Pectobacterium aroidearum sp. nov., a soft rot pathogen with preference for monocotyledonous plants

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2520-2525 ◽  
Author(s):  
Shaza Nabhan ◽  
Solke H. De Boer ◽  
Edgar Maiss ◽  
Kerstin Wydra
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Analyses ◽  
Content Type

Several pectolytic bacterial strains, mainly isolated from monocotyledonous plants and previously identified as Pectobacterium carotovorum , were thought to belong to a novel species after several taxonomic analyses including DNA–DNA hybridization. In 16S rRNA gene sequence analyses, these strains had a similarity of >97.9 % to the 16S rRNA gene sequence of strains representing six other pectobacterial species and subspecies. These strains, represented by strain SCRI 109T, also showed some unique chemotaxonomic features and quantitative differences in polar lipids, lipoquinones and fatty acids. A specific feature of strain SCRI 109T was the presence of DMK-8 lipoquinone, while the dominant fatty acids were the summed feature 3 (iso-C15 : 0 2-OH/C16 : 1ω7c), the unsaturated fatty acid C18 : 1ω7c and straight chain fatty acids, mainly C16 : 0. The DNA G+C content of strain SCRI 109T was 50.2 mol%. The taxonomic status of strain SCRI 109T and related strains in 16S rRNA gene sequence, chemotaxonomic, and physiological analyses was corroborated by the distinct clustering of these strains in multi-locus sequence analyses. It is proposed that these strains represent a novel species for which the name Pectobacterium aroidearum sp. nov. is proposed; the type strain is SCRI 109T ( = NCPPB 929T = LMG 2417T = ICMP 1522T).

scholarly journals Coinfection of Dermacentor silvarum Olenev (Acari: Ixodidae) by Coxiella-Like, Arsenophonus-Like, and Rickettsia-Like Symbionts

2013 ◽  
Vol 79 (7) ◽  
pp. 2450-2454 ◽  
Author(s):  
Limeng Liu ◽  
Lingxia Li ◽  
Jiannan Liu ◽  
Yonghong Hu ◽  
Zhao Liu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Analyses ◽  
Content Type

ABSTRACTWe report that multiple symbionts coexist inDermacentor silvarum. Based on 16S rRNA gene sequence analyses, we prove thatCoxiella-like andArsenophonus-like symbionts, with 95.6% and 96.7% sequence similarity to symbionts in the closest taxon, respectively, are novel. Moreover, we also provide evidence that theCoxiella-like symbiont appears to be the primary symbiont.

scholarly journals Roseovarius bejariae sp. nov., a moderately halophilic bacterium isolated from a hypersaline steep-sided river bed

2020 ◽  
Vol 70 (5) ◽  
pp. 3194-3201 ◽  
Author(s):  
David J. Castro ◽  
Andreina Gomez-Altuve ◽  
José Carlos Reina ◽  
Miguel Rodríguez ◽  
Inmaculada Sampedro ◽  
...  
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Moderately Halophilic Bacterium

An aerobic, Gram-stain-negative ovoid, designated as strain A21T, was isolated using the dilution-to-extinction method from a soil sample taken from Rambla Salada, an athalassohaline habitat located in Murcia (south-eastern Spain). Strain A21T is non-motile, has a respiratory metabolism and grows at NaCl concentrations within the range 0.5–15 % (w/v) [optimum, 5 % (w/v)], at 5–35 °C (optimum, 28 °C) and at pH 6–8 (optimum, pH 7.0). This strain is positive for catalase activity, oxidase activity and nitrate reduction. The 16S rRNA gene sequence indicates that it belongs to the genus Roseovarius in the class Alphaproteobacteria . The most closely related species are Roseovarius pacificus and Roseovarius halotolerans to which the strain A21T shows 16S rRNA gene sequence similarity values of 98.06 and 97.7 %, respectively. The average nucleotide identity in blast and digital DNA–DNA hybridization values between strain A21T and R. pacificus LMG 24575T are 76.8 and 21 %, respectively. The DNA G+C content based on the genome is 61.28 mol%. The major fatty acids (>5 % of the total fatty acids) of strain A21T are C18 : 1 ω7c/C18 : 1 ω6c and C16 : 0. The only detected isoprenoid quinone in strain A21T is ubiquinone 10 (Q-10). The polar lipid profile contains phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and three unidentified polar lipids. Based on the phylogenetic, genotypic, phenotypic and chemotaxonomic data, the strain represents a novel species of the genus Roseovarius , for which the name Roseovarius bejariae sp. nov. is proposed. Strain A21T (=CECT 9817T=LMG 31311T) is the type strain.

