menaquinone-6 and 2-4-diaminobutyric-acid

A Gram-stain-positive, rod-shaped, non-motile bacterial strain, designated JW-1

Topics: Actinomycetales; Aminobutyrates; Bacterial Typing Techniques; Base Composition; Cell Wall; China; DNA, Bacterial; Fatty Acids; Glycolipids; Herbicides; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Prometryne; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sewage; Vitamin K 2

A Gram-stain-positive, aerobic, non-motile, non-spore-forming and short-rod-shaped actinobacterium, designated strain 1T4Z-3

Topics: Actinomycetales; Aminobutyrates; Bacterial Typing Techniques; Base Composition; Cell Wall; China; DNA, Bacterial; Fatty Acids; Glycolipids; Phospholipids; Phylogeny; Primulaceae; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Vitamin K 2

A Gram-stain-positive, aerobic, non-motile, rod-shaped bacterial strain, designated 2C-7T, was isolated from symptomatic bark of a Populus × euramericana canker. Growth occurred between 10 and 37 °C and between pH 6 and 10, with optimal growth at 30 °C and pH 7.0-8.0. Growth was present under 0-8 % (w/v) salinity conditions (optimum 1-2 %). Growth occurred in the presence of 10 mM chromium (Cr6+). The major fatty acids (≥10 %) of the novel strain were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phospholipid, glycolipid and two unknown lipids. The major respiratory quinone was menaquinone MK-11. The cell wall amino acids were 2,4-diaminobutyric acid, alanine, glutamic acid and glycine. Strain 2C-7T was most similar to Leucobacter celer subsp. celer NAL101T (97.2 % 16S rRNA gene sequence similarity), 'Leucobacter kyeonggiensis' F3-P9T (97.1 %) and Leucobacter chromiireducens L-1T (97.1 %). In the phylogenetic tree, the isolate formed a single distinct branch separate from those of L. celer subsp. celer NAL101T, 'L. kyeonggiensis' F3-P9T and Leucobacter chironomi DSM 19883T. The DNA-DNA hybridization values between the novel strain and the reference strains were lower than the accepted bacterial threshold level of 70 % for species delineation. The DNA G+C content of strain 2C-7T was 70.0 mol%. Based on the data, strain 2C-7T represents a novel species in the genus Leucobacter, for which the name Leucobacter corticis sp. nov. is proposed. The type strain is 2C-7T (=CFCC 11901T=KCTC 39643T).

Topics: Actinomycetales; Aminobutyrates; Bacterial Typing Techniques; Cell Wall; China; DNA, Bacterial; Fatty Acids; Glycolipids; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Plant Bark; Plant Diseases; Populus; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Vitamin K 2

Strain S27

Topics: Actinobacteria; Aminobutyrates; Bacterial Typing Techniques; Base Composition; Cell Wall; DNA, Bacterial; Fatty Acids; Germany; Glycolipids; Peptidoglycan; Phospholipids; Phylogeny; Pigmentation; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sewage; Vitamin K 2

A novel Gram-reaction-positive, non-motile, aerobic bacterium, designated CFH S0483T, was isolated from a soil sample collected from Catba island in Halong Bay, Vietnam. 16S rRNA gene sequence analysis showed that the strain is a member of the genus Agromyces and has highest 16S rRNA gene sequence similarities with Agromyces humatus DSM 16389T (97.3 %) and Agromyces ramosus DSM 43045T (97.1 %), and similarities  < 97.0 % with type strains of other species of the genus Agromyces. Strain CFH S0483T was able to grow at 10-37 °C, at pH 7.0-9.0 and tolerated NaCl up to 2.0 % (w/v). The whole-cell sugars were mannose, galactose, glucose and ribose. The isolate contained l-2,4-diaminobutyric acid, d-alanine, d-glutamic acid and glycine in the cell-wall peptidoglycan. Strain CFH S0483T exhibited a menaquinone system with MK-12, and the major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The genomic DNA G+C content of strain CFH S0483T was 71.6 mol%. Based on the phylogenetic and phenotypic analysis, and low DNA-DNA hybridization values, strain CFH S0483T could not be classified into any recognized species of the genus Agromyces. Strain CFH S0483T is therefore considered to represent a novel species of the genus Agromyces, for which the name Agromyces insulae sp. nov. is proposed. The type strain is CFH S0483T ( = KCTC 39117T = CCTCC AB 2014301T).

