- Volume 49, Issue 3, 1999
Volume 49, Issue 3, 1999
- New Taxa - Gram-Positive Bacteria
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An indigo-reducing moderate thermophile from a woad vat, Clostridium isatidis sp. nov.
A Gram-positive, anaerobic, moderate thermophile, strain Wv6T, capable of reducing indigo dye, was isolated from a fermenting woad vat prepared essentially as in medieval Europe. Strain Wv6T formed rod-shaped cells, which occurred singly, in pairs or in chains and produced terminal oval endospores Strain Wv6T was saccharolytic. Growth occurred at pH 5.9-9.9 (initial pH) with an optimum at 50 °C of pH 7.2±0.2 (constant pH). At pH 7.8, the temperature range for growth was 30-55 °C with the optimum at 49-52 °C. Comparative 16S rRNA gene sequence analysis demonstrated that the bacterium represents a hitherto unknown subline within rRNA cluster I Clostridium. Based on the results of the phylogenetic analysis and phenotypic criteria, it is proposed that the unknown moderate thermophile should be classified as Clostridium isatidi sp. nov., a new species of the genus Clostridium. The type strain of Clostridium isatidis is strain Wv6T (= NCFB 3071T).
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Proposal of Virgibacillus proomii sp. nov. and emended description of Virgibacillus pantothenticus (Proom and Knight 1950) Heyndrickx et al. 1998
A polyphasic study of strains originally received as Bacillus (now Virgibacillus) pantothenticus, along with strains representing species belonging to Bacillus, Halobacillus and Paenibacilus. was undertaken using amplified rDNA restriction analysis (ARDRA), fatty acid methyl ester (FAME) analysis, SDS-PAGE of whole-cell proteins and routine diagnostic characters comprising 61 biochemical tests in the API system and 15 observations of vegetative cell and sporangial morphology. It revealed the presence within Virgibacillus of an as yet undescribed new species, for which the name Virgibacillus proomii is proposed; V. proomii can be distinguished from V. pantothenticus and members of Bacillus sensu stricto, and from members of Paenibacillus and other aerobic endospore-forming bacteria, by routine phenotypic tests. The type strain of Virgibacillus proomii is LMG 12370T.
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Note: Aerococcus christensenii sp. nov., from the human vagina
More LessPhenotypic and phylogenetic studies were performed on two strains of a hitherto undescribed Aerococcus-like organism isolated from the human vagina. Comparative 16S rRNA gene sequencing studies demonstrated that the unknown strains constitute a new subline within the genus Aerococcus. The unknown bacterium was readily distinguished from the two currently recognized Aerococcus species, Aerococcus viridans and Aerococcus urinae, by biochemical tests and electrophoretic analysis of whole-cell proteins. On the basis of phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified as Aerococcus christensenii sp. nov. The type strain of A. christensenii is CCUG 28831T.
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Fusibacter paucivorans gen. nov., sp. nov., an anaerobic, thiosulfate-reducing bacterium from an oil-producing well
A strictly anaerobic, halotolerant, spindle-shaped rod, designated strain SEBR 4211T, was isolated from an African saline oil-producing well. Cells stain Grampositive, which was confirmed by electron microscopy observations. Strain SEBR 4211T was motile by means of one to four peritrichous flagella, had a G+C content of 43 mol% and grew optimally at 37 °C, pH 7.3, with 0 to 3% (w/v) NaCI. It utilized a limited number of carbohydrates (cellobiose, glucose, fructose, mannitol and ribose) and produced acetate, butyrate, CO2 and H2 as end products from glucose fermentation. It reduced thiosulfate to sulfide. In the presence of thiosulfate, a decrease in butyrate and an increase in acetate production was observed. Phylogenetically, strain SEBR 4211T was related to members of the low G+C Clostridiales order with Clostridium halophilum as the closest relative (16S rDNA sequence similarity of 90%). On the basis of phenotypic, genotypic and phylogenetic characteristics of the isolate, it is proposed to designate it as a new species of a new genus, Fusibacter gen. nov., as Fusibacter paucivorans sp. nov. The type strain is SEBR 4211T (= DSM 12116T
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Agrococcus citreus sp. nov., isolated from a medieval wall painting of the chapel of Castle Herberstein (Austria)
A bacterial strain, D-1/1aT, isolated from a medieval wall painting of the chape of Herberstein (Styria, Austria) was characterized by a polyphasic approach. Strain D-1/1aT shared 98.1% 16S rRNA sequence similarity to Agrococcus jenensis. The chemotaxonomic characteristics including polar lipid pattern, whole cell sugars, quinone system, polyamine pattern, cell wall composition and fatty acid profile were in good agreement with those of Agrococcus jenensis. The G+C content of the DNA was determined to be 74 mol%. The value of 47% DNA reassociation obtained after DNA-DNA hybridization between DNA of Agrococcus jenensis and strain D-1/1aT as well as differences in the amino acid composition of the peptidoglycan and in physiological characteristics demonstrate that the isolate represents a new species of the genus Agrococcus. The name Agrococcus citreus sp. nov. is proposed for the new species harbouring isolate D-1/1aT. The type strain is DSM 12453T.
