- Volume 60, Issue 10, 2010
Volume 60, Issue 10, 2010
- Notification List
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Notification that new names and new combinations have appeared in volume 60, part 7, 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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Arthrobacter antarcticus sp. nov., isolated from an Antarctic marine sediment
More LessA bacterial strain, SPC26T, was isolated from a sediment sample of the Southern Ocean off Antarctica. The strain was Gram-staining- and catalase-positive and contained lysine and alanine in the cell-wall peptidoglycan. The major cellular fatty acids were anteiso-C15 : 0 (54.92 %), iso-C15 : 0 (11.47 %), anteiso-C17 : 0 (6.48 %) and anteiso-C15 : 1 (6.38 %) and the major menaquinones were MK-8, MK-9 and MK-10. The major polar lipids were phosphatidylethanolamine and diphosphatidylglycerol. The G+C content was 68±0.5 mol%. Based on 16S rRNA gene sequence similarities, the nearest phylogenetic neighbours of strain SPC26T were identified as Arthrobacter gangotriensis Lz1yT (98.8 %), A. sulfureus DSM 20167T (98.6 %), A. psychrophenolicus DSM 15454T (97.9 %) and A. kerguelensis KGN15T (97.5). With these strains, strain SPC26T exhibited DNA–DNA relatedness values of 36, 21, 12 and 10 %, respectively. Therefore, on the basis of 16S rRNA gene sequence comparisons, phylogenetic analysis, phenotypic characteristics and DNA–DNA relatedness, it is proposed that strain SPC26T represents a novel species of Arthrobacter, for which the name Arthrobacter antarcticus sp. nov. is proposed, with strain SPC26T (=LMG 24542T =NCCB 100228T) as the type strain.
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Nocardia mikamii sp. nov., isolated from human pulmonary infections in the USA
Four nocardioform bacterial strains isolated from clinical respiratory sources were characterized using a polyphasic taxonomic approach. On the basis of 16S rRNA gene sequence analyses, these strains were found to be 100 % similar to each other and were shown to belong to the genus Nocardia. Chemotaxonomic data [major menaquinone: ω-cyclic isoprene side chain MK-8(H4cycl ); major polar lipids: diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides; major fatty acids: monounsaturated fatty acids with a considerable amount of tuberculostearic acid; and mycolic acids (52–62 carbon atoms)] were consistent with the assignment of the novel strains to the genus Nocardia. Comparative phylogenetic analysis of the 16S rRNA gene sequences showed that the novel strains were related to Nocardia cerradoensis DSM 44546T (99.8 %) and Nocardia aobensis JCM 12352T (99.6 %). Analysis of gyrB gene sequences showed these strains were related to N. aobensis (96.6 %) and to N. cerradoensis (96.3 %). The results suggest that gyrB gene sequencing is a more powerful tool than 16S rRNA gene sequencing for taxonomic identification within the genus Nocardia. DNA–DNA hybridization and physiological and biochemical tests supported the genotypic and phenotypic differentiation of the novel strains from related species. These data indicated that the new strains represent a novel species within the genus Nocardia, for which the name Nocardia mikamii sp. nov. is proposed, with strain W8061T (=DSM 45174T=JCM 15508T) as the type strain.
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Nocardioides mesophilus sp. nov., isolated from soil
More LessA short coccoid- to rod-shaped, motile, mesophilic actinobacterium, strain MSL-22T, was isolated from soil on Bigeum Island, Korea. A polyphasic study was undertaken to establish the taxonomic position of this strain. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain MSL-22T formed an evolutionary lineage within the radiation of the genus Nocardioides. In particular, it formed a monophyletic lineage with Nocardioides jensenii KCTC 9134T with which it shared the highest sequence similarity of about 97.3%. However, DNA–DNA relatedness demonstrated that strain MSL-22T was distinct from its closest phylogenetic neighbours. The cell-wall peptidoglycan of strain MSL-22T contained ll-diaminopimelic acid. The predominant menaquinone was MK-8(H4). Strain MSL-22T had a cellular fatty acid profile containing straight-chain, branched, unsaturated and 10-methyl fatty acids, with iso-C16 : 0 as the major fatty acid. The DNA G+C content of the strain was 68.7 mol%. On the basis of phenotypic and phylogenetic evidence, the strain is separate from previously described members of the genus Nocardioides and represents a novel species in this genus, for which the name Nocardioides mesophilus sp. nov. is proposed. The type strain is MSL-22T (=DSM 19432T=KCTC 19310T).
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Revival and emended description of ‘Mycobacterium paraffinicum’ Davis, Chase and Raymond 1956 as Mycobacterium paraffinicum sp. nov., nom. rev.
More LessThe omission of the name ‘Mycobacterium paraffinicum’ from the Approved Lists of Bacterial Names was due to phenotypic confusion surrounding a close relationship with Mycobacterium scrofulaceum. Correspondingly, ‘M. paraffinicum’ strains grew slowly in >7 days, stained acid–alcohol-fast and produced yellow-pigmented, smooth, waxy colonies in the dark at an optimal temperature of 35 °C. However, ‘M. paraffinicum’ strains demonstrated no activity for urease, nicotinamidase or pyrazinamidase and lacked growth at 42 °C, unlike M. scrofulaceum. The mycolic acid pattern, as determined by HPLC, clustered ‘M. paraffinicum’ with M. scrofulaceum, Mycobacterium avium and Mycobacterium parascrofulaceum. Strains were fully susceptible to linezolid, rifabutin, clarithromycin and amikacin. Examination of the historical reference strain of ‘M. paraffinicum’, ATCC 12670, and five additional isolates using comparative studies with 16S rRNA, hsp65 and rpoB gene and concatenated sequences showed that they formed a tight taxonomic group that was distinct from similar non-tuberculous mycobacteria. Multilocus enzyme electrophoresis (MEE) analysis confirmed a close association of the five additional isolates with the reference strain of ‘M. paraffinicum’ with a genetic distance of 0.12 and showed that all six strains were distinct from other closely related species. These genetic results provided unambiguous evidence of the uniqueness of this slowly growing, scotochromogenic species and supported the revival of the name as Mycobacterium paraffinicum (ex Davis, Chase and Raymond 1956) sp. nov., nom. rev. We propose the previously deposited reference strain ATCC 12670T =DSM 44181T =NCIMB 10420T, located in collections worldwide, as the type strain.
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Euzebya tangerina gen. nov., sp. nov., a deeply branching marine actinobacterium isolated from the sea cucumber Holothuria edulis, and proposal of Euzebyaceae fam. nov., Euzebyales ord. nov. and Nitriliruptoridae subclassis nov.
More LessA tangerine-coloured, Gram-positive actinobacterial strain, designated F10T, was isolated from the abdominal epidermis of a sea cucumber, Holothuria edulis, collected in seawater off the coast of Japan. A 16S rRNA gene sequence analysis indicated that strain F10T was a member of the class Actinobacteria and was most closely related to Nitriliruptor alkaliphilus ANL-iso2T (87.4 % sequence similarity). Phylogenetic analyses showed that strain F10T represented a novel, deep-rooted, and distinct phylogenetic lineage within the class Actinobacteria and clustered with N. alkaliphilus and uncultured bacteria. The organism had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, and rhamnose and galactose as the diagnostic cell-wall sugars. Strain F10T contained C16 : 1 ω7c, C16 : 0 and C17 : 1 ω8c as the major cellular fatty acids. The predominant isoprenoid quinone was MK-9 (H4). The G+C content of the DNA was 68.3 mol%. Based on data from the current polyphasic study, it is proposed that the new marine isolate be placed in a novel genus and be considered a novel species designated Euzebya tangerina gen. nov., sp. nov. within the new family, order and subclass Euzebyaceae fam. nov., Euzebyales ord. nov. and Nitriliruptoridae subclassis nov. in the class Actinobacteria. The type strain of Euzebya tangerina is F10T (=NBRC 105439T =KCTC 19736T).
