scholarly journals Streptomyces endocoffea sp. nov. , an endophytic actinomycete isolated from Coffea arabica (L.)

2021 ◽  
Author(s):  
Achararak Nammali ◽  
Chakapong Intaraudom ◽  
Pattama Pittayakhajonwut ◽  
Chanwit Suriyachadkun ◽  
Sarin Tadtong ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Coffea Arabica ◽  
Gene Sequence ◽  
Novel Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
Lampang Province ◽  
Coffea Arabica L

Abstract An aerobic, non-motile, Gram-stain positive actinomycete, designated strain CA3R110T, was isolated from the surface-sterilised root of Coffea arabica L. collected from Lampang Province, Thailand. 16S rRNA gene sequence analysis indicated that strain CA3R110T is a member of the genus Streptomyces and showed the closest similarities to Streptomyces rapamycinicus NRRL B-5491T (99.1%), followed by S. iranensis HM 35T (99.0%). Strain CA3R110T contained LL-diaminopimelic acid in cell peptidoglycan, MK-9(H6), and MK-9(H8) as major menaquinone, iso-C16:0, iso-C15:0, C16:0 as major fatty acids. Diphosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositolmannoside were detected in the cell. The chemotaxonomic characteristics possessed the typical properties of the genus Streptomyces. A low digital DNA–DNA hybridization (< 55.6%) and average nucleotide identity-blast (ANIb) (< 92.2%) values revealed that strain CA3R110T could be distinguished from any known Streptomyces species. With the differences in phenotypic and genotypic data, strain CA3R110T represents a novel species of genus Streptomyces, for which the name Streptomyces endocoffea sp. nov. is proposed. The type strain is CA3R110T (= TBRC 11245T = NBRC 114296T).

scholarly journals Allobacillus salarius sp. nov., and Allobacillus saliphilus sp. nov., Isolated from Shrimp Paste (ka-pi) in Thailand

2021 ◽  
Author(s):  
Supalurk Yiamsombut ◽  
Pawina Kanchanasin ◽  
Wongsakorn Phongsopitanun ◽  
Nattakorn Kuncharoen ◽  
Ancharida Savarajara ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
Gram Stain ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
Fermented Shrimp Paste

Abstract The moderately halophilic, Gram-stain-positive, spore-forming rods, designated SKP4-8T and SKP8-2T isolated from a traditional fermented shrimp paste (Ka-pi), were taxonomic studied based on polyphasic approach. Strain SKP4-8T grew at pH 6.0-9.0 (optimum 7.0), at 25-45°C (optimum 37°C) and in 1-16 % (w/v) NaCl (optimum 5-10). Strain SKP8-2T grew at pH 6.0-9.0 (optimum 8.0), at 25-45°C (optimum 37°C) and in 0-20 % (w/v) NaCl (optimum 3-10 %). The strains contained meso-diaminopimelic acid in cell-wall peptidoglycan and the major menaquinone was MK-7. Strain SKP4-8T contained iso-C15:0, antesio-C15:0 and iso-C17:0; and strain SKP8-2T contained antesio-C15:0, iso-C15:0, iso-C16:0 and antesio-C17:0 as major cellular fatty acids.Phosphatidylglycerol, diphosphatidylglycerol, unknown phospholipids and an unknown glycolipid were detected as major polar lipids. On the basis of 16S rRNA gene sequence analysis, strains SKP4-8T and SKP8-2T belonged to the genus Allobacillus and was closely related to Allobacillus halotolerans LMG 24826T with 98.8 % and 99.3 % similarity, respectively. The comparative genome analysis based on average nucleotide identity (ANI) and digital DNA-DNA hybridization revealed that both strains showed the values below 95 and 70 %, from each other and the Allobacillus halotolerans LMG 24826T, respectively. Based on data from this polyphasic study, strains SKP4-8T and SKP8-2T represent the novel species of the genus Allobacillus and the name Allobacillus salarius sp. nov. was proposed for SKP4-8T (=KCTC 33905T =LMG 30016T =TISTR 2499T); and Allobacillus saliphilus sp. nov. for SKP8-2T (=KCTC 33906T =LMG 29682T =TISTR 2558T).

