- Volume 53, Issue 4, 2003
Volume 53, Issue 4, 2003
- New Taxa
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- Gram-Positive Bacteria
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Eubacterium pyruvativorans sp. nov., a novel non-saccharolytic anaerobe from the rumen that ferments pyruvate and amino acids, forms caproate and utilizes acetate and propionate
Two similar Gram-positive rods were isolated from 10−6 dilutions of ruminal fluid from a sheep receiving a mixed grass hay/concentrate diet, using a medium containing pancreatic casein hydrolysate as sole source of carbon and energy. The isolates did not ferment sugars, but grew on pyruvate or trypticase, forming caproate as the main fermentation product and valerate to a lesser extent. Acetate and propionate were utilized. One of these strains, I-6T, was selected for further study. Strain I-6T was a non-motile coccal rod, 1·2×0·4 μm, with a Gram-positive cell wall ultrastructure and a G+C content of 56·8 mol%. No spores were visible, and strain I-6T did not survive heating at 80 °C for 10 min. Its rate of NH3 production was 375 nmol (mg protein)−1 min−1, placing it in the ‘ammonia-hyperproducing’ (or HAP) group of ruminal bacteria. 16S rDNA sequence analysis (1296 bases) indicated that it represents a novel species within the ‘low-G+C’ Gram-positive group, for which the name Eubacterium pyruvativorans sp. nov. is proposed. Among cultivated bacteria, strain I-6T was most closely related (89 % identity) to other asaccharolytic Eubacterium isolates from the mouth and the rumen. It was 98 % identical to uncultured bacterial sequences amplified by others from ruminal digesta.
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Alkaliphilus crotonatoxidans sp. nov., a strictly anaerobic, crotonate-dismutating bacterium isolated from a methanogenic environment
More LessTwo bacterial strains were isolated from methanogenic butyrate-oxidizing mixed cultures. The cells were straight to slightly curved, Gram-positive rods that were motile by means of multiple flagella and formed endospores. Growth was observed in the temperature range 15–45 °C (optimum 37 °C) and pH range 5·5–9·0 (optimum pH 7·5). The novel isolates were strictly anaerobic chemo-organotrophs capable of utilizing yeast extract, peptone, tryptone and a variety of sugars and organic acids, but not glucose. None of the accessory electron acceptors tested (elemental sulfur, thiosulfate or fumarate) improved growth, except crotonate, which was dismutated to butyrate and acetate. The G+C content of the DNA of one of the isolates, strain B11-2T, was 30·6 mol%. Phylogenetic analysis based on 16S rDNA sequence similarity between strain B11-2T and some other strictly anaerobic, spore-forming bacteria indicated that the novel isolates represented a species in cluster XI within the low-GC Gram-positive bacteria, being most closely related to Alkaliphilus transvaalensis JCM 10712T. DNA–DNA relatedness between strain B11-2T and A. transvaalensis JCM 10712T was 21 %. On the basis of physiological and molecular properties, and cellular fatty acid and cell wall compositions, the novel isolates are proposed to represent a novel species of the genus Alkaliphilus, for which the name Alkaliphilus crotonatoxidans is proposed (type strain B11-2T=AS 1.2897T=JCM 11672T).
