatenibacter saccharivorans gen. nov., sp. nov. is proposed. The type strain of the type species is HT03-11(T) ( = YIT 12554(T) = JCM 18507(T) = DSM 26062(T)).

Fonticella tunisiensis gen. nov., sp. nov., isolated from a hot spring.

A strictly anaerobic, moderately thermophilic, halotolerant rod, designated BELH25(T), was isolated from a water sample of a Tunisian hot spring. Cells were non-motile, 2-6 µm long and 0.4-0.6 µm wide, appearing singly or in pairs. The isolate grew at 45-70 °C (optimum 55 °C), at pH 6.2-8.0 (optimum pH 7.0) and with 0-4% NaCl (optimum 0-2.0%). Sulfate, thiosulfate, elemental sulfur, sulfite, nitrate and nitrite were not used as terminal electron acceptors. Strain BELH25(T) used cellobiose, fructose, galactose, glucose, maltose, mannose, sucrose, starch and yeast extract as electron donors. The main fermentation products from glucose metabolism were formate, acetate, ethanol and CO2. The predominant cellular fatty acids were iso-C15:0, iso-C17:0 and anteiso-C15:0. The DNA G+C content was 37.2 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain BELH25(T) was most closely related to Caloramator viterbiensis JW/MS-VS5(T) and Fervidicella metallireducens AeB(T) (92.2 and 92.1% sequence similarity, respectively), and the isolate was positioned approximately equidistantly between these genera. Based on phenotypic, phylogenetic and chemotaxonomic characteristics, strain BELH25(T) is proposed to be a member of a novel species of a novel genus within the order Clostridiales, family Clostridiaceae, for which the name Fonticella tunisiensis gen. nov., sp. nov. is proposed. The type strain of the type species is BELH25(T) (=DSM 24455(T)=JCM 17559(T)).

Salisediminibacterium halotolerans gen. nov., sp. nov., a halophilic bacterium from soda lake sediment.

An orange-pigmented, Gram-reaction-positive, non-spore-forming, halophilic, alkali-tolerant rod, designated strain halo-2(T), was isolated from sediment of Xiarinaoer soda lake, in China's Inner Mongolia Autonomous Region. Strain halo-2(T) grew in a complex medium with 3-30 % (w/v) NaCl and at pH 5-10. The cell-wall peptidoglycan contained meso-diaminopimelic acid and the major respiratory isoprenoid quinone was MK-7. The predominant cellular fatty acids were anteiso-C(15 : 0) (43.6 %), anteiso-C(17 : 0) (14.8 %) and iso-C(15 : 0) (6.8 %) and the polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The genomic DNA G+C content of the novel strain was 48.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain halo-2(T) was most closely related to Bacillus agaradhaerens DSM 8721(T) (93.9 % sequence similarity). However, strain halo-2(T) could be clearly differentiated from its closest phylogenetic relatives on the basis of several phenotypic, genotypic and chemotaxonomic characteristics. Strain halo-2(T) therefore represents a novel species in a new genus for which the name Salisediminibacterium halotolerans gen. nov., sp. nov. is proposed. The type strain of the type species is halo-2(T) (= CGMCC 1.7654(T) = NBRC 104935(T)).

Characterization of an O-desmethylangolensin-producing bacterium isolated from human feces.

A bacterium that converted daidzein to O-desmethylangolensin was isolated from the feces of healthy humans. It was an obligately anaerobic, nonsporeforming, nonmotile and Gram-positive rod. The isolate used glucose, sucrose, raffinose, maltose, and fructose as carbon sources. It did not hydrolyze gelatin, esculin, or starch. The strain was urease, acid phosphatase, and arginine dihydrolase positive. It was catalase, oxidase, H(2)S, and indole negative. The major products of glucose fermentation were butyrate and lactate. Its mol% G+C was 51.2. The major cellular fatty acids were C(16:0) DMA, C(16:0), and C(16:0) aldehyde. The structural type of cell wall peptidoglycan was suggested to be A1gamma. The isolate was susceptible to beta-lactam, cefem, and macrolide antibiotics and resistant to aminoglycoside and quinolone antibiotics. The bacterium was related to Eubacterium ramulus ATCC29099(T), Eubacterium rectale ATCC33656(T), and species of the genus Roseburia, but the highest 16S rRNA gene similarity to these described species was only 94.4%, consistent with its being classified as a novel genus. Based on the above, the isolate, named strain SY8519, was identified as belonging to a novel genus in the Clostridium rRNA cluster XIVa.