Topics: Actinomycetales; Aminobutyrates; Bacterial Typing Techniques; Base Composition; Cell Wall; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Peptidoglycan; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Vietnam; Vitamin K 2

A novel actinobacterial strain, designated R1-20

Topics: Actinomycetales; Aminobutyrates; Bacterial Typing Techniques; Base Composition; Cell Wall; DNA, Bacterial; Fatty Acids; Peptidoglycan; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Vitamin K 2

Three Gram-stain-positive, irregular-rod-shaped, non-motile, non-spore-forming bacteria were isolated from nematodes collected from Santa Antao, Cabo Verde (CBX151T, CBX152T) and Kakegawa, Japan (CBX130T). Based on 16S rRNA gene sequence similarity, strains CBX130T, CBX151T and CBX152T were shown to belong to the genus Leucobacter. This affiliation was supported by chemotaxonomic data (2,4-diaminobutyric acid in the cell wall; major respiratory quinones MK-10 and MK-11; major polar lipids phosphatidylglycerol and diphosphatidylglycerol; major fatty acids anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0). Strains CBX130T and CBX152T were found to share salient characteristics. Based on morphological, physiological, chemotaxonomic and biochemical analysis, strain CBX152T represents a novel species of the genus Leucobacter, for which the name Leucobacter musarum sp. nov. (type strain CBX152T = DSM 27160T = CIP 110721T) is proposed. Two subspecies of Leucobacter musarum sp. nov. are proposed: Leucobacter musarum sp. nov. subsp. musarum subsp. nov. (type strain CBX152T = DSM 27160T = CIP 110721T) and Leucobacter musarum sp. nov. subsp. japonicus subsp. nov. (type strain CBX130T = DSM 27158T = CIP 110719T). The third novel strain, CBX151T, showed genetic similarities with Leucobacter celer NAL101T indicating that these strains belong to the same species. Based on morphological, physiological, chemotaxonomic and biochemical differences it is proposed to split the species Leucobacter celer into two novel subspecies, Leucobacter celer subsp. celer subsp. nov. (type strain NAL101T = KACC 14220T = JCM 16465T) and Leucobacter celer subsp. astrifaciens subsp. nov. (type strain CBX151T = DSM 27159T = CIP 110720T), and to emend the description of Leucobacter celerShin et al. 2011.

Topics: Actinomycetales; Aminobutyrates; Animals; Bacterial Typing Techniques; Base Composition; Caenorhabditis; Cell Wall; DNA, Bacterial; Fatty Acids; Japan; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Vitamin K 2

Strain THG-MD12T, a Gram-reaction-positive, aerobic, non-motile, rod-shaped bacterium was isolated from rhizosphere soil of Ophiopogon japonicus in PR China. THG-MD12T was closely related to members of the genus Pseudoclavibacter and showed the highest 16S rRNA gene sequence similarities with Pseudoclavibacter helvolus KCTC 19531T (98.8 %) and Pseudoclavibacter chungangensis KCTC 22691T (96.9 %). DNA-DNA hybridization showed 41.9 ± 2.1 % and 12.4 ± 0.9 % DNA reassociation with P. helvolus KCTC 19531T and P. chungangensis KCTC 22691T, respectively. Chemotaxonomic analyses revealed that strain THG-MD12T possesses menaquinone-9 as the predominant respiratory quinone, 2,4-diaminobutyric acid as the diamino acid in the peptidoglycan and anteiso-C15 : 0, iso-C16 : 0, C16 : 0 and anteiso-C17 : 0 as the major fatty acids. The polar lipid profile was found to consist of diphosphatidylglycerol, phosphatidylglycerol, two unknown glycolipids and two unknown lipids. These data corroborated the affiliation of THG-MD12T to the genus Pseudoclavibacter. Thus, the isolate represents a novel species, for which the name Pseudoclavibacter terrae sp. nov. is proposed, with THG-MD12T as the type strain ( = CCTCC AB 2015124T = KCTC 39562T).