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Leifsonia rubra sp. nov. and Leifsonia aurea sp. nov., psychrophiles from a pond in Antarctica
More LessTwo unique psychrophilic strains (CMS 76rT and CMS 81yT) were isolated from a cyanobacterial mat sample from a pond in Wright Valley, McMurdo, Antarctica. Both isolates were assigned to the genus Leifsonia, since they were Gram-positive, curved rods, non-motile, catalase-positive, contained dl-2,4-diaminobutyric acid, menaquinone MK-11, phosphatidylglycerol and diphosphatidylglycerol, had a high content of anteiso- and iso-branched fatty acids and had a DNA G+C content of 64–66 mol%. In addition, both isolates were related to the five reported species of Leifsonia at a level of about 95–96 % 16S rDNA sequence similarity and differed from one another by 2·5 %. Strains CMS 76rT and CMS 81yT also differed from one another in many other phenotypic characteristics and exhibited only 30 % relatedness at the DNA–DNA level, thus indicating that they represent two different species. Furthermore, these two isolates also showed many distinct differences with respect to the reported species of Leifsonia in terms of their phenotypic characteristics, biochemical properties, chemotaxonomic features, sensitivity to various antibiotics and 16S rDNA similarity, clearly indicating that strains CMS 76rT (=MTCC 4210T =DSM 15304T =CIP 107783T) and CMS 81yT (=MTCC 4657T =DSM 15303T =CIP 107785T) represent the type strains of two novel species of Leifsonia, for which the names Leifsonia rubra sp. nov. and Leifsonia aurea sp. nov. are proposed.
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Rhodoglobus vestalii gen. nov., sp. nov., a novel psychrophilic organism isolated from an Antarctic Dry Valley lake
More LessA novel, psychrophilic, Gram-positive bacterium (designated strain LV3T) from a lake near the McMurdo Ice Shelf, Antarctica, has been isolated and characterized. This organism formed red-pigmented colonies, had an optimal growth temperature of 18 °C and grew on a variety of media between −2 and 21 °C. Scanning electron micrographs of strain LV3T that showed small rods with unusual bulbous protuberances during all phases of growth were of particular interest. The G+C content of the genomic DNA was approximately 62 mol%. The cell walls contained ornithine as the diamino acid. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. Cells grown at −2 °C contained significant amounts of anteiso-C15 : 1. The major menaquinones found in strain LV3T were MK-11 and MK-12. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain LV3T was a member of the family Microbacteriaceae and related to, but distinct from, organisms belonging to the genera Agreia, Leifsonia and Subtercola. In addition, alignments of 16S rRNA sequences showed that the sequence of strain LV3T contained a 13 bp insertion that was found in only a few related sequences. Based on the low growth temperature, unusual cell shape, distinct 16S rRNA gene sequence and structure and cell-wall amino acid and menaquinone compositions, Rhodoglobus vestalii gen. nov., sp. nov. is proposed, with the type strain LV3T (=ATCC BAA-534T =CIP 107482T).
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Nocardia caishijiensis sp. nov., a novel soil actinomycete
More LessA soil isolate, strain F829T, which had provisionally been assigned to the genus Nocardia, was subjected to a polyphasic taxonomic study. An almost complete 16S rDNA sequence was determined for this strain; the sequence was aligned with available sequences for nocardiae and phylogenetic trees were inferred using three tree-making algorithms. The organism showed a combination of phenotypic properties typical of nocardiae and formed a distinct phyletic line within the evolutionary radiation of species of the genus Nocardia, being most closely related to Nocardia asteroides ATCC 19247T. Strain F829T was readily distinguished from representatives of species of Nocardia with validly published names on the basis of phenotypic data, notably from the type strain of N. asteroides. It is proposed that the organism be recognized as a novel species of Nocardia, Nocardia caishijiensis sp. nov. The type strain is F829T (=AS 4.1728T =JCM 11508T).
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Transfer of Hongia koreensis Lee et al. 2000 to the genus Kribbella Park et al. 1999 as Kribbella koreensis comb. nov.
More LessThe taxonomic status of Hongia koreensis was investigated by molecular systematic methods. On the basis of 16S rDNA phylogeny, H. koreensis was closely associated with Kribbella flavida and Kribbella sandramycini and formed a monophyletic clade with these species. These three taxa shared over 98 % 16S rDNA sequence similarity and many chemotaxonomic properties, which strongly indicates that they belong to the same genus. DNA–DNA pairing was employed to elucidate the genomic relatedness among these taxa. H. koreensis represented a distinct genomic species that can be differentiated from members of the genus Kribbella. Physiological characteristics and phospholipid and cellular fatty acid compositions can be also used to separate H. koreensis from species of the genus Kribbella. On the basis of data presented in this and earlier studies, it is proposed that H. koreensis Lee et al. 2000 should be transferred to the genus Kribbella Park et al. 1999 as Kribbella koreensis comb. nov.