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Actinokineospora baliensis sp. nov., Actinokineospora cibodasensis sp. nov. and Actinokineospora cianjurensis sp. nov., isolated from soil and plant litter
Six actinomycete strains isolated from soil and plant-litter samples in Indonesia were studied for their taxonomic position by using a polyphasic approach. Phylogenetically, all the strains were located in the broad cluster of the genus Actinokineospora. Chemotaxonomic data [cell-wall diamino acid, meso-diaminopimelic acid; cell-wall peptidoglycan, type III (A1γ); major sugars, galactose and arabinose; major menaquinone, MK-9(H4); major fatty acid, iso-C16 : 0; major phospholipid, phosphatidylethanolamine] supported the affiliation of all six strains to the genus Actinokineospora. The results of DNA–DNA hybridization with DNA from type strains of Actinokineospora species with validly published names revealed three DNA–DNA relatedness groups. Group I (ID03-0561T) showed low relatedness to the other strains studied. The three strains in group II (ID03-0784T, ID03-0808 and ID03-0809) formed a group with high relatedness (98–100 %) and showed low relatedness to the other strains studied. The two strains in group III (ID03-0810T and ID03-0813) showed 58–68 % relatedness to Actinokineospora terrae NBRC 15668T and showed low relatedness (2–24 %) to the other strains studied. The description of three novel species is proposed: Actinokineospora baliensis sp. nov., for the single strain in group I (type strain ID03-0561T =BTCC B-554T =NBRC 104211T), Actinokineospora cibodasensis sp. nov., for the strains in group II (type strain ID03-0784T =BTCC B-555T =NBRC 104212T), and Actinokineospora cianjurensis sp. nov., for the strains in group III (type strain ID03-0810T =BTCC B-558T =NBRC 105526T).
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Pseudonocardia babensis sp. nov., isolated from plant litter
A novel actinomycete, designated strain VN05A0561T, was isolated from plant litter collected at Ba Be National Park, Vietnam. The substrate mycelia and spore chains fragmented in a manner similar to nocardioform actinomycetes; the spores had smooth surfaces and were rod-shaped. Strain VN05A0561T had the following chemotaxonomic characteristics: meso-diaminopimelic acid in the cell-wall peptidoglycan, arabinose and galactose as characteristic sugars, MK-8(H4) as the major isoprenoid quinone, phosphatidylcholine as the diagnostic phospholipid and iso-C16 : 0 as the major cellular fatty acid. Strain VN05A0561T shared low levels of 16S rRNA gene sequence similarity (<97 %) with the type strains of recognized species of the genus Pseudonocardia and could be differentiated from its closest phylogenetic relatives based on phenotypic characteristics. These results suggested that strain VN05A0561T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia babensis sp. nov. is proposed. The type strain is VN05A0561T (=VTCC-A-1757T=NBRC 105793T).
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Agromyces bauzanensis sp. nov., isolated from soil
A Gram-stain-positive, aerobic bacterium, designated strain BZ41T, was isolated from hydrocarbon-contaminated soil. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BZ41T was related to members of the genus Agromyces and showed highest similarity with the type strain of Agromyces ramosus (96.8 %). The morphological, biochemical and chemotaxonomic characteristics of the new isolate were consistent with the description of the genus Agromyces. The cell-wall peptidoglycan of strain BZ41T was of type B2γ and contained the amino acids 2,4-diaminobutyric acid, alanine, glycine and glutamic acid in an approximate molar ratio of 1.8 : 0.7 : 1.1 : 1.0. The predominant cell-wall sugars were galactose, glucose, mannose and rhamnose. Strain BZ41T had MK-12 and MK-11 as major menaquinones and contained anteiso-C15 : 0 and anteiso-C17 : 0 as major fatty acids. The genomic DNA G+C content of strain BZ41T was 69.7 mol%. On the basis of phenotypic characteristics and genotypic analysis, strain BZ41T is considered to represent a novel species of the genus Agromyces, for which the name Agromyces bauzanensis sp. nov. is proposed. The type strain is BZ41T (=DSM 22275T =CGMCC 1.8984T).
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Nocardiopsis sinuspersici sp. nov., isolated from sandy rhizospheric soil
A polyphasic taxonomic study of a halotolerant bacterium, isolated from sandy rhizospheric soil in Sarbandar, Persian Gulf, Iran, revealed that strain HM6T represents a novel species within the genus Nocardiopsis. Results of the 16S rRNA gene sequence comparison revealed that strain HM6T clustered with strains of the genus Nocardiopsis, showing the highest degree of 16S rRNA gene sequence similarity to Nocardiopsis quinghaiensis (99.2 %), Nocardiopsis aegyptia (98.5 %) and Nocardiopsis halotolerans (98.3 %). However, DNA–DNA hybridization studies with these type strains revealed less than 39.6 % similarity. Rather than genotypic differences, there are some phenotypic discrepancies between strain HM6T and closely related species of the genus Nocardiopsis. Main morphological and chemotaxonomical features of strain HM6T include: (i) growth characteristics, i.e. the formation of a scant light-yellow to white aerial mycelium and the typical zig-zag form of the hyphae, which fragment during ageing into smooth rod-shaped spores; (ii) the presence of meso-diaminopimelic acid and glucose plus ribose in whole-cell hydrolysates; (iii) the presence of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and phosphatidylinositol, together with three unknown Nocardiopsis-specific phospholipids (close to diphosphatidylglycerol in position) in polar lipid extracts; (iv) the presence of the major menaquinones MK-10(H0), MK-10(H2) and MK-9(H0) in the non-polar fraction; (v) the presence of iso/anteiso-branched plus 10-methyl-branched fatty acids, showing the diagnostic combination for species of the genus Nocardiopsis of iso-16 : 0 (31.1 %), anteiso-17 : 0 (19.2 %), 10-methyl-17 : 0 (5.8 %) and tuberculostearic acid (8.8 %); and (vi) the absence of mycolic acids. Analysis of the 16S rRNA gene sequence revealed that strain HM6T represents a distinct taxon within the genus Nocardiopsis. Based upon genotypic and phenotypic differences from other members of the genus, a novel species, Nocardiopsis sinuspersici sp. nov., is proposed. The type strain is HM6T (=UTMC 00102T =DSM 45277T =CCUG 57624T).
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Microlunatus parietis sp. nov., isolated from an indoor wall
More LessA Gram-positive, coccoid, non-endospore-forming actinobacterium (strain 12-Be-011T) was isolated from indoor wall material. Based on 16S rRNA gene sequence comparisons, strain 12-Be-011T was clearly shown to belong to the genus Microlunatus and was most closely related to Microlunatus panaciterrae Gsoil 954T (95.7 %), Microlunatus soli CC-12602T (94.9 %), Microlunatus ginsengisoli Gsoil 633T (94.8 %), Microlunatus aurantiacus YIM 45721T (95.5 %) and Microlunatus phosphovorus DSM 10555T (94.7 %). The cell-wall peptidoglycan contained ll-diaminopimelic acid as the diagnostic diamino acid. Mycolic acids were absent. The major menaquinone was MK-9(H4). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two unknown phospholipids and one unknown glycolipid. The major fatty acids of iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0 supported the affiliation of strain 12-Be-011T to the genus Microlunatus. Physiological and biochemical test results allowed a clear phenotypic differentiation of strain 12-Be-011T from all other species of the genus Microlunatus. Hence, strain 12-Be-011T can be regarded as a representative of a novel species, for which the name Microlunatus parietis sp. nov. is proposed, with the type strain 12-Be-011T (=DSM 22083T=CCM 7636T).
