Platycodin D enhances LDLR expression and LDL uptake via down-regulation of IDOL mRNA in hepatic cells.

The root of Platycodon grandiflorum (PG) has long been used as a traditional herbal medicine in Asian country. Platycondin D (PD), triterpenoid saponin that is a main constituent of PG, exhibits various biological activities such as anti-inflammatory, anti-oxidant, anti-diabetic, and anti-cancer effects. A previous study showed that PD had cholesterol-lowering effects in mice that develop hypercholesterolemia, but the underlying molecular mechanisms have not been elucidated during the last decade. Here, we demonstrated that both PG and PD markedly increased levels of cell surface low-density lipoprotein receptor (LDLR) by down-regulation of the E3 ubiquitin ligase named inducible degrader of the LDLR (IDOL) mRNA, leading to the enhanced uptake of LDL-derived cholesterol (LDL-C) in hepatic cells. Furthermore, cycloheximide chase analysis and in vivo ubiquitination assay revealed that PD increased the half-life of LDLR protein by reducing IDOL-mediated LDLR ubiquitination. Finally, we demonstrated that treatment of HepG2 cells with simvastatin in combination with PG and PD had synergistic effects on the improvement of LDLR expression and LDL-C uptake. Together, these results provide the first molecular evidence for anti-hypercholesterolemic activity of PD and suggest that PD alone or together with statin could be a potential therapeutic option in the treatment of atherosclerotic cardiovascular disease.

Bizionia hallyeonensis sp. nov., isolated from seawater in an oyster farm.

A Gram-staining-negative, non-spore-forming, aerobic, non-flagellated, non-gliding, rod-shaped bacterium, designated strain T-y7(T), was isolated from seawater collected in an oyster farm in the South Sea, South Korea, and subjected to a polyphasic study. Strain T-y7(T) grew optimally at 25 °C, at pH 7.0-8.0 and in the presence of 2 % (w/v) NaCl. In phylogenetic analyses based on 16S rRNA gene sequences, strain T-y7(T) fell within a clade comprising Bizionia species. It formed a coherent cluster with the type strains of Bizionia algoritergicola, B. argentinensis, B. echini and B. myxarmorum, with which it exhibited 16S rRNA gene sequence similarities of 97.4-98.9 % and mean DNA-DNA relatedness values of 11-27 %. Strain T-y7(T) had MK-6 as its predominant menaquinone and iso-C(15 : 1) G, summed feature 3 (C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH), iso-C(15 : 0) and iso-C(17 : 0) 3-OH as its major fatty acids. The major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The genomic DNA G+C content was 37.1 mol%. Its phylogenetic and genetic distinctiveness and differential phenotypic properties revealed that strain T-y7(T) does not belong to any established Bizionia species. On the basis of the data presented, strain T-y7(T) is considered to represent a novel species of the genus Bizionia, for which the name Bizionia hallyeonensis sp. nov. is proposed. The type strain is T-y7(T) ( = KCTC 23881(T)  = CCUG 62110(T)).

Marivita geojedonensis sp. nov., isolated from seawater.

A Gram-negative-staining, non-motile, non-spore-forming, aerobic and rod-shaped bacterial strain, DPG-138(T), was isolated from seawater on the southern coast in Korea. Strain DPG-138(T) grew optimally at 30 °C and in the presence of 2-3 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain DPG-138(T) fell within the cluster comprising the type strains of four species of the genus Marivita (sequence similarity values of 97.8-98.2 %). The DNA G+C content was 59.9 mol%. The predominant ubiquinone of strain DPG-138(T) was Q-10, typical for the genus Marivita. The cellular fatty acid profiles of strain DPG-138(T) and type strains of four species of the genus Marivita were similar with C(18 : 1)ω7c as the most common fatty acid. The major polar lipids in strain DPG-138(T) were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and one unidentified aminolipid. Differential phenotypic properties and genetic distinctiveness of strain DPG-138(T) demonstrated that this strain is distinguishable from all four recognized species of the genus Marivita. On the basis of the data presented, strain DPG-138(T) is considered to represent a novel species of the genus Marivita, for which the name Marivita geojedonensis sp. nov. is proposed. The type strain is DPG-138(T) ( = KCTC 23882(T) = CCUG 62112(T)).