Anaerostipes butyraticus sp. nov., an anaerobic, butyrate-producing bacterium from Clostridium cluster XIVa isolated from broiler chicken caecal content, and emended description of the genus Anaerostipes.

Four butyrate-producing isolates were obtained from the caecal content of a 4-week-old broiler chicken. The 16S rRNA gene sequences were determined and confirmed the close relatedness of the four isolates, which suggested that they were derived from a single bacterial clone. Phylogenetic analysis based on 16S rRNA gene sequences showed that its closest relatives were members of cluster XIVa of the Clostridium subphylum of Gram-positive bacteria and that the closest related type strain was Anaerostipes caccae L1-92(T) (94.5 % similarity). Similarity levels of 96-98 % with sequences from uncultured bacteria from human stool samples were observed. On the basis of morphological, biochemical and phylogenetic characteristics, this strain is assigned to a novel species in the genus Anaerostipes, for which the name Anaerostipes butyraticus sp. nov. is proposed. The type strain is 35-7(T) (=LMG 24724(T) =DSM 22094(T)). An emended description of the genus Anaerostipes is also provided.

Lysinibacillus parviboronicapiens sp. nov., a low-boron-containing bacterium isolated from soil.

A spore-forming, Gram-positive-staining, motile, rod-shaped and low-boron-containing bacterium was isolated from soil. The strain, designated BAM-582(T), can tolerate 6 % (w/v) NaCl and 50 mM boron, but optimal growth was observed without addition of boron or NaCl. The optimum temperature and pH for growth were 30 degrees C (range 10-37 degrees C) and pH 7 (range pH 6-8). A comparative analysis of the 16S rRNA gene sequence demonstrated that the isolated strain was closely related to Lysinibacillus fusiformis DSM 2898(T) (97.7 % similarity) and Lysinibacillus sphaericus IAM 13420(T) (98.2 %). Levels of DNA-DNA relatedness were 33.9 % with L. fusiformis DSM 2898(T) and 29.5 % with L. sphaericus DSM 28(T). The genomic DNA G+C content of the novel strain was 38.7 mol%. The major respiratory quinone was MK-7 and the major fatty acids were iso-C(15 : 0) (37.4 %) and anteiso-C(15 : 0) (19.0 %). Analysis of cell-wall amino acids revealed that the strain contained peptidoglycan with lysine, aspartic acid, alanine and glutamic acid, as is the case with other species of the genus Lysinibacillus. Based upon its distinctive peptidoglycan composition, phylogenetic and genotypic analyses and physiological characteristics, the strain BAM-582(T) is concluded to represent a novel species in the genus Lysinibacillus, for which the name Lysinibacillus parviboronicapiens sp. nov. is proposed (type strain BAM-582(T) =NBRC 103144(T) =KCTC 13154(T)).

Thermotalea metallivorans gen. nov., sp. nov., a thermophilic, anaerobic bacterium from the Great Artesian Basin of Australia aquifer.

A strictly anaerobic, thermophilic bacterium, designated strain B2-1(T), was isolated from microbial mats colonizing a runoff channel formed by free-flowing thermal water from a Great Artesian Basin, Australia, bore well (registered number 17263). The cells of strain B2-1(T) were slightly curved rods (3.0-3.5 x 0.6-0.7 microm) which stained Gram-negative. The strain grew optimally in tryptone-yeast extract-glucose medium at 50 degrees C (temperature growth range 30-55 degrees C) and a pH of 8 (pH growth range 6.5-9). Strain B2-1(T) grew poorly on yeast extract (0.2 %) and/or tryptone (0.2 %), which were obligately required for growth on other energy sources, including a range of other carbohydrates and organic acids, but not amino acids. The end-products of glucose fermentation were ethanol and acetate. In the presence of 0.2 % yeast extract, iron(III), manganese(IV) and elemental sulfur were reduced but sulfate, thiosulfate, sulfite, nitrate and nitrite were not reduced. Growth was inhibited by chloramphenicol, streptomycin, tetracycline, penicillin, ampicillin, sodium azide and by NaCl concentrations greater than 4 % (w/v). The DNA G+C content was 48+/-1 mol% as determined by the thermal denaturation method. 16S rRNA gene sequence analysis indicated that strain B2-1(T) was a member of the family Clostridiaceae, class Clostridia, phylum Firmicutes and was most closely related to Geosporobacter subterraneus DSM 17957(T) (89.9 % similarity). On the basis of 16S rRNA gene sequence comparisons and physiological characteristics, strain B2-1(T) is considered to represent a novel species of a new genus, for which the name Thermotalea metallivorans gen. nov., sp. nov. is proposed. The type strain is B2-1(T) (=KCTC 5625(T)=JCM 15105(T)=DSM 21119(T)).