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Angustibacter luteus gen. nov., sp. nov., isolated from subarctic forest soil
An actinobacterial strain was isolated from subarctic forest soil, and subjected to polyphasic taxonomic characterization. The cell-wall peptidoglycan comprised meso-diaminopimelic acid, alanine and glutamic acid. MK-9(H4) was the predominant isoprenoid quinone, and iso-C17 : 0, iso-C15 : 0 and C16 : 0 were detected as the major cellular fatty acids. Phylogenetic analyses based on 16S rRNA gene sequences showed that this organism was related to members of the suborders Kineosporiineae and Micrococcineae. The phenotypic properties readily differentiated this organism from the phylogenetic neighbours. Based on the phenotypic and genotypic evidence, the strain is assigned to a novel species of a novel genus: Angustibacter luteus gen. nov., sp. nov. with type strain TT07R-79T (=NBRC 105387T =KACC 14249T).
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- Archaea
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Haloterrigena daqingensis sp. nov., an extremely haloalkaliphilic archaeon isolated from a saline–alkaline soil
A haloalkaliphilic archaeon, strain JX313T, was isolated from a saline–alkaline soil from Daqing, Heilongjiang Province, China. Its morphological, physiological and biochemical features and 16S rRNA gene sequence were determined. Colonies of the strain were orange–red and cells were non-motile cocci and Gram-stain-variable. The strain required at least 1.7 M NaCl for growth, with optimal growth occurring in 2.0–2.5 M NaCl. Growth was observed at 20–50 °C and pH 8.0–10.5, with optimal growth at 35 °C and pH 10.0. The G+C content of its genomic DNA was 59.3 mol%. Phylogenetic analysis of 16S rRNA gene sequences showed that strain JX313T is associated with the genera Haloterrigena and Natrinema and is most closely related to Haloterrigena salina XH-65T (96.2 % sequence similarity) and Haloterrigena hispanica FP1T (96.2 %). DNA–DNA hybridization experiments revealed that the relatedness of strain JX313T to type strains of related species of the genus Haloterrigena or Natrinema was less than 50 %. Furthermore, the cellular polar lipids of strain JX313T, identified as phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and mannose-2,6-disulfate (1→2)-glucose glycerol diether (S2-DGD), were consistent with the polar lipid characteristics of the genus Haloterrigena. Therefore, phylogenetic analysis, phenotypic assessment and chemotaxonomic data showed that JX313T represents a novel species within the genus Haloterrigena, for which the name Haloterrigena daqingensis sp. nov. is proposed. The type strain is JX313T (=CGMCC 1.8909T =NBRC 105739T).
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Halosarcina limi sp. nov., a halophilic archaeon from a marine solar saltern, and emended description of the genus Halosarcina
More LessA halophilic archaeon, strain RO1-6T, was isolated from a marine solar saltern in eastern China. Cells of strain RO1-6T were pleomorphic and motile and stained Gram-negative. Strain RO1-6T grew well on complex medium and colonies were red-pigmented. It was able to grow at 20–50 °C (optimum 37 °C), in 2.1–5.1 M NaCl (optimum 3.9 M NaCl), in 0.05–0.70 M MgCl2 (optimum 0.30 M MgCl2) and at pH 6.5–8.0 (optimum pH 7.0). Cells lysed in distilled water and the minimal NaCl concentration to prevent cell lysis was 12 % (w/v). The major polar lipids of strain RO1-6T were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and two glycolipids that were chromatographically identical to S-DGD-1 and S2-DGD. The 16S rRNA gene sequence of strain RO1-6T showed similarities of 96.9 and 96.4 % to those of the type strains of Halosarcina pallida and Halogeometricum borinquense, respectively, members of the most closely related recognized genera within the family Halobacteriaceae. The DNA G+C content of strain RO1-6T was 61.2 mol%. Phenotypic characterization and phylogenetic analysis revealed that strain RO1-6T is related to Halosarcina pallida and represents a novel species of the genus Halosarcina, for which the name Halosarcina limi sp. nov. is proposed; the type strain is RO1-6T (=CGMCC 1.8711T =JCM 16054T).
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- Bacteroidetes
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Aquimarina macrocephali sp. nov., isolated from sediment adjacent to sperm whale carcasses
More LessA Gram-negative, rod-shaped, non-spore-forming, strictly aerobic strain with gliding motility, designated JAMB N27T, was isolated from sediment adjacent to sperm whale carcasses off Kagoshima, Japan, at a depth of 219 m. Strain JAMB N27T contained MK-6 as the major isoprenoid quinone and iso-C15 : 0, iso-C15 : 1, C16 : 1 and iso-C17 : 1 as the predominant fatty acids. Casein, chitin, gelatin and starch were degraded. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JAMB N27T represented a separate lineage within the genus Aquimarina. The DNA G+C content of strain JAMB N27T was 33.1 mol%. DNA–DNA relatedness values between strain JAMB N27T and type strains of species of the genus Aquimarina were significantly lower than the cut-off value accepted for the definition of a novel species. Therefore, strain JAMB N27T represents a novel species, for which the name Aquimarina macrocephali sp. nov. is proposed. The type strain is JAMB N27T (=JCM 15542T=NCIMB 14508T).
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Salinimicrobium marinum sp. nov., a halophilic bacterium of the family Flavobacteriaceae, and emended descriptions of the genus Salinimicrobium and Salinimicrobium catena
Two novel heterotrophic, facultatively anaerobic, gliding and yellow-pigmented bacteria, designated strains KMM 6270T and KMM 6320, were isolated from different marine environments and studied using a polyphasic taxonomic approach. 16S rRNA gene sequence analysis placed the strains within the family Flavobacteriaceae. Strains KMM 6270T and KMM 6320 were most closely related to the type strains of recognized species of the genus Salinimicrobium (95.0–96.6 % 16S rRNA gene sequence similarity). The G+C content of the genomic DNA was 40–41 mol%. The strains grew with 0.5–15 % (w/v) NaCl (optimum 4 % NaCl) and at 4–41 °C (optimum 28–32 °C). Aesculin and gelatin were hydrolysed, but agar, casein, DNA and chitin were not. The phylogenetic data taken together with the results of the genotypic and phenotypic studies permit the classification of strains KMM 6270T and KMM 6320 as members of a novel species of the genus Salinimicrobium, for which the name Salinimicrobium marinum sp. nov. is proposed. The type strain is KMM 6270T (=KCTC 12719T=LMG 25395T).
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Nitritalea halalkaliphila gen. nov., sp. nov., an alkaliphilic bacterium of the family ‘Cyclobacteriaceae’, phylum Bacteroidetes
More LessA novel Gram-negative, rod-shaped, non-motile bacterium, designated strain LW7T, was isolated from a water sample collected at a depth of 4.5 m from Lonar Lake in Buldhana district, Maharastra, India. The cell suspension was dark-reddish orange due to the presence of carotenoids. The fatty acids were dominated by large amounts of iso-C15 : 0 (59.6 %) and iso-C17 : 0 3-OH (8.9 %). Strain LW7T contained MK-4 and MK-5 as the major respiratory quinones and phosphatidylglycerol and phosphatidylethanolamine as the major phospholipids. 16S rRNA gene sequence analysis indicated that Belliella baltica, a member of family ‘Cyclobacteriaceae’ (phylum Bacteroidetes), is the closest related species, with a sequence similarity of 94.0 % to the type strain. Other members of the family ‘Cyclobacteriaceae’ had sequence similarities of <93.3 %. Based on the above-mentioned phenotypic and phylogenetic characteristics, strain LW7T is proposed as a representative of a new genus and species, Nitritalea halalkaliphila gen. nov., sp. nov. The type strain of Nitritalea halalkaliphila is LW7T (=CCUG 57665T =JCM 15946T =NCCB 100279T). The genomic DNA G+C of strain LW7T is 49 mol%.
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Sphingobacterium shayense sp. nov., isolated from forest soil
A Gram-staining-negative, yellow-coloured, strictly aerobic, non-spore-forming, rod-shaped bacterium, designated HS39T, isolated from a soil sample collected from a natural Populus euphratica forest in Xinjiang, China, was characterized using a polyphasic approach. The isolate grew optimally at 30–37 °C, at pH 6.5–8.0 and with 0–3 % NaCl. Analysis of the 16S rRNA gene sequence of strain HS39T revealed that it is a member of the genus Sphingobacterium. Sphingobacterium mizutaii ATCC 33299T was the nearest relative (94.0 % 16S rRNA gene sequence similarity). The G+C content of the genomic DNA was 40.2 mol%. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1 ω6c and/or C16 : 1 ω7c). The predominant isoprenoid quinone was MK-7. On the basis of phenotypic properties and phylogenetic inference, strain HS39T represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium shayense sp. nov. is proposed. The type strain is HS39T (=CCTCC AB 209006T =NRRL B-59203T).
