Hoeflea halophila sp. nov., a novel bacterium isolated from marine sediment of the East Sea, Korea.

Jung, Man-Young,Shin, Kee-Sun,Kim, Suyeon,Kim, So-Jeong,Park, Soo-Je,Kim, Jong-Geol,Cha, In-Tae,Kim, Mi-Na,Rhee, Sung-Keun N.V. Swets en Zeitlinger 2013 Antonie van Leeuwenhoek Vol.103 No.5

<P>A Gram-negative, aerobic, motile, straight or curved rod-shaped marine bacterium was isolated from marine sediment of the East Sea, Korea. The isolated strain, JG120-1(T), grows with 0-5 % (w/v) NaCl and at 15-30 C and pH 6-9. α-galactosidase activity test was positive. Comparative 16S rRNA gene sequence studies showed that this strain belonged to the Alphaproteobacteria and was the most closely related to Hoeflea alexandrii AM1 V30(T), Hoeflea phototrophica DFL-43(T) and Hoeflea marina LMG 128(T) (98.9, 97.9 and 97.0 % 16S rRNA gene sequence similarities, respectively). Strain JG120-1(T) was found to possess summed feature 8 (C18:1ω7c/C18:1ω6c, 71.11 %) as the major cellular fatty acid. The major ubiquinone was determined to be Q-10. Polar lipids include phosphatidylglycerol, phosphatidylethanolamine, sulfoquinovosyl diacylglycerol, phosphatidylcholine and phosphatidylmonomethylethanolamine. The G+C content of the genomic DNA of strain JG120-1(T) was determined to be 57.8 mol %. DNA-DNA relatedness data indicated that strain JG120-1(T) represents a distinct species that is separate from H. phototrophica DFL-43(T), H. marina LMG128(T) and H. alexandrii AM1 V30(T). On the basis of polyphasic evidences, it is proposed that strain JG120-1(T) (= KCTC 23107(T) = JCM 16715(T)) represents the type strain of a novel species, Hoeflea halophila sp. nov.</P>

Deinococcus radioresistens sp. nov., a UV and gamma radiation-resistant bacterium isolated from mountain soil.

Srinivasan, Sathiyaraj,Lee, Jae-Jin,Lim, Sang-Yong,Joe, Min-Ho,Im, Seong-Hun,Kim, Myung Kyum N.V. Swets en Zeitlinger 2015 Antonie van Leeuwenhoek Vol.107 No.2

<P>Two Gram-negative, non-motile, short rod-shaped bacterial strains, designated as 8A(T) and 28A, were isolated from Mount Deogyusan, Jeonbuk Province, South Korea. The isolates were analyzed by a polyphasic approach, revealing variations in their phenotypic characters but high DNA-DNA hybridisation values reciprocally, confirming that they belong to the same species. Both the isolates also showed a high resistance to UV compared with Deinococcus radiodurans, and a gamma-radiation resistance similar to other members of the genus Deinococcus. Phylogenetic analysis with the 16S rRNA gene sequences of closely related species indicated their similarities were below 97 %. Chemotaxonomic data showed the most abundant fatty acids to be C16:1??7c and C16:0. The strains can be distinguished from closely related species by the production of esterase (C4) and 관-galactosidase, and by their ability to assimilate L-alanine, L-histidine and N-acetyl-D-glucosamine. Based on the phenotypic, phylogenetic, and chemotaxonomic data, the isolates represent a novel species of the genus Deinococcus, for which the name Deinococcus radioresistens sp. nov. is proposed. The type strain is 8A(T) (KEMB 9004-109(T) = JCM 19777(T)), and a second strain is 28A (KEMB 9004-113 = JCM 19778).</P>

Geosporobacter ferrireducens sp. nov., an anaerobic iron-reducing bacterium isolated from an oil-contaminated site.