scholarly journals Bacillus halochares sp. nov., a halophilic bacterium isolated from a solar saltern

2010 ◽  
Vol 60 (6) ◽  
pp. 1432-1436 ◽  
Author(s):  
A. Pappa ◽  
C. Sánchez-Porro ◽  
P. Lazoura ◽  
A. Kallimanis ◽  
A. Perisynakis ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Optimal Growth ◽  
Halophilic Bacterium ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Gram Stain ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
Lipid Pattern

A novel halophilic bacterium, designated strain MSS4T, was isolated from the solar salterns of Mesolongi, Greece. The micro-organism, a motile, Gram-stain-positive, aerobic rod, proliferated at salinities of 1.0–4.0 M NaCl, with optimal growth at 2.5 M NaCl. Endospores were not observed. Strain MSS4T showed optimal growth at 37 °C and pH 8.0. The G+C content of its DNA was 47.2 mol%. The polar lipid pattern of strain MSS4T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidic acid and phosphatidylethanolamine. It possessed anteiso-C15 : 0, C18 : 0, C16 : 0 and anteiso-C17 : 0 as the major fatty acids (altogether representing 84.7 % of the total). The predominant isoprenoid quinone was MK-7. The cell-wall peptidoglycan contained meso-diaminopimelic acid. 16S rRNA gene sequence analysis showed that the new isolate has 96.1 % similarity to Bacillus qingdaonensis CM1T and Bacillus aidingensis 17-5T, 95.5 % to Bacillus salarius BH169T and lower similarity to other Bacillus species. These results justify the assignment of strain MSS4T to a novel species within the genus Bacillus, for which the name Bacillus halochares sp. nov. is proposed. The type strain is MSS4T (=LMG 24571T =DSM 21373T).

scholarly journals Lactobacillus similis sp. nov., isolated from fermented cane molasses

2010 ◽  
Vol 60 (1) ◽  
pp. 187-190 ◽  
Author(s):  
Maki Kitahara ◽  
Mitsuo Sakamoto ◽  
Yoshimi Benno
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Cane Molasses ◽  
Gene Sequence Analysis

The taxonomic position of strain JCM 2765T isolated from fermented cane molasses in Thailand was reinvestigated. Strain JCM 2765T was originally identified as representing Lactobacillus buchneri on the basis of biochemical and physiological characteristics. In the present study, 16S rRNA gene sequence analysis of strain JCM 2765T demonstrated a low level of similarity with the type strain of L. buchneri (92.5 %) and high levels with those of Lactobacillus collinoides (97.6 %) and Lactobacillus paracollinoides (98.0 %). Ribotyping was applied to investigate the relationships between strain JCM 2765T, L. collinoides and L. paracollinoides. The dendrogram based on ribotyping patterns showed one cluster for six strains of L. paracollinoides, and that strain JCM 2765T and L. collinoides JCM 1123T were each independent. Based on additional phenotypic findings and DNA–DNA hybridization results, strain JCM 2765T is considered to represent a novel species of the genus Lactobacillus, for which the name Lactobacillus similis sp. nov. is proposed. The type strain is JCM 2765T (=LMG 23904T).

scholarly journals Microbacterium rhizomatis sp. nov., a β-glucosidase-producing bacterium isolated from rhizome of Korean mountain ginseng

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3196-3202 ◽  
Author(s):  
Van-An Hoang ◽  
Yeon-Ju Kim ◽  
Ngoc Lan Nguyen ◽  
Chang Ho Kang ◽  
Jong-Pyo Kang ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Ginseng Root ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gram Staining ◽  
Gene Sequence Analysis ◽  
The 16S Rrna Gene