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Corynebacterium sphenisci sp. nov., isolated from wild penguins
Six unidentified Gram-positive, rod-shaped organisms recovered from the cloacae of apparently healthy wild penguins were characterized by phenotypic and molecular taxonomic methods. Chemotaxonomic investigations revealed the presence of a cell wall based on meso-diaminopimelic acid and long-chain cellular fatty acids of the straight-chain saturated and monounsaturated types, consistent with the genus Corynebacterium. Corynomycolic acids, which are characteristic of the genus, were also detected, albeit in small amounts. Comparative 16S rRNA gene sequencing studies showed that the unidentified organisms were phylogenetically related to corynebacteria and represent a novel subline associated with a small subcluster of species that includes Corynebacterium xerosis, Corynebacterium amycolatum and Corynebacterium freneyi. The unknown isolates were readily distinguished from their closest phylogenetic relatives and all other Corynebacterium species with validly published names by using a combination of biochemical and chemotaxonomic criteria. Based on both phenotypic and 16S rRNA gene sequence considerations, it is proposed that the unknown isolates recovered from penguins be classified as a novel species in the genus Corynebacterium, Corynebacterium sphenisci sp. nov. The type strain is CECT 5990T (=CCUG 46398T).
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Characterization of novel psychrophilic clostridia from an Antarctic microbial mat: description of Clostridium frigoris sp. nov., Clostridium lacusfryxellense sp. nov., Clostridium bowmanii sp. nov. and Clostridium psychrophilum sp. nov. and reclassification of Clostridium laramiense as Clostridium estertheticum subsp. laramiense subsp. nov.
Taxonomic studies were performed on four strains (D-1/D-an/IIT, C/C-an/B1T, A-1/C-an/C1T and A-1/C-an/IT) of anaerobic, Gram-positive, spore-forming bacteria originally isolated from a mat sample retrieved from a shallow, moated area around Lake Fryxell, an Antarctic freshwater lake. Phylogenetic analyses based on 16S rRNA gene sequence data indicated that these strains are affiliated with cluster I clostridia and form a coherent group with Clostridium estertheticum and Clostridium laramiense. Similarity values among 16S rRNA gene sequences within this assemblage ranged between 96·7 and 99·8 %. Despite the close phylogenetic relationship, several distinguishing phenotypic traits were found among the novel strains using a polyphasic approach. All strains were psychrophilic, but the temperature optimum for growth differed markedly, ranging from 4 to 16 °C. In addition, substrate utilization patterns, fermentation end products, cellular fatty acid profiles and morphological traits enabled a clear differentiation between the strains. DNA–DNA hybridization experiments revealed that each of the four novel strains represents a distinct species, with DNA–DNA similarity values to related strains in the range 16–62 %. In contrast, the type strains of C. estertheticum and C. laramiense shared 79 % DNA–DNA similarity, indicating a close relationship at the species level. On the basis of genetic and phenotypic properties, it is proposed to designate four novel species of the genus Clostridium to harbour the newly isolated strains: Clostridium frigoris sp. nov. (type strain D-1/D-an/IIT=DSM 14204T =ATCC BAA-579T), Clostridium lacusfryxellense sp. nov. (type strain C/C-an/B1T=DSM 14205T =ATCC BAA-580T), Clostridium bowmanii sp. nov. (type strain A-1/C-an/C1T=DSM 14206T =ATCC BAA-581T) and Clostridium psychrophilum sp. nov. (type strain A-1/C-an/IT=DSM 14207T =ATCC BAA-582T). It is also proposed to unite C. laramiense and C. estertheticum under C. estertheticum. The subspecies C. estertheticum subsp. laramiense subsp. nov. is established, represented by strain ATCC 51254T (=DSM 14864T). The type strain of C. estertheticum subsp. estertheticum remains NCIMB 12511T (=DSM 8809T).