Hong, Heeji,Kim, So-Jeong,Min, Ui-Gi,Lee, Yong-Jae,Kim, Song-Gun,Jung, Man-Young,Seo, Yong-Seok,Rhee, Sung-Keun N.V. Swets en Zeitlinger 2015 Antonie van Leeuwenhoek Vol.107 No.4

<P>In this study, an alkaliphilic and heterotrophic iron-reducing bacterial strain, IRF9(T), was isolated from an oil-contaminated soil in the Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IRF9(T) belongs to the genus Geosporobacter in the family Clostridiaceae and is most closely related to Geosporobacter subterraneus VNs68(T) (96.9?% sequence similarity). Cells of strain IRF9(T) were observed to be straight or curved rod-shaped, motile and Gram-negative. Optimal growth of strain IRF9(T) was observed at pH 9.0-9.5 and 40?C. The strain was found to grow within pH and temperature ranges of 6.5-10.0 and 25-45?C, respectively. NaCl was not required for growth. Fe(III), but not sulfate, thiosulfate or elemental sulfur can be used by strain IRF9(T) as an electron acceptor. A limited number of carbohydrates and amino acids, including D-glucose, D-fructose, D-mannitol, D-ribose and L-arginine, support growth of strain IRF9(T). The main fatty acids (>10?%) of strain IRF9(T) were identified as C14:0 (18.4?%), C16:1 cis9 (13.6?%), C16:0 (12.4?%) and C16:0 dimethyl acetal (17.7?%). Major respiratory quinone was identified as menaquinone MK-5 (V-H2). The main polar lipids were found to be phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The DNA G+C content of strain IRF9(T) was determined to be 37.2?mol%, which is lower than that of G. subterraneus VNs68(T) (42.2?mol%). Based on phenotypic, chemotaxonomic, and phylogenetic studies, we conclude that strain IRF9(T) (=JCM 19987(T)?=?KCTC 15395(T)) represents a new species of the genus Geosporobacter, for which we propose the name Geosporobacter ferrireducens sp. nov.</P>

Amycolatopsis jiangsuensis sp. nov., a novel endophytic actinomycete isolated from a coastal plant in Jiangsu, China.

Xing, Ke,Liu, Wei,Zhang, Yue-Ji,Bian, Guang-Kai,Zhang, Wen-Di,Tamura, Tomohiko,Lee, Jung-Sook,Qin, Sheng,Jiang, Ji-Hong N.V. Swets en Zeitlinger 2013 Antonie van Leeuwenhoek Vol.103 No.2

<P>A novel actinomycete, designated strain KLBMP 1262(T), was isolated from a coastal plant Dendranthema indicum (Linn.) Des Moul collected from the coastal region of Nantong, Jiangsu Province, in east China and was studied in detail for its taxonomic position. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain KLBMP 1262(T) is a member of the genus Amycolatopsis. The 16S rRNA gene sequence similarity indicated that strain KLBMP 1262(T) is most closely related to Amycolatopsis sulphurea DSM 46092(T) (97.96 %), Amycolatopsis ultiminotia RP-AC36(T) (97.50 %) and Amycolatopsis jejuensis N7-3(T) (97.44 %); similarity to other type strains of the genus Amycolatopsis was less than 97.0 %. The organism was determined to have chemical and morphological features consistent with its classification in the genus Amycolatopsis such as meso-diaminopimelic acid as the diagnostic diamino acid in the cell wall peptidoglycan and arabinose and galactose as the diagnostic sugars. The predominant menaquinone was determined to be MK-9 (H(4)). The polar lipids detected were phosphatidylmethylethanolamine, phosphatidylethanolamine, an unknown aminophospholipid, two unknown glycolipids and several unknown lipids. The major fatty acids were found to be C(16:0), iso-C(16:0) and iso-C(15:0). DNA-DNA relatedness data, together with phenotypic differences, clearly distinguished the isolate from its closest relatives. On the basis of these phenotypic and genotypic data, the isolate is considered to represent a novel species, for which the name A. jiangsuensis sp. nov. is proposed. The type strain is KLBMP 1262(T) (=KCTC 19885 (T) = NBRC 108679(T)).</P>

Paenibacillus hordei sp. nov., isolated from naked barley in Korea.

