- Volume 60, Issue 9, 2010
Volume 60, Issue 9, 2010
- Validation List
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List of new names and new combinations previously effectively, but not validly, published
The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper, to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors’ names will be included in the author index of the present issue. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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- Notification List
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Notification that new names and new combinations have appeared in volume 60, part 6, of the IJSEM
This listing of names published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol 41 (1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles). Taxonomic opinions included in this List (i.e. the creation of synonyms or the emendation of circumscriptions) cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission.
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- New Taxa
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- Actinobacteria
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Planotetraspora kaengkrachanensis sp. nov. and Planotetraspora phitsanulokensis sp. nov., isolated from soil
Two novel bacterial strains were isolated from tropical rain forest soil from Thailand. Strains A-T 0875T and A-T 1383T stained Gram-positive and were filamentous bacteria that developed cylindrical sporangia containing four oval- to rod-shaped spores at the ends of short sporangiophores on branched aerial mycelium. The cell-wall peptidoglycan contained meso-diaminopimelic acid, glutamic acid and alanine as cell-wall amino acids; whole-cell hydrolysates contained rhamnose, madurose, glucose, galactose and 3-O-methylmannose as whole-cell sugars. The predominant menaquinone was MK-9(H4). Mycolic acids were not detected. The diagnostic phospholipid was phosphatidylethanolamine. The predominant cellular fatty acids were iso-C16 : 0 and 10-methyl-C17 : 0. For both strains, the G+C content of the genomic DNA was 71 mol%. Phenotypic and chemotaxonomic analyses showed that the characteristics of the two isolates were typical of members of the genus Planotetraspora. Furthermore, 16S rRNA gene sequence analysis also indicated that the strains belonged to the genus Planotetraspora but as representatives of two novel species. Following an evaluation of our phenotypic, chemotaxonomic and genotypic studies, two novel species are proposed, Planotetraspora kaengkrachanensis sp. nov. (type strain A-T 0875T=BCC 24832T=NBRC 104272T) and Planotetraspora phitsanulokensis sp. nov. (type strain A-T 1383T=BCC 26045T=NBRC 104273T).
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Haloactinobacterium album gen. nov., sp. nov., a halophilic actinobacterium, and proposal of Ruaniaceae fam. nov.
A Gram-staining-positive, facultatively anaerobic, non-motile and moderately halophilic actinobacterium, designated YIM 93306T, was isolated from a salt lake in Xinjiang province, north-west China, and subjected to a polyphasic taxonomic study. Strain YIM 93306T grew in the presence of 2–16 % (w/v) NaCl and did not grow without NaCl. The peptidoglycan type was A4α with an l-Lys–l-Glu interpeptide bridge. The whole-cell sugars were glucosamine, arabinose, mannose and two unknown sugars. The predominant menaquinone was MK-8(H4). The major fatty acids were iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, one unknown phosphoglycolipid and one unknown phospholipid. The DNA G+C content was 68.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YIM 93306T fell within the radius of the suborder Micrococcineae. Its closest phylogenetic neighbour was the type strain of Ruania albidiflava (AS 4.3142T; 96.2 % 16S rRNA gene sequence similarity), the sole recognized species of the genus Ruania. Sequence similarities between strain YIM 93306T and members of other genera of the suborder Micrococcineae were <95.2 %. On the basis of phylogenetic analysis, phenotypic characteristics and chemotaxonomic differences, a novel genus and species, Haloactinobacterium album gen. nov., sp. nov., is proposed. The type strain of the species is YIM 93306T (=DSM 21368T =KCTC 19413T =CCTCC AB 208069T). Based on phylogenetic characteristics and 16S rRNA gene signature nucleotide patterns, the genera Ruania and Haloactinobacterium gen. nov. are proposed to belong to a novel family, Ruaniaceae fam. nov.
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Amycolatopsis xylanica sp. nov., isolated from soil
An actinomycete, designated CPCC 202699T, was isolated from soil in Qinghai province, China, and its taxonomic status was established. Strain CPCC 202699T contained meso-diaminopimelic acid in its peptidoglycan, arabinose and galactose as the diagnostic sugars in whole-cell hydrolysates, a phospholipid pattern consisting mainly of phosphatidylethanolamine, phosphatidylmethylethanolamine and phosphatidylcholine, MK-9(H4) as the predominant menaquinone and iso-C16 : 0 (18.8 %), iso-C15 : 0 (18.1 %), iso-C14 : 0 (14.2 %), C16 : 1 cis9 (10.9 %) and C17 : 1 cis9 (10.3 %) as the major fatty acids. In the phylogenetic tree based on 16S rRNA gene sequences, strain CPCC 202699T formed a separate branch within the genus Amycolatopsis. However, strain CPCC 202699T showed low 16S rRNA gene sequence similarities (<97.0 %) with type strains of species with validly published names in the genus Amycolatopsis. On the basis of genotypic and phenotypic differences from the closest phylogenetic neighbours of strain CPCC 202699T, a novel species, Amycolatopsis xylanica sp. nov., is proposed. The type strain is CPCC 202699T (=DSM 45285T =KCTC 19581T =CCM 7627T).
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Marmoricola scoriae sp. nov., isolated from volcanic ash
More LessA novel Gram-stain-positive, coccoid actinobacterium, designated strain Sco-D01T, was isolated from volcanic ash collected from Oreum (a parasitic volcanic cone) on Jeju Island, Republic of Korea. Cells were aerobic, oxidase-negative and catalase-positive. Colonies were vivid yellow, circular, smooth and convex. The diagnostic diamino acid in the cell wall was ll-diaminopimelic acid. The predominant menaquinone was MK-8(H4). The polar lipids were phosphatidylinositol, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and an unknown phospholipid. The fatty acid profile was represented by large amounts of saturated, unsaturated, 10-methyl and hydroxyl components. The DNA G+C content of strain Sco-D01T was 72.0 mol%. 16S rRNA gene sequence analysis revealed that strain Sco-D01T belonged to the family Nocardioidaceae and formed a distinct sublineage within the radiation of the genus Marmoricola. The level of DNA–DNA relatedness between strain Sco-D01T and its closest phylogenetic relative, Marmoricola aurantiacus DSM 12652T, was 30.2 % (35.4 % in duplicate measurements). On the basis of phenotypic and DNA–DNA hybridization data, strain Sco-D01T is considered to represent a novel species of the genus Marmoricola, for which the name Marmoricola scoriae sp. nov. is proposed. The type strain is Sco-D01T (=KCTC 19597T=DSM 22127T).
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Arthrobacter alpinus sp. nov., a psychrophilic bacterium isolated from alpine soil
An aerobic, Gram-reaction-positive, non-motile, psychrophilic bacterium, designated strain S6-3T, was isolated from alpine soil. Cells exhibited a rod–coccus growth cycle and produced a yellow pigment. Growth occurred at 1–25 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S6-3T was related to members of the genus Arthrobacter, sharing highest sequence similarities with the type strains of Arthrobacter psychrolactophilus (97.9 %) and Arthrobacter stackebrandtii (97.6 %). Strain S6-3T had MK-9(H2) as the major menaquinone and anteiso-C15 : 0 as the major fatty acid. The cell-wall peptidoglycan was of type A3α l-Lys–l-Thr–Ala3. The predominant cell-wall sugars were galactose and rhamnose. The genomic DNA G+C content of strain S6-3T was 61.9 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness data, strain S6-3T is considered to represent a novel species of the genus Arthrobacter, for which the name Arthrobacter alpinus sp. nov. is proposed. The type strain is S6-3T (=DSM 22274T =CGMCC 1.8950T).
