Streptomyces kebangsaanensis sp. nov., an endophytic actinomycete isolated from an ethnomedicinal plant, which produces phenazine-1-carboxylic acid

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3733-3738 ◽  
Author(s):  
Nurul’ Izzah Mohd Sarmin ◽  
Geok Yuan Annie Tan ◽  
Christopher M. M. Franco ◽  
RuAngelie Edrada-Ebel ◽  
Jalifah Latip ◽  
...  

A spore-forming streptomycete designated strain SUK12T was isolated from a Malaysian ethnomedicinal plant. Its taxonomic position, established using a polyphasic approach, indicates that it is a novel species of the genus Streptomyces . Morphological and chemical characteristics of the strain were consistent with those of members of the genus Streptomyces . Analysis of the almost complete 16S rRNA gene sequence placed strain SUK12T in the genus Streptomyces where it formed a distinct phyletic line with recognized species of this genus. The strain exhibited highest sequence similarity to Streptomyces corchorusii DSM 40340T (98.2 %) followed by Streptomyces chrestomyceticus NRRL B-3310T (98.1 %). The G+C content of the genomic DNA was 74 mol%. Chemotaxonomic data [MK-9(H8) as the major menaquinone; LL-diaminopimelic acid as a component of cell-wall peptidoglycan; C12 : 0, C14 : 0, C15 : 0 and C17 : 1 as the major fatty acids; phospholipid type II] supported the affiliation of strain SUK12T to the genus Streptomyces . The results of the phylogenetic analysis and phenotypic data derived from this and previous studies allowed the genotypic and phenotypic differentiation of strain SUK12T from the related species of the genus Streptomyces . The DNA–DNA relatedness value between strain SUK12T and S. corchorusii DSM 40340T is 18.85±4.55 %. Strain SUK12T produces phenazine-1-carboxylic acid, known as tubermycin B, an antibacterial agent. It is proposed, therefore, that strain SUK12T ( = DSM 42048T = NRRL B-24860T) be classified in the genus Streptomyces as the type strain of Streptomyces kebangsaanensis sp. nov.

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4043-4048 ◽  
Author(s):  
Salih Saricaoglu ◽  
Kamil Isik ◽  
Aysel Veyisoglu ◽  
Hayrettin Saygin ◽  
Demet Cetin ◽  
...  

A novel actinobacterial strain, designated Z1R7T, was isolated from a soil sample collected from Burgazada, in the Marmara Sea (Turkey), and the strain identity was determined using a polyphasic taxonomic approach. The organism had chemotaxonomic and morphological properties consistent with its classification in the genus Streptomyces and it formed a distinct phyletic line in the 16S rRNA gene tree, together with the type strains Streptomyces specialis GW41-1564T (95.76 %), Streptomyces mayteni YIM 60475T (95.64 %), Streptomyces hainanensis YIM 47672T (95.53 %), Streptomyces hoynatensis S1412T (95.29 %), Streptomyces avicenniae MCCC 1A01535T (94.74 %), Streptomyces sedi YIM 65188T (94.59 %) and Streptomyces zhaozhouensis NEAU-LZS-5T (94.68 %). Chomotaxonomic data revealed that strain Z1R7T possesed MK-9 (H8) as the predominant menaquinone, ll-diaminopimelic acid as the diagnostic diamino acid, and galactose, glucose and ribose as whole cell sugars. Diphosphatidylglycerol, phoshphatidylethanolamine and phosphatidylinositol were the predominant polar lipids; iso-C16 : 0, anteiso-C17 : 0 and anteiso-C15 : 0 were the major fatty acids, and the genomic DNA G+C content was 69.4 mol%. On the basis of these genotypic and phenotypic data, it is proposed that isolate Z1R7T ( = KCTC 29434T = DSM 42126T) should be classified in the genus Streptomyces as Streptomyces burgazadensis sp. nov.


