- Volume 60, Issue 4, 2010

A novel Gram-stain-positive bacterium, designated R19-04T, was isolated from a soil sample from Rishiri Island, Japan, and its taxonomic position was investigated by a polyphasic approach. Cells of strain R19-04T exhibited a rod–coccus cycle. The peptidoglycan type of the isolate was A4α; lysine was the diagnostic diamino acid. The predominant menaquinone was MK-8(H2) and the major fatty acid was anteiso-C15 : 0. The polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The DNA G+C content was 72.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain R19-04T represented a novel member of the suborder Micrococcineae. Its nearest phylogenetic neighbours were the members of the genus Oerskovia, with 16S rRNA gene sequence similarity of 97.0–97.1 %. However, strain R19-04T was clearly distinguishable from members of the genus Oerskovia and phylogenetically related genera in terms of chemotaxonomic characteristics. On the basis of the chemotaxonomic and phylogenetic characteristics, a novel genus and species are proposed, Luteimicrobium subarcticum gen. nov., sp. nov. The type strain of Luteimicrobium subarcticum is R19-04T (=NBRC 105647T =DSM 22413T).

A Gram-stain-positive, coccoid, non-endospore-forming actinobacterium (strain CC-12602T) was isolated from a spawn used for growing the edible mushroom Agaricus brasiliensis in the laboratory. On the basis of 16S rRNA gene sequence analysis, strain CC-12602T was shown to belong to the genus Microlunatus and was related most closely to the type strains of Microlunatus ginsengisoli (96.1 % similarity), M. phosphovorus (95.9 %), M. panaciterrae (95.8 %) and M. aurantiacus (95.5 %). The quinone system comprised menaquinone MK-9(H4) as the major component and the polyamine pattern consisted of spermidine and spermine as major compounds. The predominant polar lipids were phosphatidylglycerol and unknown phospholipid PL3. Moderate amounts of diphosphatidylglycerol, an unknown glycolipid and three unknown phospholipids and minor amounts of an unknown phospholipid and a polar lipid were detected. The peptidoglycan type was A3γ′, based on ll-2,6-diaminopimelic acid with an interpeptide bridge consisting of a single glycine residue and a second glycine residue at position 1 of the peptide subunit. Peptidoglycan structure and major fatty acids (anteiso-C15 : 0, iso-C16 : 0 and iso-C15 : 0) supported the affiliation of strain CC-12602T to the genus Microlunatus. The results of physiological and biochemical tests allowed strain CC-12602T to be differentiated phenotypically from recognized Microlunatus species. Strain CC-12602T is therefore considered to represent a novel species of the genus Microlunatus, for which the name Microlunatus soli sp. nov. is proposed. The type strain is CC-12602T (=DSM 21800T =CCM 7685T).

Three Gram-positive, rod-shaped bacteria (strains CC-SBCK-209T, CC-12309T and CC-5209T) were isolated from the stalk of the edible mushroom Agaricus blazei grown in the laboratory. 16S rRNA gene sequence analysis indicated that all three isolates clearly belonged to the genus Microbacterium. Strains CC-SBCK-209T and CC-12309T were most related closely to the type strain of Microbacterium halotolerans (95.9 and 96.1 %16S rRNA gene sequence similarity, respectively). These two novel strains shared 97.9 % 16S rRNA gene sequence similarity. Levels of similarity to the type strains of all other recognized Microbacterium species were lower than 95.5 %. The third strain (CC-5209T) showed the highest 16S rRNA gene sequence similarity to the type strain of Microbacterium resistens (97.6 %); levels of similarity to the type strains of all other recognized Microbacterium species were lower than 96 %. The quinone systems of strains CC-SBCK-209T, CC-12309T and CC-5209T consisted of MK-11/MK-12, MK-11/MK-10 and MK-13 as major compounds, respectively. All three strains contained ornithine in their peptidoglycan. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unknown glycolipid. The polyamine pattern consisted of spermidine and spermine as predominant components. Fatty acid profiles (anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0 as major components) supported the affiliation of all three strains to the genus Microbacterium. The results of physiological and biochemical tests and DNA–DNA hybridization experiments allowed the clear phenotypic and genotypic differentiation of strains CC-SBCK-209T and CC-12309T from M. halotolerans and other closely related Microbacterium species. Strain CC-5209T could be differentiated clearly from M. resistens both genotypically and phenotypically. Based on these data, the novel strains are considered to represent three novel species of the genus Microbacterium. The names proposed for these organisms are Microbacterium agarici sp. nov. [type strain CC-SBCK-209T (=DSM 21798T=CCM 7686T)], Microbacterium humi sp. nov. [type strain CC-12309T (=DSM 21799T=CCM 7687T)] and Microbacterium pseudoresistens sp. nov. [type strain CC-5209T (=DSM 22185T=CCM 7688T)].

