- Volume 63, Issue Pt_10, 2013
Volume 63, Issue Pt_10, 2013
- Notification List
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Notification that new names of prokaryotes and new combinations have appeared in volume 63, part 7, of the IJSEM
More LessThis listing of names of prokaryotes 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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- Archaea
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Halomicroarcula pellucida gen. nov., sp. nov., a non-pigmented, transparent-colony-forming, halophilic archaeon isolated from solar salt
More LessA novel halophilic strain, BNERC31T, was isolated from solar salt, ‘Sel marin de Guérande’, imported from France. Colonies on agar medium containing soluble starch, sodium citrate, sodium glutamate and inorganic salts were non-pigmented and transparent, while cells obtained by centrifuging liquid cultures were red-pigmented. Cells of strain BNERC31T were non-motile, pleomorphic, stained Gram-negative and lysed in distilled water. Growth occurred with 20–30 % (w/v) NaCl (optimum, 25 %, w/v), with 0–500 mM MgCl2 (optimum, 10 mM), at pH 6.0–8.5 (optimum, pH 7.0) and at 25–55 °C (optimum, 40 °C). Growth was dependent on soluble starch, and inhibited completely by 0.5 % organic nutrients, such as Casamino acids or yeast extract. The DNA G+C content was 64.1 mol%. Strain BNERC31T possessed at least two heterogeneous 16S rRNA genes, and the sequence of the orthologous gene (preceded by the dihydroorotate oxidase gene, pyrD) showed the highest similarity (96.5 %) to that of Haloarcula marismortui JCM 8966T. The RNA polymerase subunit B′ gene sequence showed the highest similarity (91.7 %) to that of Haloarcula amylolytica JCM 13557T. The polar lipids of strain BNERC31T were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, diglycosyl diether and sulfated diglycosyl diether, similar to those of species of the genus Halomicrobium . The phenotypic and phylogenetic characteristics showed that strain BNERC31T differed from species of the genera Haloarcula and Halomicrobium and indicated that it represents a novel species in a new genus, for which the name Halomicroarcula pellucida gen. nov., sp. nov. is proposed. The type strain of the type species is BNERC31T ( = JCM 17820T = CECT 7537T).
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Halopiger salifodinae sp. nov., an extremely halophilic archaeon isolated from a salt mine
More LessA novel extremely halophilic archaeon KCY07-B2T was isolated from a salt mine in Kuche county, Xinjiang province, China. Colonies were cream-pigmented and cells were pleomorphic rod-shaped. Strain KCY07-B2T was able to grow at 25–50 °C (optimum 37–45 °C) and pH 6.0–8.0 (optimum 7.0). The strain required at least 1.9 M NaCl for growth. MgCl2 was not required. Cells lysed in distilled water. Polar lipid analysis revealed the presence of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, derived from both C20C20 and C20C25 glycerol diethers, together with five glyolipids. The bis-sulfated glycolipid S2-DGD-1 was present. The DNA G+C content was 62.5 mol%. Analysis of the 16S rRNA gene sequence revealed that strain KCY07-B2T was closely related to Halopiger xanaduensis SH-6T and Halopiger aswanensis 56T (95.8 % and 95.5 % similarity, respectively). On the basis of its phenotypic, chemotaxonomic and genotypic characteristics, strain KCY07-B2T is considered to represent a novel species of the genus Halopiger , for which the name Halopiger salifodinae sp. nov. is proposed. The type strain is KCY07-B2T ( = JCM 18547T = CGMCC 1.12284T).
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Halopelagius longus sp. nov., a member of the family Halobacteriaceae isolated from a salt mine, and emended description of the genus Halopelagius
More LessA thermotolerant, extremely halophilic archaeon, BC12-B1T, was isolated from a salt mine in Baicheng county, Xinjiang province, China. Colonies were off-white–grey. The cells stained Gram-negative, were motile and irregularly long-rod-shaped (variation in both width and length) with abundant gas vesicles. The strain was able to grow at 20–55 °C (optimum, 48 °C), at pH 6.0–8.0 (optimum, 7.0–7.3), with 1.8–6.0 M NaCl (optimum, 3.0–3.5 M) and with 0.02–2.2 M Mg2+ (optimum, 0.1–0.2 M). Cells lysed in distilled water and the minimal NaCl concentration to prevent cell lysis was 8 % (w/v). Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain BC12-B1T was most closely related to Halopelagius inordinatus RO5-2T (98.5 %) with less than 95 % sequence similarity to other described species. The genomic DNA G+C content of strain BC12-B1T was 64.0 mol%. The DNA–DNA hybridization value between strain BC12-B1T and Hpl. inordinatus RO5-2T was 43.6 %. The major polar lipids of strain BC12-B1T were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, four glycolipids and an unknown lipid. Based on phenotypic, chemotaxonomic and genotypic characteristics, strain BC12-B1T represents a novel species of the genus Halopelagius , for which the name Halopelagius longus sp. nov. is proposed. The type strain is BC12-B1T ( = CGMCC 1.12397T = JCM 18758T). An emended description of the genus Halopelagius is also provided.
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- Actinobacteria
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Streptomyces harbinensis sp. nov., an endophytic, ikarugamycin-producing actinomycete isolated from soybean root [Glycine max (L.) Merr.]
A novel ikarugamycin-producing actinomycete, designated strain NEAU-Da3T, was isolated from soybean root [Glycine max (L.) Merr.] and characterized using a polyphasic approach. 16S rRNA gene sequence similarity studies showed that strain NEAU-Da3T belonged to the genus Streptomyces , and was most closely related to Streptomyces carpaticus NRRL B-16359T (99.5 %), Streptomyces cheonanensis VC-A46T (99.3 %) and Streptomyces xiamenensis MCCC 1A01550T (97.2 %); similarities to other type strains of species of the genus Streptomyces were lower than 97.1 %. The maximum-likelihood phylogenetic tree based on 16S rRNA gene sequences showed that the isolate formed a distinct phyletic line with S. carpaticus NRRL B-16359T, S. cheonanensis VC-A46T and S. xiamenensis MCCC 1A01550T. This branching pattern was also supported by the tree reconstructed with the neighbour-joining method. A comparative study between strain NEAU-Da3T and the type strains of the closest related species of the genus Streptomyces revealed that it differed from them in morphological, physiological and biochemical characteristics. Therefore, it is proposed that strain NEAU-Da3T represents a novel species of the genus Streptomyces , for which the name Streptomyces harbinensis sp. nov. is proposed. The type strain is NEAU-Da3T ( = CGMCC 4.7047T = DSM 42076T).
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Kribbella albertanoniae sp. nov., isolated from a Roman catacomb, and emended description of the genus Kribbella
More LessA novel actinobacterium, strain BC640T, was isolated from a biofilm sample collected in 2009 in the Saint Callistus Roman catacombs. Analysis of the 16S rRNA gene sequence showed that the strain belonged to the genus Kribbella . Phylogenetic analysis using the 16S rRNA gene and concatenated gyrB, rpoB, relA, recA and atpD gene sequences showed that strain BC640T was most closely related to the type strains of Kribbella yunnanensis and Kribbella sandramycini . Based on gyrB genetic distance analysis, strain BC640T was shown to be distinct from all Kribbella type strains. DNA–DNA hybridization experiments confirmed that strain BC640T represents a genomic species distinct from its closest phylogenetic relatives, K. yunnanensis DSM 15499T (53.5±7.8 % DNA relatedness) and K. sandramycini DSM 15626T (33.5±5.0 %). Physiological comparisons further showed that strain BC640T is phenotypically distinct from the type strains of K. yunnanensis and K. sandramycini . Strain BC640T ( = DSM 26744T = NRRL B-24917T) is thus presented as the type strain of a novel species, for which the name Kribbella albertanoniae sp. nov. is proposed.
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Janibacter cremeus sp. nov., an actinobacterium isolated from sea sediment
A novel Gram-stain-positive actinobacterium, designated HR08-44T, was isolated from a sea-sediment sample collected from the foreshore of Rishiri Island, Japan, and its taxonomic position was investigated by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain HR08-44T was closely related to the members of the genus Janibacter , with pairwise sequence similarities of 97.3–98.8 %. Strain HR08-44T had peptidoglycan type A1γ, with meso-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinone was MK-8(H4) and the major fatty acids were iso-C16 : 0, C17 : 1ω8c, C17 : 0 and C18 : 1ω9c. These data supported the affiliation of the novel strain to the genus Janibacter . Meanwhile, the results of DNA–DNA hybridization and physiological and biochemical tests indicated that strain HR08-44T can be distinguished from recognized species of the genus Janibacter . Therefore, strain HR08-44T represents a novel species of the genus Janibacter , for which the name Janibacter cremeus sp. nov. is proposed; the type strain is HR08-44T ( = NBRC 107693T = DSM 26154T).
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Nocardioides daeguensis sp. nov., a nitrate-reducing bacterium isolated from activated sludge of an industrial wastewater treatment plant
A Gram-reaction-positive, rod-shaped, non-spore-forming bacterium (strain 2C1-5T) was isolated from activated sludge of an industrial wastewater treatment plant in Daegu, South Korea. Its taxonomic position was investigated by using a polyphasic approach. On the basis of 16S rRNA gene sequence similarity, the closest phylogenetic relatives were the type strains of Nocardioides nitrophenolicus (98.6 % similarity), N. kongjuensis (98.5 %), N. caeni (98.4 %), N. simplex (98.3 %), N. aromaticivorans (98.1 %) and N. ginsengisoli (97.5 %); the phylogenetic distance from other species with validly published names within the genus Nocardioides was greater than 3 %. Strain 2C1-5T was characterized chemotaxonomically as having ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-8(H4) as the predominant menaquinone and iso-C16 : 0, C16 : 0 and C17 : 1ω6c as the major fatty acids. The G+C content of the genomic DNA was 74.9 mol%. These chemotaxonomic properties and phenotypic characteristics supported the affiliation of strain 2C1-5T to the genus Nocardioides . The results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 2C1-5T from existing species with validly published names. Therefore, strain 2C1-5T represents a novel species of the genus Nocardioides , for which the name Nocardioides daeguensis sp. nov. is proposed, with the type strain 2C1-5T ( = JCM 17460T = KCTC 19799T).
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Streptomyces kebangsaanensis sp. nov., an endophytic actinomycete isolated from an ethnomedicinal plant, which produces phenazine-1-carboxylic acid
A spore-forming streptomycete designated strain SUK12T was isolated from a Malaysian ethnomedicinal plant. Its taxonomic position, established using a polyphasic approach, indicates that it is a novel species of the genus Streptomyces . Morphological and chemical characteristics of the strain were consistent with those of members of the genus Streptomyces . Analysis of the almost complete 16S rRNA gene sequence placed strain SUK12T in the genus Streptomyces where it formed a distinct phyletic line with recognized species of this genus. The strain exhibited highest sequence similarity to Streptomyces corchorusii DSM 40340T (98.2 %) followed by Streptomyces chrestomyceticus NRRL B-3310T (98.1 %). The G+C content of the genomic DNA was 74 mol%. Chemotaxonomic data [MK-9(H8) as the major menaquinone; LL-diaminopimelic acid as a component of cell-wall peptidoglycan; C12 : 0, C14 : 0, C15 : 0 and C17 : 1 as the major fatty acids; phospholipid type II] supported the affiliation of strain SUK12T to the genus Streptomyces . The results of the phylogenetic analysis and phenotypic data derived from this and previous studies allowed the genotypic and phenotypic differentiation of strain SUK12T from the related species of the genus Streptomyces . The DNA–DNA relatedness value between strain SUK12T and S. corchorusii DSM 40340T is 18.85±4.55 %. Strain SUK12T produces phenazine-1-carboxylic acid, known as tubermycin B, an antibacterial agent. It is proposed, therefore, that strain SUK12T ( = DSM 42048T = NRRL B-24860T) be classified in the genus Streptomyces as the type strain of Streptomyces kebangsaanensis sp. nov.