Author(s):  
Yuparat Saimee ◽  
Kannika Duangmal

A novel actinobacterium, designated strain DW4-2T, was isolated from duckweed (Spirodela sp.) collected from an agricultural pond in Kasetsart University, Bangkok, Thailand. The morphological, chemotaxonomic and phylogenetic characteristics were consistent with its classification in the genus Streptomyces . Strain DW4-2T showed the highest 16S rRNA gene sequence similarity values to Streptomyces qinglanensis DSM 42035T (98.5 %), S treptomyces smyrnaeus DSM 42105T (98.4 %) and Streptomyces oryzae S16-07T (98.4 %). Digital DNA–DNA hydridization and average nucleotide identity values between the genome sequences of strain DW4-2T with S. qinglanensis DSM 42035T (29.8 and 87.8 %), S. smyrnaeus DSM 42105T (33.1 and 89.0 %) and S. oryzae S16-07T (33.0 and 88.9 %) were below the thresholds of 70 and 95–96 % for prokaryotic conspecific assignation. Chemotaxonomic data revealed that strain DW4-2T possessed MK-9(H6) and MK-9(H8) as the predominant menaquinones. It contained ll -diaminopimelic acid as the diagnostic diamino acid and glucose, ribose and trace amount of madurose in whole-cell sugars. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, an unidentified aminolipid, an unidentified lipid and an unidentified phospholipid. The predominant cellular fatty acids were anteiso-C17 : 0, anteiso-C15 : 0 and iso-C16 : 0. The genomic DNA size of the strain DW4-2T was 7 310 765 bp with DNA G+C content 71.0 mol%. Genomic analysis of the genome indicated that the strain DW4-2T had the potential to produce bioactive compounds. On the basis of these genotypic and phenotypic data, it is supported that strain DW4-2T represents a novel species of the genus Streptomyces , for which the name Streptomyces spirodelae sp. nov. is proposed. The type strain is strain DW4-2T (=TBRC 13095T=NBRC 114803T).


2014 ◽  
Vol 64 (Pt_10) ◽  
pp. 3520-3525 ◽  
Author(s):  
Ying-Qian Kang ◽  
Hong Ming ◽  
Tohru Gonoi ◽  
Yuru Chen ◽  
Yu Cao ◽  
...  

A second novel clinical actinobacterial strain, designated IFM 10348T, was isolated from the sputum of the same Japanese patient with bacterial pneumonia from whom the type strain of Gordonia araii had been isolated. The strains differed in phylogenetic position and drug-resistance profiles. The taxonomic position of strain IFM 10348T was clarified by phenotypic, chemotaxonomic and phylogenetic studies. Phylogenetic analyses based on 16S rRNA gene sequences clearly demonstrated that strain IFM 10348T occupied a distinct clade within the genus Gordonia and was related closely to Gordonia malaquae DSM 45064T and Gordonia hirsuta DSM 44140T (97.3 and 97.1 % similarities, respectively). Strain IFM 10348T was also clearly differentiated from G. malaquae DSM 45064T and G. hirsuta DSM 44140T based on gyrB and secA1 gene sequence similarity values. Strain IFM 10348T had MK-9(H2) as the predominant menaquonine, contained meso-diaminopimelic acid, arabinose, galactose and glucosamine as cell-wall components, and contained C18 : 1ω9c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0 as the major cellular fatty acids. Mycolic acids were present. The DNA G+C content of strain IFM 10348T was 68.0 mol%. DNA–DNA relatedness data coupled with the combination of genotypic and phenotypic data indicated that strain IFM 10348T represents a novel species of the genus Gordonia , for which the name Gordonia iterans sp. nov. is proposed. The type strain is IFM 10348T ( = CCTCC M2011245T = NCCB 100436T).