Strain RuGl7T was isolated from a soil sample collected at the periphery of the glacial Lake Roopkund in the Himalayan mountain range, India. Cells of RuGl7T were Gram-positive, aerobic, rod-shaped, motile and grew optimally between 15 and 18 °C. Cells of RuGl7T contained 2,4-diaminobutyric acid in the cell-wall peptidoglycan and the major menaquinones were MK-10, MK-11 and MK-12. The polar lipids present were diphosphatidylglycerol and phosphatidylglycerol and an unknown lipid and the major fatty acid was anteiso-C15 : 0. Based on the above characteristics, strain RuGl7T was assigned to the genus Cryobacterium. Strain RuGl7T shared a 16S rRNA gene sequence similarity of 97.0 and 99.0 % with Cryobacterium psychrotolerans JCM 13925T and Cryobacterium psychrophilum JCM 1463T, respectively. However, DNA–DNA relatedness values between strain RuGl7T and C. psychrotolerans and C. psychrophilum were 28 and 23 %, respectively. Furthermore, strain RuGl7T exhibited several phenotypic and genotypic differences when compared with C. psychrotolerans, C. psychrophilum and Cryobacterium mesophilum. Based on these differentiating characteristics, strain RuGl7T was identified as a novel species of the genus Cryobacterium for which the name Cryobacterium roopkundense sp. nov. is proposed. The type strain is RuGl7T (=DSM 21065T=JCM 15131T).

A non-lipophilic coryneform bacterium, strain 3105T, was isolated from various tissues of a ferret with lethal sepsis. The strain was characterized by phenotypic and chemotaxonomic methods, which suggested an assignment of the isolate to the genus Corynebacterium. Strain 3105T exhibited the following peculiar features that made it possible to differentiate it phenotypically from all other corynebacteria: its distinctive ‘humid cellar’-like odour, strong adherence to agar and a greenish-beige pigment. Strain 3105T exhibited more than 2.8 % 16S rRNA gene sequence divergence from its closest phylogenetic neighbour, Corynebacterium pseudotuberculosis NCTC 3450T (97.12 % sequence similarity). Analysis of the highly variable region within the rpoB gene sequence showed that strain 3105T exhibited more than 14 % divergence from its closest phylogenetic relative, again C. pseudotuberculosis. Based on the data presented, it is proposed that the ferret isolate should be classified within a novel species, Corynebacterium mustelae sp. nov. (type strain 3105T =CCUG 57279T =DSM 45274T).

Brevibacterium stationis ATCC 14403T, Corynebacterium ammoniagenes ATCC 6872 and two clinical isolates were found to form a single taxon group consistent with the genus Corynebacterium, designated here as Corynebacterium stationis comb. nov. The type strain of Corynebacterium stationis is ATCC 14403T =CCUG 43497T =CIP 104228T =DSM 20302T =NBRC 12144T =JCM 11611T =VKM B-1228T. These strains can utilize citrate; therefore, inclusion of C. stationis requires that the description of the genus Corynebacterium be amended to include citrate-positive strains.

A Gram-positive-staining, non-motile, rod- or coccoid-shaped bacterium, strain CLGT, was isolated from beach sand from Lianyungang, Jiangsu Province, PR China. The organism grew optimally at 30 °C and pH 7.0. Strain CLGT contained l-Lys–d-Asp as the peptidoglycan type and galactose, rhamnose and xylose as the whole-cell sugars. It contained anteiso-C15 : 0 and iso-C15 : 0 as the major fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phospholipid, phosphatidylinositol, three phosphoglycolipids and one unidentified lipid. The DNA G+C content was 70.3 mol%. The 16S rRNA gene sequence similarity of strain CLGT with Isoptericola dokdonensis DS-3T was 99.4 % but the DNA–DNA relatedness between strain CLGT and I. dokdonensis DS-3T was 58.7 %. There were also many phenotypic properties that distinguished strain CLGT from recognized species of the genus Isoptericola. The results showed that strain CLGT represents a novel species of the genus Isoptericola, for which the name Isoptericola jiangsuensis sp. nov. is proposed. The type strain is CLGT (=DSM 21863T=CCTCC AB208287T).