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Haloechinothrix alba gen. nov., sp. nov., a halophilic, filamentous actinomycete of the suborder Pseudonocardineae
More LessA novel halophilic, filamentous actinomycete strain, designated YIM 93221T, was isolated from a salt lake in Xinjiang province, north-west China, and subjected to a polyphasic taxonomic characterization. The isolate grew with 9–23 % (w/v) NaCl and did not grow without NaCl. The isolate formed spiny aerial mycelium and did not form spores at maturity. The isolate contained meso-diaminopimelic acid as the diagnostic diamino acid and glucose, glucosamine, mannose and an unknown sugar as the major whole-cell sugars. The phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides and an unknown phospholipid. MK-8(H4) was the predominant menaquinone. The major fatty acid was iso-C16 : 0. The DNA G+C content was 68.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM 93221T formed a distinct lineage within the suborder Pseudonocardineae and showed 91.9–94.8 % 16S rRNA gene sequence similarity with members of the suborder Pseudonocardineae. On the basis of the evidence from this polyphasic study, a novel genus and species, Haloechinothrix alba gen. nov., sp. nov., are proposed. The type strain of Haloechinothrix alba is YIM 93221T (=DSM 45207T =CCTCC AB 208140T).
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- Archaea
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Fervidicoccus fontis gen. nov., sp. nov., an anaerobic, thermophilic crenarchaeote from terrestrial hot springs, and proposal of Fervidicoccaceae fam. nov. and Fervidicoccales ord. nov.
Two novel thermophilic and slightly acidophilic strains, Kam940T and Kam1507b, which shared 99 % 16S rRNA gene sequence identity, were isolated from terrestrial hot springs of the Uzon caldera on the Kamchatka peninsula. Cells of both strains were non-motile, regular cocci. Growth was observed between 55 and 85 °C, with an optimum at 65–70 °C (doubling time, 6.1 h), and at pH 4.5–7.5, with optimum growth at pH 5.5–6.0. The isolates were strictly anaerobic organotrophs and grew on a narrow spectrum of energy-rich substrates, such as beef extract, gelatin, peptone, pyruvate, sucrose and yeast extract, with yields above 107 cells ml−1. Sulfate, sulfite, thiosulfate and nitrate added as potential electron acceptors did not stimulate growth when tested with peptone. H2 at 100 % in the gas phase inhibited growth on peptone. Glycerol dibiphytanyl glycerol tetraethers (GDGTs) with zero to four cyclopentyl rings were present in the lipid fraction of isolate Kam940T. The G+C content of the genomic DNA of strain Kam940T was 37 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolates were archaea of the phylum Crenarchaeota, only distantly related to the cultured members of the class Thermoprotei (no more than 89 % identity), and formed an independent lineage adjacent to the orders Desulfurococcales and Acidilobales and clustering only with uncultured clones from hot springs of Yellowstone National Park and Iceland as the closest relatives. On the basis of their phylogenetic position and novel phenotypic features, isolates Kam940T and Kam1507b are proposed to be assigned to a new genus and species, Fervidicoccus fontis gen. nov., sp. nov. The type strain of Fervidicoccus fontis is strain Kam940T (=DSM 19380T =VKM B-2539T). The phylogenetic data as well as phenotypic properties suggest that the novel crenarchaeotes form the basis of a new family, Fervidicoccaceae fam. nov., and order, Fervidicoccales ord. nov., within the class Thermoprotei.
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Halopelagius inordinatus gen. nov., sp. nov., a new member of the family Halobacteriaceae isolated from a marine solar saltern
Two extremely halophilic archaea, strains RO5-2T and RO5-14, were isolated from Rudong marine solar saltern in Jiangsu, China. Cells of the two strains were pleomorphic, motile and stained Gram-negative. Colonies were red-pigmented. Strains RO5-2T and RO5-14 were able to grow at 20–50 °C (optimum 37 °C), at 2.6–4.8 M NaCl (optimum 3.4–3.9 M NaCl), at 0.03–0.7 M MgCl2 (optimum 0.5 M MgCl2) and at pH 5.5–8.0 (optimum pH 6.5–7.0). Cells lyse in distilled water and the minimal NaCl concentration to prevent cell lysis was 12 % (w/v). The major polar lipids of the two strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and two major glycolipids chromatographically identical to sulfated mannosyl glucosyl diether (S-DGD-1) and mannosyl glucosyl diether (DGD-1). The 16S rRNA gene sequences of strains RO5-2T and RO5-14 showed 93.4–93.8 % similarity to the closest cultivated relative, Halosarcina pallida. The DNA G+C content of strains RO5-2T and RO5-14 was 61.0 mol% and 59.9 mol%, respectively. The DNA–DNA relatedness between strains RO5-2T and RO5-14 was 86.0 %. The phenotypic, chemotaxonomic and phylogenetic properties suggest that strains RO5-2T and RO5-14 represent a novel species in a new genus within the family Halobacteriaceae, for which the name Halopelagius inordinatus gen. nov., sp. nov. is proposed. The type strain is RO5-2T (=CGMCC 1.7739T =JCM 15773T).
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Methanoculleus hydrogenitrophicus sp. nov., a methanogenic archaeon isolated from wetland soil
More LessAn obligately anaerobic, methanogenic archaeon, strain HCT, was isolated from soil of the Zoige wetland on the Tibetan plateau, China. The strain was isolated through construction of an artificial butyrate-degrading consortium in co-culture with a syntrophic bacterium, ‘Syntrophomonas erecta subsp. sporosyntropha’ JCM 13344. Cells of strain HCT were irregular coccoids, 0.8–2 μm in diameter, that occurred singly and utilized only H2/CO2 for growth and methane production. Growth occurred at 18–45 °C (optimum around 37 °C). The pH for growth was 5.0–8.5 (optimal growth around pH 6.6). The G+C content of the genomic DNA was 60.2 mol%. 16S rRNA gene sequence analysis indicated that strain HCT was affiliated to the genus Methanoculleus, with sequence similarities of 94.8–97.2 % to existing members. However, strain HCT was distinguished from described Methanoculleus species by not using formate for growth or methane formation and not requiring acetate as a growth factor. On the basis of phylogenetic analysis and phenotypic characteristics, the novel species Methanoculleus hydrogenitrophicus sp. nov. is proposed, with strain HCT (=CGMCC 1.5146T =JCM 16311T) as the type strain.
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- Bacteroidetes
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Vitellibacter aestuarii sp. nov., isolated from tidal-flat sediment, and an emended description of the genus Vitellibacter
More LessA Gram-reaction-negative, aerobic, yellowish-orange-pigmented bacterial strain, designated JC2436T, was isolated from tidal-flat sediment of Oi Island in Korea. Comparative 16S rRNA gene sequence analysis indicated its close affiliation to Vitellibacter vladivostokensis, with 96 % sequence similarity to the type strain. Cells grew with 2–6 % NaCl and at 10–41 °C. Orange flexirubin pigments were present. The major isoprenoid quinone was MK-6, the DNA G+C content was 48.7 mol% and the predominant fatty acids (>10 %) were iso-C15 : 0 and iso-C17 : 0 3-OH. The data obtained from this polyphasic study support the classification of this isolate within a novel species in the genus Vitellibacter, for which the name Vitellibacter aestuarii sp. nov. is proposed. The type strain is JC2436T (=IMSNU 14137T =KACC 13727T =KCTC 22361T =JCM 15496T).
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Chryseobacterium treverense sp. nov., isolated from a human clinical source
More LessA yellow-pigmented, Gram-reaction-negative bacterium isolated from a human clinical source was investigated using a polyphasic approach in order to clarify its taxonomic status. Comparative 16S rRNA gene sequence analysis showed that the new isolate constituted a distinct phyletic line within the genus Chryseobacterium, displaying >2.8 % sequence divergence with recognized species of this genus. The generic assignment was confirmed by chemotaxonomic data which revealed a fatty acid profile consisting of straight-chain saturated, monounsaturated and branched-chain fatty acids of iso-/anteiso-types as well as 3-hydroxylated fatty acids; a menaquinone with six isoprene units (MK-6) as the predominant respiratory quinone and sym-homospermidine as the predominant polyamine. The novel isolate could be distinguished from other members of the genus Chryseobacterium by a set of distinct biochemical properties. On the basis of phenotypic and phylogenetic evidence, it is proposed that the new isolate represents a novel species of the genus Chryseobacterium for which the name Chryseobacterium treverense sp. nov. is proposed. The type strain is IMMIB L-1519T (=DSM 22251T=CCUG 57657T).