2020 ◽  
Vol 70 (4) ◽  
pp. 2750-2759 ◽  
Author(s):  
Hayrettin Saygin ◽  
Hilal Ay ◽  
Kiymet Guven ◽  
Demet Cetin ◽  
Nevzat Sahin

A novel actinobacterial strain, designated 13K301T, was isolated from a soil sample collected from the Karakum Desert, Turkmenistan. The taxonomic position of strain 13K301T was revealed by using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain 13K301T belongs to the genus Streptomyces and had highest sequence similarity to ‘Streptomyces qaidamensis’ S10T (99.2 %), Streptomyces flavovariabilis NRRL B-16367T (98.9 %) and Streptomyces phaeoluteigriseus DSM 41896T (98.8 %), but the strain formed a distinct clade in the phylogenetic tree. The DNA–DNA relatedness and average nucleotide identity values as well as evolutionary distances based on multilocus (atpD, gyrB, recA, rpoB and trpB) sequences between strain 13K301T and closely related type strains were significantly lower than the recommended threshold values. The cell wall contained ll-diaminopimelic acid and the whole-cell hydrolysates were glucose and ribose. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol were determined as the predominant polar lipids. The major menaquinones were identified as MK-9(H8) and MK-9(H6). On the basis of these genotypic and phenotypic data, it is proposed that strain 13K301T should be classified as representative of a novel species of the genus Streptomyces , for which the name Streptomyces cahuitamycinicus sp. nov. is proposed. The type strain is 13K301T (=DSM 106873T=KCTC 49110T). In addition, the whole genome-based comparisons as well as the multilocus sequence analysis revealed that the type strains of Streptomyces galilaeus and Streptomyces bobili belong to a single species. It is, therefore, proposed that S. galilaeus be recognised as a heterotypic synonym of S. bobili for which an emended description is given.


2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1254-1260 ◽  
Author(s):  
Mustafa Camas ◽  
Nevzat Sahin ◽  
Anil Sazak ◽  
Cathrin Spröer ◽  
Hans-Peter Klenk

A novel actinomycete, designated strain KT2025T, was isolated from arid soil collected from Magusa, northern Cyprus. The taxonomic position of the novel strain was established by using a polyphasic approach. The organism had chemical and morphological features consistent with its classification in the genus Amycolatopsis . Phylogenetic analyses based on 16S rRNA gene sequences supported the classification of the isolate in the genus Amycolatopsis and showed that the organism formed a cluster with Amycolatopsis nigrescens CSC17-Ta-90T, Amycolatopsis minnesotensis 32U-2T, Amycolatopsis sacchari DSM 44468T and Amycolatopsis dongchuanensis YIM 75904T. 16S rRNA gene sequence similarity analysis indicated that strain KT2025T was most closely related to Amycolatopsis lurida DSM 43134T (97.5 %), Amycolatopsis keratiniphila subsp. keratiniphila DSM 44409T (97.4 %), Amycolatopsis keratiniphila subsp. nogabecina DSM 44586T (97.1 %), Amycolatopsis nigrescens DSM 44992T (97.1 %), Amycolatopsis azurea DSM 43854T (97.1 %) and Amycolatopsis minnesotensis DSM 44988T (96.9 %). The organism was found to have chemical features typical of members of the genus Amycolatopsis such as meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, and arabinose and galactose as diagnostic sugars. The predominant menaquinone was MK-9(H4). The polar lipids detected were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and hydroxy-phosphatidylethanolamine. The major fatty acids were iso-C16 : 0, iso-C15 : 0 and iso-C14 : 0. The G+C content of the genomic DNA was 70.8 mol%. Phenotypic data clearly distinguished the isolate from its closest relatives. The combined genotypic and phenotypic data and low levels of DNA–DNA relatedness with its closest relatives indicated that strain KT2025T represents a novel species of the genus Amycolatopsis , for which the name Amycolatopsis magusensis sp. nov. is proposed. The type strain is KT2025T ( = DSM 45510T = KCTC 29056T).