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Chryseobacterium culicis sp. nov., isolated from the midgut of the mosquito Culex quinquefasciatus
More LessA yellow-pigmented bacterial strain, R4-1AT, isolated from the midgut of the mosquito Culex quinquefasciatus (a vector of lymphatic filariasis), was studied using a polyphasic approach. Cells of the isolate were rod-shaped and stained Gram-negative. A comparison of the 16S rRNA gene sequence of this organism with sequences of type strains of the most closely related species clearly showed an allocation to the genus Chryseobacterium, with the highest sequence similarities (all 97.9 %) to Chryseobacterium jejuense JS17-8T, C. indologenes ATCC 29897T, C. arthrosphaerae CC-VM-7T and C. aquifrigidense CW9T. 16S rRNA gene sequence similarities to type strains of other Chryseobacterium species were below 97.5 %. The fatty acid profile of strain R4-1AT included the major fatty acids iso-15 : 0, summed feature 4 (comprising iso-15 : 0 2-OH and/or 16 : 1ω7c), iso-17 : 1ω9c and iso-17 : 0 3-OH. DNA–DNA hybridizations with C. jejuense KACC 12501T, C. indologenes CCUG 14556T, C. arthrosphaerae CC-VM-7T and C. aquifrigidense KCTC 12894T resulted in relatedness values of 38.3 % (reciprocal 30.5 %), 29.4 % (32.1 %), 23.2 % (37.2 %) and 29.5 % (47.1 %), respectively. These results and the differentiating biochemical and chemotaxonomic properties show that strain R4-1AT represents a novel species, for which the name Chryseobacterium culicis sp. nov. is proposed. The type strain is R4-1AT (=LMG 25442T =CCM 7716T).
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Adhaeribacter aerophilus sp. nov., Adhaeribacter aerolatus sp. nov. and Segetibacter aerophilus sp. nov., isolated from air samples
More LessThree bacterial isolates from air samples in Korea, designated strains 6424S-25T, 6515J-31T and 6424S-61T, were characterized using a polyphasic approach. The cells were strictly aerobic, Gram-stain-negative, non-motile, non-spore-forming and rod-shaped. Phylogenetic analysis of their 16S rRNA gene sequences revealed a clear affiliation with the phylum Bacteroidetes. Strains 6424S-25T and 6515J-31T showed 16S rRNA gene sequence similarities of 92.7–94.8 % to type strains of recognized species of the genus Adhaeribacter and strain 6424S-61T was closely related to Segetibacter koreensis Gsoil 664T (93.9 % similarity). The G+C contents of the DNA of strains 6424S-25T, 6515J-31T and 6424S-61T were 44.5, 43.9 and 38.4 mol%, respectively. Major fatty acids of strains 6424S-25T and 6515J-31T were summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B), iso-C15 : 0 and C16 : 1 ω5c. The fatty acid content of strain 6424S-61T mainly comprised iso-C15 : 1 G and iso-C15 : 0. Comparative analysis of phenotypic and phylogenetic traits indicated that strains 6424S-25T and 6515J-31T represented two novel species of the genus Adhaeribacter and that strain 6424S-61T should be considered as a novel species of the genus Segetibacter. The names Adhaeribacter aerophilus sp. nov. (type strain 6424S-25T =KACC 14118T =NBRC 106134T), Adhaeribacter aerolatus sp. nov. (type strain 6515J-31T =KACC 14117T =NBRC 106133T) and Segetibacter aerophilus sp. nov. (type strain 6424S-61T =KACC 14119T =NBRC 106135T) are proposed for these organisms.
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Mucilaginibacter gossypii sp. nov. and Mucilaginibacter gossypiicola sp. nov., plant-growth-promoting bacteria isolated from cotton rhizosphere soils
Two isolates from rhizosphere soil of cotton, designated Gh-67T and Gh-48T, which produced large amounts of extracellular polysaccharide and possessed plant-growth-promoting traits, were characterized phenotypically and genotypically. The strains were Gram-negative and cells were non-motile rods that grew optimally at 28 °C and grew between pH 4 and 7. 16S rRNA gene sequence analysis of strains Gh-67T and Gh-48T placed them in the genus Mucilaginibacter, with pairwise sequence similarity between them and type strains from related genera ranging from 93.9 to 98.2 %. The major fatty acids were iso-C15 : 0, C16 : 0 and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH). The strains contained MK-7 as the major isoprenoid quinone. The DNA G+C contents of strains Gh-67T and Gh-48T were 46.7 and 44.2 mol%, respectively. The low DNA–DNA hybridization value (18 %) and a number of phenotypic differences between strains Gh-48T and Gh-67T indicated that they represent two separate species. Results of phenotypic, phylogenetic and genotypic analysis revealed that the strains were separated from the species of Mucilaginibacter described to date. Therefore, strains Gh-67T and Gh-48T represent novel species of Mucilaginibacter, for which we propose the names Mucilaginibacter gossypii sp. nov. (type strain Gh-67T =NCIMB 14470T =KCTC 22380T) and Mucilaginibacter gossypiicola sp. nov. (type strain Gh-48T =NCIMB 14471T =KCTC 22379T).
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Prevotella saccharolytica sp. nov., isolated from the human oral cavity
More LessTwo strains of anaerobic, Gram-stain-negative bacilli isolated from the human oral cavity (D033B-12-2T and D080A-01) were subjected to a comprehensive range of phenotypic and genotypic tests and were found to be distinct from any previously described species. 16S rRNA gene sequence analysis revealed that the strains were related most closely to the type strain of Prevotella marshii (93.5 % sequence identity). The novel strains were saccharolytic and produced acetic acid and succinic acid as end products of fermentation. The principal cellular long-chain fatty acids were C16 : 0, iso-C14 : 0, C14 : 0, anteiso-C15 : 0, iso-C16 : 0 and C16 : 0 3-OH. The G+C content of the DNA of strain D033B-12-2T was 44 mol%. Strains D033B-12-2T and D080A-01 are considered to represent a single novel species of the genus Prevotella, for which the name Prevotella saccharolytica sp. nov. is proposed. The type strain is D033B-12-2T (=DSM 22473T =CCUG 57944T).
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- Firmicutes And Related Organisms
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Cohnella thailandensis sp. nov., a xylanolytic bacterium from Thai soil
A xylanolytic bacterium, strain S1-3T, was isolated from soil collected in Nan province, Thailand. It was characterized taxonomically based on phenotypic characteristics and 16S rRNA gene sequence comparison. The strain was a Gram-stain-positive, facultatively anaerobic, spore-forming, rod-shaped bacterium. It contained meso-diaminopimelic acid in the cell-wall peptidoglycan. The major menaquinone was MK-7. Iso-C16 : 0 (39.5 %) and anteiso-C15 : 0 (26.8 %) were predominant cellular fatty acids. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and lysyl-phosphatidylglycerol were the major polar lipids. The DNA G+C content was 53.3 mol%. Phylogenetic analysis using 16S rRNA gene sequences showed that strain S1-3T was affiliated to the genus Cohnella, and was closely related to Cohnella ginsengisoli GR21-5T and Cohnella thermotolerans CCUG 47242T with 95.7 and 95.3 % sequence similarity, respectively. Strain S1-3T could be clearly distinguished from related species of the genus Cohnella by its physiological and biochemical characteristics as well as by its phylogenetic position. Therefore, the strain represents a novel species of the genus Cohnella, for which the name Cohnella thailandensis sp. nov. is proposed. The type strain is S1-3T (=KCTC 22296T =TISTR 1890T =PCU 306T).