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Cryptobacterium curtum gen. nov., sp. nov., a new genus of Gram-positive anaerobic rod isolated from human oral cavities
Novel Eubacterium-like isolates, strains 12-3T and KV43-B, which were isolated from the periodontal pocket of an adult patient with periodontal disease and necrotic dental pulp, respectively, were studied taxonomically and phylogenetically. The morphological and differential biochemical characteristics of these organisms are also described in this paper. These organisms were Gram-positive, anaerobic, non-spore-forming, rod-shaped bacteria that were inert in most of the conventional biochemical tests and closely resembled members of asaccharolytic oral Eubacterium species. On the other hand, protein profiles of whole cells in SDS-PAGE and Western immunoblotting reaction analysis distinguished these isolates from strains of the previously described genus Eubacterium. The G+C content of the DNAs from the novel isolates was 50 and 51 mol%, respectively. The levels of DNA-DNA relatedness to other asaccharolytic oral Eubacterium species, including Eubacterium brachy, Eubacterium lentum, Eubacterium nodatum, Eubacterium timidum, Eubacterium saphenum, Eubacterium minutum and Eubacterium exiguum, was less than 11 %. These organisms also exhibited a very low level of reassociation with the DNA of Eubacterium limosum, the type species of the genus Eubacterium. The results of 16S rDNA sequence comparisons revealed that these organisms represent a novel lineage distinct from all previously described genera of Gram-positive, rod-shaped bacteria. On the basis of our results, it is suggested that strains 12-3T and KV43-B should be classified in a new genus and species, for which the name Cryptobacterium curtum gen. nov., sp. nov. is proposed. The type strain of Cryptobacterium curtum is 12-3T (= ATCC 700683T).
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Clostridium methoxybenzovorans sp. nov., a new aromatic o-demethylating homoacetogen from an olive mill wastewater treatment digester
More LessA strictly anaerobic, spore-forming bacterium (3.0-5.0 × 0.4-0.8 μm), designated strain SR3T (T=type strain), which stained Gram-positive and possessed a Grampositive type cell wall was isolated from a methanogenic pilot-scale digester fed with olive mill wastewater (Sfax, Tunisia). It utilized a number of carbohydrates (glucose, fructose, sorbose, galactose, myo-inositol, sucrose, lactose, cellobiose), organic compounds (lactate, betaine, sarcosine, dimethylglycine, methanethiol, dimethylsulfide), alcohol (methanol) and all methoxylated aromatic compounds only in the presence of yeast extract (0.1%). The end products from carbohydrate fermentation were H2, CO2, formate, acetate and ethanol, that from lactate was methanol, those from methoxylated aromatics were acetate and butyrate, and that from betaine, sarcosine, dimethylglycine, methanethiol and dimethylsulfide was only acetate. Strain SR3T was non-motile, had a G+C content of 44 mol% and grew optimally at 37 °C and pH 7.4 on a glucose-containing medium. Phylogenetically, the closest relatives of strain SR3T were the non-methoxylated aromatic-degrading Clostridium xylanolyticum, Clostridium aerotolerans, Clostridium sphenoides and Clostridium celerecrescens (mean similarity of 98%). On the basis of the phenotypic, genotypic and phylogenetic characteristics of the isolate, it is proposed to designate strain SR3T as Clostridium methoxybenzovorans sp. nov. The type strain is SR3T (=DSM 12182T).
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Note: Relationship of Bacillus subtilis clades associated with strains 168 and W23: A proposal for Bacillus subtilis subsp. subtilis subsp. nov. and Bacillus subtilis subsp. spizizenii subsp. nov.