Kim, Jeong Myeong,Lee, Se Hee,Lee, Seung Hyeon,Choi, Eun Jin,Jeon, Che Ok N.V. Swets en Zeitlinger 2013 Antonie van Leeuwenhoek Vol.103 No.1

<P>A Gram-staining positive, facultative aerobic bacterium, designated strain RH-N24(T), was isolated from naked barley in South Korea. Cells of the isolate were observed to be motile rods by means of peritrichous flagella and showed catalase-positive and oxidase-negative reactions. Growth of strain RH-N24(T) was observed at 4-40?C (optimum: 35-37?C) and at pH 5.0-9.0 (optimum: pH 6.0-7.0). Chemotaxonomic data (major isoprenoid quinone: MK-7; DNA G?+?C content: 53.5?mol?%; cell wall type: A1γ-meso-diaminopimelic acid; major fatty acids: anteiso-CB(15:0) and CB(16:0B)) supported the affiliation of the isolate to the genus Paenibacillus. The major cellular polar lipids were identified as phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and two unidentified polar lipids. Phylogenetic analysis based on 16S rRNA gene sequences also supported the conclusion that strain RH-N24(T) belonged to the genus Paenibacillus. Comparative 16S rRNA gene sequence analysis showed that strain RH-N24(T) was most closely related to Paenibacillus hunanensis FeL05(T) and Paenibacillus illinoisensis NRRL NRS-1356(T) with similarities of 94.64 and 94.54?%, respectively. On the basis of phenotypic and molecular properties, strain RH-N24(T) represents a novel species within the genus Paenibacillus for which the name Paenibacillus hordei sp. nov. is proposed. The type strain is RH-N24(T) (=KACC 15511(T)?=?JCM 17570(T)).</P>

Flavobacterium vireti sp. nov., isolated from soil.

Singh, Hina,Du, Juan,Won, KyungHwa,Yang, Jung-Eun,Akter, Shahina,Kim, Ki-Young,Yi, Tae-Hoo N.V. Swets en Zeitlinger 2015 Antonie van Leeuwenhoek Vol.107 No.6

<P>A novel Gram-negative, aerobic, yellow-pigmented, non-motile and rod-shaped bacterium, designated as THG-SM1(T), was isolated from field soil collected from Suwon, South Korea. The strain was found to grow optimally at 28?C, at pH 7.0 and in the absence of NaCl. Based on 16S rRNA gene sequence similarities, strain THG-SM1(T) belongs to the genus Flavobacterium and is most closely related to Flavobacterium terrae KACC 11731(T), followed by Flavobacterium columnare KACC 11683(T) and Flavobacterium enshiense KCTC 23775(T). The DNA G+C content of the novel isolate was determined to be 38.5?mol%. In DNA-DNA hybridization tests, the DNA relatedness between strain THG-SM1(T) and its closest phylogenetic neighbour F. terrae was below 50?%. Flexirubin-type pigments were found to be present. The major polar lipid and isoprenoid quinone were phosphatidylethanolamine and menaquinone 6 (MK-6), respectively. The main cellular fatty acids were identified as iso-C15:1G, iso-C15:0 3OH, iso-C16:0 and iso-C15:0. The DNA-DNA hybridization result and differentiating chemotaxonomic and phenotypic characteristics showed that strain THG-SM1(T) represents a novel species of the genus Flavobacterium, for which the name Flavobacterium vireti sp. nov. is proposed. The type strain is THG-SM1(T) (=KACC 18371(T)?=?CCTCC AB2014312(T)).</P>

Taibaiella yonginensis sp. nov., a bacterium isolated from soil of Yongin city.