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Amycolatopsis cihanbeyliensis sp. nov., a halotolerant actinomycete isolated from a salt mine
More LessA novel halotolerant actinomycete, designated strain BNT52T, was isolated from soil collected from Cihanbeyli Salt Mine in the central Anatolia region of Turkey, and examined using a polyphasic taxonomic approach. The isolate was found to have chemical and morphological properties typical of the genus Amycolatopsis and formed a distinct phyletic line in the 16S rRNA gene tree. Strain BNT52T was most closely related to Amycolatopsis nigrescens CSC17Ta-90T (96.7 %), Amycolatopsis magusensis KT2025T (96.6 %), Amycolatopsis sulphurea DSM 46092T (96.6 %), Amycolatopsis dongchuanensis YIM 75904T (96.5 %), Amycolatopsis ultiminotia RP-AC36T (96.4 %) and Amycolatopsis sacchari DSM 44468T (96.4 %). Sequence similarities with other strains of species of the genus Amycolatopsis were lower than 96.2 %. The isolate grew at 20–37 °C, pH 6–12 and in the presence of 0–10 % (w/v) NaCl. The cell wall of the novel strain contained meso-diaminopimelic acid and arabinose and galactose as the diagnostic sugars. Major fatty acids were iso-C16 : 0 2-OH and iso-C16 : 0. The predominant menaquinone was MK-9(H4). The polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylmethylethanolamine. The genomic DNA G+C content was 68.8 mol%. On the basis of the data from this polyphasic taxonomic study, strain BNT52T represents a novel species within the genus Amycolatopsis for which the name Amycolatopsis cihanbeyliensis sp. nov. is proposed (type strain BNT52T = KCTC 29065T = NRRL B-24886T = DSM 45679T).
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Saccharothrix saharensis sp. nov., an actinomycete isolated from Algerian Saharan soil
The taxonomic position of a novel actinomycete, strain SA152T, isolated from a sample of Algerian Saharan soil, was determined using a polyphasic taxonomic approach. The strain produced abundant aerial mycelium and fragmented substrate mycelium on most media tested. Chemotaxonomically and phylogenetically, the strain was related to the members of the genus Saccharothrix . Results of 16S rRNA gene sequence comparison revealed that strain SA152T shared the highest degree of 16S rRNA gene sequence similarity with Saccharothrix xinjiangensis NBRC 101911T (99.3 %) and Saccharothrix texasensis NRRL B-16134T (98.9 %). However, DNA–DNA hybridization studies showed only 16.2 % relatedness with S. xinjiangensis DSM 44896T and 33.9 % relatedness with S. texasensis DSM 44231T. Based upon genotypic and phenotypic differences from other members of the genus, a novel species, Saccharothrix saharensis sp. nov., is proposed, with SA152T ( = DSM 45456T = CCUG 60213T) as the type strain.
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Lechevalieria nigeriaca sp. nov., isolated from arid soil
A novel actinobacterium, designated strain NJ2035T, was isolated from soil collected from Abuja, Nigeria and was characterized to determine its taxonomic position. The isolate was found to have chemical and morphological properties associated with members of the genus Lechevalieria . Phylogenetic analyses based on almost-complete 16S rRNA gene sequences indicated that the isolate was closely related to members of the genus Lechevalieria , and was shown to form a distinct phyletic line in the Lechevalieria phylogenetic tree. Strain NJ2035T was most closely related to Lechevalieria roselyniae C81T, Lechevalieria atacamensis C61T and Lechevalieria deserti C68T (98.5 % 16S rRNA gene sequence similarity). Sequence similarities with other members of the genus Lechevalieria were less than 98.2 %. The cell wall of the novel strain contained meso-diaminopimelic acid, and galactose, mannose and rhamnose as the diagnostic sugars. The predominant menaquinone was MK-9(H4). The polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol. DNA–DNA relatedness and phenotypic data showed that the novel isolate and L. roselyniae C81T, L. atacamensis C61T and L. deserti C68T belong to distinct genomic species. On the basis of data from this taxonomic study using a polyphasic approach, strain NJ2035T represents a novel species of the genus Lechevalieria , for which the name Lechevalieria nigeriaca sp. nov. is proposed. The type strain is NJ2035T ( = DSM 45680T = KCTC 29057T = NRRL B-24881T).
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Saccharomonospora amisosensis sp. nov., isolated from deep marine sediment
More LessA novel actinomycete, strain DS3030T, was isolated from a deep sediment sample, collected from the southern Black Sea coast, Turkey, and was examined using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain DS3030T was shown to belong to the genus Saccharomonospora and to be related most closely to Saccharomonospora marina XMU15T (99.6 % similarity). Sequence similarities with other strains of the genus Saccharomonospora were lower than 97.0 %. The organism had chemical and morphological features typical of the genus Saccharomonospora . The cell wall of the novel strain contained meso-diaminopimelic acid, arabinose and galactose as diagnostic sugars. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The predominant menaquinone was MK-9(H4). Major fatty acids were iso-C16 : 0, iso-C16 : 0 2-OH and C16 : 1 cis 9. Phenotypic data clearly distinguished the new isolate from its closest relative, S. marina XMU15T. The combined genotypic and phenotypic data and low DNA–DNA relatedness with its closest related strain reveal that strain DS3030T represents a novel species of the genus, for which the name Saccharomonospora amisosensis sp. nov. is proposed. The type strain is DS3030T ( = DSM 45685T = KCTC 29069T = NRRL B-24885T).
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Actinopolyspora mzabensis sp. nov., a halophilic actinomycete isolated from an Algerian Saharan soil
A halophilic actinomycete strain, designated H55T, was isolated from Saharan soil sampled in the Mzab region (Ghardaïa, southern Algeria) and was characterized in a taxonomic study using a polyphasic approach. The cell wall was determined to contain meso-diaminopimelic acid and the characteristic whole-cell sugars were arabinose and galactose. The predominant menaquinones were found to be MK-10(H4) and MK-9(H4). The predominant cellular fatty acids were determined to be anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 0. The diagnostic phospholipid detected was phosphatidylcholine. The morphological and chemotaxonomic characteristics of the strain were consistent with those of members of the genus Actinopolyspora , and 16S rRNA gene sequence analysis confirmed that strain H55T was a member of this genus. DNA–DNA hybridization values between strain H55T and the type strains of the nearest species of the genus Actinopolyspora , Actinopolyspora erythraea and A. alba , were clearly below the 70 % threshold. The genotypic and phenotypic data showed that the organism represents a novel species of the genus Actinopolyspora , for which the name Actinopolyspora mzabensis sp. nov. is proposed, with the type strain H55T ( = DSM 45460T = CCUG 62965T).
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Nocardioides salsibiostraticola sp. nov., isolated from biofilm formed in coastal seawater
More LessA Gram-staining-positive, non-motile, aerobic, non-spore-forming and short rod-shaped bacterial strain, PAMC 26527T, was isolated from biofilm formed in coastal seawater of the Norwegian Sea. Analysis of the 16S rRNA gene sequence of strain PAMC 26527T revealed a clear affiliation with the genus Nocardioides . Based on phylogenetic analysis, strain PAMC 26527T showed the closest phylogenetic relationship with Nocardioides caricicola YC6903T with 16S rRNA gene sequence similarity of 96.3 %. Strain PAMC 26527T grew in the presence of 0–5.0 % sea salts. The optimum temperature and pH for growth were 20 °C and pH 7.5. The major cellular fatty acids of strain PAMC 26527T were iso-C16 : 0, C17 : 1ω8c and C18 : 1ω9c and the major isoprenoid quinone was MK-8(H4). Cell-wall analysis showed that strain PAMC 26527T contained ll-diaminopimelic acid. The genomic DNA G+C content was 69.3 mol%. The combined phenotypic, chemotaxonomic and phylogenetic data showed that strain PAMC 26527T could be clearly distinguished from recognized members of the genus Nocardioides . Thus, strain PAMC 26527T should be classified as representing a novel species in the genus Nocardioides , for which the name Nocardioides salsibiostraticola sp. nov. is proposed. The type strain is PAMC 26527T ( = KCTC 29158T = JCM 18743T).
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Micromonospora schwarzwaldensis sp. nov., a producer of telomycin, isolated from soil
A Gram-stain-positive, spore-forming actinomycete strain (HKI0641T) was isolated from a soil sample collected in the Black Forest, Germany. During screening for antimicrobial natural products this bacterium was identified as a producer of the antibiotic telomycin. Morphological characteristics and chemotaxonomic data indicated that the strain belonged to the genus Micromonospora . The peptidoglycan of strain HKI0641T contained meso-diaminopimelic acid, and the fatty acid profile consisted predominantly of anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and C16 : 0. MK-10(H4), MK-10(H2) and MK-10 were identified as the major menaquinones. To determine the taxonomic positioning of strain HKI0641T, we computed a binary tanglegram of two rooted phylogenetic trees that were based upon 16S rRNA and gyrB gene sequences. The comparative analysis of the two common classification methods strongly supported the phylogenetic affiliation with the genus Micromonospora , but it also revealed discrepancies in the assignment at the level of the genomic species. 16S rRNA gene sequence analysis identified Micromonospora coxensis DSM 45161T (99.1 % sequence similarity) and Micromonospora marina DSM 45555T (99.0 %) as the nearest taxonomic neighbours, whereas the gyrB sequence of strain HKI0641T indicated a closer relationship to Micromonospora aurantiaca DSM 43813T (95.1 %). By means of DNA–DNA hybridization experiments, it was possible to resolve this issue and to clearly differentiate strain HKI0641T from other species of the genus Micromonospora . The type strains of the aforementioned species of the genus Micromonospora could be further distinguished from strain HKI0641T by several phenotypic properties, such as colony colour, NaCl tolerance and the utilization of carbon sources. The isolate was therefore assigned to a novel species of the genus Micromonospora , for which the name Micromonospora schwarzwaldensis sp. nov. is proposed. The type strain is HKI0641T ( = DSM 45708T = CIP 110415T).
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Proposal of Motilibacteraceae fam. nov., with the description of Motilibacter rhizosphaerae sp. nov.
More LessA rod-shaped actinobacterium, designated strain RS-16T, was isolated from a rhizosphere soil and its taxonomic position was determined by a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis indicated that strain RS-16T was most closely related to the type strain of Motilibacter peucedani (98.3 % sequence similarity). The cell-wall peptidoglycan contained ll-diaminopimelic acid as the diagnostic diamino acid and N-glycolylated murein. The major whole-cell sugars were glucose, galactose and mannose. The predominant menaquinone was MK-9(H4). The major fatty acids were C18 : 1ω9c and C16 : 0. The DNA G+C content was 73.1 mol%. The phenotypic and DNA–DNA hybridization data showed that strain RS-16T ( = KACC 16209T = DSM 45622T) represents a novel species of the genus Motilibacter , for which Motilibacter rhizosphaerae sp. nov. is proposed. Based on the phylogenetic position determined by 16S rRNA gene analysis and the signature nucleotide set of the 16S rRNA sequence, the genus Motilibacter represents a novel family of the suborder Frankineae , for which the name Motilibacteraceae fam. nov. is proposed.