Duganella sacchari sp. nov. and Duganella radicis sp. nov., two novel species isolated from rhizosphere of field-grown sugar cane

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1126-1131 ◽  
Author(s):  
M. Madhaiyan ◽  
S. Poonguzhali ◽  
V. S. Saravanan ◽  
K. Hari ◽  
K.-C. Lee ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis

Two strains, designated Sac-22T and Sac-41T, were isolated from rhizosphere soil and rhizoplane of field-grown sugar cane clone Co86032. Comparative 16S rRNA gene sequence analysis showed a clear affiliation of these two bacteria with the class Betaproteobacteria , their closest relatives being Pseudoduganella violaceinigra and Duganella zoogloeoides with 16S rRNA gene sequence pairwise similarities of 96.4–97.2 % to the two novel strains. Strains Sac-22T and Sac-41T shared a 16S rRNA gene sequence similarity value of 97.6 %. Cells of the two strains were Gram-reaction-negative, aerobic, motile and rod-shaped. Ubiquinone (Q-8) was the respiratory quinone and the predominant polar lipids consisted of phosphatidylglycerol and phosphatidylethanolamine. The main cellular fatty acids were C16 : 0, C16 : 1ω7c/iso-C15 : 0 2-OH, C17 : 0 cyclo, C10 : 0 3-OH and C12 : 0. The DNA G+C content of the genomic DNA was 56.4 mol% for strain Sac-22T and 54.9 mol% for strain Sac-41T. Based on the results of 16S rRNA gene sequence analysis and physiological and biochemical characterization, that differentiated strains Sac-22T and Sac-41T from all recognized species of the genus Duganella , it was concluded that strains represent two novel species in the genus Duganella for which the names Duganella sacchari sp. nov. (type strain Sac-22T = KCTC 22381T = NCIMB 14475T) and Duganella radicis sp. nov. (type strain Sac-41T = KCTC 22382T = NCIMB 14476T) are proposed.

scholarly journals Proposal of Intrasporangium mesophilum sp. nov., and reclassification of Humihabitans oryzae Kageyama et al. 2007 as Intrasporangium oryzae comb. nov.

2012 ◽  
Vol 62 (Pt_5) ◽  
pp. 1037-1041 ◽  
Author(s):  
Ling-Ling Yang ◽  
Tao Ao ◽  
Xing-Hong Wang ◽  
Jie He ◽  
Hans-Peter Klenk ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

A Gram-positive and aerobic bacterium, designated strain YIM 49065T, was isolated from rhizospheric soil of Jatropha curcas in Yunnan, China. This isolate formed branched and fragmented mycelia containing ll-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The major cellular fatty acid profile was characterized by iso-C14 : 0, iso-C15 : 0 and iso-C16 : 0, and the predominant menaquinone was MK-8(H4). The DNA G+C content was 69.6 mol%. A phylogenetic analysis based on 16S rRNA gene sequence demonstrated that strain YIM 49065T was closely associated with Intrasporangium calvum DSM 43043T and Humihabitans oryzae KV-657T, exhibiting 98.8 % and 98.6 % 16S rRNA gene sequence similarities, respectively. Furthermore, DNA–DNA hybridizations among strains YIM 49065T, I. calvum DSM 43043T and H. oryzae DSM 22331T indicated that this isolate represented a novel species in the genus Intrasporangium . On the basis of these data, we proposed one novel species, Intrasporangium mesophilum sp. nov., for strain YIM 49065T ( = DSM 23217T  = CCTCC AA 209077T). Additionally, the comparison of biochemical and phylogenetic characters supported the reclassification of Humihabitans oryzae as a separate species within the genus Intrasporangium , Intrasporangium oryzae comb. nov. (type strain KV-657T  = JCM 15924T  = NBRC 101802T  = NRRL B-24470T).