A novel Gram-staining-positive, rod-shaped bacterium, designated DCY100T, was isolated from rhizome of mountain ginseng root in Hwacheon mountain, Gangwon province, Republic of Korea. The 16S rRNA gene sequence analysis showed that strain DCY100T belonged to the genus Microbacterium and was most closely related to Microbacterium ginsengisoli KCTC 19189T (97.9 %), Microbacterium lacus JCM 15575T (97.2 %) and Microbacterium invictum DSM 19600T (97.1 %). The major menaquinones were MK-11 and MK-12. The major polar lipids were found to be diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid. The major fatty acids (>10.0 %) were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The cell-wall peptidoglycan contained the amino acids ornithine, alanine, glutamic acid and glycine; whole-cell sugars consisted of glucose, galactose, rhamnose and ribose. The DNA G+C content was 63.6 ± 0.7 mol%. The DNA–DNA hybridization relatedness values between strain DCY100T and Microbacterium ginsengisoli KCTC 19189T, Microbacterium lacus JCM 15575T and Microbacterium invictum DSM 19600T were 36.2 ± 0.4, 22.0 ± 3.0 and 15.3 ± 1.8 %, respectively. On the basis of phenotypic, chemotaxonomic and genotypic analyses, the isolate is classified as a representative of a novel species in the genus Microbacterium, for which the name Microbacterium rhizomatis DCY100T is proposed. The type strain is DCY100T ( = KCTC 39529T = JCM 30598T).

scholarly journals Amycolatopsis stemonae sp. nov., isolated from a Thai medicinal plant

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 3894-3899 ◽  
Author(s):  
Nattaporn Klykleung ◽  
Somboon Tanasupawat ◽  
Pattama Pittayakhajonwut ◽  
Moriya Ohkuma ◽  
Takuji Kudo
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Cellular Fatty Acids ◽  
Gene Sequence Analysis ◽  
Actinomycete Strain ◽  
Genotypic Characteristics ◽  
The 16S Rrna Gene

A novel actinomycete, strain ST1-08T, was isolated from the stem of Stemona sp. in Thailand. The taxonomic position of this isolate was determined by using a polyphasic approach. Strain ST1-08T contained meso-diaminopimelic acid in the cell-wall peptidoglycan, and arabinose and galactose as diagnostic sugars of the whole-cell hydrolysate, which are typical properties of members of the genus Amycolatopsis. Strain ST1-08T grew at 15–40 °C, pH 6–9 and on 5 % (w/v) NaCl. Gelatin liquefaction, starch hydrolysis and skimmed milk peptonization were positive. The strain utilized l-arabinose, d-glucose, glycerol, myo-inositol, d-mannitol and l-rhamnose. The predominant menaquinone was MK-9(H4) and the major cellular fatty acids were iso-C16 : 0 and iso-C15 : 0.The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, hydroxyl-phosphatidylethanolamine, phosphatidylinositol and phosphatidylglycerol. The 16S rRNA gene sequence analysis revealed that the strain was closely related to Amycolatopsis pretoriensis JCM 12673T (98.99 %) and Amycolatopsis lexingtonensis JCM 12672T (98.87 %). The DNA G+C content of strain ST1-08T was 71.2 mol%. The DNA–DNA relatedness values among strain ST1-08T, A. pretoriensis JCM 12673T and A. lexingtonensis JCM 12672T were lower than 70 %, the cut-off level for assigning strains to the same species. On the basis of phenotypic and genotypic characteristics, strain ST1-08T represents a novel species of the genus Amycolatopsis, for which the name Amycolatopsis stemonae is proposed. The type strain is ST1-08T( = JCM 30050T = PCU 339T = TISTR 2278T).