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Cloacibacterium rupense sp. nov., isolated from freshwater lake sediment
More LessA Gram-negative, yellow-pigmented bacterium, designated strain R2A-16T, was isolated from sediment of Rupa Lake in Nepal and analysed using a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain R2A-16T is affiliated to the genus Cloacibacterium of the family Flavobacteriaceae; 16S rRNA gene sequence similarity between strain R2A-16T and Cloacibacterium normanense CCUG 46293T was 98.07 %. The isolate contained iso-C15 : 0 (35.6 %) as the major fatty acid and menaquinone MK-6 as the predominant respiratory quinone. The G+C content of the genomic DNA was 33.3 mol%. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain R2A-16T represents a novel species of the genus Cloacibacterium, for which the name Cloacibacterium rupense sp. nov. is proposed; the type strain is R2A-16T (=CGMCC 1.7656T =NBRC 104931T).
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Soonwooa buanensis gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from seawater
More LessA Gram-negative, non-motile, non-gliding, strictly aerobic, pale yellow colony-forming, rod-shaped bacterial strain, designated HM0024T, was isolated from coastal seawater of the Yellow Sea and subjected to a polyphasic taxonomy study. Based on 16S rRNA gene sequence similarities, strain HM0024T was most closely related to Chryseobacterium balustinum LMG 8329T (94.4 %), Chryseobacterium scophthalmum LMG 13028T (94.4 %), Chryseobacterium piscium LMG 23089T (94.3 %) and Elizabethkingia meningoseptica ATCC 13253T (94.0 %) and shared less than 92 % sequence similarity with other members of the family Flavobacteriaceae. Phylogenetic analyses showed that strain HM0024T formed an independent phyletic line of descent within the family Flavobacteriaceae. The DNA G+C content of the strain was 29.6 mol% and its major cellular fatty acids (>10 %) were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C17 : 1 ω7c and summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c). The major isoprenoid quinone was MK-6 and the major polar lipids were phosphatidylethanolamine and several aminolipids. Strain HM0024T was differentiated from phylogenetically related members of the family by having lower DNA G+C content, larger proportions of summed feature 3, anteiso-C15 : 0 and iso-C16 : 0 3-OH and particular phenotypic characteristics. On the basis of phenotypic and phylogenetic data, strain HM0024T is classified as a representative of a novel genus and species, for which the name Soonwooa buanensis gen. nov., sp. nov. is proposed. The type strain of Soonwooa buanensis is HM0024T (=KCTC 22689T =CECT 7503T).
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Fontibacter flavus gen. nov., sp. nov., a member of the family ‘Cyclobacteriaceae’, isolated from a hot spring
The taxonomic position of a bright orange-pigmented bacterial strain, designated CC-GZM-130T, isolated from a water sample of the Guan-zing-ling hot spring, southern Taiwan, was studied. The strain was able to grow on nutrient agar at 25–40 °C and in the presence of 1–3 % (w/v) NaCl. Comparative analyses of the 16S rRNA gene sequence showed that the isolate was grouped in the vicinity of the genus Aquiflexum with the highest sequence similarity of 92.1 % to the type strain of Aquiflexum balticum, followed by sequence similarities of 92.0, 91.6 and 91.5 % to the type strains of Algoriphagus ornithinivorans, Algoriphagus hitonicola and Belliella baltica, respectively. The polyamine pattern showed that the major compound was sym-homospermidine. The quinone system was menaquinone MK-7. The polar lipid profile was composed predominantly of phosphatidylethanolamine, three polar lipids and one aminolipid. Minor amounts of other lipids were also detectable. The main characteristics of the fatty acid profiles of strain CC-GZM-130T, B. baltica and Aquiflexum balticum were similar, with iso-C15 : 0, iso-C17 : 1 ω9c and iso-C17 : 0 3-OH as the major fatty acids, but some qualitative and quantitative differences were observed. The DNA G+C content of the novel strain was 53.2 mol%. The isolate clearly differed genotypically and phenotypically from representatives of the most closely related genera. On the basis of these differences, a novel species in a new genus, Fontibacter flavus gen. nov., sp. nov., is proposed with CC-GZM-130T (=CCUG 57694T=CCM 7650T) as the type strain of the type species.
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Flavobacterium glycines sp. nov., a facultative methylotroph isolated from the rhizosphere of soybean
More LessAn aerobic, yellow-pigmented, facultatively methylotrophic, Gram-staining-negative, non-spore-forming bacterium, designated strain Gm-149T, was isolated from the rhizosphere of cultivated soybean in India. Cells were motile by gliding. The predominant cellular fatty acids were iso-C15 : 0, summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c), C16 : 0 3-OH and anteiso-C15 : 0, and the major isoprenoid quinone was MK-6. The G+C content of the genomic DNA of strain Gm-149T was 35.6 mol%. Comparative 16S rRNA gene sequence analysis showed that strain Gm-149T formed a distinct phyletic line within the genus Flavobacterium. Based on levels of pairwise 16S rRNA gene sequence similarity, strain Gm-149T was related most closely to the type strain of Flavobacterium daejeonense (97.1 %), but the level of DNA–DNA relatedness between these two strains was about 11.2 %. On the basis of phenotypic and genotypic data, strain Gm-149T is considered to represent a novel species of the genus Flavobacterium, for which the name Flavobacterium glycines sp. nov. is proposed. The type strain is Gm-149T (=ICMP 17618T=NBRC 105008T).
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- Firmicutes And Related Organisms
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Weissella fabaria sp. nov., from a Ghanaian cocoa fermentation
More LessTwo lactic acid bacteria, strains 257T and 252, were isolated from traditional heap fermentations of Ghanaian cocoa beans. 16S rRNA gene sequence analysis of these strains allocated them to the genus Weissella, showing 99.5 % 16S rRNA gene sequence similarity towards Weissella ghanensis LMG 24286T. Whole-cell protein electrophoresis, fluorescent amplified fragment length polymorphism fingerprinting of whole genomes and biochemical tests confirmed their unique taxonomic position. DNA–DNA hybridization experiments towards their nearest phylogenetic neighbour demonstrated that the two strains represent a novel species, for which we propose the name Weissella fabaria sp. nov., with strain 257T (=LMG 24289T =DSM 21416T) as the type strain. Additional sequence analysis using pheS gene sequences proved useful for identification of all Weissella–Leuconostoc–Oenococcus species and for the recognition of the novel species.
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Classification of ‘Anaerocellum thermophilum’ strain DSM 6725 as Caldicellulosiruptor bescii sp. nov.
The thermophilic, cellulolytic, anaerobic bacterium ‘Anaerocellum thermophilum’ strain Z-1320 was isolated from a hot spring almost two decades ago and deposited in the German Collection of Microorganisms and Cell Cultures (DSMZ) as DSM 6725. The organism was classified as representing a new genus, ‘Anaerocellum’, primarily on its growth physiology, cell-wall type and morphology. The results of recent physiological studies and of phylogenetic and genome sequence analyses of strain DSM 6725 of ‘A. thermophilum’ obtained from the DSMZ showed that its properties differed from those originally described for strain Z-1320. In particular, when compared with strain Z-1320, strain DSM 6725 grew at higher temperatures and had an expanded range of growth substrates. Moreover, the 16S rRNA gene sequence of strain DSM 6725 fell within the Caldicellulosiruptor clade. It is therefore suggested that ‘Anaerocellum thermophilum’ should be classified as a member of the genus Caldicellulosiruptor, for which the name Caldicellulosiruptor bescii sp. nov. is proposed (type strain DSM 6725T=ATCC BAA-1888T). C. bescii sp. nov. DSM 6725T is the most thermophilic cellulose-degrading organism known. The strain was able to grow up to 90 °C (pH 7.2) and degraded crystalline cellulose and xylan as well as untreated plant biomass, including potential bioenergy plants such as poplar and switchgrass.
