- Volume 60, Issue 11, 2010
Volume 60, Issue 11, 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 8, 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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Pseudonocardia tropica sp. nov., an endophytic actinomycete isolated from the stem of Maytenus austroyunnanensis
A novel strain, designated YIM 61452T, was isolated from the stem of Maytenus austroyunnanensis collected from the tropical rainforest of Xishuangbanna, Yunnan Province, south-west China. The strain was characterized taxonomically by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 61452T belonged to the genus Pseudonocardia and was most closely related to Pseudonocardia alni IMSNU 20049T (99.5 %), Pseudonocardia antarctica DVS 5a1T (99.5 %) and Pseudonocardia carboxydivorans Y8T (99.4 %). The chemotaxonomic properties of strain YIM 61452T, for example MK-8(H4) as the predominant quinone system and iso-C16 : 0 and iso-C16 : 1 H as the major fatty acids, were also consistent with its classification within the genus Pseudonocardia. Strain YIM 61452T could be differentiated from closely related species of the genus Pseudonocardia by phenotypic and genotypic analysis. DNA–DNA hybridization experiments between strain YIM 61452T and closely related reference strains further confirmed that strain YIM 61452T represented a novel taxon of the genus Pseudonocardia. Therefore, strain YIM 61452T represents a novel species, for which the name Pseudonocardia tropica sp. nov. is proposed. The type strain is YIM 61452T (=DSM 45199T=CCTCC AA 208018T).
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Marisediminicola antarctica gen. nov., sp. nov., an actinobacterium isolated from the Antarctic
More LessStrain ZS314T was isolated from a sandy intertidal sediment sample collected from the coastal area off the Chinese Antarctic Zhongshan Station, east Antarctica (6 ° 22′ 13″ S 7 ° 21′ 41″ E). The cells were Gram-positive, motile, short rods. The temperature range for growth was 0–26 °C and the pH for growth ranged from 5 to 10, with optimum growth occurring within the temperature range 18–23 °C and pH range 6.0–8.0. Growth occurred in the presence of 0–6 % (w/v) NaCl, with optimum growth occurring in the presence of 2–4 % (w/v) NaCl. Strain ZS314T had MK-10 as the major menaquinone and anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0 as major fatty acids. The cell-wall peptidoglycan type was B2β with ornithine as the diagnostic diamino acid. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The genomic DNA G+C content was approximately 67 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain ZS314T represents a new lineage in the family Microbacteriaceae. On the basis of the phylogenetic analyses and phenotypic characteristics, a new genus, namely Marisediminicola gen. nov., is proposed, harbouring the novel species Marisediminicola antarctica sp. nov. with the type strain ZS314T (=DSM 22350T =CCTCC AB 209077T).
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Corynebacterium canis sp. nov., isolated from a wound infection caused by a dog bite
More LessA non-lipophilic, coryneform bacterium isolated from a patient's wound caused by a dog bite was characterized by phenotypic, chemotaxonomic and molecular genetic methods. Chemotaxonomic features suggested assignment of the unknown bacterium to the genus Corynebacterium. The isolate exhibited the following unusual features, which made it possible to phenotypically differentiate it from all other medically relevant corynebacteria: the Gram stain showed some very filamentous rods (>15 μm in length); some cells exhibited branching; colonies were domed and adherent to agar; the micro-organism was positive for pyrazinamidase, β-glucosidase, α-glucosidase and trypsin but negative for β-galactosidase. 16S rRNA gene sequencing and partial rpoB gene sequencing showed that the closest phylogenetic relative, Corynebacterium freiburgense, exhibited more than 1.9 % and 17.9 % divergence with the unknown bacterium, respectively. Based on both phenotypic and molecular genetic data, it is proposed that the isolate should be classified as a novel species, Corynebacterium canis sp. nov., with the type strain 1170T (=CCUG 58627T =DSM 45402T).
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Williamsia faeni sp. nov., an actinomycete isolated from a hay meadow
More LessThe taxonomic status of an actinomycete isolated from soil collected from a hay meadow was determined using a polyphasic approach. The strain, designated N1350T, had morphological and chemotaxonomic properties consistent with its classification in the genus Williamsia and formed a distinct phyletic line within the clade comprising the type strains of species of the genus Williamsia in the 16S rRNA gene tree. Strain N1350T shared highest 16S rRNA gene sequence similarities with Williamsia marianensis MT8T (98.1 %) and Williamsia muralis MA140-96T (98.3 %). However, strain N1350T was readily distinguished from the type strains of Williamsia species using a combination of phenotypic properties. On the basis of these data, strain N1350T is considered to represent a novel species of the genus Williamsia. The name proposed for this taxon is Williamsia faeni sp. nov., with the type strain N1350T (=DSM 45372T =NCIMB 14575T =NRRL B-24794T).
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Amycolatopsis helveola sp. nov. and Amycolatopsis pigmentata sp. nov., isolated from soil
More LessThree short spore chain-forming actinomycete strains were isolated from soil samples collected from subtropical islands in Japan. The cell-wall peptidoglycan of these strains contained meso-diaminopimelic acid (meso-A2pm), glutamic acid and alanine. The major isoprenoid quinone was MK-9(H4), iso-C16 : 0 and 2-OH iso-C16 : 0 were the major cellular fatty acids and phosphatidylethanolamine was a component of the polar lipids. The G+C content of the genomic DNA was 67–69 mol%. Phylogenetic analyses based on the 16S rRNA gene sequences showed that the novel strains consistently formed a monophyletic cluster with Amycolatopsis taiwanensis. On the basis this polyphasic taxonomical study, it is proposed that the two new isolates represent two novel species: Amycolatopsis helveola (type strain TT00-43T=NBRC 103394T=KCTC 19329T) and Amycolatopsis pigmentata (type strain TT99-32T=NBRC 103392T=KCTC 19330T).