More LessEarlier phylogenetic studies based on the inferred DNA sequences of the polC, rpoB and gyrA genes suggested that strains of the species Bacillus subtilis formed two clusters, indicating the presence two closely related taxa; one contained the laboratory strain 168 and the other the laboratory strain W23. Significant sexual isolation was found between strain 168 and members of the group containing W23, but no sexual isolation was observed between strain 168 and other members of the 168 group. DNA reassociation between the two groups ranged from 58 to 69% and intragroup DNA relatedness ranged from 82 to 100%. Because group 168 strains were highly related to the B. subtilis type strain, they were considered to be bona fide members of the species. About 99.5% sequence identity was observed between the 16S rRNA genes of the 168 and W23 groups. Ribitol and anhydroribitol were principal cell wall constituents of the W23 but not of the 168 group. These observations revealed two closely related but genetically and phenotypically distinct groups within B. subtilis that correspond to two historically important strains. Subspecies distinction is proposed for the 168 and W23 groups, with the names Bacillus subtilis subsp. subtilis subsp. nov. and Bacillus subtilis subsp. spizizenii subsp. nov., respectively. The type strain of the former is NRRL NRS-744T and the latte NRRL B-23049T.
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Note: Arthrobacter rhombi sp. nov., isolated from Greenland halibut (Reinhardtius hippoglossoides)
More LessTwo strains of a hitherto undescribed Gram-positive coryneform bacterium isolated from Greenland halibut (Reinhardtius hippoglossoides) were characterized by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing studies demonstrated that the unknown strains constitute a new line within the genus Arthrobacter. The nearest relatives of the bacterium from fish were members of the Arthrobacter nicotianael Arthrobacter sulfureus group. The unknown bacterium was readily distinguished from these species by phenotypic methods. Based on phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified as Arthrobacter rhombi sp. nov. The type strain of Arthrobacter rhombi is CCUG 38813T.
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Streptococcus pluranimalium sp. nov., from cattle and other animals
Strains from subclinical mastitis, from the genital tract and tonsils of cattle, from tonsils of a goat and a cat and from the crop and the respiratory tract of canaries were found to constitute a new streptococcal species, for which the name Streptococcus pluranimalium sp. nov. is proposed. Sequencing of 16S rRNA showed that Streptococcus thoraltensis and Streptococcus hyovaginalis were its closest known phylogenetic relatives. The new species showed some phenotypic resemblance to the poorly described species Streptococcus acidominimus, but whole-cell protein analysis and 16S rRNA sequencing revealed that the new species was only distantly related to the type strain of S. acidominimus. Identification of these bacteria, which showed heterogeneous biochemical reaction patterns, was most reliably made by whole-cell protein analysis. Nevertheless, a number of biochemical reactions can be used to differentiate S. pluranimalium from other animal streptococci. Strain LMG 14177T, isolated from mastitic milk of a dairy cow, was designated as the type strain of S. pluranimalium sp. nov.
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Nocardia uniformis nom. rev.
More LessA soil isolate representing the putatively novel species ‘Nocardia uniformis’ was found to have morphological, staining and chemotaxonomic properties consistent with its classification in the genus Nocardia. An almost complete sequence of the 16S rDNA of the strain was determined following cloning and sequencing of the amplified gene. The sequence was aligned with those available for nocardiae and phylogenetic trees were inferred using four tree-making algorithms. The organism was consistently associated with the type strain of Nocardia otitidiscaviarum albeit with a relatively low bootstrap value recorded for neighbour-joining analysis. The strain was also readily separated from representatives of all validly described Nocardia species using a set of phenotypic properties. The genotypic and phenotypic data indicate that the strain should be assigned to the genus Nocardia as a new species. The name proposed for the new species is Nocardia uniformis. The type strain is JCM 3224T.
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Note: Facklamia tabacinasalis sp. nov., from powdered tobacco
More LessAn unknown Gram-positive, catalase-negative, facultatively anaerobic, coccus-shaped organism originating as a contaminant of snuff was characterized by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing studies demonstrated that the bacterium represents a new subline within the genus Facklamia. The unknown bacterium was readily distinguished from Facklamis hominis and Facklamia ignava by biochemical tests and electrophoretic analysis of whole-cell proteins. On the basis of phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified as Facklamia tabacinasalis sp. nov., the type strain of which is CCUG 30090T.
