- Volume 60, Issue 4, 2010
Volume 60, Issue 4, 2010
- Notification List
-
-
-
Notification that new names and new combinations have appeared in volume 60, part 1, of the IJSEM
This listing of names published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol 41 (1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles). Taxonomic opinions included in this List (i.e. the creation of synonyms or the emendation of circumscriptions) cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission.
-
-
- New Taxa
-
- Actinobacteria
-
-
Reclassification of Streptomyces hygroscopicus strains as Streptomyces aldersoniae sp. nov., Streptomyces angustmyceticus sp. nov., comb. nov., Streptomyces ascomycinicus sp. nov., Streptomyces decoyicus sp. nov., comb. nov., Streptomyces milbemycinicus sp. nov. and Streptomyces wellingtoniae sp. nov.
More LessA polyphasic study was undertaken to determine the taxonomic status of six strains received as Streptomyces hygroscopicus. The strains had chemotaxonomic and morphological properties typical of members of the genus Streptomyces and formed distinct phyletic lines in the Streptomyces 16S rRNA gene tree. These strains were distinguished from one another and from phylogenetically close neighbours using a combination of phenotypic properties. The combined genotypic and phenotypic data showed that all six strains form distinct centres of taxonomic variation within the genus Streptomyces. The following novel species are proposed to accommodate the strains: Streptomyces aldersoniae sp. nov. (type strain DSM 41909T =NRRL 18513T), Streptomyces angustmyceticus sp. nov., comb. nov. (type strain DSM 41683T=NRRL B-2347T), Streptomyces ascomycinicus sp. nov. (type strain DSM 40822T =NBRC 13981T), Streptomyces decoyicus sp. nov., comb. nov. (type strain DSM 41427T =NRRL 2666T), Streptomyces milbemycinicus sp. nov. (type strain DSM 41911T =NRRL 5739T) and Streptomyces wellingtoniae sp. nov. (type strain DSM 40632T =NRRL B-1503T).
-
-
-
Luteimicrobium subarcticum gen. nov., sp. nov., a new member of the suborder Micrococcineae
A novel Gram-stain-positive bacterium, designated R19-04T, was isolated from a soil sample from Rishiri Island, Japan, and its taxonomic position was investigated by a polyphasic approach. Cells of strain R19-04T exhibited a rod–coccus cycle. The peptidoglycan type of the isolate was A4α; lysine was the diagnostic diamino acid. The predominant menaquinone was MK-8(H2) and the major fatty acid was anteiso-C15 : 0. The polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The DNA G+C content was 72.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain R19-04T represented a novel member of the suborder Micrococcineae. Its nearest phylogenetic neighbours were the members of the genus Oerskovia, with 16S rRNA gene sequence similarity of 97.0–97.1 %. However, strain R19-04T was clearly distinguishable from members of the genus Oerskovia and phylogenetically related genera in terms of chemotaxonomic characteristics. On the basis of the chemotaxonomic and phylogenetic characteristics, a novel genus and species are proposed, Luteimicrobium subarcticum gen. nov., sp. nov. The type strain of Luteimicrobium subarcticum is R19-04T (=NBRC 105647T =DSM 22413T).
-
-
-
Microlunatus soli sp. nov., isolated from soil
A Gram-stain-positive, coccoid, non-endospore-forming actinobacterium (strain CC-12602T) was isolated from a spawn used for growing the edible mushroom Agaricus brasiliensis in the laboratory. On the basis of 16S rRNA gene sequence analysis, strain CC-12602T was shown to belong to the genus Microlunatus and was related most closely to the type strains of Microlunatus ginsengisoli (96.1 % similarity), M. phosphovorus (95.9 %), M. panaciterrae (95.8 %) and M. aurantiacus (95.5 %). The quinone system comprised menaquinone MK-9(H4) as the major component and the polyamine pattern consisted of spermidine and spermine as major compounds. The predominant polar lipids were phosphatidylglycerol and unknown phospholipid PL3. Moderate amounts of diphosphatidylglycerol, an unknown glycolipid and three unknown phospholipids and minor amounts of an unknown phospholipid and a polar lipid were detected. The peptidoglycan type was A3γ′, based on ll-2,6-diaminopimelic acid with an interpeptide bridge consisting of a single glycine residue and a second glycine residue at position 1 of the peptide subunit. Peptidoglycan structure and major fatty acids (anteiso-C15 : 0, iso-C16 : 0 and iso-C15 : 0) supported the affiliation of strain CC-12602T to the genus Microlunatus. The results of physiological and biochemical tests allowed strain CC-12602T to be differentiated phenotypically from recognized Microlunatus species. Strain CC-12602T is therefore considered to represent a novel species of the genus Microlunatus, for which the name Microlunatus soli sp. nov. is proposed. The type strain is CC-12602T (=DSM 21800T =CCM 7685T).
-
-
-
Microbacterium agarici sp. nov., Microbacterium humi sp. nov. and Microbacterium pseudoresistens sp. nov., isolated from the base of the mushroom Agaricus blazei
Three Gram-positive, rod-shaped bacteria (strains CC-SBCK-209T, CC-12309T and CC-5209T) were isolated from the stalk of the edible mushroom Agaricus blazei grown in the laboratory. 16S rRNA gene sequence analysis indicated that all three isolates clearly belonged to the genus Microbacterium. Strains CC-SBCK-209T and CC-12309T were most related closely to the type strain of Microbacterium halotolerans (95.9 and 96.1 %16S rRNA gene sequence similarity, respectively). These two novel strains shared 97.9 % 16S rRNA gene sequence similarity. Levels of similarity to the type strains of all other recognized Microbacterium species were lower than 95.5 %. The third strain (CC-5209T) showed the highest 16S rRNA gene sequence similarity to the type strain of Microbacterium resistens (97.6 %); levels of similarity to the type strains of all other recognized Microbacterium species were lower than 96 %. The quinone systems of strains CC-SBCK-209T, CC-12309T and CC-5209T consisted of MK-11/MK-12, MK-11/MK-10 and MK-13 as major compounds, respectively. All three strains contained ornithine in their peptidoglycan. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unknown glycolipid. The polyamine pattern consisted of spermidine and spermine as predominant components. Fatty acid profiles (anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0 as major components) supported the affiliation of all three strains to the genus Microbacterium. The results of physiological and biochemical tests and DNA–DNA hybridization experiments allowed the clear phenotypic and genotypic differentiation of strains CC-SBCK-209T and CC-12309T from M. halotolerans and other closely related Microbacterium species. Strain CC-5209T could be differentiated clearly from M. resistens both genotypically and phenotypically. Based on these data, the novel strains are considered to represent three novel species of the genus Microbacterium. The names proposed for these organisms are Microbacterium agarici sp. nov. [type strain CC-SBCK-209T (=DSM 21798T=CCM 7686T)], Microbacterium humi sp. nov. [type strain CC-12309T (=DSM 21799T=CCM 7687T)] and Microbacterium pseudoresistens sp. nov. [type strain CC-5209T (=DSM 22185T=CCM 7688T)].