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Thalassobacillus hwangdonensis sp. nov., isolated from a tidal flat sediment
More LessA Gram-staining-positive, endospore-forming, motile, rod-shaped bacterium, strain AD-1T, was isolated from a tidal flat sediment of the coast of Hwangdo on the Yellow Sea, Korea. Strain AD-1T grew optimally at pH 7.0–7.5 and 40 °C and in the presence of 5–10 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AD-1T was most closely related to Thalassobacillus devorans G-19.1T (98.0 % sequence similarity) and Thalassobacillus cyri HS286T (97.8 %). The cell-wall peptidoglycan was based on meso-diaminopimelic acid and MK-7 was the predominant menaquinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and two unidentified lipids. The major fatty acids (>10 % of total fatty acids) were iso-C15 : 0, iso-C17 : 0 and anteiso-C15 : 0. The DNA G+C content of strain AD-1T was 45.2 mol%. It appears reasonable to classify strain AD-1T as a member of the genus Thalassobacillus. There were differences in fatty acid profiles and phenotypic and genetic characteristics between strain AD-1T and the type strains of the two Thalassobacillus species. On the basis of the data presented, strain AD-1T represents a novel species within the genus Thalassobacillus, for which the name Thalassobacillus hwangdonensis sp. nov. is proposed. The type strain is AD-1T (=KCTC 13254T =CCUG 56607T).
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Vagococcus penaei sp. nov., isolated from spoilage microbiota of cooked shrimp (Penaeus vannamei)
More LessA polyphasic taxonomic study, using phenotypic, phylogenetic and genotypic characterization, was performed on five Gram-stain-positive, catalase-negative, coccus-shaped Vagococcus-like bacteria isolated from the spoilage microbiota of cooked shrimp. Comparative 16S rRNA gene sequence analysis indicated that the isolates belonged to the genus Vagococcus. The five isolates shared 100% 16S rRNA gene sequence similarity, and representative strain CD276T formed a branch that was distinct from the type strains of the six recognized species of the genus Vagococcus (Vagococcus fluvialis CCUG 32704T, V. salmoninarum NCFB 2777T, V. lutrae CCUG 39187T, V. fessus M2661/98/1T, V. carniphilus ATCC BAA-340T and V. elongatus PPC9T). The taxonomic position of strain CD276T was clarified using DNA–DNA hybridization, pulsed-field gel electrophoresis of whole-genome DNA, G+C content determination, cell-wall peptidoglycan typing, fatty acid analysis and biochemical characterization. On the basis of this evidence, a novel species, Vagococcus penaei sp. nov., is proposed. The type strain is CD276T (=LMG 24833T =CIP 109914T).
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Paenibacillus prosopidis sp. nov., isolated from the nodules of Prosopis farcta
A bacterial strain, designated PW21T, was isolated from root nodules of Prosopis farcta in Tunisia. Phylogenetic analysis based on 16S rRNA gene sequences placed the isolate into the genus Paenibacillus, with its closest relatives being Paenibacillus glycanilyticus DS-1T and Paenibacillus castaneae Ch-32T with identity values of 96.9 %. DNA–DNA hybridization measurements showed values of less than 25 % with respect to these two species. The isolate was a Gram-variable, motile and sporulating rod. Catalase activity was positive and oxidase activity was weakly positive. Aesculin, CM-cellulose, xylan and starch were hydrolysed but casein and gelatin were not. Acetoin production was weakly positive and nitrate reduction was negative. Urease production was negative. Growth was supported by many carbohydrates and organic acids as carbon sources. MK-7 was the predominant menaquinone and anteiso-C15 : 0, iso-C16 : 0 and iso-C15 : 0 were the major fatty acids. Major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, a glycolipid, six phospholipids, an unidentified lipid and two unknown aminophosphoglycolipids. meso-Diaminopimelic acid was not detected in the peptidoglycan. The DNA G+C content of the isolate was 52.9 mol%. Phylogenetic, chemotaxonomic and phenotypic analyses showed that strain PW21T should be considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus prosopidis sp. nov. is proposed. The type strain is PW21T (=LMG 25259T =CECT 7506T =DSM 22405T).
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Weissella beninensis sp. nov., a motile lactic acid bacterium from submerged cassava fermentations, and emended description of the genus Weissella
Four Gram-positive, catalase-negative, short rod-shaped or coccoid, heterofermentative lactic acid bacterial strains (2L24P13T, 1L48P15, 1L24P31 and 1L24P34) with unusual phenotypic and genotypic properties were isolated from submerged fermenting cassava on MRS agar. All strains were motile, grew at 15 °C, produced dl-lactic acid from glucose with gas formation and produced ammonia from arginine. Acid was produced from d-fructose, d-galactose, d-glucose, lactose, maltose, d-mannose, melibiose, d-raffinose, sucrose, N-acetylglucosamine and d-mannitol, but not from d-arabinose or xylose. 16S rRNA gene sequence analysis revealed that the strains belonged to the genus Weissella and were most closely related to Weissella ghanensis LMG 24286T . Low DNA−DNA reassociation values were obtained between the isolates and W. ghanensis DSM 19935T. Based on the genetic and phenotypic results, the strains are considered to represent a novel species, for which the name Weissella beninensis sp. nov. is proposed. The type strain is 2L24P13T (=DSM 22752T=LMG 25373T).
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Bacillus rigui sp. nov., isolated from wetland fresh water
More LessTwo Gram-stain-positive strains, WPCB074T and WPCB165, were isolated from fresh water collected from the Woopo wetland (Republic of Korea). Both strains were strictly aerobic, motile, endospore-forming rods. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains WPCB074T and WPCB165 belonged to the genus Bacillus and that strain WPCB074T was most closely related to Bacillus solisalsi YC1T (98.4 % sequence similarity), B. barbaricus V2-BIII-A2T (97.7 %), B. macauensis ZFHKF-1T (96.9 %), B. arsenicus Con a/3T (96.4 %) and B. gelatini LMG 21880T (95.1 %). The 16S rRNA gene sequences of strains WPCB074T and WPCB165 differed at one position (99.9 % similarity), suggesting that these two strains constitute a single species. DNA–DNA relatedness between strain WPCB074T and the type strains of B. solisalsi, B. barbaricus, B. macauensis, B. arsenicus and B. gelatini were 26, 17, 20, 14 and 7 %, respectively. Strain WPCB074T was characterized by having cell-wall peptidoglycan based on meso-diaminopimelic acid, MK-7 as the predominant menaquinone and iso-C15 : 0 and anteiso-C15 : 0 as the major fatty acids. The DNA G+C content of strain WPCB074T was 41.9 mol%. On the basis of phenotypic properties, phylogeny and genomic distinctiveness, strain WPCB074T represents a novel species of the genus Bacillus for which the name Bacillus rigui sp. nov. is proposed. The type strain is WPCB074T (=KCTC 13278T =JCM 16348T).
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Listeria rocourtiae sp. nov.
A Listeria-like strain isolated in Austria from pre-cut lettuce fitted the description of the genus Listeria although it could not be assigned to any of the known species. Comparison of the rrs gene (encoding 16S rRNA) sequence and gene content by DNA-array indicated affiliation to the genus Listeria. Phylogenetic distance from known species of the genus Listeria indicated that it represents a novel species. Since it can be differentiated from all other known species of the genus Listeria by using phenotypic tests, the name Listeria rocourtiae sp. nov. is proposed for the novel species. The type strain is CIP 109804T (=DSM 22097T =Allerberger 700284/02T). The type strain is avirulent as assessed by cell culture assays and inoculation of mice.