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Note: Vagococcus lutrae sp. nov., isolated from the common otter (Lutra lutra)
More LessPhenotypic and phylogenetic studies were performed on an unknown Grampositive catalase-negative coccus isolated from a common otter (Lutra lutra). Comparative 16S rRNA gene sequencing demonstrated that the unknown bacterium represents a new subline within the genus Vagococcus, close to, but distinct from, Vagococcus fluvialis and Vagococcus salmoninarum. The unknown bacterium was readily distinguished from the two currently recognized Vagococcus species by biochemical tests and electrophoretic analysis of whole-cell proteins. Based on phylogenetic and phenotypic evidence it is proposed that the unknown bacterium be classified as a new species, Vagococcus lutrae, the type strain of which is CCUG 39187T.
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Mycobacterium tuberculosis subsp. caprae subsp. nov.: A taxonomic study of a new member of the Mycobacterium tuberculosis complex isolated from goats in Spain
Isolates from the Mycobacterium tuberculosis complex cultured from caprine pathological tissue samples were biochemically and genetically characterized. The isolates were negative for nitrate reduction and niacin accumulation, they weakly hydrolysed Tween 80, were sensitive to pyrazinamide (50 μg ml−1) and were resistant to 1 and 2 μg tiophene-2-carboxylic acid hydrazide ml−1 but not to 5 or 10 μg tiophene-2-carboxylic acid hydrazide ml−1. Sequencing of the pncA gene revealed a polymorphism characteristic of M. tuberculosis, whereas oxyR, katG and gyrA sequences were characteristic of Mycobacterium bovis. The fingerprinting patterns obtained with IS6110, direct repeats and polymorphic G+C-rich sequence-associated RFLP and direct variable repeat-spacer oligonucelotide typing (spoligotyping) segregated these isolates from the other members of the complex. The results of this testing, together with the repeated association of this micro-organism with goats, suggest that a new member of this taxonomic complex not matching any of the classical species had been identified. This unusual mycobacterium may play a role in the epidemiology of animal and human tuberculosis in Spain. The name Mycobacterium tuberculosis subsp. caprae subsp. nov. is proposed for these isolates. The type strain of Mycobacterium tuberculosis subsp. caprae subsp. nov. is gM-1T (= CIP 105776T).
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- New Taxa - Yeasts
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Pichia lachancei sp. nov., associated with several Hawaiian plant species
More LessA description is given of Pichia lachancei sp. nov., a new species of yeast that occurs in association with several Hawaiian plant species of the genera Tetraplasandra, Cheirodendron and Clermontia. The new species is heterothallic and occurs in nature in the haploid as well as the diploid state. Upon conjugation of complementary mating types, zygotes are formed that reproduce by budding as diploid cells. When placed on sporulation medium, four hat-shaped spores are produced which are rapidly released from the ascus. Phylogenetic analysis showed that P. lachancei is most closely related to Pichia rhodanensis and Pichia jadinii. The diploid type strain of P. lachancei, isolated from rotting bark of Tetraplasandra hawaiiensis on the island of Hawaii, is strain UCD-FST 79-9T (= ATCC 201914T = CBS 8557T = NRRL Y-27008T).
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Mastigobasidium, a new teleomorphic genus for the perfect state of ballistosporous yeast Bensingtonia intermedia
More LessA new genus, Mastigobasidium, is proposed for teliospore-forming, xylose-lacking, ballistosporogenous, glucuronate-positive yeasts. The distinguishing features of the genus are: Germination of the teliospore by several long aseptate hyphae; curved phragmometabasidia development on the apices of these hyphae; and production of basidiospores on a peg in clusters. The type strain of heterothallic, nitrate-negative species Mastigobasidium intermedium is VKM Y-2720T (Bullera intermedia type strain) and the allotype strain is VKM Y-2727AL (Sporobolomyces weijmanii type strain).
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- Evolution, Phylogeny And Biodiversity
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Complex genomic and phenotypic characterization of the related species Staphylococcus carnosus and Staphylococcus piscifermentans
More LessOn the basis of numerical analysis of 100 phenotypic features, the strains of two species, Staphylococcus carnosus and Staphylococcus piscifermentans, were differentiated into two separate phenons corresponding with the macrorestriction patterns of their genomic DNA, as well as with the results of ribotyping and PCR amplification of enterobacterial repetitive intergenic consensus sequences. One of the S. carnosus strains, the F-2 strain, was shown to be marginal, exhibiting the lowest genomic and phenotypic similarity to the S. carnosus type strain DSM 20501T. Two of the strains studied (strains S. carnosus SK 06 and S. piscifermentans SK 05) were phenotypically convergent forming a separate phenon. They were phenotypically similar, even though the genomic DNA of one of them was homologous with that of the S. carnosus type strain, whereas that of the other was homologous with the genomic DNA of the S. piscifermentans type strain. In such cases, fingerprinting methods (particularly macrorestriction analysis and ribotyping) served as important correctives, as they allow phenotypically convergent strains to be distinguished on the basis of their genomic profiles. The results of this paper support the proposal for the new species Staphylococcus condimenti as well as the new subspecies Staphylococcus carnosus subsp. utilis.