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Lactobacillus paucivorans sp. nov., isolated from a brewery environment
More LessA Gram-stain-positive, catalase-negative and rod-shaped bacterium was isolated from a brewery environment. Its phylogenetic affiliation was determined by using 16S rRNA gene sequence analysis. It was found that strain TMW 1.1424T belongs to the genus Lactobacillus, with the three nearest neighbours Lactobacillus parabrevis LMG 11984T (97 %), Lactobacillus brevis DSM 20054T (95.9 %) and Lactobacillus hammesii DSM 16381T (96.2 %). Comparative sequencing of additional phylogenetic marker genes tuf and pheS confirmed the 16S rRNA gene sequence tree topology. The DNA G+C content of strain TMW 1.1424T is 46.6 mol%. Genomic DNA–DNA relatedness values with L. brevis DSM 20054T, L. parabrevis LMG 11984T and L. hammesii DSM 16381T do not exceed 52.8 %, revealing that the novel isolate represents a separate genomic species. The strain can be distinguished from other related species of the genus Lactobacillus by physiological and biochemical tests. Based on biochemical, physiological and phylogenetic data, it is proposed that the new isolate be classified as a novel species of the genus Lactobacillus, Lactobacillus paucivorans sp. nov. The type strain is TMW 1.1424T (=DSM 22467T =LMG 25291T).
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Bacillus siamensis sp. nov., isolated from salted crab (poo-khem) in Thailand
A Gram-positive, endospore-forming, rod-shaped bacterium, strain PD-A10T, was isolated from salted crab (poo-khem) in Thailand and subjected to a taxonomic study. Phenotypic and chemotaxonomic characteristics, including phylogenetic analyses, showed that the novel strain was a member of the genus Bacillus. The novel strain grew in medium with 0–14 % (w/v) NaCl, at 4–55 °C and at pH 4.5–9. The predominant quinone was a menaquinone with seven isoprene units (MK-7). The major fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. Polar lipid analysis revealed the presence of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, lysylphosphatidylglycerol, glycolipid and unknown lipids. The DNA G+C content was 41.4 mol%. The 16S rRNA gene sequence similarities between strain PD-A10T and Bacillus amyloliquefaciens NBRC 15535T, Bacillus subtilis DSM 10T, Bacillus vallismortis DSM 11031T and Bacillus mojavensis IFO 15718T were 99.5, 99.4, 99.4 and 99.2 %, respectively. Strain PD-A10T showed a low degree similarity of rep-PCR fingerprints and low DNA–DNA relatedness with the above-mentioned species. On the basis of the data gathered in this study, strain PD-A10T should be classified as representing a novel species of the genus Bacillus, for which the name Bacillus siamensis sp. nov. is proposed. The type strain is PD-A10T (=BCC 22614T=KCTC 13613T).
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Paenibacillus sputi sp. nov., isolated from the sputum of a patient with pulmonary disease
More LessStrain KIT 00200-70066-1T was isolated from the sputum of a patient with pulmonary disease. Cells of the strain were Gram-variable, facultatively anaerobic, motile, spore-forming rods and formed colourless to white colonies on tryptic soy agar at 30 °C and pH 7. The pathogenicity of the strain is not known. The strain contained meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, MK-7 as the predominant menaquinone, anteiso-C15 : 0, iso-C16 : 0 and C16 : 0 as the major fatty acids and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and several unknown lipids in the polar lipid profile. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belongs to the genus Paenibacillus, sharing the highest levels of sequence similarity with Paenibacillus nanensis MX2-3T, Paenibacillus agaridevorans DSM 1355T and Paenibacillus alkaliterrae KSL-134T (95.4, 95.2 and 94.8 %, respectively), and that it occupied a distinct position within this genus. Combined phylogenetic and phenotypic data supported the conclusion that strain KIT 00200-70066-1T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus sputi sp. nov. is proposed; the type strain is KIT 00200-70066-1T (=KCTC 13252T =DSM 22699T).
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Oceanobacillus neutriphilus sp. nov., isolated from activated sludge in a bioreactor
More LessA Gram-stain-positive, neutrophilic, rod-shaped bacterium, strain A1gT, was isolated from activated sludge of a bioreactor and was subjected to a polyphasic taxonomic characterization. The isolate grew in the presence of 0–17.0 % (w/v) NaCl and at pH 6.0–9.0; optimum growth was observed in the presence of 3.0–5.0 % (w/v) NaCl and at pH 7.0. Strain A1gT was motile, formed cream-coloured colonies, was catalase- and oxidase-positive and was able to hydrolyse aesculin, Tween 40 and Tween 60. Chemotaxonomic analysis revealed menaquinone-7 as the predominant respiratory quinone and anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 0 as major fatty acids. The genomic DNA G+C content of strain A1gT was 36.3 mol%. Comparative 16S rRNA gene sequence analysis revealed that the new isolate belonged to the genus Oceanobacillus and exhibited closest phylogenetic affinity to the type strains of Oceanobacillus oncorhynchi subsp. incaldanensis (97.9 % similarity) and O. oncorhynchi subsp. oncorhynchi (97.5 %), but less than 97 % sequence similarity with respect to the type strains of other recognized Oceanobacillus species. Levels of DNA–DNA relatedness between strain A1gT and reference strains O. oncorhynchi subsp. incaldanensis DSM 16557T, O. oncorhynchi subsp. oncorhynchi JCM 12661T and Oceanobacillus iheyensis DSM 14371T were 29, 45 and 38 %, respectively. On the basis of phenotypic and genotypic data, strain A1gT is considered to represent a novel species of the genus Oceanobacillus, for which the name Oceanobacillus neutriphilus sp. nov. is proposed. The type strain is A1gT (=CGMCC 1.7693T =JCM 15776T).
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Paenibacillus residui sp. nov., isolated from urban waste compost
Two bacterial strains, MC-246T and MC-247, were isolated from municipal urban waste compost and characterized by a polyphasic approach. Both isolates were Gram-stain-variable, endospore-forming rods that were catalase-, oxidase- and β-galactosidase-positive, and able to grow at 25–50 °C and pH 7.0–9.0, with optimum growth at 37 °C and pH 7. The predominant cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0 and iso-C17 : 0; the major respiratory quinone was menaquinone MK-7; the cell wall peptidoglycan was of type A1γ; and the DNA G+C content was 49 mol%. These characteristics, as well as data from 16S RNA gene sequence analysis, showed that these strains were affiliated with the genus Paenibacillus; the type strains of Paenibacillus ginsengarvi and Paenibacillus hodogayensis were among their closest neighbours (<94.2 % sequence similarity). Nevertheless, the hypothesis that strains MC-246T and MC-247 could represent a novel species was supported by the low 16S rRNA gene sequence similarity values shared with other members of the genus Paenibacillus and by the observation of distinct biochemical and physiological traits. Strains MC-246T and MC-247 shared 99.6 % 16S rRNA gene sequence similarity and showed almost identical MALDI-TOF mass spectra, but could be distinguished at the phenotypic and genotypic level. However, DNA–DNA hybridization between strains MC-246T and MC-247 resulted in values above 70 % indicating that both organisms represent a single species, for which the name Paenibacillus residui sp. nov. is proposed; the type strain is MC-246T (=DSM 22072T =CCUG 57263T).