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Microbacterium lindanitolerans sp. nov., isolated from hexachlorocyclohexane-contaminated soil
More LessA Gram-stain-positive, aerobic, rod-shaped, yellow actinobacterium, designated MNA2T, was isolated from a hexachlorocyclohexane-contaminated soil in North India. Strain MNA2T showed 95 % 16S rRNA gene sequence similarity with Microbacterium halotolerans YIM 70130T. Phylogenetic analysis of 16S rRNA gene sequences showed that strain MNA2T belonged to a clade represented by the genus Microbacterium of the family Microbacteriaceae. Strain MNA2T contained anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 0 as the predominant fatty acids and diphosphatidylglycerol, phosphatidylglycerol and two unknown polar lipids. The menaquinones were MK-12, MK-11, MK-13 and MK-10, in an approximate molar ratio of 45 : 40 : 13 : 3, respectively. The DNA G+C content was 65.3 mol%. The peptidoglycan was of the B type of cross-linkage with ornithine as the diagnostic diamino acid. The results of the phylogenetic, phenotypic and chemotaxonomic analysis indicate that strain MNA2T belongs to a previously unrecognized species of the genus Microbacterium, for which the name Microbacterium lindanitolerans sp. nov. is proposed. The type strain is MNA2T (=DSM 22422T =CCM 7585T).
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Slackia piriformis sp. nov. and Collinsella tanakaei sp. nov., new members of the family Coriobacteriaceae, isolated from human faeces
More LessThree Gram-positive, strictly anaerobic, non-spore-forming, rod-shaped organisms (strains YIT 12062T, YIT 12063T and YIT 12064) were isolated from human faeces. Strain YIT 12062T was asaccharolytic and possessed a DNA G+C content of 58.3 mol%. Cells of strain YIT 12062T were negative for catalase, oxidase, urease, hydrolysis of aesculin and gelatin, nitrate reduction and indole production. Based on 16S rRNA gene sequence analysis, strain YIT 12062T was assigned to the genus Slackia (91.7–96.0 % sequence similarities to type strains of Slackia species). Biochemical data showed that the isolate was phenotypically distinct from all recognized species of the genus Slackia. Strain YIT 12062T therefore represents a novel species in the genus Slackia, for which the name Slackia piriformis sp. nov. is proposed. The type strain is YIT 12062T (=DSM 22477T=JCM 16070T). Following 16S rRNA gene sequence analysis, strains YIT 12063T and YIT 12064, which were isolated from different subjects, were shown to be most closely related to species of the genus Collinsella (93.8–95.1 % similarities to type strains). Although their phenotypic characteristics were very similar and they shared >99 % 16S rRNA gene sequence similarity and >97±1.8 % DNA–DNA relatedness, the two isolates could be discriminated by RAPD fingerprints. The DNA G+C contents of strains YIT 12063T and YIT 12064 were 60.8 and 61.0 mol%, respectively. They were saccharolytic in API test systems, positive for aesculin hydrolysis and negative for catalase, oxidase, urease, indole production, nitrate reduction and gelatin hydrolysis. The major end products of glucose fermentation of these strains were lactate, acetate and formate. Biochemical data supported the affiliation of strains YIT 12063T and YIT 12064 to the genus Collinsella and showed that they were phenotypically distinct from all recognized species of the genus Collinsella. Strains YIT 12063T and YIT 12064 therefore represent a novel species of the genus Collinsella, for which the name Collinsella tanakaei sp. nov. is proposed. The type strain is YIT 12063T (=DSM 22478T=JCM 16071T).
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Actinomadura scrupuli sp. nov., isolated from rock
More LessA novel actinomycete, designated strain R-Ac121T, was isolated from a small stone collected from an agricultural field in Jeju, Republic of Korea. The organism formed abundant vegetative mycelium that was branched and twisted. The reverse colour of colonies was brownish-yellow. Non-motile, wrinkled arthrospores were produced directly on the substrate mycelium. Aerial mycelium and sporangia were not observed. A neighbour-joining tree based on 16S rRNA gene sequences indicated that the isolate formed a distinct clade within the radiation of the family Thermomonosporaceae. The highest 16S rRNA gene sequence identity was found with the type strain of Spirillospora rubra (97.3 % sequence similarity) followed by those of Actinoallomurus purpureus (97.0 %), Actinomadura alba (96.5 %), Actinomadura fibrosa (96.5 %) and Actinomadura echinospora (96.4 %). The cell wall contained meso-diaminopimelic acid. The whole-cell sugars were rhamnose, glucose, ribose, xylose and arabinose. The polar lipids included diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. The major menaquinone was MK-9(H6) and the predominant fatty acids were iso-C16 : 0, C16 : 0, C17 : 1 ω8c and 10-methyl C17 : 0. The DNA G+C content was 71.8 mol%. The combination of morphological, chemotaxonomic and phylogenetic data clearly supports the separation of the organism from recognized species of the genus Actinomadura and related genera. On the basis of the data presented here, strain R-Ac121T represents a novel species of the genus Actinomadura, for which the name Actinomadura scrupuli sp. nov. is proposed. The type strain is strain R-Ac121T (=KCTC 19488T =DSM 45225T).
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Phytohabitans suffuscus gen. nov., sp. nov., an actinomycete of the family Micromonosporaceae isolated from plant roots
More LessAn actinomycete strain, K07-0523T, was isolated from the roots of an orchid collected in Okinawa prefecture, Japan. 16S rRNA gene sequence analysis indicated that the new strain belonged to the family Micromonosporaceae and the similarity values between strain K07-0523T and the type species of 24 genera in the family Micromonosporaceae were 93.3–97.7 %. Strain K07-0523T contained d-glutamic acid, glycine, d-alanine, meso-diaminopimelic acid, hydroxydiaminopimelic acid and l-lysine in the cell wall. The major menaquinones were MK-9(H6), MK-10(H4) and MK-10(H6). Galactose, glucose, mannose, ribose and xylose were present in the whole-cell sugars. The acyl type of the peptidoglycan was glycolyl. Major fatty acids were anteiso-C17 : 0, iso-C17 : 0, iso-C16 : 0 and iso-C15 : 0. Phosphatidylethanolamine was detected as the major phospholipid and corresponded to phospholipid type II. The G+C content of the genomic DNA was 73 mol%. On the basis of phylogenetic and chemotaxonomic data, the new strain represents a member of a new genus and novel species, namely Phytohabitans suffuscus gen. nov., sp. nov., in the family Micromonosporaceae. The type strain of the type species is K07-0523T (=DSM 45306T=NBRC 105367T).