Topics: Actinomycetales; Aminobutyrates; Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Glycolipids; Nucleic Acid Hybridization; Ophiopogon; Phylogeny; Rhizosphere; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Vitamin K 2

A novel yellow-pigmented, aerobic, rod-shaped, non-motile bacterium, designated strain CCMF41T, was isolated from rhizosphere soil of maize (Zea mays) collected in Wufeng District, Taichung, Taiwan. Strain CC-MF41T exhibited 16S rRNA gene sequence similarity of 97.5, 97.3, 97.2 and 97.1% to Leucobacter chironomi MM2LBT (and ‘Leucobacter kyeonggiensis’F3-P9 and ‘L. humi’ Re-6, the names of which have not been validly published), Leucobactertardus K70/01T, L. komagatae IFO 15245T and ‘Leucobacter margaritiformis’ A23. However,CC-MF41T and ‘L. margaritiformis’ A23 formed a loosely bound phylogenetic lineage (with alow bootstrap value) associated with species of the genus Leucobacter. In DNA–DNA reassociation experiments, the relatedness of strain CC-MF41T to L. chironomi DSM 19883T was 57.1% (reciprocal value 29.1 %). The DNA G+C content of strain CC-MF41T was 72.1 mol% and the cell-wall peptidoglycan contained 2,4-diaminobutyric acid, alanine, glycine,glutamic acid and threonine. The major menaquinone was MK-11 and the predominant fatty acids were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The polar lipid profile of strain CCMF41T contained major amounts of diphosphatidylglycerol followed by an unidentified glycolipid, phosphatidylglycerol and an unknown phospholipid. Based on its phylogenetic,phenotypic and chemotaxonomic distinctiveness, strain CC-MF41T represents a novel species of Leucobacter, for which the name Leucobacter zeae sp. nov. is proposed. The type strain isCC-MF41T (=BCRC 80515T=LMG 27265T).

Topics: Actinomycetales; Aminobutyrates; Bacterial Typing Techniques; Base Composition; Cell Wall; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Pigmentation; Rhizosphere; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Taiwan; Vitamin K 2; Zea mays

A novel Gram-stain-positive, non-motile, rod-shaped bacterium, designated 5GHs34-4(T), was isolated from greenhouse soil in Yongin, Republic of Korea. Growth occurred in the temperature range of 10-37 °C (optimum 28-30 °C) and at pH 5.0-9.0 (optimum pH 7.0). It can tolerate up to 3 % (w/v) NaCl. The strain showed 16S rRNA gene sequence similarity levels of 95.1-97.0 % with species of the genus Leifsonia, 95.7-96.7 % with species of the genus Herbiconiux, 95.1-96.4 % with species of the genus Salinibacterium and 96.1 % with Labedella gwakjiensis and Homoserinimonas aerilata. The highest sequence similarities (97.0 %) were with Leifsonia aquatica JCM 1368(T), Leifsonia poae VKM Ac-1401(T) and Leifsonia psychrotolerans LI1(T). The peptidoglycan type determined for strain 5GHs34-4(T) was B2γ with dl-2,4-diaminobutyric acid at position 3. The murein was of the acetyl type. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. The menaquinones detected were MK-13, MK-12 and MK-14, and the major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), anteiso-C17 : 0 and anteiso-C15 : 0. The phenotypic and phylogenetic traits of strain 5GHs34-4(T) differed in some respects from those of members of the family Microbacteriaceae. Therefore, strain 5GHs34-4(T) is considered to represent a novel species of a new genus in the family Microbacteriaceae, for which the name Rudaibacter terrae gen. nov., sp. nov. is proposed. The type strain is 5GHs34-4(T) ( = KACC 15523(T) = NBRC 108754(T)).

Topics: Actinomycetales; Aminobutyrates; Bacterial Typing Techniques; Base Composition; Cell Wall; DNA, Bacterial; Environment, Controlled; Fatty Acids; Molecular Sequence Data; Peptidoglycan; Phenotype; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Vitamin K 2

A Gram-stain-positive, aerobic, non-motile, non-spore-forming, short rod-shaped actinobacterium, designated strain PB243(T), was isolated from grass soil sampled in Daejeon, Republic of Korea. Comparative 16S rRNA gene sequence studies showed the isolate was clearly affiliated with the class Actinobacteria, and most closely related to Amnibacterium kyonggiense KEMC 51201-037(T), showing 98.8 % 16S rRNA gene sequence similarity. Cells of strain PB243(T) formed yellow colonies on R2A agar, contained MK-11 and MK-12 as the predominant menaquinones, l-2,4-diaminobutyric acid as the diagnostic cell-wall diamino acid, and anteiso-C15:0 and iso-C16:0 among the major fatty acids. The acyl type of the muramic acid was acetyl. The G+C content of the genomic DNA of strain PB243(T) was 71.5 mol%. Thus, the combined genotypic and phenotypic data supported the conclusion that strain PB243(T) represents a novel species of the genus Amnibacterium, for which the name Amnibacterium soli sp. nov. is proposed. The type strain is PB243(T) ( = KCTC 33147(T) = JCM 19015(T)).