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Lactobacillus florum sp. nov., a fructophilic species isolated from flowers
More LessThree strains of fructophilic lactic acid bacteria were isolated from flowers in South Africa. The isolates formed a subcluster in the Lactobacillus buchneri phylogenetic group, closely related to Lactobacillus fructivorans, Lactobacillus homohiochii, Lactobacillus lindneri and Lactobacillus sanfranciscensis according to phylogenetic analysis based on the 16S rRNA gene sequences. Levels of DNA–DNA relatedness indicated that the three strains belonged to the same taxon and formed a genetically distinct group, well separated from their phylogenetic relatives. The three strains produced acids from only two of the 49 carbohydrates tested, i.e. d-glucose and d-fructose. d-Fructose was more rapidly fermented than d-glucose. Good growth was recorded on d-fructose or d-glucose in the presence of external electron acceptors. However, delayed growth was recorded on d-glucose without electron acceptors. The novel strains produced lactic acid, ethanol and acetic acid from d-glucose at a ratio of 1 : 0.8 : 0.2. These characteristics were distinct from other species of the genus Lactobacillus. Based on the data provided, the three isolates represent a fructophilic and novel species of the genus Lactobacillus, for which the name Lactobacillus florum sp. nov. is proposed. The type strain is F9-1T (=JCM 16035T=DSM 22689T=NRIC 0771T).
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Alkalibaculum bacchi gen. nov., sp. nov., a CO-oxidizing, ethanol-producing acetogen isolated from livestock-impacted soil
More LessPhenotypic and phylogenetic studies were performed on three strains of an acetogenic bacterium isolated from livestock-impacted soil. The bacterium stained Gram-negative and was a non-spore-forming rod that was motile by peritrichous flagella. The novel strains had an optimum pH for growth of 8.0–8.5 and utilized H2 : CO2, CO : CO2, glucose, fructose, mannose, turanose, ribose, trimethylamine, pyruvate, methanol, ethanol, n-propanol and n-butanol as growth substrates. Acetate was produced from glucose. Acetate, CO2 and ethanol were produced from CO : CO2. 16S rRNA gene sequence analysis indicated that the novel strains formed a new subline in the family Eubacteriaceae (rRNA cluster XV) of the low G+C-containing Gram-positive bacteria of the class Clostridia. The DNA G+C base composition was 34 mol%. Cell wall analysis revealed the existence of a novel B-type peptidoglycan similar to the B2α-type (B4) configuration with a variation containing aspartic acid. Based on phylogenetic and phenotypic evidence, it is proposed that the new isolates represent a novel genus and species, for which the name Alkalibaculum bacchi gen. nov., sp. nov. is proposed. The type strain of the type species is CP11T (=ATCC BAA-1772T=DSM 22112T).
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Bacillus methylotrophicus sp. nov., a methanol-utilizing, plant-growth-promoting bacterium isolated from rice rhizosphere soil
More LessA Gram-positive bacterium, designated strain CBMB205T, was isolated from the rhizosphere soil of traditionally cultivated, field-grown rice. Cells were strictly aerobic, motile, rod-shaped and formed endospores. The best growth was achieved at 30 °C and pH 7.0 in ammonium mineral salts (AMS) medium containing 600 mM methanol. A comparative 16S rRNA gene sequence-based phylogenetic analysis placed strain CBMB205T in a clade with the species Bacillus amyloliquefaciens, Bacillus vallismortis, Bacillus subtilis, Bacillus atrophaeus, Bacillus mojavensis and Bacillus licheniformis and revealed pairwise similarities ranging from 98.2 to 99.2 %. DNA–DNA hybridization experiments revealed a low level (<36 %) of DNA–DNA relatedness between strain CBMB205T and its closest relatives. The major components of the fatty acid profile were C15 : 0 anteiso, C15 : 0 iso, C16 : 0 iso and C17 : 0 anteiso. The diagnostic diamino acid of the cell wall was meso-diaminopimelic acid. The G+C content of the genomic DNA was 45.0 mol%. The lipids present in strain CBMB205T were diphosphatidylglycerol, phosphatidylglycerol, a minor amount of phosphatidylcholine and two unknown phospholipids. The predominant respiratory quinone was MK-7. Studies of DNA–DNA relatedness, morphological, physiological and chemotaxonomic analyses and phylogenetic data based on 16S rRNA gene sequencing enabled strain CBMB205T to be described as representing a novel species of the genus Bacillus, for which the name Bacillus methylotrophicus sp. nov. is proposed. The type strain is CBMB205T (=KACC 13105T=NCCB 100236T).
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- Proteobacteria
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Phylogeny and differentiation of species of the genus Gluconacetobacter and related taxa based on multilocus sequence analyses of housekeeping genes and reclassification of Acetobacter xylinus subsp. sucrofermentans as Gluconacetobacter sucrofermentans (Toyosaki et al. 1996) sp. nov., comb. nov.
More LessThree housekeeping genes (dnaK, groEL and rpoB) of strains belonging to the genus Gluconacetobacter (37 strains) or related taxa (38 strains) were sequenced. Reference strains of the 15 species of the genus Gluconacetobacter were included. Phylogenetic trees generated using these gene sequences confirmed the existence of two phylogenetic groups within the genus Gluconacetobacter. These groups clustered separately in trees constructed using concatenated sequences of the three genes, indicating that the genus Gluconacetobacter should not remain a single genus and should be split, as suggested previously. Multilocus sequence analysis (MLSA) of the three housekeeping genes also proved useful for species differentiation in the family Acetobacteraceae. It also suggested that Gluconacetobacter xylinus LMG 18788, better known as the type and only strain of Acetobacter xylinus subsp. sucrofermentans, represents a distinct species in the genus Gluconacetobacter, and is not a true G. xylinus strain. In previous studies, this strain showed less than 70 % DNA relatedness to the type strains of G. xylinus and Gluconacetobacter nataicola, the phylogenetically nearest relatives, and could be distinguished from them phenotypically. Additionally, AFLP and (GTG)5-PCR DNA fingerprinting data supported its reclassification within a distinct species. The name Gluconacetobacter sucrofermentans (Toyosaki et al. 1996) sp. nov., comb. nov. is proposed.
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Shewanella corallii sp. nov., a marine bacterium isolated from a Red Sea coral
More LessA marine bacterial strain, designated fav-2-10-05T, was isolated from the mucus layer of a coral of the genus Favia, collected from the coral reef in the Gulf of Eilat, Israel (29.5 ° N 34.9 ° E). On the basis of 16S rRNA gene sequence comparisons, strain fav-2-10-05T was affiliated with the family Shewanellaceae. The closest relatives of strain fav-2-10-05T were Shewanella marisflavi SW-117T (96.0 % 16S rRNA gene sequence similarity) and Shewanella haliotis DW-1T (95.9 %). Strain fav-2-10-05T was Gram-negative, rod-shaped and motile by means of a single polar flagellum and formed yellow–brownish colonies within 2 days of incubation at 26 °C. Strain fav-2-10-05T demonstrated antibacterial activity against indicator strains and grew in the presence of 0.5–8.0 % (w/v) NaCl and at 10–37 °C. The major fatty acids were C17 : 1 ω8c (21.6 %), iso-C15 : 0 (18.6 %), C15 : 0 (9.1 %) and iso-C13 : 0 (8.9 %). The DNA G+C content was 49.1 mol%. The phylogenetic and phenotypic analyses of strain fav-2-10-05T suggested that it belongs to a novel species of the genus Shewanella, for which the name Shewanella corallii sp. nov. is proposed. The type strain is fav-2-10-05T (=LMG 24563T =DSM 21332T).
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Pusillimonas soli sp. nov., isolated from farm soil
More LessA Gram-negative, motile, non-spore-forming bacterial strain, designated MJ07T, was isolated from a farm soil and was characterized to determine its taxonomic position by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain MJ07T belongs to the family Alcaligenaceae, class Betaproteobacteria, and is related most closely to Pusillimonas ginsengisoli KCTC 22046T (98.6 % sequence similarity) and Pusillimonas noertemannii BN9T (96.9 %). The levels of 16S rRNA gene sequence similarity between strain MJ07T and members of all other recognized species of the family Alcaligenaceae were below 95.2 %. The G+C content of the genomic DNA of strain MJ07T was 59.4 mol%. The detection of a quinone system with ubiquinone Q-8 as the major respiratory lipoquinone, putrescine as the predominant polyamine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unknown aminolipids as major polar lipids and a fatty acid profile with C16 : 0 (32.0 %), C17 : 0 cyclo (24.7 %) and C19 : 0 cyclo ω8c (11.5 %) as the major components supported the affiliation of strain MJ07T to the genus Pusillimonas. Strain MJ07T exhibited relatively low levels of DNA–DNA relatedness with respect to P. ginsengisoli KCTC 22046T (50±8 %) and P. noertemannii KACC 13183T (18±7 %). On the basis of its phenotypic and genotypic properties together with its phylogenetic distinctiveness, strain MJ07T (=KCTC 22455T =JCM 16386T) should be classified in the genus Pusillimonas as the type strain of a novel species, for which the name Pusillimonas soli sp. nov. is proposed.
