Shewanella dokdonensis sp. nov., isolated from seawater

2012 ◽  
Vol 62 (Pt_7) ◽  
pp. 1636-1643 ◽  
Author(s):  
Hye-Ri Sung ◽  
Jung-Hoon Yoon ◽  
Sa-Youl Ghim
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type ◽  
Gram Staining ◽  
The Republic

A novel bacterial strain, designated UDC329T, was isolated from a sample of seawater collected at Dong-do, on the coast of Dokdo Island, in the East Sea of the Republic of Korea. The Gram-staining-negative, motile, facultatively anaerobic, non-spore-forming rods of the strain developed into dark orange–yellow colonies. The strain grew optimally between 25 and 30 °C, with 1 % (w/v) NaCl and at pH 7. It grew in the absence of NaCl, but not with NaCl at >7 % (w/v). The predominant menaquinone was MK-7, the predominant ubiquinones were Q-7 and Q-8, and the major fatty acids were iso-C15 : 0 (33.52 %) and C17 : 1ω8c (11.73 %). The genomic DNA G+C content of strain UDC329T was 50.2 mol%. In phylogenetic analyses based on 16S rRNA and gyrB gene sequences, strain UDC329T was grouped with members of the genus Shewanella and appeared most closely related to Shewanella fodinae JC15T (97.9 % 16S rRNA gene sequence similarity), Shewanella indica KJW27T (95.0 %), Shewanella algae ATCC 51192T (94.8 %), Shewanella haliotis DW01T (94.5 %) and Shewanella chilikensis JC5T (93.9 %). The level of DNA–DNA relatedness between strain UDC329T and S. fodinae JC15T was, however, only 27.4 %. On the basis of phenotypic, genotypic and DNA–DNA relatedness data, strain UDC329T represents a novel species in the genus Shewanella , for which the name Shewanella dokdonensis sp. nov. is proposed. The type strain is UDC329T ( = KCTC 22898T = DSM 23626T).

scholarly journals Frigoribacterium endophyticum sp. nov., an endophytic actinobacterium isolated from the root of Anabasis elatior (C. A. Mey.) Schischk

2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1207-1212 ◽  
Author(s):  
Hong-Fei Wang ◽  
Yong-Guang Zhang ◽  
Ji-Yue Chen ◽  
Jian-Wei Guo ◽  
Li Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type ◽  
Endophytic Actinobacterium

A novel endophytic actinobacterium, designated EGI 6500707T, was isolated from the surface-sterilized root of a halophyte Anabasis elatior (C. A. Mey.) Schischk collected from Urumqi, Xinjiang province, north-west China, and characterized using a polyphasic approach. Cells were Gram-stain-positive, non-motile, short rods and produced white colonies. Growth occurred at 10–45 °C (optimum 25–30 °C), at pH 5–10 (optimum pH 8) and in presence of 0–4 % (w/v) NaCl (optimum 0–3 %). The predominant menaquinone was MK-9. The diagnostic phospholipids were diphosphatidylglycerol and phosphatidylglycerol. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The DNA G+C content of strain EGI 6500707T was 69.1 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain EGI 6500707T should be placed in the genus Frigoribacterium (family Microbacteriaceae , phylum Actinobacteria ), and that the novel strain exhibited the highest 16S rRNA gene sequence similarity to Frigoribacterium faeni JCM 11265T (99.1 %) and Frigoribacterium mesophilum MSL-08T (96.5 %). DNA–DNA relatedness between strain EGI 6500707T and F. faeni JCM 11265T was 47.2 %. On the basis of phenotypic and chemotaxonomic characteristics, phylogenetic analysis and DNA–DNA relatedness data, strain EGI 6500707T represents a novel species of the genus Frigoribacterium , for which the name Frigoribacterium endophyticum sp. nov. is proposed. The type strain is EGI 6500707T ( = JCM 30093T = KCTC 29493T).