2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1771-1775 ◽  
Author(s):  
Xuefang Zhang ◽  
Jianli Zhang ◽  
Yabo Zhang ◽  
Yuhua Xin ◽  
Hongju He

A novel actinomycete, strain W6T, was isolated from a soil sample of Yunnan Province, China. The bacterium was aerobic, non-motile, non-spore-forming and Gram-stain-positive. Genetic, phenotypic and chemical properties of the isolate were studied. 16S rRNA gene sequence data suggested that the novel isolate belonged to the genus Friedmanniella and shared 98.6 % sequence similarity with Friedmanniella antarctica DSM 11053T and Friedmanniella okinawensis DSM 21744T, the most closely related species. The cell-wall peptidoglycan contained ll-diaminopimelic acid, and mycolic acids were absent. The main menaquinone was MK-9(H4) and the predominant fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The phospholipid profile contained phosphatidylglycerol, phosphatidylinositol, phosphatidylcholine and diphosphatidylglycerol. The DNA G+C content of strain W6T was 72 mol%. Strain W6T showed 30.0 % and 28.5 % DNA–DNA relatedness, respectively, to F. antarctica DSM 11053T and F. okinawensis DSM 21744T. The combined genotypic and phenotypic data showed that strain W6T should be assigned to the genus Friedmanniella as a representative of a novel species, for which the name Friedmanniella flava sp. nov. is proposed. The type strain is W6T ( = CGMCC 4.6856T = JCM 17701T).


2012 ◽  
Vol 62 (Pt_8) ◽  
pp. 2011-2017 ◽  
Author(s):  
Anil Sazak ◽  
Mustafa Camas ◽  
Cathrin Spröer ◽  
Hans-Peter Klenk ◽  
Nevzat Sahin

A novel actinobacterium, strain A8036T, isolated from soil, was investigated by using a polyphasic taxonomic approach. The organism formed extensively branched substrate hyphae that generated spiral chains of spores with irregular surfaces. The cell wall contained meso-diaminopimelic acid (type III) and cell-wall sugars were glucose, madurose, mannose and ribose. The predominant menaquinones were MK-9(H6) and MK-9(H4). The phospholipids were diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The major cellular fatty acids were iso-C16 : 0, C17 : 1 cis9, C16 : 0, C15 : 0 and 10-methyl C17 : 0. Based on 16S rRNA gene sequence analysis, the closest phylogenetic neighbours of strain A8036T were Actinomadura meyerae DSM 44715T (99.23 % similarity), Actinomadura bangladeshensis DSM 45347T (98.9 %) and Actinomadura chokoriensis DSM 45346T (98.3 %). However, DNA–DNA relatedness and phenotypic data demonstrated that strain A8036T could be clearly distinguished from the type strains of all closely related Actinomadura species. Strain A8036T is therefore considered to represent a novel species of the genus Actinomadura , for which the name Actinomadura geliboluensis sp. nov. is proposed. The type strain is A8036T ( = DSM 45508T = KCTC 19868T).


2014 ◽  
Vol 64 (Pt_10) ◽  
pp. 3513-3519 ◽  
Author(s):  
Learn-Han Lee ◽  
Adzzie-Shazleen Azman ◽  
Nurullhudda Zainal ◽  
Shu-Kee Eng ◽  
Nurul-Syakima Ab Mutalib ◽  
...  

Strain MUSC 115T was isolated from mangrove soil of the Tanjung Lumpur river in the state of Pahang, Peninsular Malaysia. Cells of this strain stained Gram-positive and were non-spore-forming, short rods that formed yellowish-white colonies on different agar media. The taxonomy of strain MUSC 115T was studied by a polyphasic approach, and the organism showed a range of phylogenetic and chemotaxonomic properties consistent with those of the genus Microbacterium . The cell-wall peptidoglycan was of type B2β, containing the amino acids ornithine, alanine, glycine, glutamic acid and homoserine. The muramic acid was of the N-glycolyl form. The predominant menaquinones detected were MK-12, MK-13 and MK-11. The polar lipids consisted of phosphatidylglycerol, phosphoglycolipid, diphosphatidylglycerol, two unidentified lipids, three unidentified phospholipids and four unidentified glycolipids. The major fatty acids of the cell membrane were anteiso-C15 : 0 and anteiso-C17 : 0. The whole-cell sugars detected were ribose, glucose, mannose and galactose. Based on the 16S rRNA gene sequence, strain MUSC 115T showed the highest sequence similarity to Microbacterium immunditiarum SK 18T (98.1 %), M. ulmi XIL02T (97.8 %) and M. arborescens DSM 20754T (97.5 %) and lower sequence similarity to strains of other species of the genus Microbacterium . DNA–DNA hybridization experiments revealed a low level of DNA–DNA relatedness (less than 24 %) between strain MUSC 115T and the type strains of closely related species. Furthermore, BOX-PCR fingerprint comparison also indicated that strain MUSC 115T represented a unique DNA profile. The DNA G+C content determined was 70.9±0.7 mol%, which is lower than that of M. immunditiarum SK 18T. Based on the combination of genotypic and phenotypic data, it is proposed that strain MUSC 115T represents a novel species of the genus Microbacterium , for which the name Microbacterium mangrovi sp. nov. is proposed. The type strain is MUSC 115T ( = MCCC 1K00251T = DSM 28240T = NBRC 110089T).