-
-
-
Cryobacterium roopkundense sp. nov., a psychrophilic bacterium isolated from glacial soil
More LessStrain RuGl7T was isolated from a soil sample collected at the periphery of the glacial Lake Roopkund in the Himalayan mountain range, India. Cells of RuGl7T were Gram-positive, aerobic, rod-shaped, motile and grew optimally between 15 and 18 °C. Cells of RuGl7T contained 2,4-diaminobutyric acid in the cell-wall peptidoglycan and the major menaquinones were MK-10, MK-11 and MK-12. The polar lipids present were diphosphatidylglycerol and phosphatidylglycerol and an unknown lipid and the major fatty acid was anteiso-C15 : 0. Based on the above characteristics, strain RuGl7T was assigned to the genus Cryobacterium. Strain RuGl7T shared a 16S rRNA gene sequence similarity of 97.0 and 99.0 % with Cryobacterium psychrotolerans JCM 13925T and Cryobacterium psychrophilum JCM 1463T, respectively. However, DNA–DNA relatedness values between strain RuGl7T and C. psychrotolerans and C. psychrophilum were 28 and 23 %, respectively. Furthermore, strain RuGl7T exhibited several phenotypic and genotypic differences when compared with C. psychrotolerans, C. psychrophilum and Cryobacterium mesophilum. Based on these differentiating characteristics, strain RuGl7T was identified as a novel species of the genus Cryobacterium for which the name Cryobacterium roopkundense sp. nov. is proposed. The type strain is RuGl7T (=DSM 21065T=JCM 15131T).
-
-
-
Corynebacterium mustelae sp. nov., isolated from a ferret with lethal sepsis
More LessA non-lipophilic coryneform bacterium, strain 3105T, was isolated from various tissues of a ferret with lethal sepsis. The strain was characterized by phenotypic and chemotaxonomic methods, which suggested an assignment of the isolate to the genus Corynebacterium. Strain 3105T exhibited the following peculiar features that made it possible to differentiate it phenotypically from all other corynebacteria: its distinctive ‘humid cellar’-like odour, strong adherence to agar and a greenish-beige pigment. Strain 3105T exhibited more than 2.8 % 16S rRNA gene sequence divergence from its closest phylogenetic neighbour, Corynebacterium pseudotuberculosis NCTC 3450T (97.12 % sequence similarity). Analysis of the highly variable region within the rpoB gene sequence showed that strain 3105T exhibited more than 14 % divergence from its closest phylogenetic relative, again C. pseudotuberculosis. Based on the data presented, it is proposed that the ferret isolate should be classified within a novel species, Corynebacterium mustelae sp. nov. (type strain 3105T =CCUG 57279T =DSM 45274T).
-
-
-
Assignment of Brevibacterium stationis (ZoBell and Upham 1944) Breed 1953 to the genus Corynebacterium, as Corynebacterium stationis comb. nov., and emended description of the genus Corynebacterium to include isolates that can alkalinize citrate
Brevibacterium stationis ATCC 14403T, Corynebacterium ammoniagenes ATCC 6872 and two clinical isolates were found to form a single taxon group consistent with the genus Corynebacterium, designated here as Corynebacterium stationis comb. nov. The type strain of Corynebacterium stationis is ATCC 14403T =CCUG 43497T =CIP 104228T =DSM 20302T =NBRC 12144T =JCM 11611T =VKM B-1228T. These strains can utilize citrate; therefore, inclusion of C. stationis requires that the description of the genus Corynebacterium be amended to include citrate-positive strains.
-
-
-
Isoptericola jiangsuensis sp. nov., a chitin-degrading bacterium
More LessA Gram-positive-staining, non-motile, rod- or coccoid-shaped bacterium, strain CLGT, was isolated from beach sand from Lianyungang, Jiangsu Province, PR China. The organism grew optimally at 30 °C and pH 7.0. Strain CLGT contained l-Lys–d-Asp as the peptidoglycan type and galactose, rhamnose and xylose as the whole-cell sugars. It contained anteiso-C15 : 0 and iso-C15 : 0 as the major fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phospholipid, phosphatidylinositol, three phosphoglycolipids and one unidentified lipid. The DNA G+C content was 70.3 mol%. The 16S rRNA gene sequence similarity of strain CLGT with Isoptericola dokdonensis DS-3T was 99.4 % but the DNA–DNA relatedness between strain CLGT and I. dokdonensis DS-3T was 58.7 %. There were also many phenotypic properties that distinguished strain CLGT from recognized species of the genus Isoptericola. The results showed that strain CLGT represents a novel species of the genus Isoptericola, for which the name Isoptericola jiangsuensis sp. nov. is proposed. The type strain is CLGT (=DSM 21863T=CCTCC AB208287T).
-
-
-
Brevibacterium sandarakinum sp. nov., isolated from a wall of an indoor environment
More LessA Gram-stain-positive, rod-shaped, non-endospore-forming, orange-pigmented (coloured) actinobacterium (01-Je-003T) was isolated from the wall of an indoor environment primarily colonized with moulds. On the basis of 16S rRNA gene sequence similarity studies, strain 01-Je-003T was shown to belong to the genus Brevibacterium and was most similar to the type strains of Brevibacterium picturae (98.8 % similarity), Brevibacterium marinum (97.3 %) and Brevibacterium aurantiacum (97.2 %). Chemotaxonomic data [predominant quinone menaquinone MK-8(H2); polar lipid profile consisting of major compounds diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid; characteristic cell-wall diamino acid meso-diaminopimelic acid; polyamine pattern showing major compounds putrescine and cadaverine; major fatty acids anteiso-C15 : 0 and anteiso-C17 : 0] supported the affiliation of strain 01-Je-003T to the genus Brevibacterium. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 01-Je-003T from the two most closely related species, B. picturae and B. marinum. Strain 01-Je-003T therefore represents a novel species, for which the name Brevibacterium sandarakinum sp. nov. is proposed, with the type strain 01-Je-003T (=DSM 22082T =CCM 7649T).