Exiguobacterium aquaticum sp. nov., a member of the genus Exiguobacterium

2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2150-2155 ◽  
Author(s):  
Revti Raichand ◽  
Siddhika Pareek ◽  
Nitin Kumar Singh ◽  
Shanmugam Mayilraj
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

A Gram-positive, motile, short rod-shaped, orange pigmented bacterium, designated strain IMTB-3094T, was isolated from a water sample collected from Tikkar Tal Lake, Haryana, and subjected to detailed polyphasic taxonomic analysis. Strain IMTB-3094T possessed most of the phenotypic and chemotaxonomic properties of the genus Exiguobacterium and, based on 16S rRNA gene sequence analysis, was assigned to this genus. Strain IMTB-3094T exhibited the highest 16S rRNA gene sequence similarity to Exiguobacterium mexicanum MTCC 7759T (99.5 %) followed by Exiguobacterium aurantiacum MTCC 6414T (99.1 %), Exiguobacterium aestuarii MTCC 7750T (98.0 %), Exiguobacterium profundum MTCC 10851T (98.0 %) and Exiguobacterium marinum MTCC 7751T (98.0 %). The G+C content of the genomic DNA of strain IMTB-3094T was 53.2 mol% and a DNA–DNA relatedness study confirmed that it represents a novel species. The major fatty acids of strain IMTB-3094T were iso-C17 : 0 (16.1 %), anteiso-C13 : 0 (19.0 %), iso-C13 : 0 (11.9 %), iso-C15 : 0 (9.8 %) and iso-C17 : 1 (12.7 %). The predominant quinones were MK-7 (55.0 %) and MK-6 (26.0 %) with minor amounts of MK-8 (12.0 %). Based on phenotypic, chemotaxonomic and phylogenetic analyses, strain IMTB-3094T represents a novel species of the genus Exiguobacterium , for which the name Exiguobacterium aquaticum sp. nov. is proposed. The type strain is IMTB-3094T ( = MTCC 10958T  = JCM 17977T).

Plasticicumulans lactativorans sp. nov., a polyhydroxybutyrate-accumulating gammaproteobacterium from a sequencing-batch bioreactor fed with lactate

2014 ◽  
Vol 64 (Pt_1) ◽  
pp. 33-38 ◽  
Author(s):  
Yang Jiang ◽  
Dimitry Y. Sorokin ◽  
Helena Junicke ◽  
Robbert Kleerebezem ◽  
Mark C. M. van Loosdrecht
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Polar Lipids ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

A bacterial consortium that accumulated more than 90 % (w/w) polyhydroxybutyrate (PHB) from lactate was selected in a laboratory-scale bioreactor with a ‘feast–famine’ regime. Bacterial strain YDT, representing a dominant species in this enrichment, was isolated and characterized. Analysis of the 16S rRNA gene sequence revealed that the isolate is a member of the class Gammaproteobacteria , forming an independent phylogenetic lineage. The closest relative of the isolate was Plasticicumulans acidivorans TUD-YJ37T, with 94 % 16S rRNA gene sequence similarity. Strain YDT was an obligate aerobe with large, ovoid, Gram-negative cells, motile by means of a polar flagellum. It utilized a relatively broad spectrum of substrates (e.g. carbohydrates, fatty acids) as carbon and energy sources. The temperature range for growth was 20–45 °C, with an optimum at 40 °C; the pH range was pH 6.0–8.0, with an optimum at pH 7.0. The major respiratory lipoquinones were Q-8 (91 %) and Q-7 (9 %). The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine and an unidentified aminolipid. The predominant fatty acids in the membrane polar lipids were C16 : 1ω7c, C16 : 0 and C18 : 1ω7c. The G+C content of the genomic DNA was 68.5 mol%. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, the isolate is proposed to represent a novel species in the genus Plasticicumulans , for which the name Plasticicumulans lactativorans sp. nov. is proposed. The type strain is YDT ( = DSM 25287T = NCCB 100398T).

scholarly journals Qingshengfania soli gen. nov., sp. nov., a member of the order Rhizobiales isolated from the soil of a pesticide factory

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4608-4614 ◽  
Author(s):  
Long Zhang ◽  
Qing-Xin Zhou ◽  
Man Song ◽  
Xiao-Long Chen ◽  
Xi-Hui Xu ◽  
...  
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons