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Sphingopyxis panaciterrulae sp. nov., isolated from soil of a ginseng field
A Gram-negative, rod-shaped, motile bacterium was isolated from the soil of a ginseng field in Daejeon, South Korea, and characterized in order to determine its taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequence analysis revealed that strain DCY34T belonged to the family Sphingomonadaceae, and the highest degree of sequence similarity was found with Sphingopyxis witflariensis W-50T (97.1 %), Sphingopyxis ginsengisoli Gsoil 250T (97.0 %), Sphingopyxis chilensis S37T (96.9 %), Sphingopyxis macrogoltabida IFO 15033T (96.8 %), Sphingopyxis alaskensis RB2256T (96.7 %) and Sphingopyxis taejonensis JSS54T (96.7 %). Chemotaxonomic data revealed that strain DCY34T possessed ubiquinone Q-10 as the predominant respiratory lipoquinone, which is common to members of the genus Sphingopyxis. The predominant fatty acids were C18 : 1 ω7c (27.5 %), summed feature 4 (C16 : 1 ω7c and/or C15 : 0 iso 2-OH; 18.6 %), C16 : 0 (15.6 %) and summed feature 8 (C19 : 1 ω6c and/or unknown 18.864; 15.4 %). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid and an unknown polar lipid. The results of physiological and biochemical tests clearly demonstrated that strain DCY34T represented a separate species and supported its affiliation to the genus Sphingopyxis. Based on these data, the new isolate represents a novel species, for which the name Sphingopyxis panaciterrulae sp. nov. is proposed. The type strain is DCY34T (=KCTC 22112T=JCM 14844T).
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Camelimonas lactis gen. nov., sp. nov., isolated from the milk of camels
Three strains of Gram-negative, rod-shaped, non-spore-forming bacteria (M 2040T, M 1973 and M 1878-SK2), isolated from milk of camels at a camel-milk production farm in the United Arab Emirates, were investigated for their taxonomic allocation. On the basis of 16S rRNA gene sequence similarities, all three strains were shown to belong to the Alphaproteobacteria and were most closely related to Chelatococcus asaccharovorans and Chelatococcus daeguensis (95.1 and 95.2 % sequence similarity to the respective type strains). meso-Diaminopimelic acid was detected as the characteristic peptidoglycan diamino acid. The predominant compound in the polyamine pattern was spermidine, and sym-homospermidine was not detectable. The quinone system was ubiquinone Q-10. The polar lipid profile included the major compounds phosphatidylcholine and diphosphatidylglycerol and moderate amounts of phosphatidylethanolamine, phosphatidylglycerol, an unidentified glycolipid and two unidentified aminolipids. Minor lipids were also detected. The major fatty acid profile, consisting of C19 : 0 cyclo ω8c and C18 : 1 ω7c, with C18 : 0 3-OH as the major hydroxylated fatty acid, was similar to those of the genus Chelatococcus. The results of DNA–DNA hybridization experiments and physiological and biochemical tests allowed both genotypic and phenotypic differentiation of the isolates from described Chelatococcus species. Isolates M 2040T, M 1973 and M 1878-SK2 were closely related on the basis of DNA–DNA reassociation and therefore represent a single novel species. In summary, low 16S rRNA gene sequence similarities of 95 % with Chelatococcus asaccharovorans and marked differences in polar lipid profiles as well as in polyamine patterns support the description of a novel genus and species to accommodate these strains, for which the name Camelimonas lactis gen. nov., sp. nov. is proposed. The type strain of Camelimonas lactis is M 2040T (=CCUG 58638T =CCM 7696T).
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Emended description of the genus Pantoea, description of four species from human clinical samples, Pantoea septica sp. nov., Pantoea eucrina sp. nov., Pantoea brenneri sp. nov. and Pantoea conspicua sp. nov., and transfer of Pectobacterium cypripedii (Hori 1911) Brenner et al. 1973 emend. Hauben et al. 1998 to the genus as Pantoea cypripedii comb. nov.
Bacterial strains belonging to DNA hybridization groups (HG) II, IV and V, in the Erwinia herbicola–Enterobacter agglomerans complex, of Brenner et al. [Int J Syst Bacteriol 34 (1984), 45–55] were suggested previously to belong to the genus Pantoea, but have never been formally described and classified. Additionally, it has been shown in several studies that Pectobacterium cypripedii is more closely related to species of Pantoea than to those of Pectobacterium. In this study, the phylogenetic positions of Brenner's DNA HG II, IV and V and Pectobacterium cypripedii were re-examined by both 16S rRNA gene sequencing and multilocus sequence analyses (MLSA) based on the gyrB, rpoB, atpD and infB genes. The analyses revealed that DNA HG II, IV and V and Pectobacterium cypripedii form five separate branches within the genus Pantoea (strains from HG V were split into two branches). DNA–DNA hybridization data further confirmed that DNA HG II, IV and V constitute four separate species. Pectobacterium cypripedii was shown to be a close phylogenetic relative of Pantoea dispersa and DNA HG IV by both 16S rRNA gene sequence and MLSA analyses. Biochemical analyses performed on strains from DNA HG II, IV and V and Pectobacterium cypripedii confirmed their taxonomic position within the genus Pantoea and revealed phenotypic characteristics that allow the differentiation of these species from each other and from their closest phylogenetic neighbours. It is proposed to emend the description of the genus Pantoea and to describe Pantoea septica sp. nov. for DNA HG II (type strain LMG 5345T =BD 874T =CDC 3123-70T), Pantoea eucrina sp. nov. for DNA HG IV (type strain LMG 2781T =BD 872T =CDC 1741-71T =LMG 5346T), Pantoea brenneri sp. nov. for strains of DNA HG V excluding LMG 24534 (type strain LMG 5343T =BD 873T =CDC 3482-71T) and Pantoea conspicua sp. nov. for the remaining strain of DNA HG V (type strain LMG 24534T =BD 805T =CDC 3527-71T) and to transfer Pectobacterium cypripedii to the genus as Pantoea cypripedii comb. nov. (type strain LMG 2657T =ATCC 29267T =DSM 3873T =LMG 2655T).
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Moraxella porci sp. nov., isolated from pigs
Nine Gram-negative, catalase- and oxidase-positive, coccus-shaped bacteria were isolated from pigs affected by different pathological processes. Phenotypic and genotypic methods were adopted to determine the relationships of these new isolates to recognized species of the genus Moraxella. Analysis of the 16S rRNA gene sequences demonstrated that the clinical isolates represented a new lineage within the genus Moraxella. The isolates were closely related to Moraxella cuniculi and Moraxella pluranimalium with 16S rRNA gene sequence similarities of 98.1 % and 99.1 %, respectively. The isolates displayed DNA–DNA relative binding ratios of 74 % to each other, but distinctly lower levels of DNA–DNA hybridization were observed with phylogenetically closely related moraxellae (<32 %). The new isolates could be distinguished from all other recognized species of the genus Moraxella by physiological and biochemical tests. On the basis of the phenotypic and molecular data, the nine new isolates from pigs represent a novel species within the genus Moraxella, for which the name Moraxella porci sp. nov. is proposed. The type strain is SN9-4MT (=CECT 7294T=CCUG 54912T).