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Proteiniclasticum ruminis gen. nov., sp. nov., a strictly anaerobic proteolytic bacterium isolated from yak rumen
More LessTwo strictly anaerobic, proteolytic bacterial strains, designated strain D3RC-2T and D3RC-3r, were isolated from a cellulose-degrading mixed culture enriched from yak rumen content. The strains were Gram-stain negative and non-spore-forming with cell sizes of 0.5–0.8×0.6–2.0 μm. The temperature range for growth was 24–46 °C (optimum 38–39 °C) and the pH range was between 5.6 and 8.7 (optimum 7.0–7.3). Both strains used soya peptone, tryptone, l-phenylalanine, l-leucine, l-methionine, l-serine, l-valine, l-threonine and l-histidine as carbon and nitrogen sources, but did not use any of the saccharides tested. The major fermentation products from PY medium were acetate, propionate and iso-butyrate. The DNA G+C contents of strains D3RC-2T and D3RC-3r were 41.0±0.1 mol% and 41.3±0.1 mol% (HPLC), respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the two strains represented a new phyletic sublineage within the family Clostridiaceae, with <93.8 % 16S rRNA gene sequence similarity to recognized species. On the basis of the phenotypic, genotypic and physiological evidence, strains D3RC-2T and D3RC-3r are proposed as representing a novel species of a new genus, for which the name Proteiniclasticum ruminis gen. nov., sp. nov. is proposed. The type strain of the type species is D3RC-2T (=AS 1.5057T=JCM 14817T).
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Laceyella tengchongensis sp. nov., a thermophile isolated from soil of a volcano
More LessA thermophilic strain, designated YIM 10002T, was isolated from a soil sample of Big Empty Volcano in Tengchong county, Yunnan province, south-west China, and a polyphasic approach was used to investigate its taxonomic position. Strain YIM 10002T formed endospores on both aerial and substrate mycelia. Whole-cell hydrolysates contained meso-diaminopimelic acid, ribose, xylose and glucose. The major fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The predominant menaquinone was MK-9. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides, together with some unknown phospholipids. The G+C content of its genomic DNA was 48.6 mol%. All of these chemotaxonomic data together with morphological characters consistently assigned strain YIM 10002T to the genus Laceyella. 16S rRNA gene sequence analysis showed that strain YIM 10002T was most closely related to Laceyella sacchari KCTC 9790T and Laceyella putida KCTC 3666T (99.9 and 98.0 % 16S rRNA gene sequence similarity, respectively). However, strain YIM 10002T showed relatively low DNA–DNA relatedness (34.0 and 39.0 %, respectively) with the above strains. Therefore, strain YIM 10002T represents a novel species of the genus Laceyella, for which the name Laceyella tengchongensis sp. nov. is proposed. The type strain is YIM 10002T (=DSM 45262T =CCTCC AA 208050T).
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Clostridium arbusti sp. nov., an anaerobic bacterium isolated from pear orchard soil
More LessAn obligately anaerobic, Gram-positive, spore-forming bacterial strain, designated SL206T, was isolated from pear orchard soils. Strain SL206T cells were straight or slightly curved rods, with motility by peritrichate flagella. Cell walls contained meso-diaminopimelic acid; wall sugars were glucose, rhamnose and mannose. The major fatty acids were C16 : 0, C18 : 1 ω9c and summed feature 10 (containing C18 : 1 ω11c/9t/6t). API 20A reactions were negative for oxidase, catalase and acid production from l-rhamnose, sucrose, trehalose, d-xylose, melezitose, salicin and d-sorbitol, and positive for acid production from d-glucose, sucrose, maltose, d-mannose and raffinose. Glucose was fermented to acetate, butyrate, CO2, H2 and ethanol in culture. The G+C content of the genomic DNA was 31.1 mol%. Based on comparative 16S rRNA gene sequence analysis, the isolate belonged to the genus Clostridium and formed a clade with Clostridium pasteurianum. The species most closely related to strain SL206T were C. pasteurianum (98.6 % similarity) and Clostridium acidisoli (97.8 % similarity). In DNA–DNA relatedness studies, the isolate had 59.5 % relatedness with C. pasteurianum and thus represented a unique species. On the basis of these studies, strain SL206T (=KCTC 5449T =JCM 14858T) is proposed to represent the type strain of a novel species, Clostridium arbusti sp. nov.
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- Other Bacteria
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Deinococcus wulumuqiensis sp. nov., and Deinococcus xibeiensis sp. nov., isolated from radiation-polluted soil
The taxonomic positions of two gamma- and UV-ray-resistant strains isolated from radiation-polluted soil in north-west China were determined in a polyphasic study. The organisms, designated R12T and R13T, were Gram-stain-positive, non-spore-forming cocci, which contained MK-8 as the major respiratory quinone and C16 : 1 ω7c and C16 : 0 as major fatty acids. The cell walls of strains R12T and R13T contained ornithine. Phylogenetic analysis based on 16S rRNA gene sequences and DNA–DNA hybridizations showed that strains R12T and R13T are members of novel species belonging to the genus Deinococcus, with Deinococcus radiodurans DSM 20539T as the closest relative. The isolates R12T and R13T shared 97 and 97.1 % 16S rRNA gene similarity, respectively, and 29.5 and 33.3 % DNA–DNA relatedness, respectively, with D. radiodurans DSM 20539T. The DNA G+C contents of isolates R12T and R13T were 66.7 and 63.8 %, respectively. On the basis of phenotypic tests and other results, two species, Deinococcus wulumuqiensis sp. nov. (type strain R12T =CGMCC 1.8884T =NBRC 105665T) and Deinococcus xibeiensis sp. nov. (type strain R13T =CGMCC 1.8885T =NBRC 105666T), are proposed.
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Staphylococcus rostri sp. nov., a haemolytic bacterium isolated from the noses of healthy pigs
More LessTwenty coagulase-negative Staphylococcus strains displaying α-haemolysis (δ-haemolysin) on sheep-blood agar were isolated from the noses of different pigs in Switzerland. The strains were Gram-stain-positive, non-motile cocci, catalase-positive and coagulase-negative. Sequence analysis of the 16S rRNA gene, sodA, rpoB, dnaJ and hsp60 and phylogenetic characteristics revealed that the strains showed the closest relatedness to Staphylococcus microti CCM 4903T and Staphylococcus muscae DSM 7068T. The strains can be differentiated from S. microti by the absence of mannose fermentation and arginine arylamidase and from S. muscae by the absence of β-glucuronidase activity and production of alkaline phosphatase. The chosen type strain ARI 262T shared 20.1 and 31.9 % DNA relatedness with S. microti DSM 22147T and S. muscae CCM 4903T, respectively, by DNA–DNA hybridization. iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0 were the most common fatty acids. Cell-wall structure analysis revealed the peptidoglycan type A3α l-Lys–Gly2–l-Ser–Gly (type A11.3). The presence of teichoic acid was determined by sequencing the N-acetyl-β-d-mannosaminyltransferase gene tarA, which is involved in biosynthesis of ribitol teichoic acid. Menaquinone 7 (MK-7) was the predominant respiratory quinone. The G+C content of ARI 262T was 38.8 mol%. The isolated strains represent a novel species of the genus Staphylococcus, for which we propose the name Staphylococcus rostri sp. nov. The type strain is ARI 262T (=DSM 21968T =CCUG 57266T) and strain ARI 602 (=DSM 21969 =CCUG 57267) is a reference strain.
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Caldithrix palaeochoryensis sp. nov., a thermophilic, anaerobic, chemo-organotrophic bacterium from a geothermally heated sediment, and emended description of the genus Caldithrix
A novel thermophilic, strictly anaerobic, chemo-organotrophic bacterium, designated MCT, was isolated from a geothermally heated sediment of a marine hydrothermal system at Palaeochory Bay, Milos, Greece. Cells of strain MCT were rods of variable length (4–12 μm) and width (0.2–0.3 μm), occurring as single cells or forming large aggregates that were visible as flocs. Strain MCT grew optimally at pH 7.0 and 60 °C and with 3 % (w/v) NaCl. Strain MCT grew chemo-organoheterotrophically and fermented peptides and di- and polysaccharides in the presence of 0.1 g yeast extract l−1. The DNA G+C content of strain MCT was 43.3 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed strain MCT within the genus Caldithrix. However, strain MCT possessed certain phenotypic features that differentiated it from the type strain of the only species of the genus Caldithrix described to date. On the basis of phylogenetic and phenotypic characteristics, it is proposed that strain MCT represents a novel species, Caldithrix palaeochoryensis sp. nov. The type strain is MCT (=DSM 21940T =VKM B-2536T). In addition, an emended description of the genus Caldithrix is presented.