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Comparative phylogeny of rrs and nifH genes in the Bacillaceae
More LessThe rrs (16S rDNA) gene sequences of nitrogen-fixing endospore-forming bacilli isolated from the rhizosphere of wheat and maize were determined in order to infer their phylogenetic position in the Bacillaceae. These rhizosphere strains form a monophyletic cluster with Paenibacillus azotofixans, Paenibacillus polymyxa and Paenibacillus macerans. Two of them (RSA19 and TOD45) had previously been identified as Bacillus circulans (group 2) by phenotypic characterization (APl 50CH). Evidence for nitrogen fixation by P. azotofixans, P. polymyxa, P. macerans and putative B. circulans strains RSA19 and TOD45 was provided by acetylene-reduction activity, and confirmed by amplifying and sequencing a nifH fragment (370 nt). The phylogenetic tree of nifH-derived amino acid sequences was compared to the phylogenetic tree of rrs sequences. All Paenibacillus nifH sequences formed a coherent cluster distinct from that of related nitrogen-fixing anaerobic clostridia and Gram-positive high-G+C-content frankiae. The nifH gene was neither detected in the B. circulans type strain (ATCC 4513T) nor in the type strains of Bacillus subtilis, Bacillus cereus, Bacillus alcalophilus, Bacillus simplex, Brevibacillus brevis and Paenibacillus validus. Accordingly, nitrogen fixation among aerobic endospore-forming Firmicutes seems to be restricted to a subset of species in the genus Paenibacillus.
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rRNA gene RFLP as an identification tool for Corynebacterium species
More LessThe value of rRNA gene RFLP analysis (ribotyping) as a tool for Corynebacterium and Turicella species identification was evaluateed. Seventy-four strains representing 26 different species or subspecies were analysed by BstEll, Smal and Sphl ribotyping. Numerical analysis of the resulting rDNA banding patterns was performed by Dice coefficient correlation in order to establish a database for species identification. In general, most of the strains belonging to the same species clustered together. Interestingly, BstEll clustering of many species followed known phylogenetic lineages. This was not evident with the more heterogeneous Smal and Sphl patterns. The Smal patterns contained a 1800 bp band in the digests of all species studied with the exception of Corynebacterium urealyticum. Sphl digestion resulted in the most heterogeneous patterns. The information provided by all three enzymes was considered essential for the reliable linking of starins of unknown identity with defined species in the database. It is concluded that ribotyping provides an useful tool for screening and charactrization of potentially new Corynebacterium species.
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Genetic diversity within Lactobacillus sakei and Lactobacillus curvatus and design of PCR primers for its detection using randomly amplified polymorphic DNA
More LessThe genotypic and phenotypic diversity among isolates of the Lactobacillus curvatus/Lactobacillus graminis/Lactobacillus sakei group was evaluated by comparing RAPD data and results of biochemical tests, such as hydrolysis of arginine, D-lactate production, melibiose and xylose fermentation, and the presence of haem-dependent catalase. Analyses were applied to five type strains and to a collection of 165 isolates previously assigned to L. sakei or L. curvatus. Phenotypic and RAPD data were compared with each other and with previous DNA-DNA hybridization data. The phenotypic and genotypic separation between L. sakei, L. curvatus and L graminis was clear, and new insights into the detailed structure within L. sakei and L. curvatus were obtained. Individual strains could be typed by RAPD and, after the elimination of similar or identical isolates, two sub-groups in both L. curvatus and L. sakei were defined. The presence or absence of catalase activity further distinguished the two L. curvatus sub-groups. By cloning and sequencing specific RAPD products, pairs of PCR primers were developed that can be used to specifically detect L. curvatus, L. sakei and each of the L. sakei sub-groups.
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Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 72 (2022 - 2023)
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Volume 71 (2020 - 2021)
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Volume 70 (2020)
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Volume 69 (2019)
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Volume 68 (2018)
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Volume 67 (2017)
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