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- Firmicutes and Related Organisms
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Lysinibacillus manganicus sp. nov., isolated from manganese mining soil
More LessA Gram-stain-positive, aerobic, motile, rod-shaped bacterium, designated strain Mn1-7T, was isolated from manganese mining soil in Tianjin, China. The closest phylogenetic relatives were Lysinibacillus massiliensis CCUG 49529T (97.2 % 16S rRNA gene sequence similarity), L. xylanilyticus XDB9T (96.7 %), L. sinduriensis JCM 15800T (96.2 %), L. odysseyi NBRC 100172T (95.9 %) and L. boronitolerans NBRC 103108T (95.4 %) (the type species of the genus). DNA–DNA hybridization values for strain Mn1-7T with the type strains of L. massiliensis and L. sinduriensis were 24.9 and 27.7 %, respectively. The genomic DNA G+C content was 38.4 mol%. The major menaquinone was MK-7 and the major fatty acids were iso-C15 : 0, iso-C16 : 0 and iso-C14 : 0. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The cell-wall peptidoglycan was type A4α (l-Lys–d-Asp), and the predominant cell-wall sugar was xylose. DNA–DNA hybridization results and comparison of phenotypic and chemotaxonomic characters between strain Mn1-7T and the phylogenetically most closely related strains revealed that the isolate represents a novel species of the genus Lysinibacillus , for which the name Lysinibacillus manganicus sp. nov. is proposed. The type strain is Mn1-7T ( = DSM 26584T = CCTCC AB 2012916T).
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Desulfotomaculum intricatum sp. nov., a sulfate reducer isolated from freshwater lake sediment
More LessA novel spore-forming, sulfate-reducing bacterium, strain SR45T, was isolated from sediment of a freshwater lake, Lake Mizugaki, in Japan. Cells of strain SR45 were rod-shaped (1.0–1.5×2.0–5.0 µm) and weakly motile; Gram staining and the KOH lysis test were negative. For growth, the optimum pH was 6.4–6.8 and the optimum temperature was 42–45 °C. Strain SR45T used sulfate, thiosulfate, sulfite and elemental sulfur as electron acceptors but not Fe(III). The G+C content of the genomic DNA was 41.1 mol%. Phylogenetic analyses based on genes for the 16S rRNA and DNA gyrase (gyrB) revealed that the isolated strain belonged to the family Peptococcaceae in the class Clostridia . The closest relative is Desulfotomaculum acetoxidans 5575T, with 16S rRNA gene sequence similarity of 92–94 %. It is suggested that the strain is the second isolated member of Desulfotomaculum subcluster Ie. The isolate had multiple 16S rRNA gene copies, with 13 different sequences. On the basis of phylogenetic and phenotypic characterization, the name Desulfotomaculum intricatum sp. nov. is proposed, with the type strain SR45T ( = NBRC 109411T = DSM 26801T).
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A thermophilic, hydrogenogenic and carboxydotrophic bacterium, Calderihabitans maritimus gen. nov., sp. nov., from a marine sediment core of an undersea caldera
More LessA hydrogenogenic, carboxydotrophic marine bacterium, strain KKC1T, was isolated from a sediment core sample taken from a submerged marine caldera. Cells were non-motile, Gram-stain-negative, 1.0–3.0 µm straight rods, often observed with round endospores. Strain KKC1T grew at 55–68 °C, pH 5.2–9.2 and 0.8–14 % (w/v) salinity. Optimum growth occurred at 65 °C, pH 7.0–7.5 and 2.46 % salinity with a doubling time of 3.7 h. The isolate grew chemolithotrophically, producing H2 from carbon monoxide (CO) oxidation with reduction of various electron acceptors, e.g. sulfite, thiosulfate, fumarate, ferric iron and AQDS (9,10-anthraquinone 2,6-disulfonate). KKC1T grew heterotrophically on pyruvate, lactate, fumarate, glucose, fructose and mannose with thiosulfate as an electron acceptor. When grown mixotrophically on CO and pyruvate, C16 : 0 constituted almost half of the total cellular fatty acids. The DNA G+C content was 50.6 mol%. The 16S rRNA gene sequence of KKC1T was most closely related to those of members of the genus Moorella with similarity ranging from 91 to 89 %. Based on physiological and phylogenetic novelty, we propose the isolate as a representative of a new genus and novel species with the name Calderihabitans maritimus gen. nov., sp. nov.; the type strain of the type species is KKC1T ( = DSM 26464T = NBRC 109353T).
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Pectinatus sottacetonis sp. nov., isolated from a commercial pickle spoilage tank
More LessA strictly anaerobic, Gram-stain-negative, non-spore-forming, motile bacterium, designated strain FSRU B0405T, was isolated from a commercial pickle spoilage tank and characterized by biochemical, physiological and molecular biological methods. Analyses of the 16S rRNA gene sequence of strain FSRU B0405T showed affiliation to the class Negativicutes in the phylum Firmicutes , with the closest relatives being the type strains of Pectinatus haikarae (96 %) and Pectinatus brassicae (95 %). In maximum-likelihood and neighbour-joining phylogenetic trees, strain FSRU B0405T clustered definitively (in 100 % of bootstrapped trees) within the genus Pectinatus , but not specifically with any characterized species within this genus. Strain FSRU B0405T was a slightly curved rod, varying from 3 to 30 µm in length, motile with a distinctive X-wise movement, having flagella only on the concave side of the cell. The isolate produced acetate and propionate from fructose and glucose as major metabolites similar to type strains of species of the genus Pectinatus . The major fatty acids were C11 : 0, C13 : 0, C15 : 0, C13 : 0 3-OH, C17 : 1 and C18 : 1ω11t. Strain FSRU B0405T differed from the pickle wastewater strain, Pectinatus brassicae TYT, due to its lack of susceptibility to vancomycin, acetoin production, growth temperature range, acid production from adonitol, erythritol, glycerol, inositol, lactose, maltose, mannose, ribose, salicin, sorbitol, trehalose and xylitol and lack of hydrolysis of milk. Strain FSRU B0405T could be differentiated from other species of the genus Pectinatus both phenotypically and genetically. The results indicate that strain FSRU B0405T represents a novel species of the genus Pectinatus , for which the name Pectinatus sottacetonis sp. nov. is proposed. The type strain is FSRU B0405T ( = ATCC BAA-2501T = VTT E-113163T). An emended description of the genus Pectinatus is also provided.
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Alicyclobacillus consociatus sp. nov., isolated from a human clinical specimen
More LessA Gram-stain-positive, aerobic organism, isolated from a blood sample from a 51-year-old woman, was studied for its taxonomic position. Based on 16S rRNA gene sequence similarity comparisons, strain CCUG 53762T was grouped into the genus Alicyclobacillus , most closely related to the type strain of Alicyclobacillus pohliae (94.7 %). The 16S rRNA gene sequence similarity to other species of the genus Alicyclobacillus was ≤91 % and similarity to species of the genus Tumebacillus was 91.3–93 %. The occurrence of menaquinone MK-7 as the major respiratory quinone, meso-diaminopimelic acid as the diagnostic diamino acid of the cell wall and the fatty acid profile supported the allocation of the strain to the genus Alicyclobacillus . Major fatty acids were iso- and anteiso-branched fatty acids. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and three unknown phospholipids. The absence of the iso-branched fatty acids iso-C16 : 0 and iso-C17 : 0 allowed differentiation of strain CCUG 53762T from A. pohliae CIP 109385T. In addition, the results of physiological and biochemical tests also allowed phenotypic differentiation of strain CCUG 53762T from this most closely related species. The G+C content of the DNA was 47 mol%. Strain CCUG 53762T therefore represents a novel species of the genus Alicyclobacillus , for which we propose the name Alicyclobacillus consociatus sp. nov., with CCUG 53762T ( = CCM 8439T) as the type strain.
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Paenibacillus taihuensis sp. nov., isolated from an eutrophic lake
More LessTwo Gram-stain-negative, facultatively anaerobic and endospore-forming rod-shaped bacterial strains, THMBG22T and R24, were isolated from decomposing algal scum. Phylogenetic analysis of 16S rRNA gene sequences showed that the two strains were closely related to each other (99.7 % similarity) and that they were also closely related to Paenibacillus sacheonensis DSM 23054T (97–97.1 %) and Paenibacillus phyllosphaerae DSM 17399T (96.1–96.4 %). This affiliation was also supported by rpoB-based phylogenetic analyses. Growth was observed at 20–40 °C (optimum, 30–37 °C) and at pH 5.0–9.0 (optimum, pH 6.0–7.0). The cells contained MK-7 as the sole respiratory quinone and anteiso-C15 : 0 as the major cellular fatty acid. Their cellular polar lipids were composed of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and 12 unidentified polar lipids. The diamino acid of their cell-wall peptidoglycan was meso-diaminopimelic acid. The DNA–DNA hybridization value between THMBG22T and R24 was 84 %, and DNA–DNA relatedness to the most closely related species with a validly published name ( P. sacheonensis ) was 35–37 %. These results supported the assignment of the new isolates to the genus Paenibacillus and also distinguished them from the previously described species of the genus Paenibacillus . Hence, it is proposed that strains THMBG22T and R24 represent a novel species of the genus Paenibacillus , with the name Paenibacillus taihuensis sp. nov. The type strain is THMBG22T ( = CGMCC 1.10966T = NBRC 108766T).
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Oceanobacillus chungangensis sp. nov., isolated from a sand dune
More LessA Gram-stain-positive, spore-forming, rod-shaped, motile, strictly aerobic bacterial strain, designated CAU 1051T, was isolated from a sand dune and its taxonomic position was investigated using a polyphasic approach. Strain CAU 1051T grew optimally at pH 5.0 and 30 °C. NaCl was not required for growth but up to 10.0 % (w/v) NaCl was tolerated. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CAU 1051T formed a distinct lineage within the genus Oceanobacillus and was most closely related to Oceanobacillus profundus CL-MP28T, Oceanobacillus caeni S-11T, and Oceanobacillus picturae LMG 19492T (96.8 %, 95.6 % and 95.3 % similarity, respectively). DNA–DNA reassociation analysis showed that strain CAU 1051T displayed 28.2±0.7 % relatedness to O. profundus KCTC 13625T. Strain CAU 1051T contained MK-7 as the only isoprenoid quinone and anteiso-C15 : 0 as the major fatty acid. The cell wall peptidoglycan of strain CAU 1051T contained meso-diaminopimelic acid. The polar lipids were composed of diphosphatidylglycerol, phosphatidylglycerol, six unidentified phospholipids, an unidentified glycolipid, and six unidentified polar lipids. The major whole-cell sugars were glucose and ribose. The DNA G+C content was 36.3 mol%. On the basis of phenotypic data and phylogenetic inference, strain CAU 1051T represents a novel species of the genus Oceanobacillus for which the name Oceanobacillus chungangensis sp. nov. is proposed. The type strain is CAU 1051T ( = KCTC 33035T = CCUG 63270T).