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- Proteobacteria
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Reclassification of Bacteroides ureolyticus as Campylobacter ureolyticus comb. nov., and emended description of the genus Campylobacter
More LessThe protein profiles, genomic amplified fragment length polymorphism patterns and 16S rRNA and cpn60 gene sequences of a diverse collection of 26 Bacteroides ureolyticus strains, along with published data on their DNA base, respiratory quinone and cellular fatty acid compositions, were used to reassess the taxonomy of this bacterial species. The results demonstrate that this organism is most appropriately allocated in the genus Campylobacter. The presence of much higher amounts of 18 : 1ω7c in its cellular fatty acid profile and its ability to digest gelatin and casein are the characteristics that differentiate it from present species of the genus Campylobacter. Therefore we propose to reclassify this species incertae sedis into the genus Campylobacter as Campylobacter ureolyticus with strain LMG 6451T (=CCUG 7319T =NCTC 10941T) as the type strain.
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Catellibacterium aquatile sp. nov., isolated from fresh water, and emended description of the genus Catellibacterium Tanaka et al. 2004
More LessA Gram-negative, rod-shaped, non-pigmented, non-spore-forming bacterial strain that was motile by a single polar flagellum, designated A1-9T, was isolated from Daqing reservoir in north-east China and its taxonomic position was studied using a polyphasic approach. Strain A1-9T was non-halophilic, strictly aerobic and heterotrophic and lacked carotenoids, internal membranes and genes for photosynthesis (puf genes). Strain A1-9T grew at 10–40 °C (optimum, 25–30 °C) and pH 5.5–9.0 (optimum, pH 6.0–6.5) and tolerated up to 1.0 % NaCl (w/v). Neither phototrophic nor fermentative growth was observed. The predominant ubiquinone was Q-10 and the major fatty acid was C18 : 1 ω7c (70 %). The DNA G+C content was 64.4 mol% (T m). Phylogenetic analyses based on the 16S rRNA gene sequence revealed that strain A1-9T, together with Catellibacterium nectariphilum AST4T, formed a deep line within the ‘Rhodobacter clade’ of the family Rhodobacteraceae and strain A1-9T showed 94.2 % 16S rRNA gene sequence similarity to C. nectariphilum AST4T. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain A1-9T is considered to represent a novel species of the genus Catellibacterium, for which the name Catellibacterium aquatile sp. nov. is proposed. The type strain is A1-9T (=CGMCC 1.7029T =NBRC 104254T).
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Agaricicola taiwanensis gen. nov., sp. nov., an alphaproteobacterium isolated from the edible mushroom Agaricus blazei
A Gram-negative, beige-pigmented, aerobic, motile, club-shaped bacterium, designated strain CC-SBABM117T, was isolated from the stipe of the edible mushroom Agaricus blazei Murrill. 16S rRNA gene sequence analysis demonstrated that the strain shared <93 % similarity with the type strains of species in the genera Pannonibacter, Methylopila, Nesiotobacter and Stappia. The organism was unable to produce acid from carbohydrates, but utilized a number of organic acids and amino acids. Ubiquinone 10 (Q-10) was the major respiratory quinone and C18 : 1 ω7c, C19 : 0 cyclo ω8c, C16 : 0 and C18 : 0 were the predominant fatty acids. The predominant polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content of strain CC-SBABM117T was 62.7 mol%. On the basis of 16S rRNA gene sequence analysis and chemotaxonomic and physiological data, strain CC-SBABM117T is considered to represent a novel species of a new genus, for which the name Agaricicola taiwanensis gen. nov., sp. nov. is proposed. The type strain of Agaricicola taiwanensis is CC-SBABM117T (=BCRC 17964T =CCM 7684T).
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Burkholderia acidipaludis sp. nov., aluminium-tolerant bacteria isolated from Chinese water chestnut (Eleocharis dulcis) growing in highly acidic swamps in South-East Asia
More LessTwo strains of aluminium-tolerant bacteria, SA33T and 7A078, were isolated from Chinese water chestnut (Eleocharis dulcis) growing in highly acidic swamps (pH 2–4) in actual acid sulfate soil areas of Vietnam (SA33T) and Thailand (7A078). The strains were Gram-negative, aerobic, non-spore-forming rods, 0.6–0.7 μm wide and 1.3–1.7 μm long. These strains showed good growth at pH 3.0–8.0 and 17–37 °C. The organisms contained ubiquinone Q-8 as the predominant isoprenoid quinone and C16 : 0, C18 : 1 ω7c and C17 : 0 cyclo as the major fatty acids. Their fatty acid profiles were similar to those reported for other Burkholderia species. The DNA G+C content of these strains was 64 mol%. On the basis of 16S rRNA gene sequence similarity, the strains were shown to belong to the genus Burkholderia. Although the 16S rRNA gene sequence similarity values calculated for strain SA33T to 7A078 and the type strains of Burkholderia kururiensis, B. sacchari and B. tuberum were 100, 97.3, 97.1 and 97.0 %, respectively, strains SA33T and 7A078 formed a group that was distinct in the phylogenetic trees; the DNA–DNA relatedness of strain SA33T to 7A078 and these three type strains were respectively 90, 47, 46 and 45 %. The results of physiological and biochemical tests, including whole-cell protein pattern analysis, allowed phenotypic differentiation of these strains from described Burkholderia species. Therefore, strains SA33T and 7A078 represent a novel species, for which the name Burkholderia acidipaludis sp. nov. is proposed. The type strain is SA33T (=NBRC 101816T =VTCC-D6-6T). Strain 7A078 (=NBRC 103872 =BCC 36999) is a reference strain.
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Aeromonas taiwanensis sp. nov. and Aeromonas sanarellii sp. nov., clinical species from Taiwan
Two clinical Aeromonas strains (A2-50T and A2-67T) recovered from the wounds of two patients in Taiwan could not be assigned to any known species of this genus based on their 16S rRNA gene sequences, which showed similarities of 99.6–99.8 % to those of the type strains of Aeromonas caviae, A. trota and A. aquariorum. The rpoD phylogenetic tree allocated these strains to two novel and independent phylogenetic lines, the neighbouring species being A. caviae, the type strain of which showed 93.2 % similarity (56 bp differences) to strain A2-50T and 92.2 % (63 bp differences) to strain A2-67T. A multilocus phylogenetic analysis of five housekeeping genes (gyrB, rpoD, recA, dnaJ and gyrA; 3684 bp) confirmed that the two strains formed independent phylogenetic lineages within the genus. These data, together with phenotypic characterization and DNA–DNA reassociation results, revealed that these strains represent novel Aeromonas species, for which the names Aeromonas taiwanensis sp. nov. (type strain A2-50T =CECT 7403T =LMG 24683T) and Aeromonas sanarellii sp. nov. (type strain A2-67T =CECT 7402T =LMG 24682T) are proposed.