A Gram-stain-positive, rod-shaped, non-endospore-forming, orange-pigmented (coloured) actinobacterium (01-Je-003T) was isolated from the wall of an indoor environment primarily colonized with moulds. On the basis of 16S rRNA gene sequence similarity studies, strain 01-Je-003T was shown to belong to the genus Brevibacterium and was most similar to the type strains of Brevibacterium picturae (98.8 % similarity), Brevibacterium marinum (97.3 %) and Brevibacterium aurantiacum (97.2 %). Chemotaxonomic data [predominant quinone menaquinone MK-8(H2); polar lipid profile consisting of major compounds diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid; characteristic cell-wall diamino acid meso-diaminopimelic acid; polyamine pattern showing major compounds putrescine and cadaverine; major fatty acids anteiso-C15 : 0 and anteiso-C17 : 0] supported the affiliation of strain 01-Je-003T to the genus Brevibacterium. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 01-Je-003T from the two most closely related species, B. picturae and B. marinum. Strain 01-Je-003T therefore represents a novel species, for which the name Brevibacterium sandarakinum sp. nov. is proposed, with the type strain 01-Je-003T (=DSM 22082T =CCM 7649T).

A novel actinobacterium, strain P30T, was isolated from jeotgal, a traditional Korean fermented seafood. Cells were aerobic, Gram-positive, non-motile and coccoid. Optimal growth occurred at 30–37 °C, at pH 8–9 and in the presence of 0–2 % (w/v) NaCl. Based on 16S rRNA gene sequence analysis, strain P30T was phylogenetically closely related to Kocuria carniphila, Kocuria gwangalliensis, Kocuria rhizophila, Kocuria marina, Kocuria rosea and K. varians with levels of similarity of 98.6, 98.2, 98.1, 97.4, 97.3 and 97.3 %, respectively, to the type strains of these species. Levels of DNA–DNA relatedness between strain P30T and the type strains of K. carniphila, K. rhizophila, K. marina, K. rosea and K. varians were 37, 43, 37, 25 and 17 %, respectively. The predominant menaquinone of strain P30T was MK-7. Major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0. The genomic DNA G+C content of strain P30T was 70.2 mol%. Based on these data, strain P30T is considered to represent a novel species of the genus Kocuria, for which the name Kocuria atrinae sp. nov. is proposed. The type strain is P30T (=KCTC 19594T=JCM 15914T).

Two novel actinomycetes, designated MN07-A0368T and MN07-A0371T, were isolated from soil of Terelj, Töv Province, Mongolia, and subjected to phenotypic and genotypic characterization. They produced well-developed, non-fragmenting, extensively branched substrate hyphae from which oval to irregular sporangia were produced. Chemotaxonomic characteristics, i.e. cell wall diaminopimelic acid, whole-cell sugars, fatty acid components and major menaquinones, suggested that the two organisms belonged to the genus Actinoplanes. A comparative analysis of 16S rRNA gene sequences indicated that strains MN07-A0368T and MN07-A0371T formed a distinct clade within the genus and were closely related to the type strains of: Actinoplanes ferrugineus (97.7 % sequence similarity); Actinoplanes brasiliensis (97.7–97.8 %); Actinoplanes deccanensis (97.6–97.9 %); Actinoplanes durhamensis (96.9–97.0 %); and Actinoplanes globisporus (96.5–96.8 %). Strains MN07-A0368T and MN07-A0371T could be differentiated from each other and from strains of closely related species of the genus Actinoplanes by DNA–DNA hybridization, physiological and biochemical characteristics, fatty acid composition, and whole-cell sugar components. The broad range of phenotypic and genetic characters supported the suggestion that these strains represent two novel species of the genus Actinoplanes, for which the names Actinoplanes toevensis sp. nov. (type strain MN07-A0368T=NBRC 105298T=VTCC D9-11T) and Actinoplanes tereljensis sp. nov. (type strain MN07-A0371T=NBRC 105297T=VTCC D9-10T) are proposed.

A novel actinomycete strain, designated MS498T, was isolated from an ocean sediment sample collected from the South China Sea. It was subjected to a polyphasic analysis to determine its taxonomic position. The phylogenetic tree based on 16S rRNA gene sequences showed that strain MS498T had the highest similarity (96.5 %) with members of the genus Prauserella and was loosely associated with Prauserella rugosa DSM 43194T and Saccharomonospora halophila DSM 44411T. Based on 16S rRNA gene sequence analysis, phenotypic characteristics and chemotaxonomic data, the new isolate is proposed to represent a novel species of the genus Prauserella, named Prauserella marina sp. nov. (type strain MS498T=CCTCC AA 208056T =DSM 45268T).