Deinococcus humi sp. nov., isolated from soil

2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 2844-2850 ◽  
Author(s):  
Sathiyaraj Srinivasan ◽  
Jae-Jin Lee ◽  
Sangyong Lim ◽  
Minho Joe ◽  
Myung Kyum Kim
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type ◽  
Gram Staining

A Gram-staining-positive, strictly aerobic, spherical, non-motile, red-pigmented bacterium, designated strain MK03T, was isolated from a soil sample collected in South Korea. The taxonomic position of the novel strain was investigated using a polyphasic approach. In phylogenetic analyses based on 16S rRNA gene sequences, strain MK03T was placed in a clade formed by members of the genus Deinococcus in the family Deinococcaceae and appeared to be most closely related to Deinococcus aerolatus 5516T-9T (97.4 % sequence similarity), Deinococcus marmoris AA-63T (97.2 %), Deinococcus radiopugnans ATCC 19172T (97.2 %) and Deinococcus saxicola AA-1444T (96.9 %). The genomic DNA G+C content of the novel strain was 64.5 mol%. The chemotaxonomic characteristics of strain MK03T were typical of members of the genus Deinococcus : MK-8 was identified as the predominant respiratory quinine, the major fatty acids were C16 : 1ω7c, C15 : 1ω6c, C16 : 0 and C15 : 0, ornithine was found to be the diamino acid in the cell-wall peptidoglycan and the novel strain showed resistance to gamma radiation, with a D10 value (i.e. the dose required to reduce the bacterial population by 10-fold) in excess of 9 kGy. In hybridization experiments, only low DNA–DNA relatedness values (11.6–34.5 %) were recorded between the novel strain and its closest relatives in the genus Deinococcus . Based on the phylogenetic, chemotaxonomic, phenotypic and DNA–DNA relatedness data, strain MK03T represents a novel species of the genus Deinococcus , for which the name Deinococcus humi sp. nov. is proposed. The type strain is MK03T ( = KCTC 13619T  = JCM 17915T).

Chryseobacterium viscerum sp. nov., isolated from diseased fish

2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 2934-2940 ◽  
Author(s):  
L. Zamora ◽  
A. I. Vela ◽  
M. A. Palacios ◽  
C. Sánchez-Porro ◽  
L. A. Svensson-Stadler ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type ◽  
Gram Staining

A taxonomic study was carried out on five Gram-staining-negative, catalase- and oxidase-positive, rod-shaped bacteria isolated from the gills and livers of five diseased rainbow trout. The five novel isolates were designated strains 687B-08T, 445-08, 452-08, 453B-08 and 967B-08. In phylogenetic analyses based on 16S rRNA gene sequences, the five novel strains appeared almost identical (99.0–100 % sequence similarity) and to belong to the genus Chryseobacterium . Strain 687B-08T (the strain selected to represent the five novel isolates) was found to be most closely related to Chryseobacterium oncorhynchi 701B-08T (98.9 % sequence similarity), Chryseobacterium ureilyticum F-Fue-04IIIaaaaT (98.6 %), Chryseobacterium indologenes ATCC 29897T (98.3 %), Chryseobacterium jejuense JS17-8T (98.1 %) and Chryseobacterium gleum ATCC 35910T (98.1 %). In DNA–DNA hybridizations, DNA–DNA relatedness values of 99–100 % were recorded between the five novel strains. Lower DNA–DNA relatedness values (21–57 %) were recorded between strain 687B-08T and C. oncorhynchi 701B-08T, C. ureilyticum F-Fue-04IIIaaaaT and the type strains of other closely related, established species of the genus Chryseobacterium . The predominant respiratory quinone of strain 687B-08T was MK-6 and the major cellular fatty acids were iso-C15 : 0, iso-C17 : 1ω9c, iso-C17 : 0 3-OH and C16 : 1ω6c. The G+C content of the genomic DNA of strain 687B-08T was 38.6 mol%. Based on the phenotypic and genotypic evidence, the five novel strains isolated from rainbow trout represent a single, novel species of the genus Chryseobacterium , for which the name Chryseobacterium viscerum sp. nov. is proposed. The type strain is 687B-08T ( = CECT 7793T  = CCUG 60103T).

scholarly journals Planomicrobium soli sp. nov., isolated from soil

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2700-2705 ◽  
Author(s):  
Xiaonan Luo ◽  
Jianli Zhang ◽  
Dai Li ◽  
Yuhua Xin ◽  
Di Xin ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Morphological Properties ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gram Staining