Salinimonas lutimaris sp. nov., a polysaccharide-degrading bacterium isolated from a tidal flat.

A Gram-negative, non-motile, non-endospore-forming bacterial strain, designated DPSR-4(T), was isolated from a tidal flat sediment on the southern coast of Korea. Strain DPSR-4(T) grew optimally at 25-30°C, at pH 7.0-7.5 and in the presence of 2% (w/v) NaCl. A Neighbour-Joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain DPSR-4(T) clustered with Salinimonas chungwhensis BH030046(T) by a high bootstrap resampling value of 99.7%. Strain DPSR-4(T) exhibited 96.2% 16S rRNA gene sequence similarity to that of S. chungwhensis BH030046(T) and 93.7-96.6% sequence similarity to the sequences of type strains of Alteromonas species. Strain DPSR-4(T) contained Q-8 as the predominant ubiquinone and iso-C(15:0) 2-OH and/or C(16:1) ω7c, C(16:0) and C(18:1) ω7c as the major fatty acids. The major polar lipids detected in strain DPSR-4(T) and S. chungwhensis KCTC 12239(T) were phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. The DNA G+C content was 53.4 mol%. Differential phenotypic properties and phylogenetic distinctiveness of strain DPSR-4(T) demonstrated that this strain is distinguishable from the sole recognized species of the genus Salinimonas, S. chungwhensis. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain DPSR-4(T) is considered to represent a novel species of the genus Salinimonas, for which the name Salinimonas lutimaris sp. nov. is proposed. The type strain is DPSR-4(T) (KCTC 23464(T), CCUG 60743(T)).

Mucilaginibacter litoreus sp. nov., isolated from marine sand.

A Gram-staining-negative, non-spore-forming, facultatively anaerobic, non-flagellated, non-gliding, rod-shaped bacterium, designated strain BR-18(T), was isolated from marine sand collected on the western coast of South Korea. The taxonomic position of the novel strain was determined using a polyphasic approach. Strain BR-18(T) grew optimally at 25 °C, at pH 6.5-7.0 and in the absence of NaCl. In phylogenetic analyses based on 16S rRNA gene sequences, the novel strain fell within a clade comprising members of the genus Mucilaginibacter and appeared most closely related to Mucilaginibacter lutimaris BR-3(T) (96.6 % sequence similarity) and Mucilaginibacter rigui WPCB133(T) (95.9 %). The novel strain showed lower levels of 16S rRNA gene sequence similarity with the type strains of other members of the genus Mucilaginibacter (93.4-95.5 %) and those of other species included in the phylogenetic analyses (<91.6 %). Strain BR-18(T) contained MK-7 as its predominant menaquinone, summed feature 3 (C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH) and iso-C(15 : 0) as its major fatty acids, phosphatidylethanolamine and an unidentified aminophospholipid as its major polar lipids, and sphingolipids. The genomic DNA G+C content of the novel strain was 42.4 mol%. Based on the phylogenetic and phenotypic data, strain BR-18(T) represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter litoreus sp. nov. is proposed. The type strain is BR-18(T) ( = KCTC 23697(T)  = CCUG 61484(T)).

Namhaeicola litoreus gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from seawater.