Topics: Actinobacteria; Aminobutyrates; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; Poaceae; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Vitamin K 2

A Gram-positive, strictly aerobic, rod-shaped, non-motile bacterial strain, designated MJ28T, was isolated from a sludge sample from the Daejeon sewage disposal plant in South Korea. A polyphasic approach was applied to study the taxonomic position of strain MJ28T. Strain MJ28T showed highest 16S rRNA gene sequence similarity to Pseudoclavibacter soli KP02T (95.2 %). Levels of 16S rRNA gene sequence similarity to the type strains of other Pseudoclavibacter species were less than 94.0 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MJ28T belonged to the clade formed by members of the genus Pseudoclavibacter in the family Microbacteriaceae. The G+C content of the genomic DNA of strain MJ28T was 65.8 mol%. The chemotaxonomic characteristics of strain MJ28T showed features typical of the genus Pseudoclavibacter, with MK-9 as the predominant respiratory quinone, 2,4-diaminobutryic acid as the diamino acid in the peptidoglycan, and anteiso-C17:0 (44.6 %), anteiso-C15:0 (35.7 %) and C16:0 (9.5 %) as the major fatty acids. On the basis of phylogenetic inference, fatty acid profile and other phenotypic properties, strain MJ28T is considered to represent a novel species of the genus Pseudoclavibacter, for which the name Pseudoclavibacter caeni sp. nov. is proposed. The type strain is MJ28T (=KCTC 19773T=JCM 16921T).

Topics: Actinomycetales; Aminobutyrates; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Peptidoglycan; Phylogeny; Republic of Korea; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sewage; Vitamin K 2

A Gram-positive, non-motile bacterium, designated KSL51201-037(T), was isolated from Anyang stream, Republic of Korea, and was characterized using a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis showed that strain KSL51201-037(T) belonged to the family Microbacteriaceae of the class Actinobacteria and exhibited 96.9 % gene sequence similarity to Labedella gwakjiensis KSW2-17(T), 96.0 % to Leifsonia ginsengi wged11(T) and 95.9 % to Microterricola viridarii KV-677(T). The G+C content of the genomic DNA was 72.7 mol%. Strain KSL51201-037(T) had l-2,4-diaminobutyric acid as the diagnostic cell-wall diamino acid, MK-11 and MK-12 as the major menaquinones, anteiso-C(15 : 0) (47.8 %) and iso-C(16 : 0) (24.0 %) as the major fatty acids and phosphatidylglycerol and three unknown phospholipids as the major polar lipids. On the basis of phenotypic and genotypic properties and phylogenetic distinctiveness, it is suggested that strain KSL51201-037(T) represents a novel species of a new genus in the family Microbacteriaceae for which the name Amnibacterium kyonggiense gen. nov., sp. nov. is proposed. The type strain of the type species is KSL51201-037(T) (=KEMC 51201-037(T)=JCM 16463(T)).

Topics: Actinomycetales; Aminobutyrates; Base Composition; Cell Wall; Cluster Analysis; DNA, Bacterial; DNA, Ribosomal; Fatty Acids; Korea; Molecular Sequence Data; Phospholipids; Phylogeny; Rivers; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Vitamin K 2

Strain M1-8(T) was isolated from jeotgal, a Korean salt-fermented food. Cells were aerobic, non-motile, Gram-reaction-positive and rod-shaped. Colonies were cream-coloured and circular with entire margins. Strain M1-8(T) exhibited optimal growth at 25-30 °C and pH 7.0-8.0 and in 0-4  % (w/v) NaCl. The strain tolerated up to 10.0 mM Cr(VI). Phylogenetic analyses of 16S rRNA gene sequences indicated that strain M1-8(T) represents a novel species in the genus Leucobacter. The 16S rRNA gene sequence of M1-8(T) exhibited 98.1  % similarity to that of Leucobacter chromiireducens subsp. chromiireducens L-1(T). The new isolate was clustered with Leucobacter species on a 16S rRNA gene sequence-based phylogenetic tree. The chromosomal DNA G+C content of strain M1-8(T) was 62.8 %. Its cell-wall peptidoglycan contained 2,4-diaminobutyric acid, glutamic acid, alanine, glycine and γ-aminobutyric acid. The major menaquinone was MK-11 and the predominant fatty acids were anteiso-C₁₅:₀ (63.6 %), anteiso-C₁₇:₀ (16.7 %) and iso-C₁₆:₀ (14.2  %). The polar lipid profile of strain M1-8(T) contained diphosphatidylglycerol and one unknown glycolipid. Significant genotypic and phenotypic differences were found between strain M1-8(T) and other Leucobacter species. These differentiating characteristics indicate that strain M1-8(T) represents a novel species of the genus Leucobacter, for which the name Leucobacter salsicius sp. nov. is proposed. The type strain is M1-8(T) (=KACC 21127(T) =JCM 16362(T)).