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Bacillus thermotolerans sp. nov., a thermophilic bacterium capable of reducing humus
More LessA novel thermotolerant bacterium, designated SgZ-8T, was isolated from a compost sample. Cells were non-motile, endospore-forming, Gram-staining positive, oxidase-negative and catalase-positive. The isolate was able to grow at 20–65 °C (optimum 50 °C) and pH 6.0–9.0 (optimum 6.5–7.0), and tolerate up to 9.0 % NaCl (w/v) under aerobic conditions. Anaerobic growth occurred with anthraquinone-2,6-disulphonate (AQDS), fumarate and NO3 - as electron acceptors. Phylogenetic analysis based on the16S rRNA and gyrB genes grouped strain SgZ-8T into the genus Bacillus , with the highest similarity to Bacillus badius JCM 12228T (96.2 % for 16S rRNA gene sequence and 83.5 % for gyrB gene sequence) among all recognized species in the genus Bacillus . The G+C content of the genomic DNA was 49.3 mol%. The major isoprenoid quinone was menaquinone 7 (MK-7) and the polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. The major cellular fatty acid was iso-C16 : 0. On the basis of its phenotypic and phylogenetic properties, chemotaxonomic analysis and the results of physiological and biochemical tests, strain SgZ-8T ( = CCTCC AB 2012108T = KACC 16706T) was designated the type strain of a novel species of the genus Bacillus , for which the name Bacillus thermotolerans sp. nov. is proposed.
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Aminivibrio pyruvatiphilus gen. nov., sp. nov., an anaerobic, amino-acid-degrading bacterium from soil of a Japanese rice field
More LessA novel anaerobic bacterium that could ferment amino acids and organic acids was isolated from an anaerobic, propionate-oxidizing enrichment culture originating from soil of a rice field in Japan. Cells of the isolate, designated strain 4F6ET, were Gram-staining-negative, oxidase- and catalase-negative, non-spore-forming, vibrio-shaped, motile rods (0.8×2.0–2.5 µm) with two or three lateral flagella. Growth occurred at 20–42 °C (optimum at 37–40 °C), at pH 6.4–8.4 (optimum at pH 7.3) and at 0–1.5 % (w/v) NaCl (optimum at 0–0.5 %). Good growth occurred on glycine, serine, cysteine, pyruvate and citrate, whereas poor growth was observed on threonine, glutamine, l-malate, α-ketoglutarate, peptone and Casamino acids. In co-culture with the hydrogen-utilizing methanogen Methanobacterium formicicum JCM 10132T, strain 4F6ET oxidized alanine, valine, leucine, isoleucine, methionine, aspartate, glutamate, histidine, asparagine and fumarate. Yeast extract was required for growth. The G+C content of genomic DNA was 61.9 mol%. A phylogenetic analysis based on comparison of the 16S rRNA gene sequence showed that the type strains of Fretibacterium fastidiosum , Aminobacterium colombiense and Aminobacterium mobile , members of the family Synergistaceae , were the closest relatives of strain 4F6ET, with low sequence similarities (89.3, 89.5 and 86.2 %, respectively). Strain 4F6ET contained iso-C13 : 0 (24.43 %), iso-C15 : 0 (16.47 %) and C19 : 1ω11c/C19 : 1ω9c (16.32 %) as the major fatty acids, which differed from those of F. fastidiosum , Aminobacterium colombiense and Aminobacterium mobile . On the basis of phenotypic, chemotaxonomic and phylogenetic differences between strain 4F6ET and the type strains of F. fastidiosum and Aminobacterium species, we propose that strain 4F6ET represents a novel genus and species, Aminivibrio pyruvatiphilus gen. nov., sp. nov. The type strain of Aminivibrio pyruvatiphilus is strain 4F6ET ( = JCM 18417T = DSM 25964T).
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Fusicatenibacter saccharivorans gen. nov., sp. nov., isolated from human faeces
More LessThree Gram-stain-positive, obligately anaerobic, non-motile, non-spore-forming, spindle-shaped bacterial strains (HT03-11T, KO-38 and TT-111), isolated from human faeces were characterized by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing showed that the strains were highly related to each other genetically (displaying >99 % sequence similarity) and represented a previously unknown subline within the Blautia coccoides rRNA group of organisms (cluster XIVa). The closest phylogenetic neighbours of strain HT03-11T were Clostridium bolteae WAL 16351T (93.7 % 16S rRNA gene sequence similarity) and Clostridium saccharolyticum WM1T (93.7 % similarity). All isolates produced lactic acid, formic acid, acetic acid and succinic acid as fermentation end products from glucose. Their chemotaxonomic properties included lysine as the cell wall diamino acid and C16 : 0, C18 : 1ω7c DMA and C16 : 0 DMA as the major fatty acids. The G+C contents of the genomic DNA were 46.9–47.2 mol% (HPLC). Several phenotypic and chemotaxonomic characteristics could be readily used to differentiate the isolates from phylogenetically related clostridia. Therefore, strains HT03-11T, KO-38 and TT-111 represent a novel species in a new genus of the family Lachnospiraceae , for which the name Fusicatenibacter saccharivorans gen. nov., sp. nov. is proposed. The type strain of the type species is HT03-11T ( = YIT 12554T = JCM 18507T = DSM 26062T).
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Lactobacillus delbrueckii subsp. jakobsenii subsp. nov., isolated from dolo wort, an alcoholic fermented beverage in Burkina Faso
Lactobacillus delbrueckii is divided into five subspecies based on phenotypic and genotypic differences. A novel isolate, designated ZN7a-9T, was isolated from malted sorghum wort used for making an alcoholic beverage (dolo) in Burkina Faso. The results of 16S rRNA gene sequencing, DNA–DNA hybridization and peptidoglycan cell-wall structure type analyses indicated that it belongs to the species L. delbrueckii . The genome sequence of isolate ZN7a-9T was determined by Illumina-based sequencing. Multilocus sequence typing (MLST) and split-decomposition analyses were performed on seven concatenated housekeeping genes obtained from the genome sequence of strain ZN7a-9T together with 41 additional L. delbrueckii strains. The results of the MLST and split-decomposition analyses could not establish the exact subspecies of L. delbrueckii represented by strain ZN7a-9T as it clustered with L. delbrueckii strains unassigned to any of the recognized subspecies of L. delbrueckii . Strain ZN7a-9T additionally differed from the recognized type strains of the subspecies of L. delbrueckii with respect to its carbohydrate fermentation profile. In conclusion, the cumulative results indicate that strain ZN7a-9T represents a novel subspecies of L. delbrueckii closely related to Lactobacillus delbrueckii subsp. lactis and Lactobacillus delbrueckii subsp. delbrueckii for which the name Lactobacillus delbrueckii subsp. jakobsenii subsp. nov. is proposed. The type strain is ZN7a-9T = DSM 26046T = LMG 27067T.
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Description of Lactobacillus iwatensis sp. nov., isolated from orchardgrass (Dactylis glomerata L.) silage, and Lactobacillus backii sp. nov.
Two bacterial strains, designated IWT246T and IWT248, were isolated from orchardgrass (Dactylis glomerata L.) silage from Iwate prefecture, Japan, and examined for a taxonomic study. Both organisms were rod-shaped, Gram-stain-positive, catalase-negative, facultatively anaerobic and homofermentative. The cell wall did not contain meso-diaminopimelic acid and the major fatty acids were C18 : 1ω9c and C19 cyclo 9,10/:1. Comparative analyses of 16S rRNA, pheS and rpoA gene sequences revealed that these strains were novel and belonged to the genus Lactobacillus . Based on 16S rRNA gene sequence similarity, the isolates were most closely related to the type strains of the following members of the genus Lactobacillus : Lactobacillus coryniformis subsp. coryniformis (96.7 % similarity), L. coryniformis subsp. torquens (96.6 %), L. bifermentans (95.5 %) and L. rennini (94.1 %). However, the 16S rRNA gene sequences of both IWT246T and IWT248 were 99.7 % similar to that of ‘ Lactobacillus backi’ JCM 18665; this name has not been validly published. Genotypic, phenotypic and chemotaxonomic analyses confirmed that these novel strains occupy a unique taxonomic position. DNA–DNA hybridization experiments demonstrated genotypic separation of the novel isolates from related Lactobacillus species. The name Lactobacillus iwatensis sp. nov. is proposed for the novel isolates, with strain IWT246T ( = JCM 18838T = DSM 26942T) as the type strain. Our results also suggest that ‘L. backi’ does represent a novel Lactobacillus species. The cells did not contain meso-diaminopimelic acid in their cell-wall peptidoglycan and the major fatty acids were C16 : 0, C19 cyclo 9,10/:1 and summed feature 10 (one or more of C18 : 1ω11c, C18 : 1ω9t, C18 : 1ω6t and unknown ECL 17.834). We therefore propose the corrected name Lactobacillus backii sp. nov., with the type strain JCM 18665T ( = LMG 23555T = DSM 18080T = L1062T).
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- Proteobacteria
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Albimonas pacifica sp. nov., isolated from seawater of the Pacific, and emended description of the genus Albimonas
A Gram-stain-negative, aerobic, catalase- and oxidase-positive, non-flagellated, rod-shaped bacterium, designated strain P-50-3T, was isolated from seawater of the Pacific. The strain grew at 10–40 °C (optimum at 30 °C) and with 0–12 % (w/v, optimum 2 %) NaCl. It reduced nitrate to nitrite but did not hydrolyse gelatin, starch or Tween 80. Analysis of 16S rRNA gene sequences showed that strain P-50-3T clustered tightly with the genus Albimonas and shared the highest 16S rRNA gene sequence similarity (94.3 %) with the type strain of Albimonas donghaensis . The major respiratory quinone was Q-10 and the major cellular fatty acids were C18 : 1ω7c, C18 : 0, 11-methyl C18 : 1ω7c and C16 : 0. Polar lipids included phosphatidylglycerol (PG), phosphatidylcholine (PC), two unidentified aminolipids and an unidentified lipid. The genomic DNA G+C content of strain P-50-3T was 69.0 mol%. On the basis of the data obtained in this polyphasic study, strain P-50-3T represents a novel species within the genus Albimonas , for which the name Albimonas pacifica sp. nov. is proposed. The type strain of Albimonas pacifica is P-50-3T ( = KACC 16527T = CGMCC 1.11030T). An emended description of the genus Albimonas Lim et al. 2008 is also proposed.
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Francisella guangzhouensis sp. nov., isolated from air-conditioning systems
Four strains (08HL01032T, 09HG994, 10HP82-6 and 10HL1960) were isolated from water of air-conditioning systems of various cooling towers in Guangzhou city, China. Cells were Gram-stain-negative coccobacilli without flagella, catalase-positive and oxidase-negative, showing no reduction of nitrate, no hydrolysis of urea and no production of H2S. Growth was characteristically enhanced in the presence of l-cysteine, which was consistent with the properties of members of the genus Francisella . The quinone system was composed of ubiquinone Q-8 with minor amounts of Q-9. The polar lipid profile consisted of the predominant lipids phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, two unidentified phospholipids (PL2, PL3), an unidentified aminophospholipid and an unidentified glycolipid (GL2). The polyamine pattern consisted of the major compounds spermidine, cadaverine and spermine. The major cellular fatty acids were C10 : 0, C14 : 0, C16 : 0, C18 : 1ω9c and C18 : 1 3-OH. A draft whole-genome sequence of the proposed type strain 08HL01032T was generated. Comparative sequence analysis of the complete 16S and 23S rRNA genes confirmed affiliation to the genus Francisella , with 95 % sequence identity to the closest relatives in the database, the type strains of Francisella philomiragia and Francisella noatunensis subsp. orientalis . Full-length deduced amino acid sequences of various housekeeping genes, recA, gyrB, groEL, dnaK, rpoA, rpoB, rpoD, rpoH, fopA and sdhA, exhibited similarities of 67–92 % to strains of other species of the genus Francisella . Strains 08HL01032T, 09HG994, 10HP82-6 and 10HL1960 exhibited highly similar pan-genome PCR profiles. Both the phenotypic and molecular data support the conclusion that the four strains belong to the genus Francisella but exhibit considerable divergence from all recognized Francisella species. Therefore, we propose the name Francisella guangzhouensis sp. nov., with the type strain 08HL01032T ( = CCUG 60119T = NCTC 13503T).