A novel Gram-stain-negative, rod-shaped, non-motile bacterium, strain LW1T, was isolated from a water sample collected at a depth of 3.5 m from Lonar Lake, Buldhana district, Maharashtra, India. The cell suspension was reddish-orange due to the presence of carotenoids. Strain LW1T was positive for catalase, oxidase, ornithine decarboxylase and lysine decarboxylase and negative for gelatinase, urease and lipase. Fatty acids were dominated by branched-chain fatty acids (>76 %), with a high abundance of iso-C15 : 0 (48 %), anteiso-C15 : 0 (7 %) and iso-C17 : 0 3-OH (11 %). Strain LW1T contained MK-4 and MK-7 as the major respiratory quinones and phosphatidylglycerol, phosphatidylcholine and phosphatidylethanolamine as the major phospholipids. A blast sequence similarity search based on 16S rRNA gene sequences indicated that members of the genera Belliella and Aquiflexum were the nearest phylogenetic neighbours with similarities of 91.8–92.3 %. Phylogenetic analyses indicated that strain LW1T formed a deep-rooted lineage distinct from the clades represented by the genera Belliella, Aquiflexum, Cyclobacterium, Echinicola and Algoriphagus. Based on the above-mentioned phenotypic and phylogenetic characteristics, it is proposed that strain LW1T represents a novel species in a new genus, Indibacter alkaliphilus gen. nov., sp. nov. (type strain LW1T=KCTC 22604T=CCUG 57479T). The genomic DNA G+C content of strain LW1T is 42.7±1 mol%.

A Gram-stain-negative, non-flagellated, motile (by gliding), yellow-pigmented, rod-shaped bacterial strain, designated L-4T, was isolated from seawater of Baekdo harbour in the East Sea, Korea. Strain L-4T grew optimally at 37 °C, at pH 6.5–7.0 and in the presence of 2 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain L-4T clustered with Olleya marilimosa CAM030T, a member of the family Flavobacteriaceae. Strain L-4T exhibited 16S rRNA gene sequence similarity values of 97.2 % to O. marilimosa CAM030T and less than 95.8 % to other members of the family Flavobacteriaceae. Strain L-4T and O. marilimosa CIP 108537T contained MK-6 as the predominant menaquinone. The fatty acid and polar lipid profiles of strain L-4T were similar to those of O. marilimosa CIP 108537T. The DNA G+C content of strain L-4T was 35 mol% and DNA–DNA relatedness between strain L-4T and O. marilimosa CIP 108537T was 7 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, enable strain L-4T to be distinguished from O. marilimosa. On the basis of these data, strain L-4T is considered to represent a novel species of the genus Olleya for which the name Olleya aquimaris sp. nov. is proposed; the type strain is L-4T (=KCTC 22661T =CCUG 58074T). An emended description of the genus Olleya is also provided.

A bacterial strain, designated KMM 6177T, was isolated from the sea urchin Strongylocentrotus intermedius and subjected to a polyphasic taxonomic investigation. The bacterium was found to be heterotrophic, aerobic, non-motile by gliding and orange-pigmented. Comparative phylogenetic analysis based on 16S rRNA gene sequencing placed the marine isolate in the genus Bizionia, a member of the family Flavobacteriaceae, with 16S rRNA gene sequence similarity of 94.9–98.6 % with recognized Bizionia species. Strain KMM 6177T grew at 4–39 °C and with 1–8 % NaCl. It produced alkaline phosphatase, catalase and oxidase and hydrolysed aesculin, gelatin, DNA and Tween 20. The predominant fatty acids were iso-C15 : 1, iso-C15 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH and a summed feature (comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c). The DNA G+C content was 34.4 mol%. A combination of phylogenetic, genotypic and phenotypic data clearly indicated that strain KMM 6177T represents a novel species in the genus Bizionia, for which the name Bizionia echini sp. nov. is proposed. The type strain is KMM 6177T (=KCTC 22015T=LMG 25220T).

A Gram-positive, non-motile and coccoid-, short rod- or rod-shaped bacterial strain, ISL-16T, was isolated from a marine solar saltern in Korea and its taxonomic position was investigated using a polyphasic taxonomic approach. Strain ISL-16T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ISL-16T joined the cluster comprising species of the genus Planococcus. Its 16S rRNA gene sequence contained the same signature nucleotides as those defined for the genus Planococcus. Strain ISL-16T exhibited 16S rRNA gene sequence similarity values of 96.9–98.2 % to the type strains of species of the genus Planococcus. Strain ISL-16T contained MK-8 and MK-7 as the predominant menaquinones and anteiso-C15 : 0, C16 : 1 ω7c alcohol and anteiso-C17 : 0 as the major fatty acids. The DNA G+C content was 48.3 mol%. DNA–DNA relatedness values between strain ISL-16T and the type strains of species of the genus Planococcus were 15–28 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, enabled strain ISL-16T to be differentiated from recognized species of the genus Planococcus. On the basis of the data presented, strain ISL-16T is considered to represent a novel species of the genus Planococcus, for which the name Planococcus salinarum sp. nov. is proposed. The type strain is ISL-16T (=KCTC 13584T=CCUG 57753T). An emended description of the genus Planococcus is also given.