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Vogesella mureinivorans sp. nov., a peptidoglycan-degrading bacterium from lake water
More LessA novel, non-pigmented, rod-shaped, Gram-negative strain was isolated from mesotrophic lake water in Zealand, Denmark. Phylogenetic analysis of the 16S rRNA gene sequence of the bacterium, designated strain 389T, indicated that the strain belonged to the genus Vogesella and formed a monophyletic group with Vogesella perlucida DS-28T (99.1 % nucleotide similarity); it was less related to Vogesella indigofera ATCC 19706T (96.9 % similarity) and Vogesella lacus LMG 24504T (96.8 % similarity). Hybridization of DNA from strain 389T and V. perlucida demonstrated a reassociation of 50.6±9.6 %. The DNA G+C content of strain 389T was 61.2 mol%. The fatty acid profile of the strain differed from those of the other strains representing the genus Vogesella by a high content of C16 : 1 ω7c and/or iso-C15 : 0 2-OH (71.6 %) and a lower content of C16 : 0. Strain 389T was capable of degrading peptidoglycan and had chitinase and lysozyme activities, possibly associated with the degradation of peptidoglycan, and had capacity for degradation of several other polymer compounds. Based on phenotypic and genotypic characteristics, strain 389T represents a novel species, for which we propose the name Vogesella mureinivorans sp. nov. The type strain is 389T (=DSM 21247T =LMG 25302T).
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Sphingobium vulgare sp. nov., isolated from freshwater sediment
More LessA Gram-negative, motile, non-spore-forming bacterial strain, designated HU1-GD12T, was isolated from freshwater sediment. The strain was characterized by using a polyphasic approach in order to determine its taxonomic position. Comparative analysis of the 16S rRNA gene sequence showed that the isolate constituted a distinct branch within the genus Sphingobium, showing the highest level of sequence similarity with respect to Sphingobium ummariense RL-3T (96.2 %). Strain HU1-GD12T had a genomic DNA G+C content of 66.8 mol% and Q-10 as the predominant respiratory quinone. Furthermore, the major polyamine component (spermidine) in the cytoplasm and the presence of sphingoglycolipids suggested that strain HU1-GD12T belonged to the family Sphingomonadaceae. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain HU1-GD12T represents a novel species of the genus Sphingobium, for which the name Sphingobium vulgare sp. nov. is proposed. The type strain is HU1-GD12T (=LMG 24321T=KCTC 22289T).
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- Eukaryotic Micro-Organisms
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Ogataea pignaliae sp. nov., the teleomorph of Candida pignaliae
More LessSix ascosporulating Candida pignaliae strains were isolated from epigeal plant parts in Hungary. They share identical D1/D2 LSU rRNA gene sequences with the type strain of C. pignaliae, and the physiological characteristics investigated are also very similar to that of the type strain. The only substantial difference compared to the type strain of C. pignaliae is their ability to assimilate β-glucosides (cellobiose, salicin and arbutin). The majority of the isolation sources of the strains reported in this study have the common feature of containing tannic acid, while the type strain of C. pignaliae was recovered from tanning fluid. We were able to induce ascosporulation also in the type strain of C. pignaliae. Therefore, Ogataea pignaliae Péter, Tornai-Lehoczki & Dlauchy sp. nov. is proposed as the teleomorph of C. pignaliae (F. H. Jacob) S. A. Meyer & Yarrow. The type strain is CBS 6071T.
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Rhodotorula rosulata sp. nov., Rhodotorula silvestris sp. nov. and Rhodotorula straminea sp. nov., novel myo-inositol-assimilating yeast species in the Microbotryomycetes
More LessThree novel species are described as Rhodotorula rosulata sp. nov. (type strain VKM Y-2962T =CBS 10977T), Rhodotorula silvestris sp. nov. (type strain VKM Y-2971T =CBS 11420T) and Rhodotorula straminea sp. nov. (type strain VKM Y-2964T =CBS 10976T) based on the study of eight isolates from needle litter. The new species, phylogenetically located within the Microbotryomycetes, are related to glucuronate-assimilating species of the genus Rhodotorula. Sequencing of the D1/D2 domains of the LSU rDNA gene and the internal transcribed spacer (ITS) region, as well as physiological characterization, revealed their distinct taxonomic positions.
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- Evolution, Phylogeny And Biodiversity
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Delineation of two Helicobacter bilis genomospecies: implications for systematics and evolution
More LessThe evolution and taxonomy of Helicobacter bilis strains isolated in Italy and Finland were studied by phylogenetic analysis of different genes, comparative analysis of small rRNA gene intervening sequence (IVS), amplified fragment length polymorphism analysis and DNA–DNA hybridization. The results of this study divided the H. bilis strains into two distinct and divergent genomic groups. In the absence of a specific phenotype or pathotype to distinguish these groups, however, they may be referred to as two genomospecies: H. bilis sensu stricto and Helicobacter sp. FL56. The phylogenetic network of gyrB and ureB gene sequences, as well as the comparative analysis of small rRNA gene IVS, suggests independent evolution of the two genomospecies. In particular, Helicobacter sp. FL56 seems to be the result of adaptation of an ancestral H. bilis strain in a new host. The phenomenon of adaptation to different hosts, or different intestinal niches in the same host, associated with high mutation and recombination rates could explain the evolution and the complex taxonomy of the genus Helicobacter. A comprehensive phylogenomics study of this genus would be useful to properly investigate this hypothesis.
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Further refinement of the phylogeny of the Halobacteriaceae based on the full-length RNA polymerase subunit B′ (rpoB′) gene
More LessA considerable number of species of the Halobacteriaceae possess multiple copies of the 16S rRNA gene that exhibit more than 5 % divergence, complicating phylogenetic interpretations. Two additional problems have been pointed out: (i) the genera Haloterrigena and Natrinema show a very close relationship, with some species being shown to overlap in phylogenetic trees reconstructed by the neighbour-joining method, and (ii) alkaliphilic and neutrophilic species of the genus Natrialba form definitely separate clusters in neighbour-joining trees, suggesting that these two clusters could be separated into two genera. In an attempt to solve these problems, the RNA polymerase B′ subunit has been used as an additional target molecule for phylogenetic analysis, using partial sequences of 1305 bp. In this work, a primer set was designed that consistently amplified the full-length RNA polymerase B′ subunit gene (rpoB′) (1827–1842 bp) from 85 strains in 27 genera of the Halobacteriaceae. Differences in sequence length were found within the first 15 to 31 nt, and their downstream sequences (1812 bp) were aligned unambiguously without any gaps or deletions. Phylogenetic trees reconstructed from nucleotide sequences and deduced amino acid sequences by the maximum-likelihood method demonstrated that multiple species/strains in most genera individually formed cohesive clusters. Two discrepancies were observed: (i) the two species of Natronolimnobius were placed in definitely different positions, in that Natronolimnobius innermongolicus was placed in the Haloterrigena/Natrinema cluster, while Natronolimnobius baerhuensis was closely related to Halostagnicola larsenii, and (ii) Natronorubrum tibetense was segregated from the three other Natronorubrum species in the protein tree, while all four species formed a cluster in the gene tree, although supported by a bootstrap value of less than 50 %. The six Haloterrigena species/strains and the five species of Natrinema formed a large cluster in both trees, with Halopiger xanaduensis and Nln. innermongolicus located in the cluster in the protein tree and Nln. innermongolicus in the gene tree. Hpg. xanaduensis broke into the cluster of the genus Halobiforma, instead of the Haloterrigena/Natrinema cluster, in the gene tree. The six Natrialba species formed a tight cluster with two subclusters, of neutrophilic species and alkaliphilic species, in both trees. Overall, our data strongly suggest that (i) Nln. innermongolicus is a member of Haloterrigena/Natrinema, (ii) Nrr. tibetense might represent a new genus and (iii) the two genera Haloterrigena and Natrinema might constitute a single genus. As more and more novel species and genera are proposed in the family Halobacteriaceae, the full sequence of the rpoB′ gene may provide a supplementary tool for determining the phylogenetic position of new isolates.
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Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 72 (2022 - 2023)
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Volume 71 (2020 - 2021)
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Volume 70 (2020)
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Volume 69 (2019)
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