Nocardioides ungokensis sp. nov., isolated from lake sediment

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4857-4862 ◽  
Author(s):  
Yan Zhao ◽  
Qingmei Liu ◽  
Myung-Suk Kang ◽  
Fengxie Jin ◽  
Hongshan Yu ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Bacterium Strain

A Gram-reaction-positive, aerobic, coccus- to rod-shaped, non-motile, non-spore-forming bacterium (strain UKS-03T) was isolated from a sediment sample of Ungok Lake in Gochang, Republic of Korea. The taxonomic position of this bacterium was determined in an investigation based on a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain UKS-03T was shown to belong to the family Nocardioidaceae and to be related most closely to Nocardioides ginsengisegetis Gsoil 485T (98.5 % similarity), Nocardioides koreensis MSL-09T (98.4 %) and ‘Nocardioides panaciterrulae’ Gsoil 958 (97.3 %). Strain UKS-03T was characterized chemotaxonomically as having ll-2,6-diaminopimelic acid in its cell-wall peptidoglycan, MK-8(H4) as the predominant menaquinone, diphosphatidylglycerol and phosphatidylglycerol as the main polar lipids, and iso-C16 : 0, C17 : 1ω8c and C17 : 0 10-methyl as its major fatty acids. The G+C content of the genomic DNA was 71.9 mol%. Mean DNA–DNA relatedness values between strain UKS-03T and N. ginsengisegetis Gsoil 485T, N. koreensis KCTC 19272T and ‘N. panaciterrulae’ Gsoil 958 were 37.5 ± 7.2, 6.8 ± 0.9 and 3.1 ± 0.7 %, respectively. On the basis of the data from this polyphasic taxonomic study, strain UKS-03T represents a novel species of the genus Nocardioides, for which the name Nocardioides ungokensis sp. nov. is proposed. The type strain is UKS-03T ( = KACC 18304T = LMG 28591T).

scholarly journals Paenibacillus antarcticus sp. nov., a novel psychrotolerant organism from the Antarctic environment

2004 ◽  
Vol 54 (5) ◽  
pp. 1521-1526 ◽  
Author(s):  
Ma Jesús Montes ◽  
Elena Mercadé ◽  
Núria Bozal ◽  
Jesús Guinea
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Major Cellular Fatty Acid ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Antarctic

An endospore-forming strain, 20CMT, was isolated from Antarctic sediment and identified as a member of the genus Paenibacillus on the basis of phenotypic and phylogenetic analyses. The organism stained Gram-variable and was facultatively anaerobic. Strain 20CMT was psychrotolerant, growing optimally at 10–15 °C. Like other Paenibacillus species, it contained anteiso-C15 : 0 as the major cellular fatty acid. The DNA G+C content was 40·7 mol%. 16S rRNA gene sequence analysis placed strain 20CMT within the Paenibacillus cluster, with a similarity value of 99·5 % to Paenibacillus macquariensis DSM 2T. DNA–DNA hybridization experiments between the Antarctic isolate and P. macquariensis DSM 2T revealed a reassociation value of 47 %, indicating that strain 20CMT and P. macquariensis DSM 2T belong to different species. Based on evaluation of morphological, physiological, chemotaxonomic and phylogenetic analyses, a novel species, Paenibacillus antarcticus sp. nov., is proposed; the type strain is 20CMT (=LMG 22078T=CECT 5836T).

Arenibacter certesii sp. nov., a novel marine bacterium isolated from the green alga Ulva fenestrata

2004 ◽  
Vol 54 (4) ◽  
pp. 1173-1176 ◽  
Author(s):  
Olga I. Nedashkovskaya ◽  
Seung Bum Kim ◽  
Suk Kyun Han ◽  
Anatoly M. Lysenko ◽  
Valery V. Mikhailov ◽  
...  
Keyword(s):  
Green Alga ◽  
Dna Hybridization ◽  
Marine Bacterium ◽  
Gene Sequence ◽  
Novel Species ◽  
The Sea Of Japan ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Ulva Fenestrata ◽  
Gene Sequence Analysis

The taxonomic position of a novel, marine, heterotrophic, aerobic, pigmented, non-motile bacterium that was isolated from a green alga, Ulva fenestrata, inhabiting the Sea of Japan, was determined. 16S rRNA gene sequence analysis revealed that the strain, KMM 3941T, is a member of the genus Arenibacter. The results of DNA–DNA hybridization experiments, supported by phenotypic and chemotaxonomic data, showed that the isolate represents a novel species of the genus Arenibacter, for which the name Arenibacter certesii sp. nov. is proposed. The type strain is KMM 3941T (=KCTC 12113T=CCUG 48006T).