-
-
-
Kocuria atrinae sp. nov., isolated from traditional Korean fermented seafood
More LessA novel actinobacterium, strain P30T, was isolated from jeotgal, a traditional Korean fermented seafood. Cells were aerobic, Gram-positive, non-motile and coccoid. Optimal growth occurred at 30–37 °C, at pH 8–9 and in the presence of 0–2 % (w/v) NaCl. Based on 16S rRNA gene sequence analysis, strain P30T was phylogenetically closely related to Kocuria carniphila, Kocuria gwangalliensis, Kocuria rhizophila, Kocuria marina, Kocuria rosea and K. varians with levels of similarity of 98.6, 98.2, 98.1, 97.4, 97.3 and 97.3 %, respectively, to the type strains of these species. Levels of DNA–DNA relatedness between strain P30T and the type strains of K. carniphila, K. rhizophila, K. marina, K. rosea and K. varians were 37, 43, 37, 25 and 17 %, respectively. The predominant menaquinone of strain P30T was MK-7. Major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0. The genomic DNA G+C content of strain P30T was 70.2 mol%. Based on these data, strain P30T is considered to represent a novel species of the genus Kocuria, for which the name Kocuria atrinae sp. nov. is proposed. The type strain is P30T (=KCTC 19594T=JCM 15914T).
-
-
-
Actinoplanes toevensis sp. nov. and Actinoplanes tereljensis sp. nov., isolated from Mongolian soil
More LessTwo novel actinomycetes, designated MN07-A0368T and MN07-A0371T, were isolated from soil of Terelj, Töv Province, Mongolia, and subjected to phenotypic and genotypic characterization. They produced well-developed, non-fragmenting, extensively branched substrate hyphae from which oval to irregular sporangia were produced. Chemotaxonomic characteristics, i.e. cell wall diaminopimelic acid, whole-cell sugars, fatty acid components and major menaquinones, suggested that the two organisms belonged to the genus Actinoplanes. A comparative analysis of 16S rRNA gene sequences indicated that strains MN07-A0368T and MN07-A0371T formed a distinct clade within the genus and were closely related to the type strains of: Actinoplanes ferrugineus (97.7 % sequence similarity); Actinoplanes brasiliensis (97.7–97.8 %); Actinoplanes deccanensis (97.6–97.9 %); Actinoplanes durhamensis (96.9–97.0 %); and Actinoplanes globisporus (96.5–96.8 %). Strains MN07-A0368T and MN07-A0371T could be differentiated from each other and from strains of closely related species of the genus Actinoplanes by DNA–DNA hybridization, physiological and biochemical characteristics, fatty acid composition, and whole-cell sugar components. The broad range of phenotypic and genetic characters supported the suggestion that these strains represent two novel species of the genus Actinoplanes, for which the names Actinoplanes toevensis sp. nov. (type strain MN07-A0368T=NBRC 105298T=VTCC D9-11T) and Actinoplanes tereljensis sp. nov. (type strain MN07-A0371T=NBRC 105297T=VTCC D9-10T) are proposed.
-
-
-
Prauserella marina sp. nov., isolated from ocean sediment of the South China Sea
More LessA novel actinomycete strain, designated MS498T, was isolated from an ocean sediment sample collected from the South China Sea. It was subjected to a polyphasic analysis to determine its taxonomic position. The phylogenetic tree based on 16S rRNA gene sequences showed that strain MS498T had the highest similarity (96.5 %) with members of the genus Prauserella and was loosely associated with Prauserella rugosa DSM 43194T and Saccharomonospora halophila DSM 44411T. Based on 16S rRNA gene sequence analysis, phenotypic characteristics and chemotaxonomic data, the new isolate is proposed to represent a novel species of the genus Prauserella, named Prauserella marina sp. nov. (type strain MS498T=CCTCC AA 208056T =DSM 45268T).
-
- Bacteroidetes
-
-
Indibacter alkaliphilus gen. nov., sp. nov., an alkaliphilic bacterium isolated from a haloalkaline lake
More LessA novel Gram-stain-negative, rod-shaped, non-motile bacterium, strain LW1T, was isolated from a water sample collected at a depth of 3.5 m from Lonar Lake, Buldhana district, Maharashtra, India. The cell suspension was reddish-orange due to the presence of carotenoids. Strain LW1T was positive for catalase, oxidase, ornithine decarboxylase and lysine decarboxylase and negative for gelatinase, urease and lipase. Fatty acids were dominated by branched-chain fatty acids (>76 %), with a high abundance of iso-C15 : 0 (48 %), anteiso-C15 : 0 (7 %) and iso-C17 : 0 3-OH (11 %). Strain LW1T contained MK-4 and MK-7 as the major respiratory quinones and phosphatidylglycerol, phosphatidylcholine and phosphatidylethanolamine as the major phospholipids. A blast sequence similarity search based on 16S rRNA gene sequences indicated that members of the genera Belliella and Aquiflexum were the nearest phylogenetic neighbours with similarities of 91.8–92.3 %. Phylogenetic analyses indicated that strain LW1T formed a deep-rooted lineage distinct from the clades represented by the genera Belliella, Aquiflexum, Cyclobacterium, Echinicola and Algoriphagus. Based on the above-mentioned phenotypic and phylogenetic characteristics, it is proposed that strain LW1T represents a novel species in a new genus, Indibacter alkaliphilus gen. nov., sp. nov. (type strain LW1T=KCTC 22604T=CCUG 57479T). The genomic DNA G+C content of strain LW1T is 42.7±1 mol%.