A Gram-staining-positive bacterium, designated strain XN13T, was isolated from a soil sample collected from ALaShan National Geological Park in Inner Mongolia Autonomous Region, China and subjected to a taxonomic study using a polyphasic approach. Strain XN13T was found to have a range of chemical and morphological properties consistent with its classification in the genus Planomicrobium . Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain XN13T was related to members of the genus Planomicrobium . The closest phylogenetic relatives were Planomicrobium okeanokoites NBRC 12536T, Planomicrobium koreense JG07T, Planomicrobium mcmeekinii S23F2T and Planomicrobium flavidum ISL-41T with 98.2 %, 97.8 %, 97.8 % and 97.7 % 16S rRNA gene sequence similarity, respectively. The major cellular fatty acids were anteiso-C15 : 0, C16 : 1ω7c alcohol, iso-C14 : 0 and C16 : 1ω11c. The predominant menaquinones were MK-8 and MK-7. The DNA G+C content was 40.3 mol%. The DNA–DNA relatedness values between strain XN13T and Planomicrobium okeanokoites KCTC 3672T, Planomicrobium koreense KCTC 3684T, P. mcmeekinii CGMCC 1.2724T, Planomicrobium flavidum KCTC 13261T, Planomicrobium chinense CGMCC 1.3454T and Planomicrobium glaciei CGMCC 1.6846T were 36 %, 30 %, 34 %, 29 %, 30 % and 31 %, respectively. The organism is different from recognized species of the genus Planomicrobium in several phenotypic characteristics. On the basis of phenotypic and genotypic properties, strain XN13T represents a novel species of the genus Planomicrobium , for which the name Planomicrobium soli sp. nov. is proposed. The type strain is XN13T ( = CGMCC 1.12259T = KCTC 33047T).

Mariniflexile maritimum sp. nov., isolated from seawater of the South Sea in the Republic of Korea

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
So-Ra Ko ◽  
Ve Van Le ◽  
Long Jin ◽  
Sang-Ah Lee ◽  
Chi-Yong Ahn ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Republic Of Korea ◽  
Rrna Gene ◽  
The South ◽  
Content Type ◽  
Link Type ◽  
South Sea ◽  
The Republic

A novel Gram-stain-negative, rod-shaped, aerobic, non-motile bacterial strain, designated M5A1MT, was isolated from seawater collected from the South Sea of the Republic of Korea. Based on 16S rRNA gene sequence similarity, strain M5A1MT was closely related to Mariniflexile gromovii KMM 6038T (95.3 %), Mariniflexile fucanivorans SW5T (95.2 %), Mariniflexile soesokkakense RSSK-9T (95.1 %), Yeosuana aromativorans GW1-1T (94.6 %) and Confluentibacter lentus HJM-3T (94.6 %). Genome-based phylogenetic analyses revealed that strain M5A1MT formed a distinct cluster with the type strains of the genus Mariniflexile . The major cellular fatty acid constituents (>5 % of the total fatty acids) were iso-C15:0, anteiso-C15 : 0, iso-C15 : 0 3-OH, iso-C15 : 1 G, iso-C16:03-OH and iso-C17 : 0 3-OH. The respiratory quinone was identified as MK-6. The major polar lipids were phosphatidylethanolamine and one unidentified polar lipid. The genomic DNA G+C content of strain M5A1MT was determined to be 37.7 mol%. On the basis of its phenotypic, phylogenetic and chemotaxonomic characteristics, strain M5A1MT is considered to represent a novel species within the genus Mariniflexile , for which the name Mariniflexile maritimum sp. nov. is proposed. The type strain is M5A1MT (=KCTC 72895T=JCM 33982T).