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Clostridium caminithermale sp. nov., a slightly halophilic and moderately thermophilic bacterium isolated from an Atlantic deep-sea hydrothermal chimney
A strictly anaerobic, slightly halophilic and moderately thermophilic, sporulating rod designated strain DVird3T was isolated from deep-sea hydrothermal vent samples collected at a depth of approximately 800 m on the Atlantic Ocean Ridge. Strain DVird3T possessed a few laterally inserted flagella, had a DNA G+C content of 33·1 mol% and grew optimally at pH 6·6 and at 45 °C. Growth was observed at temperatures between 20 and 58 °C and at pH values between 5·8 and 8·2. The optimum NaCl concentration for growth was 3 % sea salt (30 g l−1); no growth was observed in the presence of 15 or 60 g sea salt l−1. Strain DVird3T is heterotrophic and utilizes some sugars and various single amino acids. Acetate was the main fatty acid detected from carbohydrate fermentation, together with H2 and CO2. Gelatin was used as an energy source. It performed the Stickland reaction. Phylogenetically, strain DVird3T branched with members of cluster XI of the order Clostridiales, with Clostridium halophilum as its closest relative (similarity of 94·6 %). On the basis of its phenotypic, genotypic and phylogenetic characteristics, strain DVird3T (=DSM 15212T =CIP 107654T) is proposed as the type strain of a novel species of the genus Clostridium, Clostridium caminithermale sp. nov.
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Paenibacillus agarexedens sp. nov., nom. rev., and Paenibacillus agaridevorans sp. nov.
Twenty-two agarolytic, aerobic, spore-forming strains were characterized taxonomically by DNA–DNA reassociation experiments, riboprint analyses, 16S rDNA sequencing and phenetic similarity analyses. Based on riboprint analyses, the strains formed eight ribogroups, six of which contained 2–6 strains and two encompassed single strains. Within the multi-strain ribogroups, similarities ranged from 91–99 %. Phylogenetic analyses of representatives of the eight groups by 16S rDNA sequence analysis showed that the strains were affiliated to the genus Paenibacillus, but relatedness to described Paenibacillus species was only moderate (<97·8 % sequence similarity). Published DNA–DNA similarity values for most of the agarolytic strains, supplemented with new data, supported the distinctiveness of the eight ribogroups. Intragroup DNA–DNA similarity values ranged from 80 to 104 %, while intergroup DNA–DNA similarities were <35 %. Based on genomic distinctiveness and supported by the presence of distinguishing phenotypic properties, multi-strain groups 1 and 2 are proposed as novel species, Paenibacillus agarexedens sp. nov., nom. rev. (type strain, DSM 1327T=CIP 107437T) and Paenibacillus agaridevorans sp. nov. (type strain, DSM 1355T=CIP 107436T).
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Halobacillus karajensis sp. nov., a novel moderate halophile
More LessA moderately halophilic, Gram-positive, spore-forming bacterium was isolated from surface saline soil of the Karaj region, Iran. The strain, designated MA-2T, was strictly aerobic with rod-shaped cells that occurred singly, in pairs or short chains. It contained l-orn–d-Asp-type peptidoglycan and the major respiratory lipoquinone was MK-7. It was non-motile and had an ellipsoidal endospore located centrally or subterminally. Growth occurred at 10–49 °C and in the pH range 6·0–9·6. Strain MA-2T grew at salinities of 1–24 % (w/v) NaCl, showing optimal growth at 10 % (w/v). The DNA G+C content was 41·3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MA-2T was associated with Bacillus rRNA group 1. The micro-organisms showing the closest phylogenetic relationship to strain MA-2T were Halobacillus litoralis and Halobacillus trueperi. On the basis of phenotypic and chemotaxonomic characteristics, 16S rRNA gene sequence analysis and DNA–DNA similarity data, it is proposed that strain MA-2T (=DSM 14948T =LMG 21515T) should be placed in the genus Halobacillus as the type strain of a novel species, Halobacillus karajensis sp. nov.