-
-
-
Description of Olleya aquimaris sp. nov., isolated from seawater, and emended description of the genus Olleya Mancuso Nichols et al. 2005
More LessA Gram-stain-negative, non-flagellated, motile (by gliding), yellow-pigmented, rod-shaped bacterial strain, designated L-4T, was isolated from seawater of Baekdo harbour in the East Sea, Korea. Strain L-4T grew optimally at 37 °C, at pH 6.5–7.0 and in the presence of 2 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain L-4T clustered with Olleya marilimosa CAM030T, a member of the family Flavobacteriaceae. Strain L-4T exhibited 16S rRNA gene sequence similarity values of 97.2 % to O. marilimosa CAM030T and less than 95.8 % to other members of the family Flavobacteriaceae. Strain L-4T and O. marilimosa CIP 108537T contained MK-6 as the predominant menaquinone. The fatty acid and polar lipid profiles of strain L-4T were similar to those of O. marilimosa CIP 108537T. The DNA G+C content of strain L-4T was 35 mol% and DNA–DNA relatedness between strain L-4T and O. marilimosa CIP 108537T was 7 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, enable strain L-4T to be distinguished from O. marilimosa. On the basis of these data, strain L-4T is considered to represent a novel species of the genus Olleya for which the name Olleya aquimaris sp. nov. is proposed; the type strain is L-4T (=KCTC 22661T =CCUG 58074T). An emended description of the genus Olleya is also provided.
-
-
-
Bizionia echini sp. nov., isolated from a sea urchin
More LessA bacterial strain, designated KMM 6177T, was isolated from the sea urchin Strongylocentrotus intermedius and subjected to a polyphasic taxonomic investigation. The bacterium was found to be heterotrophic, aerobic, non-motile by gliding and orange-pigmented. Comparative phylogenetic analysis based on 16S rRNA gene sequencing placed the marine isolate in the genus Bizionia, a member of the family Flavobacteriaceae, with 16S rRNA gene sequence similarity of 94.9–98.6 % with recognized Bizionia species. Strain KMM 6177T grew at 4–39 °C and with 1–8 % NaCl. It produced alkaline phosphatase, catalase and oxidase and hydrolysed aesculin, gelatin, DNA and Tween 20. The predominant fatty acids were iso-C15 : 1, iso-C15 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH and a summed feature (comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c). The DNA G+C content was 34.4 mol%. A combination of phylogenetic, genotypic and phenotypic data clearly indicated that strain KMM 6177T represents a novel species in the genus Bizionia, for which the name Bizionia echini sp. nov. is proposed. The type strain is KMM 6177T (=KCTC 22015T=LMG 25220T).
-
- Firmicutes And Related Organisms
-
-
Planococcus salinarum sp. nov., isolated from a marine solar saltern, and emended description of the genus Planococcus
More LessA Gram-positive, non-motile and coccoid-, short rod- or rod-shaped bacterial strain, ISL-16T, was isolated from a marine solar saltern in Korea and its taxonomic position was investigated using a polyphasic taxonomic approach. Strain ISL-16T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ISL-16T joined the cluster comprising species of the genus Planococcus. Its 16S rRNA gene sequence contained the same signature nucleotides as those defined for the genus Planococcus. Strain ISL-16T exhibited 16S rRNA gene sequence similarity values of 96.9–98.2 % to the type strains of species of the genus Planococcus. Strain ISL-16T contained MK-8 and MK-7 as the predominant menaquinones and anteiso-C15 : 0, C16 : 1 ω7c alcohol and anteiso-C17 : 0 as the major fatty acids. The DNA G+C content was 48.3 mol%. DNA–DNA relatedness values between strain ISL-16T and the type strains of species of the genus Planococcus were 15–28 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, enabled strain ISL-16T to be differentiated from recognized species of the genus Planococcus. On the basis of the data presented, strain ISL-16T is considered to represent a novel species of the genus Planococcus, for which the name Planococcus salinarum sp. nov. is proposed. The type strain is ISL-16T (=KCTC 13584T=CCUG 57753T). An emended description of the genus Planococcus is also given.
-
-
-
Streptococcus dentapri sp. nov., isolated from the wild boar oral cavity
More LessFour Gram-stain-positive, catalase-negative, coccoid-shaped isolates were obtained from the oral cavities of wild boars and characterized by phenotypic and phylogenetic studies. On the results of biochemical tests, the organisms were tentatively identified as a streptococcal species. Comparative 16S rRNA gene sequencing studies confirmed that the organisms are members of the genus Streptococcus, with Streptococcus equi subsp. equi ATCC 33398T as their closest phylogenetic relative (94.7 % similarity). DNA–DNA hybridization analysis showed that the isolates displayed less than 10 % relatedness to Streptococcus equi subsp. equi DSM 20561T. From the phylogenetic and phenotypic evidence, the four isolates represent a novel species of the genus Streptococcus, for which the name Streptococcus dentapri sp. nov. (type strain NUM 1529T =JCM 15752T =DSM 21999T) is proposed.
-
-
-
Cellulosilyticum ruminicola gen. nov., sp. nov., isolated from the rumen of yak, and reclassification of Clostridium lentocellum as Cellulosilyticum lentocellum comb. nov.
More LessAn obligate anaerobic, Gram-staining-negative, mesophilic, cellulolytic bacterium, strain H1T, was isolated from the rumen content of yak. Cells were straight to slightly curved rods, 0.8–1.0×3.0–4.0 μm in size, non-motile and encapsulated with mucous materials. Elliptical and terminal spores that swelled the cells were produced occasionally. The strain grew at 25–45 °C (optimum, 38 °C) and pH 6.0–7.8 (optimum, pH 6.7). Cellulose, cellobiose, xylan, xylose and maltose were used as carbon and energy sources, but not glucose. Products from cellulose and cellobiose fermentation were formic acid, acetic acid, carbon dioxide and trace amounts of ethanol, lactic acid and succinic acid. The genomic DNA G+C content was 33.7±1.2 mol%. The predominant fatty acids were C16 : 0 (27.1 %), C14 : 0 (9.2 %) and iso-C16 : 0 (6.4%). Based on the 16S rRNA gene sequence analysis, strain H1T was affiliated to the clostridial rRNA cluster XIVb and showed the highest 16S rRNA gene sequence similarity to Clostridium lentocellum DSM 5427T (96.0 %). These two strains formed a distinct lineage of the family ‘Lachnospiraceae’. Based on data from this polyphasic taxonomic study, a new genus, Cellulosilyticum gen. nov., is proposed. Cellulosilyticum ruminicola sp. nov. is proposed for strain H1T. The type strain of Cellulosilyticum ruminicola sp. nov. is strain H1T (=CGMCC 1.5065T=JCM 14822T). Clostridium lentocellum was reclassified in the new genus as Cellulosilyticum lentocellum comb. nov. (type strain RHM5T=ATCC 49066T=DSM 5427T=NCIMB 11756T).