A Gram-staining-negative, non-flagellated, non-gliding and pleomorphic bacterial strain, designated DPG-25(T), was isolated from seawater in a seaweed farm in the South Sea in Korea and its taxonomic position was investigated by using a polyphasic approach. Strain DPG-25(T) grew optimally at 25 °C, at pH 7.0-7.5 and in the presence of 2 % (w/v) NaCl. Flexirubin-type pigments were not produced. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DPG-25(T) formed a cluster with the type strains of Actibacter sediminis, Aestuariicola saemankumensis and Lutimonas vermicola. Strain DPG-25(T) exhibited 16S rRNA gene sequence similarity values of 95.3, 93.1 and 93.6 % to the type strains of Actibacter sediminis, Aestuariicola saemankumensis and L. vermicola, respectively. Strain DPG-25(T) contained MK-6 as the predominant menaquinone and iso-C(15 : 0) and iso-C(17 : 0) 3-OH as the major fatty acids. The major polar lipids detected in strain DPG-25(T) were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content was 39.9 mol%. Differential phenotypic properties and the phylogenetic distinctiveness of strain DPG-25(T) demonstrated that this strain is distinguishable from Actibacter sediminis, Aestuariicola saemankumensis and L. vermicola. On the basis of the data presented here, strain DPG-25(T) represents a novel species in a novel genus of the family Flavobacteriaceae, for which the name Namhaeicola litoreus gen. nov., sp. nov. is proposed. The type strain of Namhaeicola litoreus is DPG-25(T) (= KCTC 23702(T) = CCUG 61485(T)).

Kangiella geojedonensis sp. nov., isolated from seawater.

A Gram-stain-negative, non-motile, non-spore-forming bacterial strain, YCS-5(T), was isolated from seawater off the southern coast of Korea. Strain YCS-5(T) grew optimally at 30 °C and in the presence of 2% (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain YCS-5(T) fell within the clade comprising Kangiella species. Strain YCS-5(T) exhibited 16S rRNA gene sequence similarity values of 96.6, 95.7 and 97.9% to the type strains of Kangiella koreensis, Kangiella aquimarina and Kangiella japonica, respectively, and less than 89.8% to strains of other species used in the phylogenetic analysis. Strain YCS-5(T) contained Q-8 as the predominant ubiquinone and iso-C(17:0), iso-C(15:0), iso-C(11:0) 3-OH and iso-C(17:1)ω9c as the major fatty acids. The polar lipid profile of strain YCS-5(T) was similar to that of K. koreensis SW-125(T), with phosphatidylglycerol and an unidentified aminolipid as major polar lipids. The DNA G+C content was 47 mol%. The mean DNA-DNA relatedness value between strain YCS-5(T) and K. japonica JCM 16211(T) was 12%. Differential phenotypic properties and the phylogenetic and genetic distinctiveness of strain YCS-5(T) demonstrated that this strain is distinguishable from other Kangiella species. On the basis of the data presented, strain YCS-5(T) is considered to represent a novel species of the genus Kangiella, for which the name Kangiella geojedonensis sp. nov. is proposed; the type strain is YCS-5(T) (=KCTC 23420(T)=CCUG 60526(T)).

Mucilaginibacter lutimaris sp. nov., isolated from a tidal flat sediment.

A Gram-staining-negative, non-spore-forming, facultatively aerobic, non-motile, rod-shaped bacterial strain, BR-3(T), was isolated from a tidal flat on the western coast of Korea, and subjected to a polyphasic study. Strain BR-3(T) grew optimally at 25 °C, at pH 6.5-7.0 and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain BR-3(T) fell within the clade comprising species of the genus Mucilaginibacter, joining the type strain of Mucilaginibacter rigui, with which it exhibited highest 16S rRNA gene sequence similarity (98.2%). 16S rRNA gene sequence similarity values between strain BR-3(T) and the type strains of the other species of the genus Mucilaginibacter were in the range 93.8-95.9%. A mean DNA-DNA relatedness value between strain BR-3(T) and M. rigui KCTC 12534(T) was 21%. Strain BR-3(T) contained MK-7 as the predominant menaquinone and C(16:1)ω7c and/or iso-C(15:0) 2-OH and iso-C(15:0) as the major fatty acids. The major polar lipids were phosphatidylethanolamine and an unidentified aminophospholipid. The DNA G+C content was 49.8 mol%. Differential phenotypic properties and phylogenetic and genetic distinctiveness of strain BR-3(T) demonstrated that this strain is separate from M. rigui as well as the other species of the genus Mucilaginibacter. On the basis of the data presented, strain BR-3(T) is considered to represent a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter lutimaris sp. nov. is proposed. The type strain is BR-3(T) (=KCTC 23461(T) =CCUG 60742(T)).