Williamsia sterculiae sp. nov., isolated from a Chinese medicinal plant

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4158-4162 ◽  
Author(s):  
Xiao-Mei Fang ◽  
Jing Su ◽  
Hao Wang ◽  
Yu-Zhen Wei ◽  
Tao Zhang ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Type Strains ◽  
Chinese Medicinal Plant

Two actinobacterial strains, CPCC 203464T and CPCC 203448, isolated from surface-sterilized stems of medicinal plants were subjected to a polyphasic taxonomic study. These two aerobic organisms formed pale yellow colonies on tryptic soy agar (TSA). Cells were Gram-stain-positive, non-acid-fast, non-motile, rod- or coccoid-like elements. Comparative 16S rRNA gene sequence analysis indicated that strains CPCC 203464T and CPCC 203448 were most closely related to the type strains of the species of the genus Williamsia . Chemotaxonomic properties such as containing meso-diaminopimelic acid in the cell wall, arabinose, galactose and ribose being the whole-cell hydrolysate sugars, phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phosphatidylinositol (PI) as the phospholipids, and C16 : 0, 10-methyl C18 : 0, C18 : 1ω9c, C16 : 1ω7c and/or iso-C15 : 0 2-OH as major fatty acids supported the affiliation of strains CPCC 203464T and CPCC 203448 to the genus Williamsia . The DNA–DNA hybridization values in combination with differentiating chemotaxonomic and physiological characteristics strongly suggested that these two isolates should be classified as representatives of a novel species of the genus Williamsia . The name Williamsia sterculiae sp. nov. is proposed, with strain CPCC 203464T ( = DSM 45741T = KCTC 29118T) as the type strain.

scholarly journals Stenotrophomonas ginsengisoli sp. nov., isolated from a ginseng field

2010 ◽  
Vol 60 (7) ◽  
pp. 1522-1526 ◽  
Author(s):  
Ho-Bin Kim ◽  
Sathiyaraj Srinivasan ◽  
Gayathri Sathiyaraj ◽  
Lin-Hu Quan ◽  
Se-Hwa Kim ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Gene Sequence Analysis ◽  
Stenotrophomonas Nitritireducens ◽  
Physiological And Biochemical

A Gram-negative, non-spore-forming, rod-shaped bacterium, designated strain DCY01T, was isolated from soil from a ginseng field in South Korea and was characterized in order to determine its taxonomic position. 16S rRNA gene sequence analysis revealed that strain DCY01T belonged to the Gammaproteobacteria and was most closely related to Stenotrophomonas koreensis KCTC 12211T (98.4 % similarity), Stenotrophomonas humi R-32729T (97.2 %), Stenotrophomonas terrae R-32768 (97.1 %), Stenotrophomonas maltophilia DSM 50170T (96.9 %) and Stenotrophomonas nitritireducens DSM 12575T (96.8 %). Chemotaxonomic analyses revealed that strain DCY01T possessed a quinone system with Q-8 as the predominant compound, and iso-C15 : 0 (28.2 %), C16 : 0 10-methyl (13.2 %), iso-C15 : 1 F (10.8 %) and C15 : 0 (7.5 %) as major fatty acids, corroborating assignment of strain DCY01T to the genus Stenotrophomonas. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The results of DNA–DNA hybridization and physiological and biochemical tests clearly demonstrated that strain DCY01T represents a species distinct from recognized Stenotrophomonas species. Based on these data, DCY01T (=KCTC 12539T=NBRC 101154T) should be classified as the type strain of a novel species of the genus Stenotrophomonas, for which the name Stenotrophomonas ginsengisoli sp. nov. is proposed.

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