-
-
-
Bacillus galliciensis sp. nov., isolated from faeces of wild seahorses (Hippocampus guttulatus)
More LessA Gram-positive-staining, motile, rod-shaped, endospore-forming bacterium (BFLP-1T) was isolated from faeces of wild long-snouted seahorses (Hippocampus guttulatus) captured in north-west Spain (Toralla, Galicia). Strain BFLP-1T grew at 10–30 °C and pH 5.5–9 (optimally at 20 °C and pH 7.2) and with 0–7 % (w/v) NaCl (optimally with 2 % NaCl). The G+C content of the DNA was 48.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BFLP-1T was a member of the genus Bacillus and was most closely related to Bacillus herbersteinensis D-1,5aT (96.6 %), B. shackletonii LMG 18435T (96.0 %) and B. isabeliae CVS-8T (95.9 %). Chemotaxonomic data (peptidoglycan type, meso-diaminopimelic acid; major menaquinone, MK-7; predominant fatty acids, anteiso-C15 : 0, anteiso-C17 : 0 and C16 : 1 ω11c; major polar lipids, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unknown aminoglycophospholipid) supported the affiliation of strain BFLP-1T to the genus Bacillus. Comparative analysis of 16S rRNA gene sequences and chemotaxonomic and phenotypic features indicated that strain BFLP-1T represents a novel species within the genus Bacillus, for which the name Bacillus galliciensis sp. nov. is proposed. The type strain is BFLP-1T (=DSM 21539T =LMG 24668T).
-
-
-
Gracilibacillus thailandensis sp. nov., from fermented fish (pla-ra)
A novel strain, designated TP2-8T, was isolated from fermented fish (pla-ra) in Thailand. It stained Gram-positive and the cells were aerobic, endospore-forming rods. The strain grew at pH 6–8 (optimum pH 7), 15–55 °C (optimum 37 °C) and 1–22 % (w/v) NaCl (optimum 5–10 %). It contained meso-diaminopimelic in the cell-wall peptidoglycan. MK-7 and cellular fatty acids anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0 were major components. Polar lipids diphosphatidylglycerol and phosphatidylglycerol and unidentified lipids were detected. The DNA G+C content was 37.6 mol%. Comparison of the 16S rRNA gene sequence of strain TP2-8T with those of other members of the family Bacillaceae indicated that it was a member of the genus Gracilibacillus (94.9–99.2 % sequence similarity) and was closely related to Gracilibacillus saliphilus YIM 91119T (99.2 % similarity), G. lacisalsi BH312T (98.6 %), G. orientalis XH-63T (97.7 %), ‘G. quinghaiensis’ YIM C229 (97.7 %) and G. boraciitolerans T-16XT (97.2 %). Strain TP2-8T showed low DNA–DNA relatedness (≤49 %) to G. saliphilus YIM 91119T, G. lacisalsi DSM 19029T, G. orientalis CCM 7326T, ‘G. quinghaiensis’ DSM 17858 and G. boraciitolerans JCM 21714T. On the basis of the physiological and biochemical characteristics and molecular data presented, strain TP2-8T is proposed to represent a novel species, Gracilibacillus thailandensis sp. nov. (type strain TP2-8T =JCM 15569T =PCU 304T =TISTR 1881T).
-
-
-
Geomicrobium halophilum gen. nov., sp. nov., a moderately halophilic and alkaliphilic bacterium isolated from soil
More LessTwo moderately halophilic and alkaliphilic bacteria, designated strains BH1T and HN5, were isolated from forest soil and garden soil, respectively, in Japan. Cells of strains BH1T and HN5 were non-motile, aerobic, bean-shaped, formed irregular clusters with 2–20 cells, Gram-positive and contained A1γ, meso-diaminopimelic acid-type murein. Spore formation was not detected. Growth occurred in 5–25 % (w/v) NaCl (optimum, 10–15 %, w/v), at pH 6.0–10.0 (optimum, pH 8.5–9.0) and at 20–40 °C (optimum, 30 °C). The predominant isoprenoid quinones were menaquinone-7 and menaquinone-6. The phospholipids were diphosphatidylglycerol and phosphatidylglycerol. The major cellular fatty acids were i-C15 : 0, i-C17 : 0 and i-C18 : 0. The DNA G+C content of strains BH1T and HN5 was 45 and 46 mol%, respectively. The 16S rRNA gene sequences of the two strains were 99.9 % similar. DNA–DNA hybridization results indicated high levels of relatedness (88 and 85 % reciprocally). Similarities with recognized species were less than 90.2 %. The phylogenetic and phenotypic characteristics indicated that strains BH1T and HN5 represent a novel species in a new genus, for which the name Geomicrobium halophilum gen. nov., sp. nov. is proposed. The type strain is BH1T (=JCM 15647T=DSM 21769T).
-
- Other Bacteria
-
-
Deinococcus aetherius sp. nov., isolated from the stratosphere
A pink-red pigmented, non-motile, coccoid bacterial strain, ST0316T, was isolated from dust samples collected from the stratosphere in Japan. Phylogenetic analysis based on 16S rRNA gene sequences showed that it belonged to the genus Deinococcus. DNA G+C content (69.8 mol%), desiccation tolerance, and resistance to gamma-rays [D10 (dose required to reduce the bacterial population by 10-fold) >8 kGy] and UV radiation (D10 1000 J m−2) supported the affiliation of strain ST0316T to the genus Deinococcus. The major peptidoglycan amino acids were d-glutamic acid, glycine, d-alanine, l-alanine and ornithine. Predominant fatty acids were C16 : 1 ω7c, C16 : 0, C17 : 0 and iso-C17 : 0. Strain ST0316T diverged from recognized species of the genus Deinococcus, showing less than 93.0 % similarity values to its closest relatives Deinococcus apachensis, D. aerius, D. geothermalis and D. murrayi. Strain ST0316T also differed from the type strains of closely related species in its polar lipid profile, nitrate reduction and carbon-source assimilation tests. Therefore, we propose a new species of the genus Deinococcus, Deinococcus aetherius sp. nov. (type strain, ST0316T =JCM 11751T =DSM 21230T).