Tenacibaculum geojense sp. nov., isolated from seawater.

A Gram-negative, non-flagellated, non-spore-forming bacterium, designated YCS-6(T), that was motile by gliding, was isolated from seawater on the southern coast of Korea. Strain YCS-6(T) grew optimally at 30 °C and with 2% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YCS-6(T) fell within the genus Tenacibaculum and was most closely associated with Tenacibaculum litopenaei B-I(T), with which the isolate exhibited 95.9% 16S rRNA gene sequence similarity. Sequence similarity between strain YCS-6(T) and other members of the genus Tenacibaculum was 93.8-95.7%. Strain YCS-6(T) contained menaquinone-6 (MK-6) as the predominant respiratory quinone and iso-C(15:0), summed feature 3 (iso-C(15:0) 2-OH and/or C(16:1)ω7c), iso-C(15:0) 3-OH and iso-C(15:1) G as the major fatty acids. The DNA G+C content was 32.7 mol%. Differential phenotypic properties and phylogenetic distinctiveness distinguished strain YCS-6(T) from all other members of the genus Tenacibaculum. On the basis of our phenotypic, chemotaxonomic and phylogenetic data, strain YCS-6(T) is considered to represent a novel species of the genus Tenacibaculum, for which the name Tenacibaculum geojense sp. nov. is proposed. The type strain is YCS-6(T) (=KCTC 23423(T) =CCUG 60527(T)).

Roseovarius halocynthiae sp. nov., isolated from the sea squirt Halocynthia roretzi.

A Gram-negative, motile, ovoid- to rod-shaped bacterial strain, designated MA1-10T, was isolated from a sea squirt (Halocynthia roretzi) collected from the South Sea, Korea. Strain MA1-10T grew optimally at pH 7.0-8.0, at 30 °C and in the presence of 2 % (w/v) NaCl. In the neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, strain MA1-10T clustered with Roseovarius crassostreae CV919-312T, with which it exhibited 97.1 % sequence similarity, at a bootstrap resampling value of 96.2 %. It exhibited 93.3-95.8 % 16S rRNA gene sequence similarity to the type strains of other recognized Roseovarius species. Strain MA1-10T contained Q-10 as the predominant ubiquinone and C18:1ω7c as the major fatty acid, which is consistent with data for the genus Roseovarius. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid and an unidentified lipid. The DNA G+C content of strain MA1-10T was 55.4 mol%. Mean DNA-DNA relatedness between strain MA1-10T and R. crassostreae DSM 16950T was 13 %. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, demonstrated that strain MA1-10T could be distinguished from all recognized Roseovarius species. On the basis of the data presented, strain MA1-10T is considered to represent a novel species of the genus Roseovarius, for which the name Roseovarius halocynthiae sp. nov. is proposed; the type strain is MA1-10T (=KCTC 23462T=CCUG 60745T).

Ruegeria halocynthiae sp. nov., isolated from the sea squirt Halocynthia roretzi.

A Gram-negative, non-motile, rod-shaped bacterial strain, designated MA1-6T, was isolated from a sea squirt (Halocynthia roretzi) collected from the South Sea, Korea, and was characterized to determine its taxonomic position. Strain MA1-6T grew optimally at pH 7.0-8.0, at 30 °C and in the presence of 2-3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MA1-6T fell within the clade comprising Ruegeria species and exhibited 95.3-96.5 % similarity to the type strains of recognized Ruegeria species. Strain MA1-6T contained Q-10 as the predominant ubiquinone and C18:1ω7c as the major fatty acid, which is consistent with data for Ruegeria species. The major polar lipids detected in strain MA1-6T and Ruegeria atlantica KCTC 12424T were phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid and an unidentified lipid. The DNA G+C content of strain MA1-6T was 58.6 mol%. Differential phenotypic properties, together with phylogenetic distinctiveness, demonstrated that strain MA1-6T can be distinguished from recognized Ruegeria species. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain MA1-6T is considered to represent a novel species of the genus Ruegeria, for which the name Ruegeria halocynthiae sp. nov. is proposed; the type strain is MA1-6T (=KCTC 23463T=CCUG 60744T).