Two Gram-stain negative, coccoid to oval-shaped, non-spore-forming bacteria (LR4T and LR4-1), isolated from the soil of a pesticide factory in Nanjing, China, were investigated for their taxonomic allocation by using a polyphasic approach. Both strains grew optimally at pH 7.0, 30 °C and in the absence of NaCl. Both strains were positive for catalase and oxidase activities. Q-10 was the predominant respiratory ubiquinone. The major polar lipids were phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and two unknown aminolipids. The major fatty acids (>10 % of the total fatty acids) were C18:1ω7c/C18:1ω6c (summed feature 8) and C17:1 iso I/C17:1 anteiso B (summed feature 4). Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the two isolates formed a distinct line within a clade containing the genera Chelatococcus, Bosea, Camelimonas, Salinarimonas, Psychroglaciecola, Microvirga, Methylobacterium, Albibacter, Hansschlegelia and Methylopila in the order Rhizobiales, with the highest 16S rRNA gene sequence similarity to Chelatococcus asaccharovorans TE2T (94.12 %), followed by Bosea thiooxidans DSM 9653T (93.25 %). Strains LR4T and LR4-1 were closely related on the basis of DNA–DNA reassociation and therefore represent a single novel species. Based on phenotypic, chemotaxonomic and phylogenetic data, strains LR4T and LR4-1 represent a novel species of a new genus in the order Rhizobiales, for which the name Qingshengfania soli gen. nov., sp. nov. is proposed. The type strain of the type species is LR4T ( = CCTCC AB 2015036T = KCTC 42463T).

scholarly journals Sphingorhabdus lacus sp. nov. and Sphingorhabdus profundilacus sp. nov., isolated from freshwater environments

2020 ◽  
Vol 70 (5) ◽  
pp. 3202-3209 ◽  
Author(s):  
Miri Park ◽  
Ilsuk Jung ◽  
Jaeho Song ◽  
Jang-Cheon Cho
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Two Gram-stain-negative, aerobic, non-motile bacteria, designated IMCC1753T and IMCC26285T, were isolated from a shallow eutrophic pond and a deep oligotrophic lake, respectively. Results of 16S rRNA gene sequence analysis indicated that the two strains shared 99.8 % sequence similarity and were most closely related to Sphingorhabdus contaminans JC216T(98.7–98.8 %). The whole genome sequences of strains IMCC1753T and IMCC26285T were 3.5 and 2.9 Mbp in size with 56.6 and 55.5 mol% DNA G+C content, respectively. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the two strains were 82.2 and 25.8 %, respectively, indicating that they are separate species. The two strains showed ≤98.8 % 16S rRNA gene sequence similarities and ≤82.2 % ANI and ≤28.7 % dDDH values to closely related species of the genus Sphingorhabdus , indicating that the two strains each represent novel species. Major fatty acid constituents of strain IMCC1753T were C17 : 1  ω6c, C17 : 1  ω8c and summed features 3 (C16 : 1  ω6c and/or C16 : 1  ω7c) and 8 (C18 : 1  ω6c and/or C18 : 1  ω7c); those of strain IMCC26285T were summed features 3 and 8. The predominant isoprenoid quinone detected in both strains was ubiquinone-10 and the most abundant polyamine was spermidine. Both strains contained phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol and sphingoglycolipid as major polar lipids. On the basis of the phylogenetic and phenotypic characteristics, strains IMCC1753T and IMCC26285T were considered to represent two distinct novel species in the genus Sphingorhabdus , for which the names Sphingorhabdus lacus (IMCC1753T=KCTC 52480T=KACC 18985T=NBRC 112442T) and Sphingorhabdus profundilacus (IMCC26285T=KCTC 52479T=KACC 18986T=NBRC 112454T) are proposed, respectively.

scholarly journals Faecalicoccus acidiformans gen. nov., sp. nov., isolated from the chicken caecum, and reclassification of Streptococcus pleomorphus (Barnes et al. 1977), Eubacterium biforme (Eggerth 1935) and Eubacterium cylindroides (Cato et al. 1974) as Faecalicoccus pleomorphus comb. nov., Holdemanella biformis gen. nov., comb. nov. and Faecalitalea cylindroides gen. nov., comb. nov., respectively, within the family Erysipelotrichaceae