-
-
-
Thermus arciformis sp. nov., a thermophilic species from a geothermal area
Xin-Qi Zhang, Yi Ying, Ying Ye, Xue-Wei Xu, Xu-Fen Zhu and Min WuTwo aerobic, Gram-negative, non-motile, non-sporulating, yellow-pigmented bacteria, strains TH92T and TH91, were isolated from a hot spring located in Laibin, Guangxi, in the south-eastern geothermal area of China. The isolates grew at 40–77 °C (optimally at 70 °C) and at pH 6.0–9.5 (optimally at pH 7.5–8.0). Phylogenetic analysis of 16S rRNA gene sequences and levels of DNA–DNA relatedness together indicated that the new isolates represented a novel species of the genus Thermus with closest affinity to Thermus aquaticus, Thermus igniterrae and Thermus thermophilus. Compared with their closest relatives, strains TH92T and TH91 were able to assimilate a wider range of carbohydrates, amino acids and organic acids as sole carbon sources for growth, such as lactose and melibiose. The new isolates had lower combined levels of C16 : 0 and iso-C16 : 0 compared with their closest relatives. On the basis of polyphasic taxonomic characterization, strains TH92T and TH91 are considered to represent a single novel species of the genus Thermus, for which the name Thermus arciformis sp. nov. is proposed. The type strain is TH92T (=CGMCC 1.6992T =JCM 15153T).
-
-
-
Meiothermus cateniformans sp. nov., a slightly thermophilic species from north-eastern China
More LessTwo aerobic, non-motile and non-sporulating bacteria, strains LY1T and L462, were recovered from a hot spring located in the Qianshan area of north-eastern China. The novel strains had Gram-negative cell walls and grew at 30–66 °C (optimum 55–60 °C) and pH 5.5–10.0 (optimum pH 8.0–8.5).16S rRNA gene sequence similarity analysis revealed that strains LY1T and L462 were most closely related to Meiothermus ruber ATCC 35948T, M. taiwanensis WR-30T and M. cerbereus GY-1T, with 97.1–98.4 % sequence similarity. Phylogenetic analysis indicated that the new isolates represented a novel species by forming a distinctive lineage within genus Meiothermus, which was confirmed by DNA–DNA reassociation values. Strain LY1T was obviously different from its closest relatives in a number of phenotypic characteristics, such as the inability to hydrolyse casein or to assimilate melibiose, trehalose, sucrose and lactose. Strain L462 was distinct in its ability to reduce nitrate. In addition, the novel strains were distinct in having larger amounts of anteiso-C17 : 0 than their closest phylogenetic neighbours. On the basis of this polyphasic taxonomic characterization, the name Meiothermus cateniformans sp. nov. is proposed for the novel species, currently represented by the type strain LY1T (=CGMCC 1.6990T =JCM 15151T) and strain L462 (=CGMCC 1.6989 =JCM 15150).
-
-
-
Dethiosulfovibrio salsuginis sp. nov., an anaerobic, slightly halophilic bacterium isolated from a saline spring
More LessA mesophilic, strictly anaerobic, slightly halophilic bacterium, designated strain USBA 82T, was isolated from a terrestrial saline spring in the Colombian Andes. The non-spore-forming curved rods (5–7×1.3 μm) with pointed or rounded ends, stained Gram-negative and were motile by means of laterally inserted flagella. The strain grew optimally at 30 °C (growth range 20–40 °C), pH 7.3 (growth range pH 5.5–8.5) and 2 % (w/v) NaCl (growth range 0.1–7 % NaCl). The strain fermented peptides, amino acids and a few organic acids, but growth was not observed on carbohydrates, alcohols or fatty acids. The strain reduced thiosulfate and sulfur to sulfide. Sulfate, sulfite, nitrate and nitrite were not used as electron acceptors. On peptone alone, acetate, succinate, propionate and traces of ethanol were formed, but in the presence of thiosulfate, acetate and succinate were formed. The G+C content of the chromosomal DNA was 52 mol% (T m).16S rRNA gene sequence analysis indicated that strain USBA 82T was affiliated to Dethiosulfovibrio peptidovorans within the phylum Synergistetes with a similarity value of approximately 93 %. Based on the differences between the new strain and the type species of the genus Dethiosulfovibrio, we suggest that strain USBA 82T represents a novel species of the genus for which the name Dethiosulfovibrio salsuginis sp. nov. is proposed. The type strain is USBA 82T (=DSM 21565T=KCTC 5659T).
-
-
-
Thermococcoides shengliensis gen. nov., sp. nov., a new member of the order Thermotogales isolated from oil-production fluid
More LessA novel thermophilic, strictly anaerobic, heterotrophic bacterium, strain 2SM-2T, was isolated from the Shengli oilfield, China. This organism was identified as a member of the order Thermotogales on the basis of its 16S rRNA gene sequence and the presence of an external membranous toga-like structure. Cells stained Gram-negative, were non-motile, appeared as irregular cocci 0.7–0.9 μm in diameter, and occurred in clusters of two to six cells, with cells located within a ballooning toga-like membrane. Its optimum temperature, pH and NaCl concentration for growth were 65 °C, 7.0 and 15 g l−1, respectively. Under the optimum growth conditions, the doubling time was approximately 105 min. Strain 2SM-2T fermented a variety of simple and complex substrates such as glucose, acetate, methanol, starch and peptone while reducing elemental sulfur, sulfate and thiosulfate. The end products identified during growth on glucose were acetate, lactate, l-alanine, H2 and CO2. The DNA G+C content of this organism was 36.4 mol%. The results of 16S rRNA gene-based sequence comparisons revealed that the strain represented a new lineage within the family Thermotogaceae of the order Thermotogales. Based on the phenotypic and phylogenetic characteristics, it is proposed that this organism represents a novel species in a new genus within the family Thermotogaceae, for which the name Thermococcoides shengliensis gen. nov., sp. nov. is proposed. The type strain is 2SM-2T (=ACCC 00496T=DSM 22460T).
-
- Proteobacteria
-
-
Porticoccus litoralis gen. nov., sp. nov., a gammaproteobacterium isolated from the Yellow Sea
More LessA marine bacterium, designated IMCC2115T, was isolated from coastal seawater (Yellow Sea, Korea) using a high throughput cultivation method based on dilution-to-extinction, and taxonomically investigated. Cells of the strain formed tiny, beige to off-white colonies and were Gram-stain-negative, obligately aerobic, chemoheterotrophic, non-motile cocci. Based on 16S rRNA gene sequence comparisons, the strain was most closely related to the genera Marinimicrobium (92.0–92.4 %) and Microbulbifer (91.6–92.8 %), but phylogenetic trees showed that the strain formed a distinct phyletic line in the class Gammaproteobacteria adjacent to the OM60 and SAR92 clades. The DNA G+C content of the strain was 47.8 mol% and the predominant cellular fatty acids were anteiso-C15 : 0 (67.6 %), anteiso-C17 : 0 (14.4 %) and C16 : 0 (6.9 %). The 16S rRNA gene sequence analyses and phenotypic and chemotaxonomic tests allowed the differentiation of IMCC2115T from other related genera in the class Gammaproteobacteria. Therefore, strain IMCC2115T (=KCCM 42369T =NBRC 102686T) is proposed as the representative of a new genus and species, for which the name Porticoccus litoralis gen. nov., sp. nov. is proposed.