Tropicimonas aquimaris sp. nov., isolated from seawater, and emended description of the genus Tropicimonas Harwati et al. 2009.

A Gram-staining-negative, aerobic, non-motile and rod-shaped bacterial strain, designated DPG-21(T), was isolated from seawater from the South Sea in Korea, and investigated using a polyphasic taxonomic approach. Strain DPG-21(T) grew optimally at pH 7.0-8.0, at 30 °C and in the presence of 2% (w/v) NaCl. In a neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, strain DPG-21(T) clustered with Tropicimonas isoalkanivorans B51(T) (with a sequence similarity of 97.1%); the novel strain showed lower 16S rRNA gene sequence similarities (<95.4%) with the other species included in the tree. The mean DNA-DNA relatedness value between strain DPG-21(T) and T. isoalkanivorans DSM 19548(T) was 12%. The predominant ubiquinones of strain DPG-21(T) were Q-10 and Q-9 while C(18:1)ω7c was the strain's major fatty acid. The polar lipid profile of strain DPG-21(T) was similar to that of T. isoalkanivorans DSM 19548(T). The genomic DNA G+C content of the novel strain was 69.6 mol%. Some phenotypic properties and the phylogenetic and genetic data indicated that strain DPG-21(T) was distinct from T. isoalkanivorans and represents a novel species of the genus Tropicimonas, for which the name Tropicimonas aquimaris sp. nov. is proposed. The type strain is DPG-21(T) (=KCTC 23424(T)=CCUG 60524(T)).

Algoriphagus namhaensis sp. nov., isolated from seawater.

A Gram-staining-negative, non-motile, non-spore-forming bacterial strain, DPG-3(T), was isolated from seawater from the South Sea in Korea, and its taxonomic position was investigated using a polyphasic approach. Strain DPG-3(T) grew optimally at 30 °C and in the presence of 2% (w/v) NaCl. In a neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, strain DPG-3(T) fell within a clade comprising Algoriphagus species and appeared most closely related to Algoriphagus halophilus JC 2051(T) (96.1%16S rRNA gene sequence similarity) and Algoriphagus lutimaris S1-3(T) (96.4%). The type strains of other Algoriphagus species showed 16S rRNA gene sequence similarities of 92.9-96.0% with strain DPG-3(T). The predominant menaquinone of strain DPG-3(T) was MK-7. The major fatty acids were iso-C(15:0) and iso-C(15:0) 2-OH and/or C(16:1)ω7c (summed feature 3). The major polar lipids detected in strain DPG-3(T) were phosphatidylcholine, phosphatidylethanolamine and an unidentified lipid. The genomic DNA G+C content was 44.8 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain DPG-3(T) is considered to represent a novel species of the genus Algoriphagus, for which the name Algoriphagus namhaensis sp. nov. is proposed. The type strain is DPG-3(T) (=KCTC 23419(T)=CCUG 60523(T)).

Marivita hallyeonensis sp. nov., isolated from seawater, reclassification of Gaetbulicola byunsanensis as Marivita byunsanensis comb. nov. and emended description of the genus Marivita Hwang et al. 2009.