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Frischella perrara gen. nov., sp. nov., a gammaproteobacterium isolated from the gut of the honeybee, Apis mellifera
More LessThe gut of the Western honeybee, Apis mellifera, is colonized by a characteristic set of bacteria. Two distinct gammaproteobacteria are consistent members of this unique microbial community, and one has recently been described in a new genus and species with the name Gilliamella apicola . Here, we present the isolation and characterization of PEB0191T, a strain belonging to the second gammaproteobacterial species present in the honeybee gut microbiota, formerly referred to as ‘Gammaproteobacterium-2’. Cells of strain PEB0191T were mesophilic and had a mean length of around 2 µm, and optimal growth was achieved under anaerobic conditions. Growth was not obtained under aerobic conditions and was reduced in a microaerophilic environment. Based on 16S rRNA gene sequence analysis, strain PEB0191T belongs to the family Orbaceae , and its closest relatives, with around 95 % sequence similarity, are species of the genera Orbus and Gilliamella . Phylogenetic analyses suggest that PEB0191T is more closely related to the genus Orbus than to the genus Gilliamella . In accordance with its evolutionary relationship, further similarities between strain PEB0191T and other members of the family Orbaceae were revealed based on the respiratory quinone type (ubiquinone 8), the fatty acid profile and the DNA G+C content. Interestingly, like strains of the genus Gilliamella , PEB0191T exhibited a high level of resistance to oxytetracycline. The similar levels of sequence divergence from the genera Gilliamella and Orbus and its uncertain phylogenetic position within the family Orbaceae indicate that strain PEB0191T represents a novel species of a new genus, with the proposed name Frischella perrara gen. nov., sp. nov. The type strain of Frischella perrara is PEB0191T ( = NCIMB 14821T = ATCC BAA-2450T).
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Vibrio hemicentroti sp. nov., an alginate lyase-producing bacterium, isolated from the gut microflora of sea urchin (Hemicentrotus pulcherrimus)
More LessAn alginate lyase-producing bacterium, designated AlyHP32T, was isolated from the gut of sea urchin (Hemicentrotus pulcherrimus) obtained from the South Sea, Republic of Korea. Cells of strain AlyHP32T were Gram-reaction-negative and motile with a single polar flagellum. The strain grew with 1–6 % (w/v) NaCl (optimum 2–4 %) and at 4–30 °C (optimum 15–25 °C). Phylogenetic analysis based on sequences of the 16S rRNA gene and five housekeeping genes (atpA, pyrH, recA, rpoA and rpoD) revealed that strain AlyHP32T belonged to the genus Vibrio and formed a compact clade with the Vibrio splendidus group. However, DNA–DNA hybridization and fingerprints using the repetitive primers BOX and REP indicated that strain AlyHP32T was distinct from closely related species of the genus Vibrio . The major fatty acids were summed feature 3 (C16:1ω7c and/or C16:1ω6c) and C16:0. The DNA G+C content was 44.1 mol%. The predominant quinone was ubiquinone Q-8. Based on genotypic, phenotypic and DNA–DNA hybridization analysis, strain AlyHP32T represents a novel species of the genus Vibrio ; the name Vibrio hemicentroti sp. nov. (type strain AlyHP32T = KCTC 32085T = DSM 26178T) is proposed for this novel taxon.
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Hansschlegelia beijingensis sp. nov., an aerobic, pink-pigmented, facultatively methylotrophic bacterium isolated from watermelon rhizosphere soil
A novel Gram-stain-negative, aerobic, rod-shaped strain designated PG04T was isolated from the rhizosphere of watermelon plants cultivated in Beijing, China. A polyphasic taxonomic study was performed on the new isolate. On the basis of 16S rRNA gene sequence similarity studies, isolate PG04T belonged clearly to the genus Hansschlegelia and was most closely related to Hansschlegelia zhihuaiae (97.3 % similarity to the type strain). The predominant respiratory quinone was ubiquinone 10 (Q-10) and the polar lipid profile was composed of the major lipids diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The major fatty acids were C18 : 1ω7c (41.3 %), C19 : 0 cyclo ω8c (30.6 %) and C16 : 0 (19.1 %). The G+C content of the DNA was about 64.4 mol%. DNA–DNA hybridization experiments showed 34.4 % relatedness between strain PG04T and H. zhihuaiae DSM 18984T. The results of physiological and biochemical tests and differences in fatty acid profiles allowed clear phenotypic differentiation of strain PG04T from the most closely related species in the genus, H. zhihuaiae . Strain PG04T therefore represents a novel species within the genus Hansschlegelia , for which the name Hansschlegelia beijingensis sp. nov. is proposed, with the type strain PG04T ( = DSM 25481T = ACCC 05759T).
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Azoarcus olearius sp. nov., a nitrogen-fixing bacterium isolated from oil-contaminated soil
More LessA novel nitrogen-fixing strain, designated DQS-4T, was isolated from oil-contaminated soil in Taiwan and was characterized using a polyphasic taxonomic approach. Cells of strain DQS-4T stained Gram-negative, contained poly-β-hydroxybutyrate granules and were motile rods, surrounded by a thin capsule. Cells displayed a strictly aerobic type of metabolism and fixed nitrogen microaerobically. Growth occurred at 10–45 °C (optimum, 35–40 °C), at pH 7.0–8.0 (optimum, pH 7.0) and with 0–2 % NaCl (optimum, 0.5–1 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DQS-4T belonged to the genus Azoarcus , and its closest neighbours were Azoarcus indigens VB32T and Azoarcus communis SWub3T, with sequence similarities of 97.4 and 96.4 %, respectively. The major cellular fatty acids of strain DQS-4T were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c. The major cellular hydroxy fatty acid was C10 : 0 3-OH. The DNA G+C content was 64.5 mol%. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several uncharacterized aminophospholipids and phospholipids. The mean level of DNA–DNA relatedness between strain DQS-4T and A. indigens LMG 9092T was 27.4 %. On the basis of the genotypic and phenotypic data, strain DQS-4T represents a novel species in the genus Azoarcus , for which the name Azoarcus olearius sp. nov. is proposed. The type strain is DQS-4T ( = BCRC 80407T = KCTC 23918T = LMG 26893T).
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Azospirillum fermentarium sp. nov., a nitrogen-fixing species isolated from a fermenter
More LessAn aerobic, Gram-stain-negative, spiral or rod-shaped, non-spore-forming, diazotrophic bacterium (strain CC-LY743T) was isolated from a fermentative tank in Taiwan. Strain CC-LY743T was able to grow at 20–37 °C and pH 6.0–8.0 and tolerated up to 3.0 % (w/v) NaCl. It was positive for nitrogen fixation, with activity of 10.6 nmol ethylene h−1. 16S rRNA gene sequence analysis of strain CC-LY743T showed highest similarity to Azospirillum picis DSM 19922T (96.1 %), Azospirillum oryzae JCM 21588T (96.0 %) and Azospirillum rugosum DSM 19657T (96.0 %) and lower similarity (<96.0 %) to all other Azospirillum species. Highest nifH gene sequence similarities were obtained with Azospirillum brasilense BCRC 12270T (92.0 %), Azospirillum formosense BCRC 80273T (92.3 %) and A. rugosum DSM 19657T (91.8 %). It was positive in the rapid identification by a genus-specific primer set. The predominant quinone system was ubiquinone 10 (Q-10) and the DNA G+C content was 69.6±0.1 mol%. The major fatty acids found in strain CC-LY743T were n-C16 : 0, C19 : 0 cyclo ω8c, C14 : 0 3-OH/C16 : 1 iso I, C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c. Based on its phylogenetic, phenotypic and chemotaxonomic features, strain CC-LY743T is considered to represent a novel species within the genus Azospirillum for which the name Azospirillum fermentarium sp. nov. is proposed. The type strain is CC-LY743T ( = BCRC 80505T = JCM 18688T = LMG 27264T).
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Hyphomicrobium nitrativorans sp. nov., isolated from the biofilm of a methanol-fed denitrification system treating seawater at the Montreal Biodome
More LessA budding prosthecate bacterial strain, designated NL23T, was isolated from a methanol-fed denitrification system treating seawater at the Montreal Biodome, Canada. Phylogenetic analysis based on 16S rRNA (rRNA) gene sequences showed that the strain was affiliated with the genus Hyphomicrobium of the Alphaproteobacteria and was most closely related to Hyphomicrobium zavarzinii with 99.4 % sequence similarity. Despite this high level of 16S rRNA gene sequence similarity, DNA–DNA hybridization assays showed that strain NL23T was only distantly related to H. zavarzinii ZV-622T (12 %). Strain NL23T grew aerobically, but also had the capacity to grow under denitrifying conditions in the presence of nitrate without nitrite accumulation. Growth occurred at pH 7.0–9.5, with 0–1 % NaCl and at temperatures of 15–35 °C. Major fatty acids were C18 : 1ω7c or ω6c (84.6 %) and C18 : 0 (8.5 %), and major quinones were Q8 (5 %) and Q9 (95 %). The complete genome of the strain was sequenced and showed a DNA G+C content of 63.8 mol%. Genome analysis predicted open reading frames (ORF) encoding the key enzymes of the serine pathway as well as enzymes involved in methylotrophy. Also, ORF encoding a periplasmic nitrate reductase (Nap), a nitrite reductase (Nir), a nitric oxide reductase (Nor) and a nitrous oxide reductase (Nos) were identified. Our results support that strain NL23T represents a novel species within the genus Hyphomicrobium , for which the name Hyphomicrobium nitrativorans sp. nov. is proposed. The type strain is NL23T ( = ATCC BAA-2476T = LMG 27277T).
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Dyella kyungheensis sp. nov., isolated from soil of a cornus fruit field
A Gram-reaction-negative, aerobic, motile by one polar flagellum, yellow-pigmented, rod-shaped bacterium, designated strain THG-B117T, was isolated from soil of a cornus fruit field of Hoengseong province in South Korea and its taxonomic position was investigated by a polyphasic study. Strain THG-B117T grew well at 25–30 °C and at pH 6.0–8.0 in the absence of NaCl on nutrient agar. On the basis of 16S rRNA gene sequence similarity, strain THG-B117T was shown to belong to the family Xanthomonadaceae and be related to Dyella japonica XD53T (98.7 % similarity), Dyella terrae JS14-6T (98.0 %), Dyella koreensis BB4T (96.9 %), Dyella soli JS12-10T (96.9 %) and Dyella thiooxydans ATSB10T (96.7 %). DNA–DNA hybridization experiments showed that DNA relatedness between strain THG-B117T and its phylogenetically closest neighbours was below 45.1 %. The G+C content of the genomic DNA of strain THG-B117T was 64.8 mol%. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, unidentified aminolipids, unidentified aminophospholipids and unidentified phospholipids. Phenotypic and chemotaxonomic data (major ubiquinone was Q-8, and major fatty acids were iso-C15 : 0, iso-C16 : 0, iso-C17 : 0 and iso-C17 : 1ω9c) supported the affiliation of strain THG-B117T with the genus Dyella . The results of physiological and biochemical tests suggested that strain THG-B117T was different genotypically and phenotypically from recognized species of the genus Dyella , and represents a novel species of this genus. The name Dyella kyungheensis sp. nov. is proposed, with the type strain THG-B117T ( = KACC 16981T = JCM 18747T).