Singh, Hina,Du, Juan,Won, KyungHwa,Yang, Jung-Eun,Akter, Shahina,Kim, Ki-Young,Yin, ChangShik,Yi, Tae-Hoo N.V. Swets en Zeitlinger 2015 Antonie van Leeuwenhoek Vol.108 No.3

<P>A novel bacterial strain, designated as THG-SC4(T), was isolated from a soil sample collected from Yongin city in South Korea. Cells of the strain were Gram-negative, aerobic, rod-shaped and non-motile. The strain grew optimally at 28-30?C; at pH 7.0 and in the absence of NaCl. Flexirubin-type pigments were found to be present. On the basis of 16S rRNA gene sequence similarity, strain THG-SC4(T) was shown to belong to the genus Taibaiella and shares high sequence similarity with Taibaiella smilacinae KCTC 32316(T) (95.4?%), followed by Taibaiella koreensis KACC 17171(T) (94.3?%) and Taibaiella chishuiensis JCM 19637(T) (94.2?%). The DNA G+C content of the novel isolate was determined to be 43.1?mol% and MK-7 was identified as the predominant isoprenoid quinone. The only polyamine was homospermidine. The major polar lipids were phosphatidylethanolamine, an unidentified aminophospholipid and an unidentified polar lipid. The predominant fatty acids were identified as iso-C15:0, iso-C15:1 G, C16:0 and iso-C17:03-OH. On the basis of data from this polyphasic taxonomic study, strain THG-SC4(T) is considered to represent a novel species of the genus Taibaiella, for which the name Taibaiella yonginensis sp. nov. is proposed. The type strain is THG-SC4(T) (=KACC 18372(T) = CCTCC AB 2014316(T)).</P>

Comparative evaluation of three Lactobacilli with strain-specific activities for rats when supplied in drinking water.

Guo, Xiao-Hua,Zhao, Zhi-Dan,Nam, Hyang-Mi,Kim, Jae-Myung N.V. Swets en Zeitlinger 2012 Antonie van Leeuwenhoek Vol.102 No.4

<P>To test the in vivo benefits of three lactobacilli and to compare their different efficacies based on strain-specific activities by using rats as an experimental model, a growth-promotion and a challenge trial were conducted. The three strains, Lactobacillus salivarius G1-1, Lactobacillus reuteri G22-2, and Lactobacillus reuteri G8-5 shared antimicrobial, bile-salt-hydrolase and amylolytic activities in vitro, respectively. In the 17?day growth-promotion trial, 48 rats were allotted to four treatments with 12 replicates per treatment: a control group, which received saline, as well as three experimental groups, which received 10(8) cells/ml of one of the three lactobacilli in saline suspension. The results showed that compared with the control group, L. reuteri G8-5 significantly improved feed efficiency and decreased fecal pH values on days 8 and 17, concomitant with reduced faecal coliform counts on d 17 (p?<?0.05). All treatments with lactobacilli caused an increase in the moisture content of the faeces and a decrease in the serum total cholesterol and blood urea nitrogen levels. High-density lipoprotein cholesterol was only elevated for rats which received L. reuteri G22-2. In the Salmonella-challenge trial, 40 rats were allotted to five treatments (8 replicates per treatment) which consisted of a positive control (infected, no Lactobacillus pretreatment), a negative control (uninfected, no Lactobacillus pretreatment) and three Lactobacillus-pretreated groups (10(9) cells/ml in saline). The results showed that rats in all Lactobacillus pretreated groups were protected from infection with significantly higher weight gain, feed intake and feed efficiency compared with positive control rats (p?<?0.05). Rats treated with L. salivarius G1-1 and L. reuteri G22-2 tended to exhibit higher weight gains than those pretreated with L. reuteri G8-5. Significantly lower Salmonella shedding in faeces, Salmonella numbers in the spleen and the relative weight of the spleen were observed in the Lactobacillus groups (p?<?0.05). Based on the overall results, it can be concluded that not all strains within the same lactobacilli species show similar effects and that some of the beneficial functionalities to animals were strain-specific. Therefore strains for practical application need to be carefully selected based on their strain-specific characters.</P>

Lentilitoribacter donghaensis gen. nov., sp. nov., a slowly-growing alphaproteobacterium isolated from coastal seawater.