-
-
-
Stappia indica sp. nov., isolated from deep seawater of the Indian Ocean
More LessA taxonomic study was carried out on strain B106T, which was isolated from a polycyclic aromatic hydrocarbon-degrading consortium, enriched with deep seawater from the Indian Ocean. The isolate was Gram-negative, oxidase- and catalase-positive, rod-shaped and motile by means of one polar flagellum. Growth was observed at salinities of 0.5–11 % and at temperatures of 4–42 °C, and the strain was capable of nitrate reduction, but was unable to degrade Tween 80 or gelatin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain B106T belonged to the genus Stappia, with a highest sequence similarity of 97.7 % to Stappia stellulata IAM 12621T; similarity to other strains was below 95.2 %. DNA–DNA hybridization between strain B106T and S. stellulata IAM 12621T was 43 %. The major fatty acids were C16 : 0 (6.10 %), C18 : 1 ω7c (62.58 %), C18 : 0 (5.17 %), C18 : 1 ω7c 11-methyl (14.48 %) and C19 : 0 ω8c cyclo (4.70 %). The G+C content of the chromosomal DNA was 65.9 mol%. The combined genotypic and phenotypic data showed that strain B106T represents a novel species of the genus Stappia, for which the name Stappia indica sp. nov. is proposed, with the type strain B106T (=PR56-8T=CCTCC AB 208228T=LMG 24625T=MCCC 1A01226T).
-
-
-
Halomonas andesensis sp. nov., a moderate halophile isolated from the saline lake Laguna Colorada in Bolivia
More LessA moderately halophilic, motile, Gram-negative, rod-shaped bacterium, strain LC6T, was isolated from a water sample of lake Laguna Colorada in the Bolivian Andes. The major cellular fatty acids were C18 : 1 ω7c, iso-C16 : 1 ω7c 2-OH, C16 : 0 and C12 : 0 3-OH. The respiratory ubiquinones found in strain LC6T were Q-9 (97 %) and Q-8 (3 %). Strain LC6T was aerobic, heterotrophic, and able to utilize various carbohydrates and other substrates as carbon source. The G+C content of the genomic DNA of strain LC6T was 52.5 mol%. The organism was able to grow at pH 6.0–11.0 (optimum, pH 7.0–8.0), at 4–45 °C (optimum, 30–35 °C) and in the presence of 0.5–20 % (w/v) NaCl (optimum, 1–3 %, w/v). Based on 16S rRNA gene sequence analysis, strain LC6T was most closely related to Halomonas hydrothermalis DSM 15725T and Halomonas venusta DSM 4743T (98.8 % similarity), followed by Halomonas aquamarina DSM 30161T, Halomonas axialensis DSM 15723T and Halomonas meridiana DSM 5425T (98.4 %). However, levels of DNA–DNA relatedness between strain LC6T and the above type strains were low (<31 %). Strain LC6T resembled recognized Halomonas species with respect to various physiological, biochemical and nutritional characteristics. Combined phenotypic data and DNA–DNA hybridization data supported the conclusion that strain LC6T represents a novel species of the genus Halomonas, for which the name Halomonas andesensis is proposed. The type strain is LC6T (=CCUG 54844T=LMG 24243T=DSM 19434T).
-
-
-
Bartonella japonica sp. nov. and Bartonella silvatica sp. nov., isolated from Apodemus mice
Two bacterial strains, Fuji 18-1T and Fuji 23-1T, were isolated from the blood of the small Japanese field mouse (Apodemus argenteus) and the large Japanese field mouse (Apodemus speciosus), respectively, specimens of which were captured in the forest of Mount Fuji, Japan. Phenotypic characterization (growth conditions, incubation periods, biochemical properties and cell morphologies), DNA G+C contents (40.1 mol% for strain Fuji 18-1T and 40.4 mol% for strain Fuji 23-1T) and sequence analyses of the 16S rRNA genes indicated that both strains were members of the genus Bartonella. Using rpoB and gltA sequencing analysis, the highest sequence similarities between strains Fuji 18-1T, Fuji 23-1T and other recognized species of the genus Bartonella showed values considerably lower than 91.4 % and 89.9 % in the rpoB gene and 89.1 % and 90.4 % in the gltA gene, respectively. It is known that similarities of 95.4 % for the rpoB gene and 96.0 % for the gltA gene can be applied as cut-off values for the designation of novel species of the genus Bartonella. In a phylogenetic tree based on the merged set of concatenated sequences of seven loci [16S rRNA, ftsZ, gltA, groEL, ribC and rpoB genes and the intergenic spacer region (ITS)], strains Fuji 18-1T and Fuji 23-1T formed a distinct clade from other recognized species of the genus Bartonella. These data support the classification of strains Fuji 18-1T and Fuji 23-1T as novel species of the genus Bartonella. The names Bartonella japonica sp. nov. and Bartonella silvatica sp. nov. are proposed for these novel species. The type strains of Bartonella japonica sp. nov. and Bartonella silvatica sp. nov. are Fuji 18-1T (=JCM 15567T=CIP 109861T) and Fuji 23-1T (=JCM 15566T=CIP 109862T), respectively.