Alkalibacterium thalassium sp. nov., Alkalibacterium pelagium sp. nov., Alkalibacterium putridalgicola sp. nov. and Alkalibacterium kapii sp. nov., slightly halophilic and alkaliphilic marine lactic acid bacteria isolated from marine organisms and salted foods collected in Japan and Thailand.

We describe 10 new strains of marine lactic acid bacteria isolated from decaying marine algae, decaying seagrass, raw fish, salted fish and salted and fermented shrimp paste ('ka-pi') collected from a temperate area of Japan and Thailand. The isolates are Gram-positive and non-sporulating. They have motility with peritrichous flagella depending on the strains. They lack catalase and quinones. Under anaerobic conditions, lactate yields were 64-93 % of the glucose consumed; residual products were formate, acetate and ethanol with a molar ratio of approximately 2 : 1 : 1. The pH of the fermentation medium markedly affected the product composition; at higher pH, the yield of lactate decreased (15-48 % at pH 9.0) and yields of other products increased, retaining the molar ratio. Under aerobic conditions, acetate and lactate were produced from carbohydrates and related compounds. The isolates were slightly halophilic, highly halotolerant and alkaliphilic. The optimum NaCl concentration for growth ranged between 0.5 and 4.0 % (w/v), depending on the strain, with a growth range of between 0 and 17-21 % (11 % for one isolate). The optimum pH for growth ranged between 8.0 and 9.5, with a growth range of 6.0-11.0, depending on the strains. Comparative sequence analysis of the 16S rRNA genes revealed that the isolates occupied three phylogenetic positions within the genus Alkalibacterium, showing 97.1-99.8 % similarity to Alkalibacterium indicireducens. DNA-DNA hybridization values (<46 %) among the 10 isolates and phylogenetically related taxa resulted in the identification of four genomic species (designated groups GS1-GS4). The G+C contents of the DNA were 41.7 mol% (group GS1), 42.2 mol% (group GS2), 41.0-43.0 mol% (group GS3) and 38.4-39.4 mol% (group GS4). The cell-wall peptidoglycan was type A4beta, Orn-d-Asp, for three genomic species (groups GS1, GS2 and GS3), and type A4beta, Orn-d-Glu, for the remaining species (group GS4). The major components of cellular fatty acids were C(16 : 0), C(16 : 1)omega9c and C(18 : 1)omega9c (oleic acid). On the bases of phenotypic characteristics, genetic distinctiveness and phylogenetic affiliations, the four genomic species, groups GS1, GS2, GS3 and GS4, were classified as four novel species within the genus Alkalibacterium, for which the names Alkalibacterium thalassium sp. nov., Alkalibacterium pelagium sp. nov., Alkalibacterium putridalgicola sp. nov. and Alkalibacterium kapii sp. nov., respectively, are proposed. The respective type strains are T117-1-2(T) (=DSM 19181(T)=NBRC 103241(T)=NRIC 0718(T)), T143-1-1(T) (=DSM 19183(T)=NBRC 103242(T)=NRIC 0719(T)), T129-2-1(T) (=DSM 19182(T)=NBRC 103243(T)=NRIC 0720(T)) and T22-1-2(T) (=DSM 19180(T)=NBRC 103247(T)=NRIC 0724(T)).

Caloramator australicus sp. nov., a thermophilic, anaerobic bacterium from the Great Artesian Basin of Australia.