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Microbacterium radiodurans sp. nov., a UV radiation-resistant bacterium isolated from soil
Strain GIMN 1.002T, a UV radiation-tolerant bacterium, was isolated from the upper sand layers of the Gobi desert, Xinjiang, China and characterized in order to determine its taxonomic position. Cells were Gram-reaction-positive, heterotrophic, strictly aerobic, short rods. 16S rRNA gene sequence analysis revealed that strain GIMN 1.002T belonged to the genus Microbacterium and was closely related to Microbacterium arborescens DSM 20754T (98.8 % 16S rRNA gene sequence similarity) and Microbacterium imperiale DSM 20530T (98.7 %). However, strain GIMN 1.002T had low DNA–DNA relatedness with M. arborescens DSM 20754T (17.1 %) and M. imperiale DSM 20530T (12.89 %). Strain GIMN 1.002T possessed chemotaxonomic markers that were consistent with its classification in the genus Microbacterium, i.e. MK-11, MK-12 and MK-10 as major menaquinones and anteiso-C15 : 0 (38.67 %), iso-C16 : 0 (18.16 %) and iso-C15 : 0 (17.46 %) as predominant cellular fatty acids. The DNA G+C content was 67.74 mol%. The cell-wall sugar was rhamnose. On the basis of the data from this study, strain GIMN 1.002T represents a novel species of the genus Microbacterium, for which the name Microbacterium radiodurans sp. nov. is proposed. The type strain is GIMN 1.002T (=CCTCC M208212T =NRRL B-24799T).
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- Archaea
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Halarchaeum acidiphilum gen. nov., sp. nov., a moderately acidophilic haloarchaeon isolated from commercial solar salt
More LessA novel halophilic archaeon, strain MH1-52-1T, was isolated from solar salt imported from Australia. Cells were pleomorphic, non-motile and Gram-negative. Strain MH1-52-1T required at least 3.0 M NaCl and 1 mM Mg2+ for growth. Strain MH1-52-1T was able to grow at pH 4.0–6.0 (optimum, pH 4.4–4.5) and 15–45 °C (optimum, 37 °C). The diether phospholipids phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, derived from both C20C20 and C20C25 archaeol, were present. Four unidentified glycolipids were also detected. The 16S rRNA gene sequence showed the highest similarity to that of Halobacterium noricense A1T (91.7 %); there were lower levels of similarity to other members of the family Halobacteriaceae. The G+C content of its DNA was 61.4 mol%. Based on our phenotypic, genotypic and phylogenetic analyses, it is proposed that the isolate should be classified as a representative of a new genus and species, for which the name Halarchaeum acidiphilum gen. nov., sp. nov. is proposed. The type strain of Halarchaeum acidiphilum is MH1-52-1T (=JCM 16109T =DSM 22442T =CECT 7534T).
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Natronoarchaeum mannanilyticum gen. nov., sp. nov., an aerobic, extremely halophilic archaeon isolated from commercial salt
Strain YSM-123T was isolated from commercial salt made from Japanese seawater in Niigata prefecture. Optimal NaCl and Mg2+ concentrations for growth were 4.0–4.5 M and 5 mM, respectively. The isolate was a mesophilic and slightly alkaliphilic haloarchaeon, whose optimal growth temperature and pH were 37 °C and pH 8.0–9.0. Phylogenetic analysis based on 16S rRNA gene sequence analysis suggested that strain YSM-123T is a member of the phylogenetic group defined by the family Halobacteriaceae, but there were low similarities to type strains of other genera of this family (≤90 %); for example, Halococcus (similarity <89 %), Halostagnicola (<89 %), Natronolimnobius (<89 %), Halobiforma (<90 %), Haloterrigena (<90 %), Halovivax (<90 %), Natrialba (<90 %), Natronobacterium (<90 %) and Natronococcus (<90 %). The G+C content of the DNA was 63 mol%. Polar lipid analysis revealed the presence of phosphatidylglycerol, phosphatidylglycerophosphate methyl ester, disulfated diglycosyl diether and an unknown glycolipid. On the basis of the data presented, we propose that strain YSM-123T should be placed in a new genus and species, Natronoarchaeum mannanilyticum gen. nov., sp. nov. The type strain of Natronoarchaeum mannanilyticum is strain YSM-123T (=JCM 16328T =CECT 7565T).
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Methanospirillum lacunae sp. nov., a methane-producing archaeon isolated from a puddly soil, and emended descriptions of the genus Methanospirillum and Methanospirillum hungatei
More LessA mesophilic, hydrogenotrophic methanogen, designated strain Ki8-1T, was isolated from soil. Cells were strictly anaerobic, Gram-stain-negative, non-sporulating, motile by means of a single flagellum or tufted flagella, and curved or wavy rod-shaped (11–25 μm long). The temperature and pH for optimum growth were 30 °C and 7.5. The strain grew best in basal medium without the addition of NaCl. Methane was produced from H2 and formate. Acetate or yeast extract was required for growth. The G+C content of the genomic DNA of strain Ki8-1T was 45.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Ki8-1T was a member of the genus Methanospirillum and showed 95.1 % sequence similarity to Methanospirillum hungatei NBRC 100397T. On the basis of its phenotypic characteristics and phylogenetic position, strain Ki8-1T is considered to represent a novel species of the genus Methanospirillum, for which the name Methanospirillum lacunae sp. nov. is proposed. The type strain is Ki8-1T (NBRC 104920T =JCM 16384T =DSM 22751T). Emended descriptions of the genus Methanospirillum and of Methanospirillum hungatei are also provided.