2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 934-938 ◽  
Author(s):  
Wen-Ming Chen ◽  
Rey-Chang Chang ◽  
Chih-Yu Cheng ◽  
Yu-Wen Shiau ◽  
Shih-Yi Sheu

A novel bacterium, designated strain JchiT, was isolated from soil in Taiwan and characterized using a polyphasic approach. Cells of strain JchiT were aerobic, Gram-stain-negative, motile and rod-shaped. They contained poly-β-hydroxybutyrate granules and formed dark-yellow colonies. Growth occurred at 20–37 °C (optimum between 25 and 30 °C), at pH 6.0–8.0 (optimum between pH 7.0 and pH 8.0) and with 0–2 % NaCl (optimum between 0 and 1 %). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain JchiT belonged to the genus Jeongeupia and that its closest neighbour was Jeongeupia naejangsanensis BIO-TAS4-2T (98.0 % sequence similarity). The major fatty acids (>10 %) of strain JchiT were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c. The major cellular hydroxy fatty acid was C12 : 0 3-OH. The isoprenoid quinone was Q-8 and the genomic DNA G+C content was 66.1 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylserine and two unidentified phospholipids. The DNA–DNA relatedness value between strain JchiT and J. naejangsanensis BIO-TAS4-2T was about 41.0 %. On the basis of the genotypic and phenotypic data, strain JchiT represents a novel species in the genus Jeongeupia , for which the name Jeongeupia chitinilytica sp. nov. is proposed. The type strain is JchiT ( = BCRC 80367T  = KCTC 23701T).


Author(s):  
Fenfa Li ◽  
Qingyi Xie ◽  
Shuangqing Zhou ◽  
Fandong Kong ◽  
Yun Xu ◽  
...  

Strain HNM0947T, representing a novel actinobacterium, was isolated from the coral Galaxea astreata collected from the coast of Wenchang, Hainan, China. The strain was found to have morphological and chemotaxonomic characteristics consistent with the genus Nocardiopsis . The organism formed abundant fragmented substrate mycelia and aerial mycelia which differentiated into non-motile, rod-shaped spores. Whole-cell hydrolysates contained meso-diaminopimelic acid and no diagnostic sugars. The major menaquinones were MK-10(H8), MK-10(H6) and MK-10(H4). The major phospholipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The major fatty acids were iso-C16:0, anteiso-C17:0, C18:0, C18:0 10-methyl (TBSA) and anteiso-C15:0. The G+C content was 71.3 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain HNM0947T belonged to the genus Nocardiopsis and shared highest sequence similarity to Nocardiopsis salina YIM 90010T (98.8%), Nocardiopsis xinjiangensis YIM 90004T(98.5%) and Nocardiopsis kunsanensis DSM 44524T (98.3%). The strain HNM0947T was distinguished from its closest type strain by low average nucleotide identity (90.8%) and dDDH values (60.4%) respectively. Based on genotypic, chemotaxonomic and phenotypic characteristics, it was concluded that strain HNM0947T represents a novel species of the genus Nocardiopsis whose name was proposed as Nocardiopsis coralli sp. nov. The type strain was HNM0947T (=CCTCC AA 2020015 T=KCTC 49525 T).


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