A strictly anaerobic, thermophilic bacterium, designated strain RC3T, was isolated from microbial mats colonizing thermal waters of a run-off channel formed by free-flowing waters from a bore well (registered no. 17263) of the Great Artesian Basin, Australia. The slightly curved rods (2.5-4.2x0.8-1.0 microm) of strain RC3T stained Gram-positive and grew optimally in tryptone-yeast extract-glucose medium at 60 degrees C (range 45-70 degrees C) and pH 7 (range pH 5-9). Strain RC3T grew poorly on yeast extract (0.2 %) but did not grow on tryptone (0.2 %) as a sole carbon source; yeast extract was required for growth on other energy sources, which included glucose, fructose, galactose, xylose, maltose, sucrose, raffinose, mannose, cellobiose, cellulose, starch, amylopectin, xylan, peptone, amyl media (Research Achievement), threonine and pyruvate but did not include arabinose, ribose, lactose, CM-cellulose, myo-inositol, mannitol, chitin, casein, formate, acetate, succinate, propionate, lactate, benzoate, glycerol, ethanol, Casamino acids, arginine, alanine, serine, glycine, glutamine, leucine, isoleucine, methionine or aspartate. The end products of glucose fermentation were ethanol and acetate. In the presence of 0.2 % yeast extract, iron(III), manganese(IV) and elemental sulfur were reduced but not sulfate, sulfite, thiosulfate, nitrate or nitrite. Iron(III) was also reduced in the presence of peptone, tryptone, amyl media, threonine and glycerol but not chitin, xylan, pectin, starch, pyruvate, acetate, benzoate, lactate, propionate, succinate, inositol, ethanol, mannitol, arginine, glutamine or serine. Strain RC3T was not able to utilize molecular hydrogen and/or carbon dioxide in the presence or absence of iron(III). In the presence of iron(III) and glycerol, increased concentrations of Fe(II) corresponded to increased cell numbers, demonstrating that strain RC3(T) was able to conserve energy to support growth from the reduction of Fe(III) to Fe(II). Chloramphenicol, streptomycin, tetracycline, penicillin and ampicillin and NaCl concentrations greater than 2 % inhibited growth. The G+C content of the DNA was 34+/-1 mol% as determined by the thermal denaturation (Tm) method. 16S rRNA gene sequence analysis indicated that strain RC3T was affiliated to Caloramator fervidus (95.8 % similarity to the type strain) and to other Caloramator species (average similarity of 91.6 %) within the phylum Firmicutes. On the basis of phylogenetic and phenotypic characteristics, it is proposed that strain RC3T should be classified in the genus Caloramator as a representative of a novel species, Caloramator australicus sp. nov. The type strain is RC3T (=JCM 1508T =KCTC 5601T).

Proteiniborus ethanoligenes gen. nov., sp. nov., an anaerobic protein-utilizing bacterium.

A novel anaerobic, mesophilic, protein-utilizing bacterial strain, GW(T), was isolated from the mesophilic hydrogen-producing granular sludge used to treat food industry wastewater. The strain was a Gram-positive, non-spore-forming and non-motile rod. Growth of the strain was observed at 20-48 degrees C and at pH 6.4-10.0. The strain used yeast extract and peptone as carbon and energy sources. Weak growth was also observed with tryptone and Casamino acids as carbon and energy sources. The strain used none of the tested carbohydrates, alcohols or fatty acids. The fermentation products in peptone-yeast broth included ethanol, acetic acid, hydrogen and carbon dioxide. Gelatin was not hydrolysed. Nitrate was reduced. Indole was produced. NH(3) and H(2)S were not produced. The DNA G+C content of strain GW(T) was 38.0 mol%. The predominant cellular fatty acids were the saturated fatty acids C(14:0) (15.58%), C(16:0) (25.40%) and C(18:0) (12.03%). Phylogenetic analysis based on 16S rRNA gene sequence similarity revealed that strain GW(T) represented a new branch within cluster XII of the Clostridium subphylum, with <89.6% 16S rRNA gene sequence similarities to all described species. On the basis of polyphasic evidence from this study, strain GW(T) represents a new genus and novel species, for which the name Proteiniborus ethanoligenes gen. nov., sp. nov. is proposed. The type strain is GW(T) (=CGMCC 1.5055(T)=JCM 14574(T)).

Identification of oral bacterial species associated with halitosis.

BACKGROUND: The authors examined the tongue bacteria associated with oral halitosis (bad breath originating from the oral cavity), focusing on noncultivable bacteria-bacteria that cannot be identified by bacterial culture techniques. METHODS: The authors took samples from the dorsal tongue surface of eight adult subjects with halitosis and five control subjects who did not have halitosis. They identified the bacteria in these samples by using both anaerobic culture and direct amplification of 16S ribosomal DNA, a method that can identify both cultivable and noncultivable microorganisms. They analyzed the resulting microbiological data using chi(2) and correlation coefficient tests. RESULTS: Clinical measures of halitosis were correlated highly with each other and with tongue coating scores. Of 4,088 isolates and phylotypes identified from the 13 subjects, 32 species including 13 noncultivable species were found only in subjects with halitosis. Solobacterium moorei was present in all subjects with halitosis but not in any control subjects. CONCLUSIONS: Subjects with halitosis harbor some bacterial species on their dorsal tongue surfaces that are distinct from bacterial species found in control subjects. This finding is consistent with the hypothesis that halitosis has a microbial etiology. CLINICAL IMPLICATIONS: Like other oral diseases with microbial etiology, halitosis may be amenable to specific and nonspecific antimicrobial therapy targeted toward the bacteria associated with it.