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Halogeometricum rufum sp. nov., a halophilic archaeon from a marine solar saltern, and emended description of the genus Halogeometricum
Two halophilic archaea, strains RO1-4T and RO1-64, were isolated from a marine solar saltern in Jiangsu, China. Cells of the two strains were pleomorphic, motile, and stained Gram-negative. Colonies were red-pigmented. Strains RO1-4T and RO1-64 were able to grow at 25–55 °C (optimum 40–42 °C), at 2.1–5.1 M NaCl (optimum 3.9 M NaCl), at 0.05–0.7 M MgCl2 (optimum 0.3 M MgCl2) and at pH 6.0–8.5 (optimum pH 7.0). Cells lyse in distilled water and the minimal NaCl concentration to prevent cell lysis is 12 % (w/v). On the basis of 16S rRNA gene sequence analysis, strains RO1-4T and RO1-64 were closely related to Halogeometricum borinquense PR3T (98.0 and 98.2 % similarity, respectively) and Halosarcina pallida BZ256T (97.8 and 97.9 %). The major polar lipids of the two strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and two glycolipids (S-DGD-1 and DGD-1). The DNA G+C contents of strains RO1-4T and RO1-64 are 64.9 and 62.4 mol%, respectively. The DNA–DNA hybridization value between strains RO1-4T and RO1-64 was 83.0 % and both strains showed low DNA–DNA relatedness with Halogeometricum borinquense PR3T (42.5 and 50.1 % relatedness, respectively) and Halosarcina pallida BZ256T (37.6 and 42.1 % relatedness). It was concluded that strains RO1-4T and RO1-64 represent a novel species of the genus Halogeometricum, for which the name Halogeometricum rufum sp. nov. is proposed. The type strain is RO1-4T (=CGMCC 1.7736T =JCM 15770T).
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- Bacteroidetes
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Siphonobacter aquaeclarae gen. nov., sp. nov., a novel member of the family ‘Flexibacteraceae’, phylum Bacteroidetes
More LessA Gram-negative bacterium, designated P2T, was isolated from the biofilm developed on the inner surface of an ultrapure cooling water system in a Hungarian power plant and was characterized by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain P2T was affiliated with the family ‘Flexibacteraceae’ in the phylum Bacteroidetes. Its closest relative was Flectobacillus lacus CL-GP79T (88.7 % 16S rRNA gene sequence similarity) followed by Arcicella rosea TW5T (86.5 %), Arcicella aquatica NO-502T (86.4 %), Flectobacillus roseus GFA-11T (86.3 %) and Flectobacillus major DSM 103T (85.4 %). Cells of strain P2T were facultatively anaerobic, non-motile rods. The major fatty acids were C16 : 1 ω5c (42.5 %), iso-C15 : 0 2-OH (17.2 %), iso-C17 : 0 3-OH (16.1 %) and iso-C15 : 0 (8.5 %). The major menaquinone was MK-7 and the predominant polar lipid was phosphatidylethanolamine. The DNA G+C content was 54.5 mol%. Thus, the phenotypic and genotypic analyses clearly showed that strain P2T is considerably different from members of other genera in the family ‘Flexibacteraceae’. Based on these results, it is concluded that strain P2T represents a novel species in a new genus, for which the name Siphonobacter aquaeclarae gen. nov., sp. nov. is proposed, with type strain P2T (=DSM 21668T =NCAIM B 02328T).
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Bacteroides faecis sp. nov., isolated from human faeces
More LessTwo anaerobic, Gram-negative, non-motile and non-spore-forming bacterial strains, designated MAJ27T and MAJ26, were isolated from human faeces. Both isolates grew optimally at 37 °C, were oxidase- and catalase-negative, were sensitive to bile and produced acid from fermentation of several substrates, including glucose. A study based on 16S rRNA gene sequences showed that both isolates were closely related to type strains of species of the genus Bacteroides. Comparisons of the isolates with Bacteroides thetaiotaomicron VPI 5482T and Bacteroides finegoldii JCM 13345T showed high levels of 16S rRNA gene sequence similarity (98.6–98.7 and 96.9–97.0 %, respectively), but low levels of DNA–DNA relatedness (≤22 %). The DNA G+C content (42.7±1 mol%) and the major fatty acid (anteiso-C15 : 0, 39.3–42.5 %) supported the assignment of the isolates to the genus Bacteroides. Based on phenotypic, chemotaxonomic, genotypic and phylogenetic studies, we propose that strains MAJ27T and MAJ26 be classified as representing a novel species, Bacteroides faecis sp. nov. The type strain is MAJ27T (=KCTC 5823T=JCM 16478T).
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Dyadobacter soli sp. nov., a starch-degrading bacterium isolated from farm soil
More LessA Gram-negative, non-motile, aerobic bacterial strain, designated MJ20T, was isolated from farm soil near Daejeon (South Korea) and was characterized taxonomically by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain MJ20T belongs to the family Cytophagaceae, class Sphingobacteria, and was related most closely to Dyadobacter fermentans DSM 18053T (98.9 % sequence similarity), Dyadobacter beijingensis JCM 14200T (98.0 %) and Dyadobacter ginsengisoli KCTC 12589T (96.4 %). The G+C content of the genomic DNA of strain MJ20T was 48.5 mol%. The detection of MK-7 as the predominant menaquinone and a fatty acid profile with summed feature 4 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0, C16 : 0 and C16 : 1 ω5c as major components supported the affiliation of strain MJ20T to the genus Dyadobacter. The new isolate exhibited relatively low levels of DNA–DNA relatedness with respect to D. fermentans DSM 18053T (mean±sd of three determinations, 47±7 %) and D. beijingensis JCM 14200T (38±8 %). On the basis of its phenotypic and genotypic properties together with phylogenetic distinctiveness, strain MJ20T (=KCTC 22481T =JCM 16232T) should be classified in the genus Dyadobacter as the type strain of a novel species, for which the name Dyadobacter soli sp. nov. is proposed.