Four Gram-stain-positive, catalase-negative, coccoid-shaped isolates were obtained from the oral cavities of wild boars and characterized by phenotypic and phylogenetic studies. On the results of biochemical tests, the organisms were tentatively identified as a streptococcal species. Comparative 16S rRNA gene sequencing studies confirmed that the organisms are members of the genus Streptococcus, with Streptococcus equi subsp. equi ATCC 33398T as their closest phylogenetic relative (94.7 % similarity). DNA–DNA hybridization analysis showed that the isolates displayed less than 10 % relatedness to Streptococcus equi subsp. equi DSM 20561T. From the phylogenetic and phenotypic evidence, the four isolates represent a novel species of the genus Streptococcus, for which the name Streptococcus dentapri sp. nov. (type strain NUM 1529T =JCM 15752T =DSM 21999T) is proposed.

An obligate anaerobic, Gram-staining-negative, mesophilic, cellulolytic bacterium, strain H1T, was isolated from the rumen content of yak. Cells were straight to slightly curved rods, 0.8–1.0×3.0–4.0 μm in size, non-motile and encapsulated with mucous materials. Elliptical and terminal spores that swelled the cells were produced occasionally. The strain grew at 25–45 °C (optimum, 38 °C) and pH 6.0–7.8 (optimum, pH 6.7). Cellulose, cellobiose, xylan, xylose and maltose were used as carbon and energy sources, but not glucose. Products from cellulose and cellobiose fermentation were formic acid, acetic acid, carbon dioxide and trace amounts of ethanol, lactic acid and succinic acid. The genomic DNA G+C content was 33.7±1.2 mol%. The predominant fatty acids were C16 : 0 (27.1 %), C14 : 0 (9.2 %) and iso-C16 : 0 (6.4%). Based on the 16S rRNA gene sequence analysis, strain H1T was affiliated to the clostridial rRNA cluster XIVb and showed the highest 16S rRNA gene sequence similarity to Clostridium lentocellum DSM 5427T (96.0 %). These two strains formed a distinct lineage of the family ‘Lachnospiraceae’. Based on data from this polyphasic taxonomic study, a new genus, Cellulosilyticum gen. nov., is proposed. Cellulosilyticum ruminicola sp. nov. is proposed for strain H1T. The type strain of Cellulosilyticum ruminicola sp. nov. is strain H1T (=CGMCC 1.5065T=JCM 14822T). Clostridium lentocellum was reclassified in the new genus as Cellulosilyticum lentocellum comb. nov. (type strain RHM5T=ATCC 49066T=DSM 5427T=NCIMB 11756T).

A Gram-positive-staining, motile, rod-shaped, endospore-forming bacterium (BFLP-1T) was isolated from faeces of wild long-snouted seahorses (Hippocampus guttulatus) captured in north-west Spain (Toralla, Galicia). Strain BFLP-1T grew at 10–30 °C and pH 5.5–9 (optimally at 20 °C and pH 7.2) and with 0–7 % (w/v) NaCl (optimally with 2 % NaCl). The G+C content of the DNA was 48.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BFLP-1T was a member of the genus Bacillus and was most closely related to Bacillus herbersteinensis D-1,5aT (96.6 %), B. shackletonii LMG 18435T (96.0 %) and B. isabeliae CVS-8T (95.9 %). Chemotaxonomic data (peptidoglycan type, meso-diaminopimelic acid; major menaquinone, MK-7; predominant fatty acids, anteiso-C15 : 0, anteiso-C17 : 0 and C16 : 1 ω11c; major polar lipids, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unknown aminoglycophospholipid) supported the affiliation of strain BFLP-1T to the genus Bacillus. Comparative analysis of 16S rRNA gene sequences and chemotaxonomic and phenotypic features indicated that strain BFLP-1T represents a novel species within the genus Bacillus, for which the name Bacillus galliciensis sp. nov. is proposed. The type strain is BFLP-1T (=DSM 21539T =LMG 24668T).