Namhaeicola litoreus gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from seawater

2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2163-2168 ◽  
Author(s):  
Yong-Taek Jung ◽  
Ji-Hoon Kim ◽  
So-Jung Kang ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Type Strains

A Gram-staining-negative, non-flagellated, non-gliding and pleomorphic bacterial strain, designated DPG-25T, was isolated from seawater in a seaweed farm in the South Sea in Korea and its taxonomic position was investigated by using a polyphasic approach. Strain DPG-25T grew optimally at 25 °C, at pH 7.0–7.5 and in the presence of 2 % (w/v) NaCl. Flexirubin-type pigments were not produced. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DPG-25T formed a cluster with the type strains of Actibacter sediminis , Aestuariicola saemankumensis and Lutimonas vermicola . Strain DPG-25T exhibited 16S rRNA gene sequence similarity values of 95.3, 93.1 and 93.6 % to the type strains of Actibacter sediminis , Aestuariicola saemankumensis and L. vermicola , respectively. Strain DPG-25T contained MK-6 as the predominant menaquinone and iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids detected in strain DPG-25T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content was 39.9 mol%. Differential phenotypic properties and the phylogenetic distinctiveness of strain DPG-25T demonstrated that this strain is distinguishable from Actibacter sediminis , Aestuariicola saemankumensis and L. vermicola . On the basis of the data presented here, strain DPG-25T represents a novel species in a novel genus of the family Flavobacteriaceae , for which the name Namhaeicola litoreus gen. nov., sp. nov. is proposed. The type strain of Namhaeicola litoreus is DPG-25T ( = KCTC 23702T  = CCUG 61485T).

scholarly journals Elioraea rosea sp. nov., a plant promoting bacterium isolated from floodwater of a paddy field

2020 ◽  
Vol 70 (3) ◽  
pp. 2132-2136 ◽  
Author(s):  
Hyo-Jin Lee ◽  
Kyung-Sook Whang
Keyword(s):  
Paddy Field ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Phenotypic Data ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type

A Gram-stain-negative bacterium, designated strain PF-30T, was isolated from floodwater of a paddy field in South Korea. Strain PF-30T was found to be a strictly aerobic, motile and pink-pigmented rods which can grow at 25–40 °C (optimum, 28 °C), at pH 5.0–9.0 (optimum pH 7.0) and at salinities of 0.5–3.0 % NaCl (optimum 0.5 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain PF-30T belongs to the genus Elioraea , showing highest sequence similarity to Elioraea tepidiphila TU-7T (97.1%) and less than 91.3 % similarity with other members of the family Acetobacteraceae . The average nucleotide identity (ANI) and DNA–DNA relatedness between the strain PF-30T and E. tepidiphila TU-7T yielded an ANI value of 75.1 % and DNA–DNA relatedness of 11.7±0.7 %, respectively. The major fatty acids were identified as C18 : 0 and C18 : 1 ω7c. The predominant respiratory quinone was identified as Q-10. The DNA G+C content was determined to be 69.9 mol%. The strain PF-30T was observed to produce plant-growth-promoting materials such as indole-3-acetic acid (IAA), siderophore and phytase. On the basis of the results from phylogenetic, chemotaxonomic and phenotypic data, we concluded that strain PF-30T represents a novel species of the genus Elioraea , for which the name Elioraea rosea sp. nov. is proposed. The type strain is PF-30T (=KACC 19985T=NBRC 113984T).

Luteimonas deserti sp. nov., a novel strain isolated from desert soil

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Xiao-Xian Huang ◽  
Jia Shang ◽  
Lian Xu ◽  
Rui Yang ◽  
Ji-Quan Sun
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Desert Soil ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, non-motile, rod-shaped bacterial strain, named SJ-16T, was isolated from desert soil collected in Inner Mongolia, northern PR China. Strain SJ-16T grew at pH 6.0–11.0 (optimum, pH 8.0–9.0), 4–40 °C (optimum, 30–35 °C) and in the presence of 0–8 % (w/v) NaCl (optimum, 0–2 %). The strain was negative for catalase and positive for oxidase. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SJ-16T clustered with Luteimonas chenhongjianii 100111T and Luteimonas terrae THG-MD21T, and had 98.8, 98.6, 98.3 and <97.9 % of 16S rRNA gene sequence similarity to strains L. chenhongjianii 100111T, L. terrae THG-MD21T, L. aestuarii B9T and all other type strains of the genus Luteimonas , respectively. The major cellular fatty acids were iso-C15 : 0, iso-C16 : 0, summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) and summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1  ω9c). Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were the major polar lipids, and ubiquinone-8 was the only respiratory quinone. The genomic DNA G+C content was 69.3 mol%. The digital DNA–DNA hybridization and average nucleotide identity values of strain SJ-16T to L. chenhongjianii 100111T, L. terrae THG-MD21T, L. rhizosphaerae 4-12T and L. aestuarii B9T were 36.9, 37.5, 24.0 and 21.1 %, and 80.9, 80.6, 80.7 and 76.3 %, respectively. Based on phenotypic, physiological and phylogenetic results, strain SJ-16T represents a novel species of the genus Luteimonas , for which the name Luteimonas deserti is proposed. The type strain is SJ-16T (=CGMCC 1.17694T=KCTC 82207T).