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Pedobacter bauzanensis sp. nov., isolated from soil
More LessA Gram-negative, aerobic, rod-shaped, non-motile bacterium, designated BZ42T, was isolated from the soil of an industrial site. Strain BZ42T was able to grow at 5–25 °C. The major fatty acids were iso-C15 : 0 (46.2 %), C16 : 1 ω7c and/or iso-C15 : 0 2-OH (23.2 %) and iso-C17 : 0 3-OH (9.1 %). The predominant menaquinone was MK-7. The genomic DNA G+C content was 36.5 mol% (HPLC). 16S rRNA gene sequence phylogenetic analysis revealed that strain BZ42T was a member of the genus Pedobacter, family Sphingobacteriaceae, and 16S rRNA gene sequence similarities between strain BZ42T and the type strains of species of the genus Pedobacter with validly published names were 90.4–93.2 %. On the basis of phenotypic, chemotaxonomic and phylogenetic distinctiveness, strain BZ42T was considered to represent a novel species of the genus Pedobacter, for which the name Pedobacter bauzanensis sp. nov. is proposed. The type strain is BZ42T (=DSM 22554T =CGMCC 1.10187T =CIP 110134T).
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- Firmicutes And Related Organisms
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Amphibacillus jilinensis sp. nov., a facultatively anaerobic, alkaliphilic bacillus from a soda lake
More LessA facultatively anaerobic, alkaliphilic, spore-forming, Gram-positive-staining rod, designated Y1T, was isolated under strictly anaerobic conditions from sediment of a soda lake in Jilin province, China. The strain was not dependent on Na+ but was highly halotolerant and grew optimally in medium JY with 0.5 M Na+ (0.06 M NaHCO3 and 0.44 M NaCl). The optimum pH for growth was 9.0, with a range of pH 7.5–10.5. No growth occurred at pH 7.0 or 11.0. The strain was mesophilic, with a temperature range of 15–45 °C and optimum growth at 32 °C. Strain Y1T was able to use certain mono- and oligosaccharides. Soluble starch and casein were hydrolysed. The methyl red test, Voges–Proskauer test and tests for catalase and oxidase activities were negative. The predominant fatty acids were anteiso-C15 : 0 and iso-C15 : 0. Comparative 16S rRNA gene sequence analysis revealed 93.4–96.8 % sequence similarity to members of the genus Amphibacillus. The DNA G+C content was 37.7 mol% (T m method). The DNA–DNA relatedness of strain Y1T with respect to Amphibacillus tropicus DSM 13870T and Amphibacillus sediminis DSM 21624T was 48 and 37 %, respectively. On the basis of its phylogenetic position and the DNA–DNA relatedness data as well as its physiological and biochemical properties, strain Y1T represents a novel species of the genus Amphibacillus, for which the name Amphibacillus jilinensis sp. nov. is proposed. The type strain is Y1T (=CGMCC 1.5123T =JCM 16149T).
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- Proteobacteria
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Vibrio atypicus sp. nov., isolated from the digestive tract of the Chinese prawn (Penaeus chinensis O'sbeck)
More LessA culture (designated strain HHS02T) was isolated from Chinese prawn (Penaeus chinensis, O'sbeck) and determined to be a member of the genus Vibrio. Strain HHS02T comprised slightly curved, rod-shaped, non-endospore-forming, Gram-negative, catalase-negative, oxidase-positive, O/129-sensitive and facultatively anaerobic cells that were motile by means of a single polar flagellum. Growth of strain HHS02T occurred in 0.5–7 % (w/v) NaCl [optimally in 1–3 % (w/v) NaCl] and between pH 7.0 and 10.0 (optimally at pH 8.0–9.0). The strain showed growth between 16 and 30 °C (optimum 20 °C). Analysis using the 16S rRNA, gapA, gyrB, mreB, pyrH, recA and topA gene sequences of the novel isolate revealed that the organism belonged to the genus Vibrio, with ∼98, 98, 90, 88, 92, 89 and 83 % sequence similarity, respectively, with representatives of the genus Vibrio. DNA–DNA hybridization experiments indicated that the novel strain was distinct from recognized species of the genus Vibrio. The major fatty acid components were summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH, 38.7 %), C16 : 0 (22.9 %) and C18 : 1 ω7c (12.5 %). The G+C content of the genomic DNA was 44.4 mol%. On the basis of the polyphasic taxonomic evidence presented in this study, it is concluded that strain HHS02T should be classified as a novel species of the genus Vibrio, for which the name Vibrio atypicus sp. nov. is proposed. The type strain is HHS02T (=CGMCC 1.8461T=LMG 24781T).
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Mesorhizobium robiniae sp. nov., isolated from root nodules of Robinia pseudoacacia
More LessPreviously, five rhizobial strains isolated from root nodules of Robinia pseudoacacia were assigned to the same genospecies on the basis of identical 16S rRNA gene sequences and phylogenetic analyses of the nodA, nodC and nifH genes, in which the five isolates formed a well-supported group that excluded other sequences found in public databases. In this study, the 16S rRNA gene sequence similarities between the isolates and Mesorhizobium mediterraneum UPM-Ca36T and Mesorhizobium temperatum SDW018T were 99.5 and 99.6 %, respectively. The five isolates were also different from defined Mesorhizobium species using ERIC fingerprint profiles and they formed a novel Mesorhizobium lineage in phylogenetic analyses of recA and atpD gene sequences. DNA–DNA relatedness values between the representative strain, CCNWYC 115T, and type strains of defined Mesorhizobium species were found to be lower than 47.5 %. These results indicated that the isolates represented a novel genomic species. Therefore, a novel species, Mesorhizobium robiniae sp. nov., is proposed, with type strain CCNWYC 115T (=ACCC 14543T =HAMBI 3082T). Strain CCNWYC 115T can form effective nodules only on its original host.