Tindallia texcoconensis sp. nov., a new haloalkaliphilic bacterium isolated from lake Texcoco, Mexico.

A new alkaliphilic and moderately halophilic, strictly anaerobic, fermentative bacterium (strain IMP-300(T)) was isolated from a groundwater sample in the zone of the former soda lake Texcoco in Mexico. Strain IMP-300(T) was Gram-positive, non-sporulated, motile and rod-shaped. It grew within a pH range from 7.5 to 10.5, and an optimum at 9.5. The organism was obligately dependent on the presence of sodium salts. Growth showed an optimum at 35 degrees C with absence of growth above 45 degrees C. It fermented peptone and a few amino acids, preferentially arginine and ornithine, with production of acetate, propionate, and ammonium. Its fatty acid pattern was mainly composed of straight chain saturated, unsaturated, and cyclopropane fatty acids. The G + C content of genomic DNA was 40.0 mol%. Analysis of the 16S rRNA gene sequence indicated that the new isolate belongs to the genus Tindallia, in the low G + C Gram-positive phylum. Phylogenetically, strain IMP-300(T) has Tindallia californiensis, as closest relative with a 97.5% similarity level between their 16S rDNA gene sequences, but the DNA-DNA re-association value between the two DNAs was only 42.2%. On the basis of differences in genotypic, phenotypic, and phylogenetic characteristics, strain IMP-300(T) is proposed as a new species of the genus Tindallia, T. texcoconensis sp. nov. (type strain IMP-300(T ) = DSM 18041(T) = JCM 13990(T)).

Novel chemolithotrophic, thermophilic, anaerobic bacteria Thermolithobacter ferrireducens gen. nov., sp. nov. and Thermolithobacter carboxydivorans sp. nov.

Three thermophilic strains of chemolithoautotrophic Fe(III)-reducers were isolated from mixed sediment and water samples (JW/KA-1 and JW/KA-2(T): Calcite Spring, Yellowstone N.P., WY, USA; JW/JH-Fiji-2: Savusavu, Vanu Levu, Fiji). All were Gram stain positive rods (approximately 0.5 x 1.8 microm). Cells occurred singly or in V-shaped pairs, and they formed long chains in complex media. All utilized H(2) to reduce amorphous iron (III) oxide/hydroxide to magnetite at temperatures from 50 to 75 degrees C (opt. approximately 73 degrees C). Growth occurred within the pH(60C) range of 6.5-8.5 (opt. pH(60C) 7.1-7.3). Magnetite production by resting cells occurred at pH(60C) 5.5-10.3 (opt. 7.3). The iron (III) reduction rate was 1.3 mumol Fe(II) produced x h(-1) x ml(-1) in a culture with 3 x 10(7) cells, one of the highest rates reported. In the presence or absence of H(2), JW/KA-2(T) did not utilize CO. The G + C content of the genomic DNA of the type strain is 52.7 +/- 0.3 mol%. Strains JW/KA-1 and JW/KA-2(T) each contain two different 16S rRNA gene sequences. The 16S rRNA gene sequences from JW/KA-1, JW/KA-2(T), or JW/JH-Fiji-2 possessed >99% similarity to each other but also 99% similarity to the 16S rRNA gene sequence from the anaerobic, thermophilic, hydrogenogenic CO-oxidizing bacterium 'Carboxydothermus restrictus' R1. DNA-DNA hybridization between strain JW/KA-2(T) and strain R1(T) yielded 35% similarity. Physiological characteristics and the 16S rRNA gene sequence analysis indicated that the strains represent two novel species and are placed into the novel genus Thermolithobacter within the phylum 'Firmicutes'. In addition, the levels of 16S rRNA gene sequence similarity between the lineage containing the Thermolithobacter and well-established members of the three existing classes of the 'Firmicutes' is less than 85%. Therefore, Thermolithobacter is proposed to constitute the first genus within a novel class of the 'Firmicutes', Thermolithobacteria. The Fe(III)-reducing Thermolithobacter ferrireducens gen. nov., sp. nov. is designated as the type species with strain JW/KA-2(T) (ATCC 700985(T), DSM 13639(T)) as its type strain. Strain R1(T) is the type strain for the hydrogenogenic, CO-oxidizing Thermolithobacter carboxydivorans sp. nov. (DSM 7242(T), VKM 2359(T)).