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Castellaniella daejeonensis sp. nov., isolated from soil
More LessA Gram-negative, non-spore-forming, motile, facultatively anaerobic bacterium, designated strain MJ06T, was isolated from oil-contaminated soil and was characterized taxonomically by using a polyphasic approach. Strain MJ06T contained ubiquinone Q-8 as the major respiratory lipoquinone, putrescine as the predominant polyamine and phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol as major polar lipids. The G+C content of the genomic DNA of strain MJ06T was 66.2 mol%. The major fatty acids were summed feature 4 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH; 32.5 %), C16 : 0 (22.8 %) and summed feature 7 (one or more of C18 : 1 ω7c, C18 : 1 ω9t and C18 : 1 ω12t; 14.9 %). Comparative 16S rRNA gene sequence analysis showed that strain MJ06T belonged to the family Alcaligenaceae, class Betaproteobacteria, and joined the evolutionary radiation enclosed by the genus Castellaniella. Levels of 16S rRNA gene sequence similarity between strain MJ06T and its phylogenetically closest relatives, Castellaniella denitrificans NKNTAUT, Castellaniella defragrans 54PinT, Castellaniella ginsengisoli DCY36T and Castellaniella caeni Ho-11T, were 98.6, 98.3, 97.8 and 97.3 %, respectively. Levels of similarity between strain MJ06T and the type strains of all other recognized species in the family Alcaligenaceae were below 95.0 %. Strain MJ06T exhibited relatively low levels of DNA–DNA relatedness with respect to C. defragrans DSM 12141T (52 %), C. denitrificans DSM 11046T (31 %), C. ginsengisoli KCTC 22398T (18 %) and C. caeni KCTC 12197T (15 %). On the basis of its phenotypic and genotypic properties together with phylogenetic distinctiveness, strain MJ06T is considered to represent a novel species of the genus Castellaniella, for which the name Castellaniella daejeonensis sp. nov. is proposed. The type strain is MJ06T (=KCTC 22454T =JCM 16240T).
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Pseudidiomarina aestuarii sp. nov., a marine bacterium isolated from shallow coastal seawater
More LessA non-motile, rod-shaped and aerobic marine bacterium, designated strain KYW314T, was isolated from seawater collected from the South Sea, Republic of Korea. Cells were Gram-negative, catalase- and oxidase-positive and had proteolytic activity. The major fatty acids were iso-C15 : 0 (17.2 %), C16 : 0 (11.1 %), iso-C17 : 0 (10.5 %) and C18 : 1 ω7c (10.0 %). The DNA G+C content was 56.4 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain KYW314T formed a lineage within the genus Pseudidiomarina (95.4–97.3 % sequence similarity) and a distinct branch within the clade containing Pseudidiomarina taiwanensis PIT1T and Pseudidiomarina sediminum c121T. Phenotypic characteristics could distinguish strain KYW314T from members of the genus Pseudidiomarina. On the basis of the data presented, strain KYW314T represents a novel species, for which the name Pseudidiomarina aestuarii sp. nov. is proposed. The type strain is KYW314T (=KCTC 22740T =JCM 16344T).
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Pseudomonas taiwanensis sp. nov., isolated from soil
More LessA novel Gram-negative, rod-shaped, motile, non-spore-forming bacterial strain, CMST, isolated from soil was characterized using phenotypic and molecular taxonomic methods. 16S rRNA gene sequence analysis revealed that the organism belongs phylogenetically to the genus Pseudomonas. Pseudomonas monteilii, P. plecoglossicida and P. mosselii were the most closely related species, with 16S rRNA gene sequence similarities to the respective type strains of 99.79, 99.73 and 99.59 %. Relatively low gyrB gene sequence similarities (<90 %) and DNA–DNA reassociation values (<51 %) were obtained between the strain and its phylogenetically closest neighbours. The G+C content of strain CMST was 62.7 mol%. The major cellular fatty acids were C18 : 1 ω7c, summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C10 : 0 3-OH. Based on the phenotypic and genetic evidence, the strain is suggested to represent a novel species, for which the name Pseudomonas taiwanensis sp. nov. is proposed. The type strain is CMST (=BCRC 17751T =DSM 21245T).
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Rhodobacter johrii sp. nov., an endospore-producing cryptic species isolated from semi-arid tropical soils
More LessAn oval to rod-shaped, phototrophic, purple non-sulfur bacterium, strain JA192T, was isolated from an enrichment culture of a pasteurized rhizosphere soil sample from a field cultivated with jowar (sorghum) collected from Godumakunta village near Hyderabad, India. Strain JA192T is Gram-negative, motile and produces endospores. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that the strain JA192T is closely related to Rhodobacter sphaeroides 2.4.1T (99.9 % sequence similarity), Rba. megalophilus JA194T (99.8 %) and Rba. azotoformans KA25T (98.1 %) and clusters with other species of the genus Rhodobacter of the family Rhodobacteraceae. However, DNA–DNA hybridization with Rba. sphaeroides DSM 158T, Rba. megalophilus JA194T and Rba. azotoformans JCM 9340T showed relatedness of only 38–57 % with respect to strain JA192T. On the basis of 16S rRNA gene sequence analysis, DNA–DNA hybridization data and morphological, physiological and chemotaxonomic characters, strain JA192T represents a novel species of the genus Rhodobacter, for which the name Rhodobacter johrii sp. nov. is proposed. The type strain is JA192T (=DSM 18678T =JCM 14543T =MTCC 8172T).
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Brevundimonas vancanneytii sp. nov., isolated from blood of a patient with endocarditis
More LessA Gram-negative, rod-shaped, non-spore-forming bacterial strain, designated LMG 2337T, was isolated from the blood of a patient with endocarditis and characterized. The strain was affiliated with the alphaproteobacterial genus Brevundimonas, with Brevundimonas diminuta LMG 2089T (98.3 % 16S rRNA gene sequence similarity) and Brevundimonas terrae KSL-145T (97.5 %) as its closest relatives. This affiliation was supported by chemotaxonomic data: the G+C content was 66.3 mol %, the major polar lipids were phosphatidyl diacylglycerol, sulfoquinovosyl diacylglycerol and phosphatidyl glucopyranosyl diacylglycerol and the major fatty acids were summed feature 7 (one or more of C18 : 1 ω7c, C18 : 1 ω9t and C18 : 1 ω12t) and C16 : 0. Strain LMG 2337T displayed an unusually broad substrate spectrum. The results from DNA–DNA hybridization and physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain LMG 2337T from all of the type strains of hitherto-described Brevundimonas species. The strain therefore represents a novel species, for which the name Brevundimonas vancanneytii sp. nov. is proposed, with type strain LMG 2337T (=CCUG 1797T =ATCC 14736T).
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Pontibaca methylaminivorans gen. nov., sp. nov., a member of the family Rhodobacteraceae
More LessThe alphaproteobacterial strains GRP21T and PH34, which were isolated from coastal sediment of the East Sea, Korea, were subjected to a polyphasic taxonomic investigation. The strains were Gram-negative, non-motile, non-spore-forming, oval-shaped rods that produced creamy-white colonies on tryptic soy agar, required NaCl for growth, contained Q-10 as the predominant ubiquinone, contained 16 : 0, 18 : 1ω7c and 19 : 0 cyclo ω8c as major fatty acids and had polar lipid profiles consisting of phosphatidylcholine, phosphatidylglycerol, an unknown aminolipid, an unknown phospholipid and three unknown lipids. Phylogenetic analysis, based on 16S rRNA gene sequencing, showed that the strains were most closely related to Donghicola eburneus KCTC 12735T, with 94.5 % sequence similarity, but formed a separate lineage within the family Rhodobacteraceae. The combined genotypic and phenotypic data supported the conclusion that the strains represent a novel genus and species, for which the name Pontibaca methylaminivorans gen. nov., sp. nov. is proposed. The type strain of Pontibaca methylaminivorans is GRP21T (=KCTC 22497T =DSM 21219T).