A Gram-stain-negative, non-motile, non-spore-forming, aerobic, rod-shaped bacterial strain, designated DPG-28T, was isolated from seawater on the southern coast of Korea. Strain DPG-28T grew optimally at 30 °C and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain DPG-28T formed a coherent cluster with members of the genera Marivita and Gaetbulicola, with which it exhibited sequence similarity values of 97.8-98.5 %. The DNA G+C content of strain DPG-28T was 65.1 mol%. The predominant ubiquinone of strain DPG-28T was ubiquinone-10 (Q-10), consistent with data for the genera Marivita and Gaetbulicola. The cellular fatty acid profiles of strain DPG-28T and the type strains of Marivita cryptomonadis, Marivita litorea and Gaetbulicola byunsanensis were essentially similar in that the common predominant fatty acid was C18:1ω7c. Major polar lipids found in strain DPG-28T and the type strains of M. cryptomonadis, M. litorea and G. byunsanensis were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and an unidentified aminolipid. From these data, it is proposed that Gaetbulicola byunsanensis be reclassified as a member of the genus Marivita, for which the name Marivita byunsanensis comb. nov. is proposed, with the type strain SMK-114T (=CCUG 57612T=KCTC 22632T), and that strain DPG-28T be classified in the genus Marivita. Differential phenotypic properties and genetic distinctiveness of strain DPG-28T demonstrated that this strain is distinguishable from M. cryptomonadis, M. litorea and G. byunsanensis. On the basis of the data presented, strain DPG-28T is considered to represent a novel species of the genus Marivita, for which the name Marivita hallyeonensis sp. nov. is proposed. The type strain is DPG-28T (=KCTC 23421T=CCUG 60522T). An emended description of the genus Marivita is also provided.

Description of Litoreibacter meonggei sp. nov., isolated from the sea squirt Halocynthia roretzi, reclassification of Thalassobacter arenae as Litoreibacter arenae comb. nov. and emended description of the genus Litoreibacter Romanenko et al. 2011.

A Gram-negative, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated MA1-1(T), was isolated from a sea squirt (Halocynthia roretzi) collected from the South Sea, Korea. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain MA1-1(T) is phylogenetically closely related to Litoreibacter species and to Thalassobacter arenae. It exhibited 16S rRNA gene sequence similarities of 97.3, 97.1 and 97.3% to the type strains of Litoreibacter albidus, Litoreibacter janthinus and T. arenae, respectively. Strain MA1-1(T) contained Q-10 as the predominant ubiquinone and C(18:1)ω7c as the predominant fatty acid. The polar lipid profile of strain MA1-1(T) was similar to those of the type strains of L. albidus and L. janthinus. T. arenae was found to be phylogenetically and chemotaxonomically more closely related to Litoreibacter species and strain MA1-1(T) than to Thalassobacter stenotrophicus, the type species of the genus Thalassobacter. The DNA G+C content of strain MA1-1(T) was 57.9 mol%, and DNA-DNA relatedness to the type strains of the two Litoreibacter species and T. arenae was 9-14%. Differential phenotypic properties, together with the observed phylogenetic and genetic distinctiveness, distinguished strain MA1-1(T) from the two Litoreibacter species and T. arenae. On the basis of the data presented, strain MA1-1(T) is considered to represent a novel species of the genus Litoreibacter, for which the name Litoreibacter meonggei sp. nov. is proposed. The type strain is MA1-1(T) ( = KCTC 23699(T)  = CCUG 61486(T)). In this study, it is also proposed that Thalassobacter arenae is reclassified as a member of the genus Litoreibacter, Litoreibacter arenae comb. nov. (type strain GA2-M15(T)  = DSM 19593(T)  = KACC 12675(T)). An emended description of the genus Litoreibacter is also presented.

Reclassification of the three species of the genus Krokinobacter into the genus Dokdonia as Dokdonia genika comb. nov., Dokdonia diaphoros comb. nov. and Dokdonia eikasta comb. nov., and emended description of the genus Dokdonia Yoon et al. 2005.