Topics: Actinomycetales; Aminobutyrates; Base Composition; Cell Wall; Cluster Analysis; Cytoplasm; DNA, Bacterial; DNA, Ribosomal; Fatty Acids; Food Microbiology; Korea; Molecular Sequence Data; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Vitamin K 2

A Gram-positive, non-spore-forming actinobacterium (Sj 10(T)) was isolated on tryptone soy agar from the air of a duck barn after filter sampling. Based on 16S rRNA gene sequence similarity studies, strain Sj 10(T) was shown to belong to the genus Leucobacter and was closely related to Leucobacter chromiireducens subsp. chromiireducens L-1(T) (97.8 %), Leucobacter tardus DSM 19811(T) (97.3 %) and Leucobacter luti RF6(T) (97.3 %). The peptidoglycan of strain Sj 10(T) contained 2,4-diaminobutyric acid in combination with a lower amount of lysine as diagnostic diamino acids. In addition, threonine, glycine, alanine and glutamic acid were found. Menaquinone MK-11 was the major respiratory quinone; MK-12 and MK-10 were detected in minor amounts. The polar lipid pattern consisted of phosphatidylglycerol, diphosphatidylglycerol and one unknown component each of a phospholipid, glycolipid and aminoglycolipid. Strain Sj 10(T) contained the major fatty acids anteiso-C(15 : 0), iso-C(16 : 0) and anteiso-C(17 : 0), like other members of the genus Leucobacter. Results of DNA-DNA hybridization, physiological and biochemical tests enabled strain Sj 10(T) to be differentiated genotypically and phenotypically from the most closely related Leucobacter species. Strain Sj 10(T) represents a novel species of the genus Leucobacter, for which the name Leucobacter aerolatus sp. nov. is proposed, with Sj 10(T) (=DSM 22806(T) =CCM 7705(T)) as the type strain.

Topics: Actinomycetales; Air Microbiology; Aminobutyrates; Animals; Bacterial Typing Techniques; DNA, Bacterial; Ducks; Fatty Acids; Housing, Animal; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Vitamin K 2

A yellow-pigmented, Gram-positive, aerobic, non-motile, non-spore-forming, irregular rod-shaped bacterium (strain TAN 31504(T)) was isolated from the bacteriophagous nematode Caenorhabditis elegans. Based on 16S rRNA gene sequence similarity, DNA G+C content of 69.5 mol%, 2,4-diaminobutyric acid in the cell-wall peptidoglycan, major menaquinone MK-11, abundance of anteiso- and iso-fatty acids, polar lipids diphosphatidylglycerol and phosphatidylglycerol and a number of shared biochemical characteristics, strain TAN 31504(T) was placed in the genus Leucobacter. DNA-DNA hybridization comparisons demonstrated a 91 % DNA-DNA relatedness between strain TAN 31504(T) and Leucobacter chromiireducens LMG 22506(T) indicating that these two strains belong to the same species, when the recommended threshold value of 70 % DNA-DNA relatedness for the definition of a bacterial species by the ad hoc committee on reconciliation of approaches to bacterial systematics is considered. Based on distinct differences in morphology, physiology, chemotaxonomic markers and various biochemical characteristics, it is proposed to split the species L. chromiireducens into two novel subspecies, Leucobacter chromiireducens subsp. chromiireducens subsp. nov. (type strain L-1(T)=CIP 108389(T)=LMG 22506(T)) and Leucobacter chromiireducens subsp. solipictus subsp. nov. (type strain TAN 31504(T)=DSM 18340(T)=ATCC BAA-1336(T)).

Topics: Actinomycetales; Aerobiosis; Aminobutyrates; Animals; Bacterial Typing Techniques; Base Composition; Caenorhabditis elegans; Cell Wall; DNA, Bacterial; DNA, Ribosomal; Fatty Acids; Genes, rRNA; Locomotion; Molecular Sequence Data; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Pigments, Biological; RNA, Bacterial; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sequence Homology, Nucleic Acid; Vitamin K 2