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Rhizobium paknamense sp. nov., isolated from lesser duckweeds (Lemna aequinoctialis)
More LessA Gram-stain-negative, rod-shaped bacterium was isolated and designated strain L6-8T during a study of endophytic bacterial communities in lesser duckweed (Lemna aequinoctialis). Cells of strain L6-8T were motile with peritrichous flagella. The analysis of the nearly complete 16S rRNA gene sequence indicated that strain L6-8T was phylogenetically related to species of the genus Rhizobium . Its closest relatives were Rhizobium borbori DN316T (97.6 %), Rhizobium oryzae Alt 505T (97.3 %) and Rhizobium pseudoryzae J3-A127T (97.0 %). The sequence similarity analysis of housekeeping genes recA, glnII, atpD and gyrB showed low levels of sequence similarity (<91.5 %) between strain L6-8T and other species of the genus Rhizobium with validly published names. The pH range for growth was 4.0–9.0 (optimum 6.0–7.0), and the temperature range for growth was 20–45 °C (optimum 30 °C). Strain L6-8T tolerated NaCl up to 2 % (w/v) (optimum 1 % NaCl). The predominant components of cellular fatty acids were C19 : 0 cyclo ω8c (31.32 %), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 25.39 %) and C16 : 0 (12.03 %). The DNA G+C content of strain L6-8T was 60.4 mol% (T m). nodC and nifH were not amplified in strain L6-8T. DNA–DNA relatedness between strain L6-8T and R. borbori DN316T, R. oryzae Alt505T and R. pseudoryzae J3-A127T was between 11.2 and 18.3 %. Based on the sequence similarity analyses, phenotypic, biochemical and physiological characteristics and DNA–DNA hybridization, strain L6-8T could be readily distinguished from its closest relatives and represents a novel species of the genus Rhizobium , for which the name Rhizobium paknamense sp. nov. is proposed. The type strain is L6-8T ( = NBRC 109338T = BCC 55142T).
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Asticcacaulis solisilvae sp. nov., isolated from forest soil
More LessAn obligately aerobic, chemoheterotrophic, mesophilic prosthecate bacterium, designated strain CGM1-3ENT, was isolated from the enrichment cultures of forest soil from Cheonggyesan Mountain, Republic of Korea. Cells were Gram-reaction-negative, motile rods (1.3–2.4 µm long by 0.30–0.75 µm wide) with single flagella. The strain grew at 10–37 °C (optimum 25–30 °C) and at pH 4.5–9.5 (optimum 5.0–7.0). The major cellular fatty acids were C16 : 0, C18 : 1ω7c 11-methyl, C12 : 1 3-OH and summed feature 8 (comprising C18 : 1ω7c/C18 : 1ω6c). The genomic DNA G+C content of strain CGM1-3ENT was 63.7 mol%. The closest phylogenetic neighbour to strain CGM1-3ENT was identified as Asticcacaulis biprosthecium DSM 4723T (97.2 % 16S rRNA gene sequence similarity) and the DNA–DNA hybridization value between strain CGM1-3ENT and A. biprosthecium DSM 4723T was less than 24.5 %. Strain CGM1-3ENT used d-glucose, d-fructose, sucrose, maltose, trehalose, d-mannose, d-mannitol, d-sorbitol, d-galactose, cellobiose, lactose, raffinose, fumarate, pyruvate, dl-alanine and glycerol as carbon sources. Based on data from the present polyphasic study, the forest soil isolate CGM1-3ENT is considered to represent a novel species of the genus Asticcacaulis , for which the name Asticcacaulis solisilvae sp. nov. is proposed. The type strain is CGM1-3ENT ( = AIM0088T = KCTC 32102T = JCM 18544T).
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Roseovarius lutimaris sp. nov., isolated from a marine tidal flat
More LessA novel Gram-staining-negative, moderately halophilic and strictly aerobic bacterium, designated strain 112T, was isolated from a tidal flat at Taean, Korea. Cells were catalase- and oxidase-positive ovoids to rods and did not produce bacteriochlorophyll a. Optimum growth of strain 112T was observed at 30 °C, at pH 6.5–7.5 and in the presence of 2–4 % (w/v) NaCl. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0 and Q-10 was detected as the predominant ubiquinone. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid and three unidentified lipids. The genomic DNA G+C content of strain 112T was 58.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 112T formed a phyletic lineage within the genus Roseovarius of the class Alphaproteobacteria . Strain 112T was most closely related to Roseovarius mucosus DFL-24T, with 96.52 % similarity. On the basis of phenotypic, chemotaxonomic and molecular properties, strain 112T represents a novel species of the genus Roseovarius , for which the name Roseovarius lutimaris sp. nov. is proposed. The type strain is 112T ( = KACC 16185T = JCM 17743T).
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Falsochrobactrum ovis gen. nov., sp. nov., isolated from a sheep
More LessA Gram-stain-negative, rod-shaped, oxidase-positive, non-spore-forming, non-motile bacterium (B1315T) was isolated from the placenta of a sheep with abortion. On the basis of 16S rRNA gene sequence analyses the strain was assigned to the Brucella – Ochrobactrum – Paenochrobactrum – Pseudochrobactrum group with 94.5–94.8 %, 94.3–96.1 %, 95.0–95.1 %, and 95.9–96.1 % sequence similarities to type strains of species of the four genera, respectively. Phylogenetic trees indicated a close relationship to the type strains of Ochrobactrum gallinifaecis and Ochrobactrum oryzae (95.9 and 96.1 % sequence similarity, respectively). Chemotaxonomic data confirmed the allocation of strain B1315T to the family Brucellaceae (quinone system: ubiquinone Q-10 and major fatty acids: C18 : 1ω7c and C19 : 0 cyclo ω8c). The polar lipid profile contained the major lipids diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and the unidentified but unique phospholipid PL7. The polyamine pattern of strain B1315T contained the major polyamines spermidine and putrescine. On the basis of the 16S rRNA gene and recA sequence phylogeny and chemotaxonomic data strain B1315T was clearly different from the genera Brucella , Ochrobactrum , Paenochrobactrum and Pseudochrobactrum . On the basis of these data we propose the novel genus Falsochrobactrum gen. nov. with the type species Falsochrobactrum ovis sp. nov. with the type strain B1315T ( = CCM 8460T = LMG 27356T.) The taxonomic allocation of O. gallinifaecis , which grouped inconsistently together with strain B1315T on the basis of 16S rRNA gene sequence data, but shows the chemotaxonomic features of the genus Ochrobactrum , remains to be clarified.
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Sphingomonas kyungheensis sp. nov., a bacterium with ginsenoside-converting activity isolated from soil of a ginseng field
A bacterial strain THG-B283T, which has β-glucosidase activity, was isolated from soil of a ginseng field. Cells were Gram-reaction-negative, oxidase- and catalase-positive, aerobic, motile with one polar flagellum and rod-shaped. The strain was subjected to a polyphasic taxonomic study. Strain THG-B283T grew optimally at around pH 7.0, at 25–28 °C and in the absence of NaCl on R2A agar. 16S rRNA gene sequence analysis revealed that strain THG-B283T belongs to the family Sphingomonadaceae and is closely related to Sphingomonas melonis DAPP-PG 224T (98.2 %), S. aquatilis JSS7T (98.1 %), S. insulae DS-28T (97.6 %), S. mali IFO 15500T (97.1 %) and S. pruni IFO 15498T (97.0 %). Strain THG-B283T contained Q-10 as the predominant ubiquinone. The major fatty acids included summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C18 : 1ω7c, C14 : 0 2-OH and C16 : 0. The DNA G+C content was 72.2 mol%. The major component in the polyamine pattern was sym-homospermidine. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, sphingoglycolipid, diphosphatidylglycerol, an unidentified glycolipid, unidentified aminolipids, an unidentified phospholipid and unidentified lipids. Genomic and chemotaxonomic data supported the affiliation of strain THG-B283T to the genus Sphingomonas . DNA–DNA relatedness between strain THG-B283T and its closest phylogenetic neighbours was below 23 %. On the basis of phenotypic, phylogenetic and genetic data, strain THG-B283T represents a novel species of genus Sphingomonas , for which the name Sphingomonas kyungheensis sp. nov. is proposed. The type strain is THG-B283T ( = KACC 16224T = LMG 26582T).
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Amorphus suaedae sp. nov., isolated from the root of a tidal flat plant, Suaeda maritima
More LessA novel bacterial strain, YC6899T, was isolated from the root of Suaedae maritima growing on a tidal flat of Namhae Island, Korea. Cells were Gram-reaction-negative, rod-shaped, non-motile, slightly halophilic and heterotrophic. Strain YC6899T grew optimally at a salinity of 2–4 %, at 25–37 °C and at pH 6.5–8.0. Phylogenetic analysis of 16S rRNA gene sequences demonstrated that strain YC6899T was closely related to Amorphus orientalis YIM D10T (96.1 % similarity) and Amorphus coralli RS.Sph.026T (95.9 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unknown aminolipids, an unknown aminophospholipid, an unknown aminoglycolipid, unknown glycolipids and unknown lipids. The major fatty acids of strain YC6899T were C19 : 0 cyclo ω8c and C18 : 1ω7c. The G+C content of the genomic DNA was 61.3 mol%. Strain YC6899T contained ubiquinone-10 (Q-10) as the major respiratory quinone system. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain YC6899T represents a novel species within the genus Amorphus , for which the name Amorphus suaedae sp. nov. is proposed. The type strain is YC6899T ( = KACC 14912T = NBRC 107845T).
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- Bacteroidetes
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Flavobacterium marinum sp. nov., isolated from seawater
More LessA Gram-staining-negative, strictly aerobic, non-gliding, rod-shaped bacterial strain, designated SW105T, was isolated from a seawater sample collected from the Indian Ocean. The strain produced flexirubin-type pigments and grew at 15–45 °C (optimum, 35 °C), at pH 5.5–8.5 (optimum, pH 7.0–7.5) and in the presence of 0–5.0 % (w/v) NaCl (optimum, 1.0–1.5 %). The predominant cellular fatty acids were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), iso-C17 : 1ω9c and iso-C17 : 0 3-OH. The major menaquinone was menaquinone 6 (MK-6) and the major polar lipids were phosphatidylethanolamine and two unidentified aminophospholipids. The genomic DNA G+C content of strain SW105T was 36.2 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the novel isolate was related to members of the genus Flavobacterium , showing the highest similarity to Flavobacterium ummariense DS-12T and Flavobacterium ceti CCUG 52969T (94.3 and 93.0 % sequence similarity, respectively). On the basis of phylogenetic inference and phenotypic characteristics, it is proposed that strain SW105T represents a novel species of the genus Flavobacterium , for which the name Flavobacterium marinum sp. nov. is proposed. The type strain is SW105T ( = CGMCC 1.10825T = JCM 18132T).