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Legionella dresdenensis sp. nov., isolated from river water
More LessLegionella-like isolates, strains W03-356T, W03-357 and W03-359, from three independent water samples from the river Elbe, Germany, were analysed by using a polyphasic approach. Morphological and biochemical characterization revealed that they were Gram-negative, aerobic, non-spore-forming bacilli with a cut glass colony appearance that grew only on l-cysteine-supplemented buffered charcoal yeast extract agar. Phylogenetic analysis based on sequence comparisons of the 16S rRNA, macrophage infectivity potentiator (mip), gyrase subunit A (gyrA), ribosomal polymerase B (rpoB) and RNase P (rnpB) genes confirmed that the three isolates were distinct from recognized species of the genus Legionella. Phenotypic characterization of strain W03-356T based on fatty acid profiles confirmed that it was closely related to Legionella rubrilucens ATCC 35304T and Legionella pneumophila ATCC 33152T, but distinct from other species of the genus Legionella. Serotyping of the isolates showed that they were distinct from all recognized species of the genus Legionella. Strains W03-356T, W03-357 and W03-359 are thus considered to represent a novel species of the genus Legionella, for which the name Legionella dresdenensis sp. nov. is proposed. The type strain is W03-356T (=DSM 19488T=NCTC 13409T).
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Kangiella japonica sp. nov., isolated from a marine environment
More LessThree Gram-negative, aerobic, halophilic, non-motile, yellowish-pigmented bacteria, designated KMM 3896, KMM 3897 and KMM 3899T, were isolated from coastal seawater and sediment samples of the Sea of Japan, Russia. The isolates were shown to belong to the same species on the basis of 16S rRNA gene sequence similarities (99.6–99.9 %) and DNA–DNA relatedness (73–98 %). Phylogenetic analysis of 16S rRNA gene sequences demonstrated that the isolates formed a subcluster within the genus Kangiella in the class Gammaproteobacteria. 16S rRNA gene sequence similarities between strain KMM 3899T and its closest phylogenetic neighbours, Kangiella koreensis SW-125T and Kangiella aquimarina SW-154T, were 96.6 and 95.5 %, respectively. On the basis of phenotypic differences and phylogenetic distances, it is proposed that strains KMM 3896, KMM 3897 and KMM 3899T are assigned to a novel species of the genus Kangiella, Kangiella japonica sp. nov. The type strain is KMM 3899T (=NRIC 0764T =JCM 16211T).
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Photobacterium gaetbulicola sp. nov., a lipolytic bacterium isolated from a tidal flat sediment
A Gram-negative, motile, non-spore-forming and lipolytic bacterial strain, designated Gung47T, was isolated from a tidal flat on the west coast of Korea. Strain Gung47T grew optimally at 30 °C and with 2−5 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain Gung47T belonged to the genus Photobacterium. Strain Gung47T exhibited 98.1 % 16S rRNA gene sequence similarity with Photobacterium rosenbergii LMG 22223T and 94.3–96.3 % similarity with other type strains of species of the genus Photobacterium. Strain Gung47T exhibited 47 % DNA–DNA relatedness to P. rosenbergii LMG 22223T. Strain Gung47T contained Q-8 as the predominant ubiquinone and C16 : 1 ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C18 : 1 ω7c as the major fatty acids. In this study, two closely related type strains, P. rosenbergii LMG 22223T and Photobacterium halotolerans LMG 22194T, were also found to have Q-8 as the predominant ubiquinone. The DNA G+C content of strain Gung47T was 50.6 mol%. The differential phenotypic properties together with the phylogenetic and genetic distinctiveness of strain Gung47T demonstrated that this strain is distinguishable from recognized Photobacterium species. Therefore, strain Gung47T is considered to represent a novel species of the genus Photobacterium, for which the name Photobacterium gaetbulicola sp. nov. is proposed. The type strain is Gung47T (=KCTC 22804T =CCUG 58399T).
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Description of Microvirga aerophila sp. nov. and Microvirga aerilata sp. nov., isolated from air, reclassification of Balneimonas flocculans Takeda et al. 2004 as Microvirga flocculans comb. nov. and emended description of the genus Microvirga
Two bacterial strains, 5420S-12T and 5420S-16T, isolated from air samples, were characterized using a polyphasic approach. 16S rRNA gene sequence analysis showed that strain 5420S-12T was related phylogenetically to Microvirga subterranea FaiI4T (97.4 % sequence similarity) and Microvirga guangxiensis 25BT (97.1 %) and that strain 5420S-16T was closely related to Balneimonas flocculans TFBT (98.0 %) and Microvirga guangxiensis 25BT (97.2 %). The G+C content of the genomic DNA was 62.2 mol% for strain 5420S-12T and 61.5 mol% for strain 5420S-16T. The major fatty acid was C18 : 1 ω7c. The results of DNA–DNA hybridization and the phenotypic data showed that strains 5420S-12T and 5420S-16T could be distinguished from phylogenetically related species and represent two novel species within the genus Microvirga, for which the names Microvirga aerophila sp. nov. (type strain 5420S-12T =KACC 12743T =NBRC 106136T) and Microvirga aerilata sp. nov. (type strain 5420S-16T =KACC 12744T =NBRC 106137T) are proposed. Furthermore, the reclassification of Balneimonas flocculans as Microvirga flocculans comb. nov. (type strain TFBT =JCM 11936T =KCTC 12101T =IAM 15034T =ATCC BAA-817T) is proposed and an emended description of the genus Microvirga is provided.