The genera Dokdonia and Krokinobacter, members of the family Flavobacteriaceae in the phylum Bacteroidetes, were found to be phylogenetically closely related from the result of 16S rRNA gene sequence analysis. Dokdonia donghaensis DSW-1(T) exhibited 16S rRNA gene sequence similarity values of 99.3, 98.1 and 98.1% to Krokinobacter genikus Cos-13(T), Krokinobacter diaphorus MSKK-32(T) and Krokinobacter eikastus PMA-26(T), respectively. A taxonomic study of D. donghaensis DSW-1(T), K. genikus CIP 108744(T), K. diaphorus CIP 108745(T) and K. eikastus CIP 108743(T) was conducted using a polyphasic approach. The major fatty acids (>10% of the total fatty acids) in the four strains were iso-C(15:0), iso-C(15:1) G and iso-C(17:0) 3-OH, and their overall fatty acid profiles were essentially similar. The predominant menaquinone found in the type strains of the three species of the genus Krokinobacter was MK-6, in line with the genus Dokdonia. The polar lipid profiles of the type strains of the three species of the genus Krokinobacter were similar to that of D. donghaensis DSW-1(T) in that phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid were the major polar lipids. In addition, one unidentified aminophospholipid was also present as a major polar lipid in K. diaphorus CIP 108745(T) and K. eikastus CIP 108743(T). D. donghaensis DSW-1(T) was distinguishable from K. genikus CIP 108744(T), K. diaphorus CIP 108745(T) and K. eikastus CIP 108743(T) by genetic relatedness and differential phenotypic properties. On the basis of these data, it is proposed that K. genikus, K. diaphorus and K. eikastus be reclassified into the genus Dokdonia as Dokdonia genika comb. nov. (type strain is Cos-13(T) = NBRC 100811(T) = CIP 108744(T)), Dokdonia diaphoros comb. nov. (type strain is MSKK-32(T) = NBRC 100817(T) = CIP 108745(T)), and Dokdonia eikasta comb. nov. (type strain is PMA-26(T) = NBRC 100814(T) = CIP 108743(T)), respectively. An emended description of the genus Dokdonia is also presented.

Shewanella upenei sp. nov., a lipolytic bacterium isolated from bensasi goatfish Upeneus bensasi.

A Gram-staining-negative, motile, non-spore-forming and rod-shaped bacterial strain, 20-23R(T), was isolated from intestine of bensasi goatfish, Upeneus bensasi, and its taxonomic position was investigated by using a polyphasic study. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain 20-23R(T) belonged to the genus Shewanella. Strain 20-23R(T) exhibited 16S rRNA gene sequence similarity values of 99.5, 99.2, and 97.5% to Shewanella algae ATCC 51192(T), Shewanella haliotis DW01(T), and Shewanella chilikensis JC5(T), respectively. Strain 20-23R(T) exhibited 93.1-96.0% 16S rRNA gene sequence similarity to the other Shewanella species. It also exhibited 98.3-98.4% gyrB sequence similarity to the type strains of S. algae and S. haliotis. Strain 20-23R(T) contained simultaneously both menaquinones and ubiquinones; the predominant menaquinone was MK-7 and the predominant ubiquinones were Q-8 and Q-7. The fatty acid profiles of strain 20-23R(T), S. algae KCTC 22552(T) and S. haliotis KCTC 12896(T) were similar; major components were iso-C(15:0), C(16:0), C(16:1) ω7c and/or iso-C(15:0) 2-OH and C(17:1) ω8c. The DNA G+C content of strain 20-23R(T) was 53.9 mol%. Differential phenotypic properties and genetic distinctiveness of strain 20-23R(T), together with the phylogenetic distinctiveness, revealed that this strain is distinguishable from recognized Shewanella species. On the basis of the data presented, strain 20-23R(T) represents a novel species of the genus Shewanella, for which the name Shewanella upenei sp. nov. is proposed. The type strain is 20-23R(T) (=KCTC 22806(T) =CCUG 58400(T)).

Exceptional production of both prodigiosin and cycloprodigiosin as major metabolic constituents by a novel marine bacterium, Zooshikella rubidus S1-1.