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Corynebacterium atypicum sp. nov., from a human clinical source, does not contain corynomycolic acids
More LessAn unusual Gram-positive, facultatively anaerobic, catalase-positive, diphtheroid-shaped organism originating from an unknown human clinical source was characterized by biochemical, molecular chemical and molecular phylogenetic methods. Based on its morphological and biochemical characteristics and the presence of a murein based on meso-diaminopimelic acid, the unidentified organism was tentatively assigned to the genus Corynebacterium. However, the unknown organism was found to lack the distinctive, short-chain corynomycolic acids that are considered to be characteristic of this genus. Despite the absence of these characteristic lipids, comparative 16S rRNA gene sequencing showed that the unknown bacterium was phylogenetically a member of the genus Corynebacterium and was distinct from all currently known species. Based on both phenotypic and 16S rRNA sequence considerations, it is proposed that the unknown organism be classified as a novel species, Corynebacterium atypicum sp. nov. The type strain of C. atypicum is strain R2070T (=CCUG 45804T =CIP 107431T).
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Description of Enterococcus canis sp. nov. from dogs and reclassification of Enterococcus porcinus Teixeira et al. 2001 as a junior synonym of Enterococcus villorum Vancanneyt et al. 2001
Strains from anal swabs and chronic otitis externa in dogs were shown to be phylogenetically related to the Enterococcus faecium species group. They shared a number of phenotypic characteristics with these species, but they could be easily differentiated by biochemical reactions. In addition, the canine strains were unusual in their nearly complete failure to grow on sodium azide-containing enterococci-selective media and in their Voges–Proskauer reactions (usually negative). By using 16S rRNA sequencing and DNA–DNA hybridization of representative strains, as well as tDNA interspacer gene PCR and SDS-PAGE of whole-cell proteins, the group of canine strains was shown to constitute a novel enterococcal species. The name Enterococcus canis sp. nov. is proposed for this species, with LMG 12316T (=CCUG 46666T) as the type strain. Concurrently, the taxonomic situation and nomenclatural position of Enterococcus porcinus were investigated. As no phenotypic or genotypic differences were found between this species and Enterococcus villorum, the name E. porcinus is considered to be a junior synonym of E. villorum.
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Alicyclobacillus sendaiensis sp. nov., a novel acidophilic, slightly thermophilic species isolated from soil in Sendai, Japan
More LessAn acidophilic, slightly thermophilic bacterium, designated strain NTAP-1T, that produces a thermostable extracellular acid collagenase activity with potential industrial applications was isolated from soil of Aoba-yama Park, Sendai, Japan. The temperature range for growth was 40–65 °C, with an optimum at 55 °C, and the pH range for growth was 2·5–6·5, with an optimum at pH 5·5. Analysis of the 16S rDNA sequence of strain NTAP-1T showed that it is most closely related to strains of the genus Alicyclobacillus. Consistently, the major constituents of the cell-membrane lipid of strain NTAP-1T were ω-alicyclic fatty acids. However, DNA–DNA reassociation studies showed only low similarities (less than 33 %) to any type strain of Alicyclobacillus. On the basis of the phenotypic and genotypic properties, a novel species is proposed, Alicyclobacillus sendaiensis sp. nov., represented by strain NTAP-1T (=JCM 11817T =ATCC BAA-609T).