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Orbus hercynius gen. nov., sp. nov., isolated from faeces of wild boar, is most closely related to members of the orders ‘Enterobacteriales’ and Pasteurellales
A novel gammaproteobacterium, strain CN3T, was isolated from the faeces of wild boar. Strain CN3T was facultatively anaerobic and appeared coccoid or rod-shaped. The partial 16S rRNA gene sequence determined for strain CN3T suggested a distant relationship with members of the orders ‘Enterobacteriales’ and Pasteurellales. The gene sequence showed highest similarity (90.3 %) with Obesumbacterium proteus DSM 2777T, a member of the family Enterobacteriaceae. The closest relatives outside the order ‘Enterobacteriales’ according to 16S rRNA gene sequence analysis were members of the order Pasteurellales with 88.7 % similarity (Mannheimia haemolytica NCTC 9380T and Actinobacillus lignieresii NCTC 4189T). In contrast to most members of the order ‘Enterobacteriales’, strain CN3T was oxidase-positive. The pattern of fatty acids, in particular the high relative abundance of C18 : 1 ω7c (38.5 %), was clearly distinct from the conserved pattern found for members of the order Pasteurellales. EcoRI ribotyping of strain CN3T yielded no significant similarity to existing database entries. The major ubiquinone of strain CN3T was Q-8. The DNA G+C content was 36.4 mol%. Strain CN3T hosted a phage and secreted considerable amounts of three proteins into the culture supernatant. A spontaneous mutant of strain CN3T was isolated which formed long filaments. Microscopic studies revealed the presence of a capsule that the mutant strain was unable to partition after cell division. Strain CN3T thus represents a novel species within a new genus, for which the name Orbus hercynius gen. nov., sp. nov. is proposed. The type strain of the type species is CN3T (=DSM 22228T=CCUG 57622T). Classification of the novel species to the family and order level will require further investigations.
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Cupriavidus pampae sp. nov., a novel herbicide-degrading bacterium isolated from agricultural soil
More LessA bacterial consortium able to degrade the herbicide 4-(2,4-dichlorophenoxy) butyric acid (2,4-DB) was obtained from an agricultural soil of the Argentinean Humid Pampa region which has a history of long-term herbicide use. Four bacterial strains were isolated from the consortium and identified as members of the genera Cupriavidus, Labrys and Pseudomonas. A polyphasic systematic analysis was carried out on strain CPDB6T, the member of the 2,4-DB-degrading consortium able to degrade 2,4-DB as a sole carbon and energy source. The Gram-negative, rod-shaped, motile, non-sporulating, non-fermenting bacterium was shown to belong to the genus Cupriavidus on the basis of 16S rRNA gene sequence analyses. Strain CPDB6T did not reduce nitrate, which differentiated it from the type species of the genus, Cupriavidus necator; it did not grow in 0.5–4.5 % NaCl, although most species of Cupriavidus are able to grow at NaCl concentrations as high as 1.5 %; and it was able to deamidate acetamide, which differentiated it from all other species of Cupriavidus. DNA–DNA hybridization data revealed low levels of genomic DNA similarity (less than 30 %) between strain CPDB6T and the type strains of Cupriavidus species with validly published names. The major cellular fatty acids detected were cis-9-hexadecenoic (16 : 1ω7c) and hexadecanoic (16 : 0) acids. On the basis of phenotypic and genotypic characterizations, strain CPDB6T was recognized as a representative of a novel species within the genus Cupriavidus. The name Cupriavidus pampae sp. nov. is proposed, with strain CPDB6T (=CCUG 55948T=CCM-A-29:1289T) as the type strain.
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Sphingopyxis bauzanensis sp. nov., a psychrophilic bacterium isolated from soil
More LessStrain BZ30T was isolated from hydrocarbon-contaminated soil. The Gram-negative, aerobic bacterium was psychrophilic and able to grow at temperatures ranging from 1 to 30 °C. The predominant cellular fatty acids of strain BZ30T were summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH) (37.4 %), C18 : 1 ω7c (19.6 %), C16 : 0 (8.2 %), C14 : 0 2-OH (8.0 %) and C16 : 0 2-OH (5.0 %). The predominant ubiquinone was Q-10. Major polar lipids were sphingoglycolipids, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. Spermidine was the major polyamine. The genomic DNA G+C content was 64.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain BZ30T belonged to the family Sphingomonadaceae of the α-4 group of the phylum Proteobacteria, and was related to the members of the genus Sphingopyxis, sharing the highest sequence similarities with the type strains of Sphingopyxis chilensis (98.3 %), S. witflariensis (98.2 %), S. taejonensis (97.4 %) and S. ginsengisoli (97.2 %). On the basis of the phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness data, strain BZ30T represents a novel species of the genus Sphingopyxis, for which the name Sphingopyxis bauzanensis is proposed. The type strain is BZ30T (=DSM 22271T =CGMCC 1.8959T =CIP 110136T).
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Methylophilus flavus sp. nov. and Methylophilus luteus sp. nov., aerobic, methylotrophic bacteria associated with plants
More LessNovel yellow, obligately methylotrophic and restricted facultatively methylotrophic bacteria, respectively designated strains ShipT and MimT, with the ribulose monophosphate pathway of C1 assimilation are described. Cells were strictly aerobic, Gram-negative, asporogenous, non-motile rods that multiply by binary fission, were mesophilic and neutrophilic and synthesized indole-3-acetic acid and exopolysaccharide. The predominant cellular fatty acids were C16 : 0 and C16 : 1. The major ubiquinone was Q-8. The predominant phospholipids were phosphatidylethanolamine and phosphatidylglycerol; diphosphatidylglycerol was absent. The two strains lacked α-ketoglutarate dehydrogenase and glutamate dehydrogenase. They assimilated ammonium via the glutamate cycle enzymes glutamine synthetase and glutamate synthase. The DNA G+C contents of strains ShipT and MimT were 50.7 and 54.5 mol% (T m), respectively. The level of 16S rRNA gene sequence similarity between these strains was very high (99.8 %) but they shared a low level of DNA–DNA relatedness (44 %). Based on 16S rRNA gene sequence analysis and low levels of DNA–DNA relatedness with the type strains of recognized species of the genus Methylophilus (31–36 %), strains ShipT and MimT are considered to represent novel species of the genus Methylophilus, for which the names Methylophilus flavus sp. nov. (type strain ShipT =DSM 23073T =VKM B-2547T =CCUG 58411T) and Methylophilus luteus sp. nov. (type strain MimT =DSM 22949T =VKM B-2548T =CCUG 58412T) are proposed.