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Kordia antarctica sp. nov., isolated from Antarctic seawater
More LessA Gram-staining-negative, chemoheterotrophic, yellow-pigmented, non-motile, flexirubin-negative, facultatively anaerobic bacterium, designated strain IMCC3317T, was isolated from a coastal seawater sample from the Antarctic Penninsula. Optimal growth of strain IMCC3317T was observed at 20 °C, pH 8.0 and in the presence of 2–3 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IMCC3317T belonged to the genus Kordia and was closely related to Kordia algicida OT-1T (96.7 % sequence similarity) and Kordia periserrulae IMCC1412T (96.1 % sequence similarity). The major fatty acids were 10-methyl C16 : 0 and/or iso-C16 : 1ω9c, iso-C17 : 0 3-OH, iso-C15 : 0 and anteiso-C15 : 0. The G+C content of the genomic DNA was 35.1 mol%. The strain contained menaquinone-6 (MK-6) as the respiratory quinone. The polar lipids detected in the strain were phosphatidylethanolamine and unknown aminophospholipids, aminolipids and polar lipids. On the basis of phylogenetic distinction and differential phenotypic characteristics, it is suggested that strain IMCC3317T ( = KCTC 32292T = NBRC 109401T) be assigned to the genus Kordia as the type strain of a novel species, for which the name Kordia antarctica sp. nov. is proposed.
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Dyadobacter tibetensis sp. nov., isolated from glacial ice core
A Gram-stain-negative, rod-shaped, aerobic, non-motile bacterium, designated Y620-1T, was isolated from a glacier on the Tibetan Plateau, China. The 16S rRNA gene sequence of the novel isolate shared 93.6–95.1 % similarity with type strains of species of the genus Dyadobacter . The major fatty acids of strain Y620-1T were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0, C16 : 1ω5c and iso-C17 : 0 3-OH. The predominant isoprenoid quinone and polar lipid were MK-7 and phosphatidylethanolamine (PE), respectively. The DNA G+C content was 44.4±0.3 mol% (T m). Flexirubin-type pigment was produced. The novel isolate was classified in the genus Dyadobacter , but a number of phenotypic characteristics distinguished the novel isolate from type strains of species of the genus Dyadobacter . From these genotypic and phenotypic data, it is evident that strain Y620-1T represents a novel species of the genus Dyadobacter , for which the name Dyadobacter tibetensis sp. nov. is proposed. The type strain is Y620-1T ( = JCM 18589T = CGMCC 1.12215T).
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Gillisia marina sp. nov., from seashore sand, and emended description of the genus Gillisia
A Gram-staining-negative, strictly aerobic, rod-shaped bacterium, designated CBA3202T, was isolated from seashore sand on Jeju Island, Republic of Korea. Based on the 16S rRNA gene sequence analysis, strain CBA3202T was allocated to the genus Gillisia (family Flavobacteriaceae ) and was most closely related to the type strain of Gillisia mitskevichiae (99.0 % 16S rRNA gene sequence similarity). Optimal growth occurred at 25 °C and with 3 % NaCl. The only isoprenoid quinone was menaquinone-6 (MK-6), the predominant fatty acids were C16 : 0, iso-C15 : 1 G, iso-C16 : 0 and summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c), and the DNA G+C content was 34.9 mol%. The polar lipids were phosphatidylethanolamine, two unidentified aminolipids and several unidentified polar lipids. Based on phylogenetic inference and phenotypic data, we conclude that strain CBA3202T represents a novel species of the genus Gillisia , for which the name Gillisia marina sp. nov. is proposed. The type strain is CBA3202T ( = KACC 16693T = KCTC 32030T = JCM 18402T). An emended description of the genus Gillisia is also provided.
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Algibacter undariae sp. nov., isolated from a brown algae reservoir
More LessA Gram-stain-negative, non-flagellated, rod-shaped bacterial strain able to move by gliding, designated WS-MY9T, was isolated from a brown algae reservoir in South Korea. Strain WS-MY9T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain WS-MY9T clustered with the type strain of Algibacter lectus with a bootstrap resampling value of 100 %. Strain WS-MY9T exhibited 16S rRNA gene sequence similarity values of 98.5 and 96.7 % to the type strains of A. lectus and Algibacter mikhailovii , respectively, and less than 96.1 % sequence similarity to other members of the family Flavobacteriaceae . Strain WS-MY9T contained MK-6 as the predominant menaquinone and anteiso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 G and iso-C15 : 0 as the major fatty acids. The major polar lipids of strain WS-MY9T were phosphatidylethanolamine and two unidentified lipids. The DNA G+C content of strain WS-MY9T was 35.0 mol% and its DNA–DNA relatedness value with A. lectus KCTC 12103T was 15 %. The phylogenetic and genetic distinctiveness and differential phenotypic properties revealed that strain WS-MY9T is separate from the two recognized species of the genus Algibacter . On the basis of the data presented, strain WS-MY9T represents a novel species of the genus Algibacter , for which the name Algibacter undariae sp. nov. is proposed. The type strain is WS-MY9T ( = KCTC 32259T = CCUG 63684T).
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Fabibacter pacificus sp. nov., a moderately halophilic bacterium isolated from seawater
More LessA Gram-stain-negative, aerobic, moderately halophilic bacterium, strain DY53T, was isolated from a deep-seawater sample collected from the eastern Pacific Ocean. This isolate grew in the presence of 0.5–10.0 % (w/v) NaCl, at pH 6.5–8.5 and at 15–40 °C. The optimum NaCl concentration for growth of DY53T was 2 % (w/v) at 35 °C. Chemotaxonomic analysis showed MK-7 as the predominant menaquinone and iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C15 : 1 G, iso-C15 : 0 3-OH and iso-C17 : 0 3-OH as major cellular fatty acids. The genomic DNA G+C content was 40.8 mol%. Phylogenetic trees based on 16S rRNA gene sequences revealed that Fabibacter halotolerans UST030701-097T was the closest neighbour, with 96.7 % sequence similarity. Based on phylogenetic, chemotaxonomic and phenotypic data, we propose that strain DY53T represents a novel species of the genus Fabibacter , for which the name Fabibacter pacificus sp. nov. is proposed. The type strain is DY53T( = CGMCC 1.12402T = JCM 18885T).
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Taibaiella smilacinae gen. nov., sp. nov., an endophytic member of the family Chitinophagaceae isolated from the stem of Smilacina japonica, and emended description of Flavihumibacter petaseus
More LessA light-yellow-coloured bacterium, designated strain PTJT-5T, was isolated from the stem of Smilacina japonica A. Gray collected from Taibai Mountain in Shaanxi Province, north-west China, and was subjected to a taxonomic study by using a polyphasic approach. The novel isolate grew optimally at 25–28 °C and pH 6.0–7.0. Flexirubin-type pigments were produced. Cells were Gram-reaction-negative, strictly aerobic, rod-shaped and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PTJT-5T was a member of the phylum Bacteroidetes , exhibiting the highest sequence similarity to Lacibacter cauensis NJ-8T (87.7 %). The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 and iso-C17 : 0 3-OH. The only polyamine was homospermidine and the major polar lipid was phosphatidylethanolamine. The only respiratory quinone was MK-7 and the DNA G+C content was 40.3 mol%. Based on the phenotypic, phylogenetic and genotypic data, strain PTJT-5T is considered to represent a novel species of a new genus in the family Chitinophagaceae , for which the name Taibaiella smilacinae gen. nov., sp. nov. is proposed. The type strain of Taibaiella smilacinae is PTJT-5T ( = CCTCC AB 2013017T = KCTC 32316T). An emended description of Flavihumibacter petaseus is also proposed.
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Heliimonas saccharivorans gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from a mineral water aquifer, and emended description of Filimonas lacunae
More LessTwo isolates, with optimum growth temperature and pH of about 30 °C and 6.0–7.0, were recovered from a borehole head of a mineral water aquifer in Portugal. The closest relatives based on 16S rRNA gene sequence analysis were species of genera of the family Chitinophagaceae . Strains L2-4T and L2-109 formed translucent colonies and non-motile pleomorphic cells. Strains were strictly aerobic, and oxidase- and catalase-positive. The major fatty acids of strains L2-4T and L2-109 were 17 : 0 iso 3-OH, 15 : 0 iso and 15 : 1 iso G. The major polar lipids were phosphatidylethanolamine, one unidentified phospholipid, four unidentified aminophospholipids, four unidentified aminolipids and three unidentified polar lipids. Menaquinone 7 was the only respiratory quinone. The G+C content of the DNA of strains L2-4T and L2-109 was 42.0 and 41.4 mol%, respectively. Based on 16S rRNA gene sequence analysis, physiological and biochemical characteristics, strains L2-4T ( = CECT 8122T = LMG 26919T) and L2-109 ( = CECT 8121 = LMG 26920) are considered to represent a novel species of a new genus, for which the name Heliimonas saccharivorans gen. nov., sp. nov. is proposed. The type strain of Heliimonas saccharivorans is L2-4T. Due to additional results obtained in this study an emended description of Filimonas lacunae is provided.
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Fluviimonas pallidilutea gen. nov., sp. nov., a new member of the family Cytophagaceae isolated from a freshwater river
More LessA bacterial strain designated TQQ6T was isolated from a freshwater river in Taiwan and characterized using a polyphasic taxonomy approach. Cells of strain TQQ6T were strictly aerobic, Gram-staining-negative, poly-β-hydroxybutyrate-containing, non-motile, non-spore-forming, long rods surrounded by a thick capsule and forming pale orange colonies. Growth occurred at 20–40 °C (optimum, 25 °C), at pH 7.0–9.0 (optimum, pH 8.0) and with 0–0.5 % NaCl (optimum, 0 %). The predominant fatty acids were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c), iso-C17 : 0 3-OH, C16 : 1ω5c and C16 : 0. The major isoprenoid quinone was MK-7 and the DNA G+C content was 42.2 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, two uncharacterized aminophospholipids and three uncharacterized phospholipids. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TQQ6T represents a distinct phyletic line that reflects a novel generic status within the family Cytophagaceae with relatively low sequence similarities (less than 90 %) to members of other genera with validly published names. On the basis of the genotypic and phenotypic data, strain TQQ6T represents a new genus and novel species of the family Cytophagaceae , for which the name Fluviimonas pallidilutea gen. nov., sp. nov. is proposed. The type strain is TQQ6T ( = BCRC 80447T = LMG 27056T = KCTC 32035T).
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- Eukaryotic Micro-organisms
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Trichonympha burlesquei n. sp. from Reticulitermes virginicus and evidence against a cosmopolitan distribution of Trichonympha agilis in many termite hosts
More LessHistorically, symbiotic protists in termite hindguts have been considered to be the same species if they are morphologically similar, even if they are found in different host species. For example, the first-described hindgut and hypermastigote parabasalian, Trichonympha agilis (Leidy, 1877) has since been documented in six species of Reticulitermes, in addition to the original discovery in Reticulitermes flavipes. Here we revisit one of these, Reticulitermes virginicus, using molecular phylogenetic analysis from single-cell isolates and show that the Trichonympha in R. virginicus is distinct from isolates in the type host and describe this novel species as Trichonympha burlesque i n. sp. We also show the molecular diversity of Trichonympha from the type host R. flavipes is greater than supposed, itself probably representing more than one species. All of this is consistent with recent data suggesting a major underestimate of termite symbiont diversity.
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Description of Ambrosiozyma oregonensis sp. nov., and reassignment of Candida species of the Ambrosiozyma clade to Ambrosiozyma kashinagacola f.a., comb. nov., Ambrosiozyma llanquihuensis f.a., comb. nov., Ambrosiozyma maleeae f.a., comb. nov., Ambrosiozyma pseudovanderkliftii f.a., comb. nov., and Ambrosiozyma vanderkliftii f.a., comb. nov.