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Streptococcus oligofermentans sp. nov., a novel oral isolate from caries-free humans
More LessFive streptococcal strains were isolated from dental plaque and saliva of caries-free humans. The cells were Gram-positive, non-spore-forming, non-motile cocci that were arranged in short chains. The strains were catalase-negative, facultatively anaerobic and produced lactic acid exclusively from glucose fermentation. Biochemical analysis that used both conventional methods and the commercial API 20 Strep system showed that the five strains fermented only a few kinds of sugar. The mean DNA G+C content of the five novel strains was 39·5±0·8 mol%. Phylogenetic analysis based on 16S rDNA sequence homology indicated that the new isolates represented a novel member of the mitis group of the genus Streptococcus, related most closely to the recently described species Streptococcus sinensis. DNA–DNA relatedness between novel strain LMG 21535T and type strains of phylogenetically related species of oral streptococci was 7·1–16·4 %. Therefore a novel Streptococcus species, Streptococcus oligofermentans sp. nov., is proposed. The type strain is LMG 21535T=AS 1.3089T.
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Leuconostoc inhae sp. nov., a lactic acid bacterium isolated from kimchi
More LessSix strains of a hitherto unknown bacterium isolated from kimchi, a fermented vegetable food produced in Korea, were characterized by using phenotypic methods, phylogenetic analysis and DNA–DNA hybridization. The novel strains were Gram-positive, non-spore-forming, heterofermentative and spherical or lenticular lactic acid bacteria. Comparative 16S rRNA gene sequencing and DNA relatedness demonstrated that the unknown strains represented a novel clade within the genus Leuconostoc and were close to, but distinct from, Leuconostoc gelidum. The unknown strains were clearly distinguished from all described members of the genus Leuconostoc by using RFLP patterns of genus-specific 16S rRNA gene PCR products with a single endonuclease, BsmAI. Based on the polyphasic evidence, the unknown isolates are classified as Leuconostoc inhae sp. nov. The type strain is strain IH003T (=KCTC 3774T =DSM 15101T).
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Tepidibacter thalassicus gen. nov., sp. nov., a novel moderately thermophilic, anaerobic, fermentative bacterium from a deep-sea hydrothermal vent
A moderately thermophilic, anaerobic, endospore-forming bacterium (strain SC 562T) was isolated from a hydrothermal vent chimney located at 13° N on the East-Pacific Rise at a depth of 2650 m. Cells of strain SC 562T were straight to slightly curved rods, which were 0·7–0·9 μm in diameter and 3·5–6·0 μm in length with peritrichous flagella. Strain SC 562T formed round, refractile endospores in terminally swollen sporangia. The temperature range for growth was 33–60 °C, with an optimum at 50 °C. The pH range for growth was 4·8–8·5, with an optimum at pH 6·5–6·8. Growth of strain SC 562T was observed at NaCl concentrations ranging from 1·5 to 6 % (w/v). The substrates utilized by strain SC 562T included casein, peptone, albumin, yeast extract, beef extract, alanine plus proline and starch. Glucose, maltose, pyruvate, valine and arginine each slightly stimulated growth in the presence of yeast extract. The products of glucose fermentation were ethanol, acetate, H2 and CO2. Strain SC 562T reduced elemental sulfur to hydrogen sulfide. The G+C content of the DNA of strain SC 562T was 24 mol%. 16S rDNA sequence analysis revealed that the isolated organism belonged to cluster XI of the Clostridium subphylum. On the basis of its physiological properties and phylogenetic analyses, it is proposed that strain SC 562T represents the sole species of a novel genus, Tepidibacter; the name Tepidibacter thalassicus is proposed for strain SC 562T (=DSM 15285T =UNIQEM 215T).