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Methylocapsa aurea sp. nov., a facultative methanotroph possessing a particulate methane monooxygenase, and emended description of the genus Methylocapsa
An aerobic, methanotrophic bacterium, designated KYGT, was isolated from a forest soil in Germany. Cells of strain KYGT were Gram-negative, non-motile, slightly curved rods that multiplied by binary fission and produced yellow colonies. The cells contained intracellular granules of poly-β-hydroxybutyrate at each cell pole, a particulate methane monooxygenase (pMMO) and stacks of intracytoplasmic membranes (ICMs) packed in parallel along one side of the cell envelope. Strain KYGT grew at pH 5.2–7.2 and 2–33 °C and could fix atmospheric nitrogen under reduced oxygen tension. The major cellular fatty acid was C18 : 1 ω7c (81.5 %) and the DNA G+C content was 61.4 mol%. Strain KYGT belonged to the family Beijerinckiaceae of the class Alphaproteobacteria and was most closely related to the obligate methanotroph Methylocapsa acidiphila B2T (98.1 % 16S rRNA gene sequence similarity and 84.7 % pmoA sequence similarity). Unlike Methylocapsa acidiphila B2T, which grows only on methane and methanol, strain KYGT was able to grow facultatively on acetate. Facultative acetate utilization is a characteristic of the methanotrophs of the genus Methylocella, but the genus Methylocella does not produce pMMO or ICMs. Strain KYGT differed from Methylocapsa acidiphila B2T on the basis of substrate utilization pattern, pigmentation, pH range, cell ultrastructure and efficiency of dinitrogen fixation. Therefore, we propose a novel species, Methylocapsa aurea sp. nov., to accommodate this bacterium. The type strain is KYGT (=DSM 22158T =VKM B-2544T).
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- Eukaryotic Micro-Organisms
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Candida cabralensis sp. nov., a yeast species isolated from traditional Spanish blue-veined Cabrales cheese
More LessThree yeast strains, 1AD8T, 3AD15 and 3AD23, belonging to a previously unknown yeast species were isolated from two independent batches of the Spanish blue-veined Cabrales cheese, a traditional cheese manufactured without the addition of starter and mould cultures. Physiological characterization revealed that the unknown yeast is not fermentative and does not assimilate lactose; rather it assimilates dl-lactic acid and ethanol, major end products of lactic acid bacteria metabolism in cheese. The novel yeast is anamorphic. Phylogenetic tree reconstruction based on nucleotide sequence comparison of the D1/D2 region of the 26S rRNA gene showed that Pichia terricola and Pichia fermentans are the closest relatives of the unknown species. The name Candida cabralensis sp. nov. is proposed, and the isolate 1AD8T (=CECT 13027T =CBS 11679T) is the type strain of this novel taxon.
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Re-examination of strains formerly assigned to Hyphopichia burtonii, the phylogeny of the genus Hyphopichia, and the description of Hyphopichia pseudoburtonii sp. nov.
More LessOn the basis of the nucleotide divergence in the internal transcribed spacer (ITS) domain of the rRNA gene and the D1/D2 domain of the 26S rRNA gene, species of the genus Hyphopichia can be divided into different phylogenetic groups. In this study, three distinct phylogenetic clusters as well as a novel species, Hyphopichia pseudoburtonii sp. nov. with type strain CBS 2455T (=JCM 16346T), are introduced. Mating studies indicate that strains belonging to Hyphopichia pseudoburtonii are heterothallic.
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Molecular systematics of marine gregarines (Apicomplexa) from North-eastern Pacific polychaetes and nemerteans, with descriptions of three novel species: Lecudina phyllochaetopteri sp. nov., Difficilina tubulani sp. nov. and Difficilina paranemertis sp. nov.
More LessMost eugregarine apicomplexans infecting the intestines of marine invertebrates have been described within the family Lecudinidae and the type genus Lecudina. The diversity of these parasites is vast and poorly understood and only a tiny number of species has been characterized at the molecular phylogenetic level. DNA sequences coupled with high-resolution micrographs of trophozoites provide an efficient and precise approach for delimiting gregarine lineages from one another and also facilitate our overall understanding of gregarine biodiversity. In this study, phylogenetic analyses of small subunit (SSU) rDNA sequences from five (uncultivated) gregarines isolated from polychaetes and nemerteans in the North-eastern Pacific Ocean are presented. Lecudina phyllochaetopteri sp. nov. was isolated from the intestines of the parchment tubeworm Phyllochaetopterus prolifica (Polychaeta). Lecudina longissima and Lecudina polymorpha were both isolated from the intestines of Lumbrineris japonica (Polychaeta). Difficilina tubulani sp. nov. was isolated from the nemertean Tubulanus polymorpha and Difficilina paranemertis sp. nov. was isolated from the nemertean Paranemertes peregrina. This is the first report of molecular sequence data from gregarines that infect nemerteans. The two novel species of the genus Difficilina described in this study formed a strongly supported clade in the phylogenetic analyses. This Difficilina clade formed the sister group to a robust subclade of lecudinids consisting of Lecudina longissima, Lecudina phyllochaetopteri sp. nov. (which lacked epicytic folds), Lecudina tuzetae, species of the genus Lankesteria and several sequences derived from previous environmental DNA surveys of marine biodiversity.
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- International Committee On Systematics Of Prokaryotes
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- Minutes
Volumes and issues
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