More LessAmbrosiozyma oregonensis sp. nov. is described from two strains, one isolated from a mountain stream in Oregon, USA (NRRL Y-6106T = CBS 5560T), and a second (NRRL YB-4169) from an unknown substrate from Marion, Illinois, USA. The species forms four hat-shaped ascospores in each deliquescent ascus and appears to be homothallic. Abundant true hyphae are produced with some having apparent dolipore-like septa. Analyses of nuclear gene sequences for the D1/D2 domains of large-subunit rRNA, small-subunit rRNA, translation elongation factor-1α, and subunits B1 and B2 of RNA polymerase II show the proposed novel species to be distinct from other species of the Ambrosiozyma clade. Because of their placement in the Ambrosiozyma clade, Candida kashinagacola, Candida llanquihuensis, Candida maleeae, Candida pseudovanderkliftii and Candida vanderkliftii are reassigned to the genus Ambrosiozyma as new combinations, and the description of the genus Ambrosiozyma is emended to reflect the resulting changes in phenotypic characters.
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Rhodotorula portillonensis sp. nov., a basidiomycetous yeast isolated from Antarctic shallow-water marine sediment
More LessDuring the characterization of the mycobiota associated with shallow-water marine environments from Antarctic sea, a novel pink yeast species was isolated. Sequence analysis of the D1/D2 domain of the LSU rDNA gene and 5.8S-ITS regions revealed that the isolated yeast was closely related to Rhodotorula pallida CBS 320T and Rhodotorula benthica CBS 9124T. On the basis of morphological, biochemical and physiological characterization and phylogenetic analyses, a novel basidiomycetous yeast species, Rhodotorula portillonensis sp. nov., is proposed. The type strain is Pi2T ( = CBS 12733T = CECT 13081T) which was isolated from shallow-water marine sediment in Fildes Bay, King George Island, Antarctica.
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Kurtzmanomyces shapotouensis sp. nov., an anamorphic, basidiomycetous yeast isolated from desert soil crusts
More LessTwo yeast strains isolated from soil crusts in the Shapotou region of Tengger Desert (north-western China) were grouped in the genus Kurtzmanomyces based on morphological characteristics. rRNA gene sequence analyses (including the D1/D2 domain of the large subunit rRNA gene and internal transcribed spacer region) indicated that these two strains represented a novel species of the genus Kurtzmanomyces, for which the name Kurtzmanomyces shapotouensis sp. nov. is proposed (type strain: CPCC 300020T = DSM 26579T = CBS 12707T). The MycoBank number of the novel species is MB 804959.
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Starmerella neotropicalis f. a., sp. nov., a yeast species found in bees and pollen
A novel yeast species was found repeatedly and in high cell densities in underground-nesting stingless bees of the species Melipona quinquefasciata and their provisions in northern Minas Gerais (Brazil). One additional strain was isolated from bee-collected pollen in Cuba. Phylogenetic analyses based on rRNA gene sequences (D1/D2 large subunit gene and internal transcribed spacer) indicated that the novel species belongs to the Starmerella clade and is most closely related to Candida (iter. nom. Starmerella) apicola. Growth reactions on carbon and nitrogen sources were typical of those observed in related species of the Starmerella clade. PCR-fingerprinting with mini- and microsatellite specific primers allowed the distinction of the novel species from Candida apicola, Candida bombi and a yet undescribed species represented by strain CBS 4353. On the basis of phylogenetic relationships, the novel species is assigned to the genus Starmerella despite the failure to observe sexual reproduction after extensive mating tests. We propose the name Starmerella neotropicalis f. a., sp. nov. (Mycobank MB 804285) and designate UFMG PST 09T ( = MUCL 53320T = CBS 12811T) as the type strain.
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- Other Bacteria
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Seleniivibrio woodruffii gen. nov., sp. nov., a selenate- and arsenate-respiring bacterium in the Deferribacteraceae
A Gram-type-negative, obligately anaerobic, selenate-respiring bacterium, strain S4T, was isolated from activated sludge of a wastewater treatment plant in New Jersey after enrichment with 10 mM selenate as the sole electron acceptor. In addition to its selenate-respiring capability, strain S4T also respired arsenate with acetate as carbon source and electron donor. Fermentative growth was not observed. The optimum growth temperature was 37 °C and optimum pH was pH 7. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain S4T is a novel member of the family Deferribacteraceae , with the type strain of Denitrovibrio acetiphilus as its closest cultivated relative, with 91.5 % sequence similarity. The cellular fatty acid profile was composed predominantly of straight-chain fatty acids C14 : 0, C15 : 0, C16 : 0, C17 : 0 and C18 : 0, which distinguishes this organism from its closest relatives. The DNA G+C content was 47.7 mol%. Together, these findings support the conclusion that strain S4T represents a novel genus and species, for which the name Seleniivibrio woodruffii gen. nov., sp. nov. is proposed. The type strain of Seleniivibrio woodruffii is S4T ( = DSM 24984T = ATCC BAA-2290T).
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- Evolution, Phylogeny and Biodiversity
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Evaluation of the DNA-dependent RNA polymerase β-subunit gene (rpoB) for phytoplasma classification and phylogeny
More LessPhytoplasmas are classified into 16Sr groups and subgroups and ‘Candidatus Phytoplasma ’ species, largely or entirely based on analysis of 16S rRNA gene sequences. Yet, distinctions among closely related ‘Ca. Phytoplasma ’ species and strains based on 16S rRNA genes alone have limitations imposed by the high degree of rRNA nucleotide sequence conservation across diverse phytoplasma lineages and by the presence in a phytoplasma genome of two, sometimes sequence-heterogeneous, copies of the 16S rRNA gene. Since the DNA-dependent RNA polymerase (DpRp) β-subunit gene (rpoB) exists as a single copy in the phytoplasma genome, we explored the use of rpoB for phytoplasma classification and phylogenetic analysis. We sequenced a clover phyllody (CPh) phytoplasma genetic locus containing ribosomal protein genes, a complete rpoB gene and a partial rpoC gene encoding the β′-subunit of DpRp. Primers and reaction conditions were designed for PCR-mediated amplification of rpoB gene fragments from diverse phytoplasmas. The rpoB gene sequences from phytoplasmas classified in groups 16SrI, 16SrII, 16SrIII, 16SrX and 16SrXII were subjected to sequence similarity and phylogenetic analyses. The rpoB gene sequences were more variable than 16S rRNA gene sequences, more clearly distinguishing among phytoplasma lineages. Phylogenetic trees based on 16S rRNA and rpoB gene sequences had similar topologies, and branch lengths in the rpoB tree facilitated distinctions among closely related phytoplasmas. Virtual RFLP analysis of rpoB gene sequences also improved distinctions among closely related lineages. The results indicate that the rpoB gene provides a useful additional marker for phytoplasma classification that should facilitate studies of disease aetiology and epidemiology.
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- Taxonomic Note
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Taxonomic study of the genera Halogeometricum and Halosarcina : transfer of Halosarcina limi and Halosarcina pallida to the genus Halogeometricum as Halogeometricum limi comb. nov. and Halogeometricum pallidum comb. nov., respectively
More LessMembers of the haloarchaeal genera Halosarcina and Halogeometricum (family Halobacteriaceae ) are closely related to each other and show 96.6–98 % 16S rRNA gene sequence similarity. This is higher than the accepted threshold value (95 %) to separate two genera, and a taxonomic study using a polyphasic approach of all four members of the two genera was conducted to clarify their relationships. Polar lipid profiles indicated that Halogeometricum rufum RO1-4T, Halosarcina pallida BZ256T and Halosarcina limi RO1-6T are related more to each other than to Halogeometricum borinquense CGMCC 1.6168T. Phylogenetic analyses using the sequences of three different genes (16S rRNA gene, rpoB′ and EF-2) strongly supported the monophyly of these four species, showing that they formed a distinct clade, separate from the related genera Halopelagius , Halobellus , Haloquadratum , Haloferax and Halogranum . The results indicate that the four species should be assigned to the same genus, and it is proposed that Halosarcina pallida and Halosarcina limi be transferred to the genus Halogeometricum as Halogeometricum pallidum comb. nov. (type strain, BZ256T = KCTC 4017T = JCM 14848T) and Halogeometricum limi comb. nov. (type strain, RO1-6T = CGMCC 1.8711T = JCM 16054T).
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Genome sequence analyses show that Neisseria oralis is the same species as ‘ Neisseria mucosa var. heidelbergensis’
More LessPhylogenies generated from whole genome sequence (WGS) data provide definitive means of bacterial isolate characterization for typing and taxonomy. The species status of strains recently defined with conventional taxonomic approaches as representing Neisseria oralis was examined by the analysis of sequences derived from WGS data, specifically: (i) 53 Neisseria ribosomal protein subunit (rps) genes (ribosomal multi-locus sequence typing, rMLST); and (ii) 246 Neisseria core genes (core genome MLST, cgMLST). These data were compared with phylogenies derived from 16S and 23S rRNA gene sequences, demonstrating that the N. oralis strains were monophyletic with strains described previously as representing ‘ Neisseria mucosa var. heidelbergensis’ and that this group was of equivalent taxonomic status to other well-described species of the genus Neisseria . Phylogenetic analyses also indicated that Neisseria sicca and Neisseria macacae should be considered the same species as Neisseria mucosa and that Neisseria flavescens should be considered the same species as Neisseria subflava . Analyses using rMLST showed that some strains currently defined as belonging to the genus Neisseria were more closely related to species belonging to other genera within the family; however, whole genome analysis of a more comprehensive selection of strains from within the family Neisseriaceae would be necessary to confirm this. We suggest that strains previously identified as representing ‘ N. mucosa var. heidelbergensis’ and deposited in culture collections should be renamed N. oralis . Finally, one of the strains of N. oralis was able to ferment lactose, due to the presence of β-galactosidase and lactose permease genes, a characteristic previously thought to be unique to Neisseria lactamica , which therefore cannot be thought of as diagnostic for this species; however, the rMLST and cgMLST analyses confirm that N. oralis is most closely related to N. mucosa .
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Proposed reclassification of Pasteurella lymphangitidis Sneath & Stevens 1990 as Yersinia pseudotuberculosis
More LessThe 16S rRNA gene sequences of Pasteurella lymphangitidis , Yersinia pseudotuberculosis and Yersinia pestis were found to be identical and multilocus sequence analysis could not discriminate between the three species. The susceptibility to a Y. pseudotuberculosis phage and the presence of the Y. pseudotuberculosis -specific invasin gene in P. lymphangitidis indicate that the latter should be reclassified as Y. pseudotuberculosis .
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- Erratum
Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 69 (2019)
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Volume 28 (1978)
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Volume 27 (1977)
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Volume 23 (1973)
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Volume 22 (1972)
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Volume 21 (1971)
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Volume 20 (1970)
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Volume 19 (1969)
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Volume 18 (1968)
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Volume 17 (1967)
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Volume 16 (1966)
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Volume 14 (1964)
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Volume 12 (1962)
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Volume 11 (1961)
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Volume 10 (1960)
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Volume 9 (1959)
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Volume 8 (1958)
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Volume 7 (1957)
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Volume 6 (1956)
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Volume 5 (1955)
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Volume 4 (1954)
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Volume 3 (1953)
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Volume 2 (1952)
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Volume 1 (1951)