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Pseudoalteromonas lipolytica sp. nov., isolated from the Yangtze River estuary
More LessA strictly aerobic, Gram-negative, non-pigmented bacterial strain, designated LMEB 39T, was isolated from a seawater sample collected from the Yangtze River estuary near the East China Sea and was examined physiologically, chemotaxonomically and phylogenetically. The novel isolate was motile by a single polar flagellum and positive for nitrate reduction and decomposition of casein, gelatin, Tween 20 and Tween 80, but negative for indole production. Chemotaxonomic analysis revealed ubiquinone-8 as the predominant respiratory quinone and phosphatidylethanolamine and phosphatidylglycerol as major polar lipids. The major fatty acids were C16 : 1 ω7c/iso-C15 : 0 2-OH, C16 : 0, C18 : 1 ω7c, C12 : 0 3-OH, C17 : 1 ω8c and C17 : 0. The genomic DNA G+C content was 42.3 mol%. Comparative 16S rRNA gene sequence analysis revealed that the isolate belongs to the genus Pseudoalteromonas. Strain LMEB 39T exhibited the closest phylogenetic affinity to Pseudoalteromonas byunsanensis JCM 12483T (97.4 % sequence similarity). The DNA–DNA reassociation values between strain LMEB 39T and P. byunsanensis JCM 12483T and Pseudoalteromonas undina DSM 6065T (97.2 % sequence similarity) were 31.7 and 30.3 %, respectively. On the basis of phenotypic and genotypic data, strain LMEB 39T represents a novel species of the genus Pseudoalteromonas, for which the name Pseudoalteromonas lipolytica sp. nov. is proposed; the type strain is LMEB 39T (=CGMCC 1.8499T=JCM 15903T).
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Alishewanella agri sp. nov., isolated from landfill soil
More LessStrain BL06T was isolated from landfill soil in Pohang, Korea. Strain BL06T is Gram-negative, aerobic, non-motile and rod-shaped. For growth, the NaCl range is 0–6 % (w/v), the temperature range is 10–44 °C and the pH range is 5.5–12.0. Based on the 16S rRNA gene and gyrase B (gyrB) gene sequences, phylogenetic analysis showed that strain BL06T is associated with the genus Alishewanella and related closely to the type strains of Alishewanella species (98.8 % 16S rRNA gene sequence similarity to Alishewanella aestuarii, 98.7 % to Alishewanella fetalis and 98.5 % to Alishewanella jeotgali). Physiological and biochemical tests verified that strain BL06T is genotypically and phenotypically different from previously described species in the genus Alishewanella. DNA–DNA hybridization experiments showed that relatedness between the genomic DNA of strain BL06T and type strains of other Alishewanella species is <41 %. These findings suggest strongly that the strain represents a novel species, despite high 16S rRNA gene sequence similarity between strain BL06T and related strains. Therefore, strain BL06T (=KCTC 22400T=JCM 15597T) is proposed to represent a novel species in the genus Alishewanella, named Alishewanella agri sp. nov.
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Erythrobacter nanhaisediminis sp. nov., isolated from marine sediment of the South China Sea
A novel Gram-negative, orange-pigmented, slightly halophilic, rod-shaped bacterium, strain T30T, was isolated from sediment from the South China Sea. Phylogenetic analysis showed that strain T30T was a member of the genus Erythrobacter, sharing highest 16S rRNA gene sequence similarities with Erythrobacter aquimaris JCM 12189T (99.5 %) and Erythrobacter vulgaris DSM 17792T (99.0 %). Levels of DNA–DNA relatedness between strain T30T and closely related strains of Erythrobacter species ranged from 14.5 to 56.9 %.The isolate lacked bacteriochlorophyll a and contained ubiquinone-10 as the predominant respiratory lipoquinone. The major fatty acids of this strain were C18 : 1 ω7c (38.2 %) and C16 : 1 ω7c /C16 : 1 ω6c (17.4 %). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine and phosphatidylglycerol. The DNA G+C content of strain T30T was 59.5 mol%. On the basis of phenotypic and phylogenetic data, a novel species, Erythrobacter nanhaisediminis sp. nov., is proposed; the type strain is T30T (=CGMCC 1.7715T=JCM 16125T).
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- Eukaryotic Micro-Organisms
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Herpetomonas trimorpha sp. nov. (Trypanosomatidae, Kinetoplastida), a parasite of the biting midge Culicoides truncorum (Ceratopogonidae, Diptera)
More LessMonoxenous trypanosomatid Herpetomonas trimorpha sp. nov. was isolated from the digestive tract of the biting midge Culicoides truncorum (Ceratopogonidae, Diptera). This species forms three distinct morphotypes in culture: the microflagellate promastigote, the small promastigote and the long promastigote. The last form is unique for the newly described species. Phylogenetic analyses of SSU rRNA and glycosomal glyceraldehyde phosphate dehydrogenase genes showed that H. trimorpha sp. nov. is the closest relative of Herpetomonas ztiplika, another monoxenous trypanosomatid isolated from biting midges. However, morphological and randomly amplified polymorphic DNA analyses confirmed that H. trimorpha sp. nov. is distinct from H. ztiplika.
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Lachancea nothofagi sp. nov., a yeast associated with Nothofagus species in Patagonia, Argentina
More LessSix strains of a novel yeast species were isolated from Nothofagus species trees in native forests in Patagonia, Argentina. The strains were isolated from bark, fluxes and the ectomycorrhizospheric soil fraction of Nothofagus antarctica, Nothofagus nervosa and Nothofagus pumilio. Analysis of the D1/D2 large-subunit rDNA sequences indicated that the novel species belonged to the genus Lachancea and is closely related to Lachancea meyersii. The name Lachancea nothofagi sp. nov. is proposed to accommodate these strains. The type strain is UWOPS 99-807.3T (=CBS 11611T=NRRL Y-48670T).
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Cystobasidiomycetes yeasts from Patagonia (Argentina): description of Rhodotorula meli sp. nov. from glacial meltwater
More LessA basidiomycetous yeast, strain CRUB 1032T, which formed salmon-pink colonies, was isolated from glacial meltwater in Patagonia, Argentina. Morphological, physiological and biochemical characterization indicated that this strain belonged to the genus Rhodotorula. Molecular taxonomic analysis based on the 26S rDNA D1/D2 domain and internal transcribed spacer region sequences showed that strain CRUB 1032T represents an undescribed yeast species, for which the name Rhodotorula meli sp. nov. is proposed (type strain is CRUB 1032T=CBS 10797T=JCM 15319T). Phylogenetic analysis showed that Rhodotorula lamellibrachii was the closest known species, which, together with R. meli, formed a separate cluster related to the Sakaguchia clade within the Cystobasidiomycetes. Additional Patagonian yeast isolates of the class Cystobasidiomycetes are also investigated in the present work.
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- Evolution, Phylogeny And Biodiversity
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Partial recN gene sequencing: a new tool for identification and phylogeny within the genus Streptococcus
More LessPartial sequences of the recN gene (1249 bp), which encodes a recombination and repair protein, were analysed to determine the phylogenetic relationship and identification of streptococci. The partial sequences presented interspecies nucleotide similarity of 56.4–98.2 % and intersubspecies similarity of 89.8–98 %. The mean DNA sequence similarity of recN gene sequences (66.6 %) was found to be lower than those of the 16S rRNA gene (94.1 %), rpoB (84.6 %), sodA (74.8 %), groEL (78.1 %) and gyrB (73.2 %). Phylogenetically derived trees revealed six statistically supported groups: Streptococcus salivarius, S. equinus, S. hyovaginalis/S. pluranimalium/S. thoraltensis, S. pyogenes, S. mutans and S. suis. The ‘mitis’ group was not supported by a significant bootstrap value, but three statistically supported subgroups were noted: Streptococcus sanguinis/S. cristatus/S. sinensis, S. anginosus/S. intermedius/S. constellatus (the ‘anginosus’ subgroup) and S. mitis/S. infantis/S. peroris/S. oralis/S. oligofermentans/S. pneumoniae/S. pseudopneumoniae. The partial recN gene sequence comparison highlighted a high percentage of divergence between Streptococcus dysgalactiae subsp. dysgalactiae and S. dysgalactiae subsp. equisimilis. This observation is confirmed by other gene sequence comparisons (groEL, gyrB, rpoB and sodA). A high percentage of similarity was found between S. intermedius and S. constellatus after sequence comparison of the recN gene. To study the genetic diversity among the ‘anginosus’ subgroup, recN, groEL, sodA, gyrB and rpoB sequences were determined for 36 clinical isolates. The results that were obtained confirmed the high genetic diversity within this group of streptococci.
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- International Committee On Systematics Of Prokaryotes
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- Minutes
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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Volume 65 (2015)
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Volume 64 (2014)
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Volume 1 (1951)