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Isolation of Corynebacterium falsenii and description of Corynebacterium aquilae sp. nov., from eagles
Biochemical, molecular chemical and molecular genetic studies were performed on seven unidentified Gram-positive, rod-shaped organisms recovered from eagles. The strains were provisionally identified as Corynebacterium jeikeium with the commercial API Coryne system, but they were able to grow under anaerobic conditions and were non-lipophilic. Comparative 16S rRNA gene sequencing studies demonstrated that the isolates belonged phylogenetically to the genus Corynebacterium. Three strains were identified genotypically as Corynebacterium falsenii; the remaining four strains corresponded to a hitherto unknown lineage within the genus Corynebacterium, associated with a small subcluster of species that included Corynebacterium diphtheriae and its close relatives. The unknown bacterial strains were readily distinguished from these and other species of the genus by biochemical tests. Based on both phenotypic and phylogenetic evidence, it is proposed that the unknown bacterial strains from eagles should be classified as Corynebacterium aquilae sp. nov. (type strain is S-613T=CECT 5993T =CCUG 46511T).
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- Unicellular Eukaryotes
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Three new combinations from the Cryptococcus laurentii complex: Cryptococcus aureus, Cryptococcus carnescens and Cryptococcus peneaus
More LessFifteen strains of the Cryptococcus laurentii complex were reclassified based on sequence analyses of 18S rDNA, the D1/D2 region of the 26S rDNA and the internal transcribed spacer regions, as well as physiological and biochemical properties. The strains were divided into phylogenetic groups I and II. The type strain of C. laurentii (CBS 139T=ATCC 18803T =JCM 9066T =MUCL 30398T =NRRL Y-2536T) was in phylogenetic group I. Phylogenetic group II, which was phylogenetically distant from phylogenetic group I, clustered with Cryptococcus dimennae and Bullera globispora. In phylogenetic group I, the type strain of Torula aurea (CBS 318T=ATCC 32063T =IFO 0372T =NRRL Y-1582T) appeared to be a separate species from C. laurentii, and the designation Cryptococcus aureus comb. nov. is proposed for Torula aurea. Cryptococcus flavescens (formerly Torula flavescens, type strain CBS 942T=ATCC 10668T =DBVPG 6007T =MUCL 30414T) was treated as a synonym of C. laurentii; however, this is a distinct species. The type strains of Torulopsis carnescens (CBS 973T=ATCC 32064T =MUCL 30641T =NRRL Y-1503T), Rhodotorula peneaus (CBS 2409T=ATCC 13546T =MUCL 30643T =NRRL Y-2005T) and Cryptococcus victoriae belonged to phylogenetic group II. Two new combinations, Cryptococcus carnescens comb. nov. (type strain CBS 973T=ATCC 32064T =MUCL 30641T =NRRL Y-1503T) and Cryptococcus peneaus comb. nov. (type strain CBS 2409T=ATCC 13546T =MUCL 30643T =NRRL Y-2005T), are proposed from this group.
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Phylogenetic analysis identifies the ‘megabacterium’ of birds as a novel anamorphic ascomycetous yeast, Macrorhabdus ornithogaster gen. nov., sp. nov.
An organism commonly referred to as ‘megabacterium’ colonizes the gastric isthmus of many species of birds. It is weakly Gram-positive and periodic acid–Schiff-positive and stains with silver stains. Previous studies have shown that it has a nucleus and a cell wall similar to those seen in fungi. Calcofluor white M2R staining suggests that the cell wall contains chitin, a eukaryote-specific substance, and rRNA in situ hybridization demonstrates that it is a eukaryote. To characterize this organism phylogenetically, DNA was extracted from purified cells. rDNA was readily amplified by PCR with pan-fungal DNA primer sets and primer sets derived from the newly determined sequence, but not with bacteria-specific primer sets. Specific primer sets amplified rDNA from isthmus scrapings from an infected bird, but not from a non-infected bird or other control DNA. The sequence was confirmed to derive from the purified organism by in situ rRNA hybridization using a specific probe. Phylogenetic analysis of sequences of the 18S rDNA and domain D1/D2 of 26S rDNA showed the organism to be a previously undescribed anamorphic ascomycetous yeast representing a new genus. The name Macrorhabdus ornithogaster gen. nov., sp. nov. is proposed for this organism. The type material is CBS 9251T (=NRRL Y-27487T).
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