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3877-3884 ◽  
Author(s):  
Celine De Maesschalck ◽  
Filip Van Immerseel ◽  
Venessa Eeckhaut ◽  
Siegrid De Baere ◽  
Margo Cnockaert ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Strains LMG 27428T and LMG 27427 were isolated from the caecal content of a chicken and produced butyric, lactic and formic acids as major metabolic end products. The genomic DNA G+C contents of strains LMG 27428T and LMG 27427 were 40.4 and 38.8 mol%. On the basis of 16S rRNA gene sequence similarity, both strains were most closely related to the generically misclassified Streptococcus pleomorphus ATCC 29734T. Strain LMG 27428T could be distinguished from S. pleomorphus ATCC 29734T based on production of more lactic acid and less formic acid in M2GSC medium, a higher DNA G+C content and the absence of activities of acid phosphatase and leucine, arginine, leucyl glycine, pyroglutamic acid, glycine and histidine arylamidases, while strain LMG 27428 was biochemically indistinguishable from S. pleomorphus ATCC 29734T. The novel genus Faecalicoccus gen. nov. within the family Erysipelotrichaceae is proposed to accommodate strains LMG 27428T and LMG 27427. Strain LMG 27428T ( = DSM 26963T) is the type strain of Faecalicoccus acidiformans sp. nov., and strain LMG 27427 ( = DSM 26962) is a strain of Faecalicoccus pleomorphus comb. nov. (type strain LMG 17756T = ATCC 29734T = DSM 20574T). Furthermore, the nearest phylogenetic neighbours of the genus Faecalicoccus are the generically misclassified Eubacterium cylindroides DSM 3983T (94.4 % 16S rRNA gene sequence similarity to strain LMG 27428T) and Eubacterium biforme DSM 3989T (92.7 % 16S rRNA gene sequence similarity to strain LMG 27428T). We present genotypic and phenotypic data that allow the differentiation of each of these taxa and propose to reclassify these generically misnamed species of the genus Eubacterium formally as Faecalitalea cylindroides gen. nov., comb. nov. and Holdemanella biformis gen. nov., comb. nov., respectively. The type strain of Faecalitalea cylindroides is DSM 3983T = ATCC 27803T = JCM 10261T and that of Holdemanella biformis is DSM 3989T = ATCC 27806T = CCUG 28091T.

scholarly journals Kaistia terrae sp. nov., isolated from a wetland in Korea

2010 ◽  
Vol 60 (4) ◽  
pp. 949-952 ◽  
Author(s):  
Soo-Jin Kim ◽  
Hang-Yeon Weon ◽  
Yi-Seul Kim ◽  
Rangasamy Anandham ◽  
Seung-Hee Yoo ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

An ivory-coloured bacterium, designated strain 5YN7-3T, was isolated from a wetland, Yongneup, Korea. Cells of the strain were aerobic, Gram-stain-negative, non-motile and short rods. 16S rRNA gene sequence analysis demonstrated that strain 5YN7-3T belongs to the order Rhizobiales of the class Alphaproteobacteria and is closely related to Kaistia soli 5YN9-8T (97.8 %), Kaistia granuli Ko04T (97.6 %) and Kaistia adipata Chj404T (97.4 %). Strain 5YN7-3T showed DNA–DNA hybridization values of 28, 22 and 35 % with K. granuli Ko04T, K. soli 5YN9-8T and K. adipata Chj404T, respectively. The major fatty acids were C18 : 1 ω7c (51.2 %), C19 : 0 cyclo ω8c (25.0 %), C18 : 0 (12.9 %) and C16 : 0 (10.8 %) (>10 % of total fatty acids). Ubiquinone-10 was the major isoprenoid quinone and the DNA G+C content was 66.5 mol%. The phenotypic characteristics in combination with 16S rRNA gene sequence analysis and DNA–DNA hybridization data clearly define strain 5YN7-3T as a novel species of the genus Kaistia, for which the name Kaistia terrae sp. nov. is proposed. The type strain is 5YN7-3T (=KACC 12910T =DSM 21341T).

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