A Gram-negative, red-pigment-producing marine bacterial strain, designated S1-1, was isolated from the tidal flat sediment of the Yellow Sea, Korea. On the basis of phenotypic, phylogenetic, and genetic data, strain S1-1 (KCTC 11448BP) represented a new species of the genus Zooshikella. Thus, we propose the name Zooshikella rubidus sp. nov. Liquid chromatography and mass spectrometry of the red pigments produced by strain S1-1 revealed that the major metabolic compounds were prodigiosin and cycloprodigiosin. In addition, this organism produced six minor prodigiosin analogues, including two new structures that were previously unknown. To our knowledge, this is the first description of a microorganism that simultaneously produces prodigiosin and cycloprodigiosin as two major metabolites. Both prodigiosin and cycloprodigiosin showed antimicrobial activity against several microbial species. These bacteria were approximately 1.5-fold more sensitive to cycloprodigiosin than to prodigiosin. The metabolites also showed anticancer activity against human melanoma cells, which showed significantly more sensitivity to prodigiosin than to cycloprodigiosin. The secondary metabolite profiles of strain S1-1 and two reference bacterial strains were compared by liquid chromatography-mass spectrometry. Multivariate statistical analyses based on secondary metabolite profiles by liquid chromatography-mass spectrometry indicated that the metabolite profile of strain S1-1 could clearly be distinguished from those of two phylogenetically related, prodigiosin-producing bacterial strains.

Oceanisphaera ostreae sp. nov., isolated from seawater of an oyster farm, and emended description of the genus Oceanisphaera Romanenko et al. 2003.

A Gram-stain-negative, motile, non-spore-forming and short rod- or rod-shaped bacterial strain, T-w6(T), was isolated from seawater of an oyster farm in the South Sea, Korea. Strain T-w6(T) grew optimally at 25 °C and in the presence of 2% (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain T-w6(T) joined the cluster comprising Oceanisphaera species with a bootstrap resampling value of 90.8%, and this cluster joined the clade comprising members of the genera Oceanimonas and Zobellella with a bootstrap resampling value of 100%. Strain T-w6(T) exhibited 16S rRNA gene sequence similarity of 95.9 and 96.6% to the type strains of Oceanisphaera litoralis and Oceanisphaera donghaensis, respectively. Strain T-w6(T) and the type strains of Oceanisphaera litoralis and Oceanisphaera donghaensis had Q-8 as the predominant ubiquinone and iso-C(15:0) 2-OH and/or C(16:1)ω7c, C(18:1)ω7c and C(16:0) as the major fatty acids. The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content of strain T-w6(T) was 56.6 mol%. Mean DNA-DNA relatedness of strain T-w6(T) with Oceanisphaera litoralis DSM 15406(T) and Oceanisphaera donghaensis KCTC 12522(T) was 13 and 10%, respectively. Phenotypic properties of strain T-w6(T) demonstrated that this strain could be distinguished from the other Oceanisphaera species. On the basis of the data presented, strain T-w6(T) is considered to represent a novel species of the genus Oceanisphaera, for which the name Oceanisphaera ostreae sp. nov. is proposed; the type strain is T-w6(T) (=KCTC 23422(T) =CCUG 60525(T)). An emended description of the genus Oceanisphaera is also presented.

Mucilaginibacter boryungensis sp. nov., isolated from soil.

A Gram-stain-negative, non-motile, non-spore-forming bacterial strain, BDR-9(T), was isolated from soil collected from Boryung on the west coast of the Korean peninsula, and its taxonomic position was investigated by using a polyphasic study. Strain BDR-9(T) grew optimally at 25 °C, at pH 6.0-7.5 and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain BDR-9(T) fell within the clade comprising species of the genus Mucilaginibacter within the phylum Bacteroidetes. 16S rRNA gene sequence similarity values between strain BDR-9(T) and the type strains of species of the genus Mucilaginibacter were in the range 94.0-95.6 %. Strain BDR-9(T) contained MK-7 as the predominant menaquinone and iso-C(15 : 0) and C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH as the major fatty acids. The DNA G+C content was 44.3 mol%. Differential phenotypic properties and phylogenetic distinctiveness of strain BDR-9(T) demonstrated that this strain is distinguishable from species of the genus Mucilaginibacter. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain BDR-9(T) is considered to represent a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter boryungensis sp. nov. is proposed. The type strain is BDR-9(T) ( = KCTC 23157(T)  = CCUG 59599(T)).