scholarly journals Lysinibacillus varians sp. nov., an endospore-forming bacterium with a filament-to-rod cell cycle

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3644-3649 ◽  
Author(s):  
Chunjie Zhu ◽  
Guoping Sun ◽  
Xingjuan Chen ◽  
Jun Guo ◽  
Meiying Xu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Single Cells ◽  
Rrna Gene ◽  
Phylogenetic Distance ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type

Six Gram-stain-positive, motile, filamentous and/or rod-shaped, spherical spore-forming bacteria (strains GY32T, L31, F01, F03, F06 and F07) showing polybrominated diphenyl ether transformation were investigated to determine their taxonomic status. After spore germination, these organisms could grow more than one hundred microns long as intact single cells and then divide into rod cells and form endospores in 33 h. The cell-wall peptidoglycan of these strains was type A4α, the predominant menaquinone was MK-7 and the major fatty acids were iso-C16 : 0, iso-C15 : 0 and C16 : 1ω7C. Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were detected in the polar lipid profile. Analysis of the 16S rRNA gene sequences indicated that these strains should be placed in the genus Lysinibacillus and they were most closely related to Lysinibacillus sphaericus DSM 28T (99 % 16S rRNA gene sequence similarity). The gyrB sequence similarity and DNA–DNA relatedness between strain GY32T and L. sphaericus JCM 2502T were 81 % and 52 %, respectively. The G+C content of the genomic DNA of strain GY32T was 43.2 mol%. In addition, strain GY32T showed differences in nitrate reduction, starch and gelatin hydrolysis, carbon resource utilization and cell morphology. The phylogenetic distance from its closest relative measured by DNA–DNA relatedness and DNA G+C content, and its phenotypic properties demonstrated that strain GY32T represents a novel species of the genus Lysinibacillus , for which the name Lysinibacillus varians sp. nov. is proposed. The type strain is GY32T ( = NBRC 109424T = CGMCC 1.12212T = CCTCC M 2011307T).

Bizionia hallyeonensis sp. nov., isolated from seawater in an oyster farm

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 685-690 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Chul-Hyung Kang ◽  
Yong-Taek Jung ◽  
So-Jung Kang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Oyster Farm

A Gram-staining-negative, non-spore-forming, aerobic, non-flagellated, non-gliding, rod-shaped bacterium, designated strain T-y7T, was isolated from seawater collected in an oyster farm in the South Sea, South Korea, and subjected to a polyphasic study. Strain T-y7T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2 % (w/v) NaCl. In phylogenetic analyses based on 16S rRNA gene sequences, strain T-y7T fell within a clade comprising Bizionia species. It formed a coherent cluster with the type strains of Bizionia algoritergicola , B. argentinensis , B. echini and B. myxarmorum , with which it exhibited 16S rRNA gene sequence similarities of 97.4–98.9 % and mean DNA–DNA relatedness values of 11–27 %. Strain T-y7T had MK-6 as its predominant menaquinone and iso-C15 : 1 G, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0 and iso-C17 : 0 3-OH as its major fatty acids. The major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The genomic DNA G+C content was 37.1 mol%. Its phylogenetic and genetic distinctiveness and differential phenotypic properties revealed that strain T-y7T does not belong to any established Bizionia species. On the basis of the data presented, strain T-y7T is considered to represent a novel species of the genus Bizionia , for which the name Bizionia hallyeonensis sp. nov. is proposed. The type strain is T-y7T ( = KCTC 23881T  = CCUG 62110T).

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