Park, Sooyeon,Lee, Jung-Sook,Lee, Kenu-Chul,Yoon, Jung-Hoon N.V. Swets en Zeitlinger 2013 Antonie van Leeuwenhoek Vol.103 No.3

<P>A Gram-staining-negative, aerobic, non-spore-forming, non-flagellated and rod- or short rod-shaped bacterial strain, designated BH-4(T), was isolated from coastal seawater in the East Sea, South Korea. Strain BH-4(T) grew optimally at 25 C, at pH 7.0-7.5 and in the presence of 2 % (w/v) NaCl. Strain BH-4(T) exhibited the highest 16S rRNA gene sequence similarity value (96.5 %) to Hoeflea phototrophica NCIMB 14078(T). It exhibited 94.2-95.5, 94.7 and 93.8 % sequence similarity values to the type strains of the other Hoeflea species, Ahrensia kielensis and Pseudahrensia aquimaris, respectively. Neighbor-joining, maximum-likelihood and maximum-parsimony phylogenetic trees revealed that strain BH-4(T) clustered with the type strains of A. kielensis and P. aquimaris. Strain BH-4(T) contained Q-10 as the predominant ubiquinone as shown in the genera Ahrensia, Pseudahrensia and Hoeflea. The fatty acid and polar lipid profiles of strain BH-4(T) were distinguished from those of members of the genera Ahrensia, Pseudahrensia and Hoeflea. The DNA G + C content was 49.3 mol%, lower than those of the type strains of P. aquimaris and Hoeflea species. The phylogenetic data, differential chemotaxonomic and other phenotypic properties revealed that strain BH-4(T) constitutes a new genus and species within the Alphaproteobacteria, for which the name Lentilitoribacter donghaensis gen. nov., sp. nov., is proposed. The type strain of Lentilitoribacter donghaensis is BH-4(T) (=KCTC 32082(T) = CCUG 62792(T)).</P>

Draconibacterium filum sp. nov., a new species of the genus of Draconibacterium from sediment of the east coast of the Korean Peninsula.

Gwak, Joo-Han,Kim, So-Jeong,Jung, Man-Young,Kim, Jong-Geol,Roh, Seong Woon,Yim, Kyung June,Lee, Yong-Jae,Kim, Song-Gun,Park, Soo-Je,Rhee, Sung-Keun N.V. Swets en Zeitlinger 2015 Antonie van Leeuwenhoek Vol.107 No.4

<P>A Gram-stain negative, long rod shaped, facultatively anaerobic bacterium, designated strain F2(T), was isolated from coastal sediment of the Korean Peninsula. Strain F2(T) was found to grow at 10-40 A degrees C (optimum 30 A degrees C), at pH 6.0-8.5 (optimum pH 7.5) and at 0.0-8.0 % (w/v) NaCl (optimum 3.0 %). Phylogenetic analysis of the 16S rRNA gene sequence showed that strain F2(T) is closely related to Draconibacterium orientale FH5(T) (with 97.9 % 16S rRNA gene similarity) of the family Prolixibacteraceae of the phylum Bacteroidetes. The major isoprenoid quinone was identified as MK-7 and the main fatty acids as iso-C-15:0 (24.1 %), anteiso-C-15:0 (15.4 %), C-16:0 (10.7 %), iso-C-17:0 3-OH (7.6 %) and iso-C-16:0 3-OH (5.9 %). The major polar lipids were identified as phosphatidylethanolamine, phosphatidylinositol and four unidentified polar lipids. The genomic DNA G+C content of strain F2(T) was determined to be 44.7 mol% and the DNA-DNA relatedness of strain F2(T) with D. orientale DSM 25947(T) was 34.6 +/- A 4.3 %. Nitrate reduction capability and cell morphology of strain F2(T) are distinct from those of the closest relative, D. orientale DSM 25947(T). Based on these properties, we propose strain F2(T) represents a novel species within the genus Draconibacterium, with the name Draconibacterium filum sp. nov. The type strain of D. filum is F2(T) (=KCTC 32486(T) = JCM 19986(T)).</P>