Salinicoccus salsiraiae sp. nov.: a new moderately halophilic gram-positive bacterium isolated from salted skate.

Two moderately halophilic low G + C Gram-positive bacteria were isolated from a sample of salted skate (Class Chondrychthyes, Genus Raja). Phylogenetic analysis of the 16S rRNA gene sequence of strains RH1(T) and RH4 showed that these organisms represented a novel species of the genus Salinicoccus. The new isolates formed pink-red colonies and flocculated in liquid media, with optimum growth in media containing 4% NaCl and pH of about 8.0. These organisms are aerobic but reduce nitrate to nitrite under anaerobic conditions. Acid is produced from several carbohydrates. Oxidase and catalase were detected. Menaquinone 6 was the major respiratory quinone. The major fatty acids of strains RH1(T) and RH4 were 15:0 anteiso and 15:0 iso. The G + C contents of DNA were 46.2 and 46.0 mol%, respectively. The peptidoglycan was of A3alpha L-Lys-Gly(5-6) type. On the basis of the phylogenetic analyses, physiological and biochemical characteristics, we suggest that strain RH1(T) (=LMG 22840 = CIP 108576) represents a new species of the genus Salinicoccus, for which we propose the name Salinicoccus salsiraiae.

[Evaluation of API Coryne System, version 2.0, for diphteroid gram-positive rods identification with clinical relevance]. / Evaluación del sistema API coryne, versión 2.0, para la identificación de bacilos gram-positivos difteroides de importancia clínica.

The ability of the API Coryne system, version 2.0, to identify 178 strains of gram-positive rods was evaluated. Seventy eight isolates belonged to genus Corynebacterium and one hundred to related genera, all strains were isolated from clinical samples at the Laboratory of Bacteriology, Hospital de Clínicas José de San Martin (UBA) between 1995 and 2004. The isolates were identified according to von Graevenitz and Funke's scheme. One hundred and sixty two out of 178 strains (91%) were correctly identified at genus and species level (IC95 = 85.6-94.6), in 44 of them (24.7%) additional tests were needed to final identification. Sixteen strains (9%) were not correctly identified (IC95 = 5.4-14.4); none of the 178 strains remained unidentified. The API Coryne system, version 2.0, is useful to identify the majority of Cory-nebacterium species with clinical relevance: Corynebacterium jeikeium, Corynebacterium urealyticum, Corynebacterium striatum, Corynebacterium pseudodiphtheriticum, Corynebacterium amycolatum and related species such as Arcanobacterium haemolyticum, Dermabacter hominis, Listeria monocytogenes, among others. Nevertheless for yellow-pigmented diphteroid gram-positive rods (Aureobacterium spp., Leifsonia aquatica, Microbacterium spp. and Cellulomonas spp.) and for acid fast gram-positive rods (Rhodococcus, Gordonia, Tsukamurella and Nocardia) the identification usefulness the system is limited.

Alkalibacterium iburiense sp. nov., an obligate alkaliphile that reduces an indigo dye.

Three indigo-reducing obligately alkaliphilic strains, M3(T), 41A and 41C, were isolated. The isolates grew at pH 9-12, but not at pH 7-8. They were Gram-positive, facultatively anaerobic, straight rod-shaped strains with peritrichous flagella. The isolates grew in 0-14% (w/v) NaCl, with optimum growth at 3-13%. They grew at temperatures between 10 and 45 degrees C, with optimum growth at around 30-37 degrees C. They did not hydrolyse starch or gelatin. DL-lactate was the major end-product from D-glucose. No quinones could be detected. The peptidoglycan type was A4beta, Orn-d-Asp. The major cellular fatty acids were C(16:0), C(16:1)7c and C(18:1)9c. The DNA G+C content was 42.6-43.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequence data indicated that the isolates belong to the genus Alkalibacterium. DNA-DNA hybridization revealed low similarity (less than 16%) of the isolates with respect to the two closest phylogenetically related strains, Alkalibacterium olivapovliticus and Alkalibacterium psychrotolerans. On the basis of phenotypic and chemotaxonomic characteristics, phylogenetic data and DNA-DNA relatedness, the isolates merit classification as a novel species of the genus Alkalibacterium, for which the name Alkalibacterium iburiense is proposed. The type strain is M3(T) (=JCM 12662(T)=NCIMB 14024(T)).