-
-
-
Acidocella aluminiidurans sp. nov., an aluminium-tolerant bacterium isolated from Panicum repens grown in a highly acidic swamp in actual acid sulfate soil area of Vietnam
An aluminium-tolerant bacterium, strain AL46T, was isolated from a waterweed, Panicum repens, grown in a highly acidic swamp (pH 3) at an actual acid sulfate soil area of Vietnam. Cells were Gram-negative, aerobic, non-spore-forming, non-motile rods (0.3 μm wide and 1.2–1.6 μm long). 16S rRNA gene sequence analysis indicated that strain AL46T belongs to the genus Acidocella, class Alphaproteobacteria. Strain AL46T was related most closely to the type strains of Acidocella facilis and Acidocella aminolytica (99.4 and 97.8 % 16S rRNA gene sequence similarity, respectively). Levels of DNA–DNA relatedness between strain AL46T and the above type strains were 40 %. The results of physiological and biochemical tests allowed the novel strain to be differentiated phenotypically from the two recognized Acidocella species. Data for predominant cellular fatty acids (cyclopropyl C19 : 0 and C18 : 1), major isoprenoid quinone (Q-10) and DNA G+C content (65.6 mol%) were in accordance with those reported for the genus Acidocella. Therefore, strain AL46T is considered to represent a novel species of the genus Acidocella, for which the name Acidocella aluminiidurans sp. nov. is proposed. The type strain is AL46T (=NBRC 104303T =VTCC-D9-1T).
-
-
-
Sphingopyxis ummariensis sp. nov., isolated from a hexachlorocyclohexane dump site
More LessA Gram-negative, motile, rod-shaped, yellow-pigmented bacterium, strain UI2T, was isolated from a hexachlorocyclohexane (HCH) dump site located in Ummari, in northern India. 16S rRNA gene sequence analysis revealed that strain UI2T belongs to the genus Sphingopyxis and showed highest 16S rRNA gene sequence similarity with Sphingopyxis terrae IFO 15098T (98.6 %). DNA–DNA relatedness values between strain UI2T and Sphingopyxis terrae IFO 15098T and other related strains were found to be less than 46 %. The major cellular fatty acids of strain UI2T were C18 : 1 ω7c (28.3 %), C16 : 0 (14.4 %), 11-methyl C18 : 1 ω7c (10.9 %), C17 : 1 ω6c (9.6 %) and summed feature 3 (consisting of C16 : 1 ω7c and/or C15 : 0 iso 2-OH; 14.7 %). The DNA G+C content of strain UI2T was 68 mol%. On the basis of DNA–DNA hybridization, phenotypic characteristics and phylogenetic analysis, strain UI2T is found to represent a novel species of the genus Sphingopyxis, for which the name Sphingopyxis ummariensis sp. nov. is proposed. The type strain is UI2T (=CCM 7428T =MTCC 8591T).
-
-
-
Loktanella pyoseonensis sp. nov., isolated from beach sand, and emended description of the genus Loktanella
More LessA novel Gram-stain-negative, aerobic, heterotrophic, obligately halophilic bacterium, designated strain JJM85T, was isolated from beach sand in Jeju, Republic of Korea. Cells were rod-shaped and motile by means of flagella; colonies were pink, convex and smooth with an entire edge. The organism grew at pH 5.0–10.0 and 4–30 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that the organism belonged to the genus Loktanella of the class Alphaproteobacteria and formed a tight cluster with the type strain of Loktanella hongkongensis (96.0 % sequence similarity). The DNA G+C content and fatty acid profile of the novel strain supported affiliation with the genus Loktanella. However, the novel strain could be differentiated clearly from members of this genus by cell motility, some physiological properties and low 16S rRNA gene sequence similarity (93.1–96.0 %). On the basis of the polyphasic data presented here, strain JJM85T is considered to represent a novel species of the genus Loktanella, for which the name Loktanella pyoseonensis sp. nov. is proposed; the type strain is JJM85T (=KCTC 22372T =DSM 21424T).
-
-
-
Sphingomonas changbaiensis sp. nov., isolated from forest soil
More LessBacterial strain V2M44T was isolated from forest soil from the Changbai Mountains, Heilongjiang Province, China. Cells of strain V2M44T were Gram-negative, rod-shaped and 0.3–0.4 μm in diameter and 1.5–2.5 μm long. The cells were strictly aerobic and were motile by means of peritrichous flagella. Growth occurred at 20–33 °C (optimum, 29–31 °C), at pH 5–8 (optimum, pH 6.0–7.0) and in the presence of 0−0.1 % (w/v) NaCl (optimum, 0.05 %). Strain V2M44T contained C17 : 1 ω6c (38.9 %) and summed feature 7 (comprising C18 : 1 ω7c, C18 : 1 ω9t and/or C18 : 1 ω12t, 31.5 %) as the major cellular fatty acids and Q-10 as the major respiratory quinone. The major polar lipids were sphingoglycolipid, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol along with two unidentified phospholipids and four unidentified glycolipids. The major component in the polyamine pattern was sym-homospermidine. The DNA G+C content was 65.8 mol%. Analysis of 16S rRNA gene sequences indicated that strain V2M44T was phylogenetically related to members of the genus Sphingomonas, with sequence similarities ranging from 92.0–95.8 %. Based on these results, it is concluded that strain V2M44T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas changbaiensis sp. nov. is proposed. The type strain is V2M44T (=CGMCC 1.7057T=NBRC 104936T).
-
-
-
Brucella inopinata sp. nov., isolated from a breast implant infection
A Gram-negative, non-motile, non-spore-forming coccoid bacterium (strain BO1T) was isolated recently from a breast implant infection of a 71-year-old female patient with clinical signs of brucellosis. Affiliation of strain BO1T to the genus Brucella was confirmed by means of polyamine pattern, polar lipid profile, fatty acid profile, quinone system, DNA–DNA hybridization studies and by insertion sequence 711 (IS711)-specific PCR. Strain BO1T harboured four to five copies of the Brucella-specific insertion element IS711, displaying a unique banding pattern, and exhibited a unique 16S rRNA gene sequence and also grouped separately in multilocus sequence typing analysis. Strain BO1T reacted with Brucella M-monospecific antiserum. Incomplete lysis was detected with bacteriophages Tb (Tbilisi), F1 and F25. Biochemical profiling revealed a high degree of enzymic activity and metabolic capabilities. In multilocus VNTR (variable-number tandem-repeat) analysis, strain BO1T showed a very distinctive profile and clustered with the other ‘exotic’ Brucella strains, including strains isolated from marine mammals, and Brucella microti, Brucella suis biovar 5 and Brucella neotomae. Comparative omp2a and omp2b gene sequence analysis revealed the most divergent omp2 sequences identified to date for a Brucella strain. The recA gene sequence of strain BO1T differed in seven nucleotides from the Brucella recA consensus sequence. Using the Brucella species-specific multiplex PCR assay, strain BO1T displayed a unique banding pattern not observed in other Brucella species. From the phenotypic and molecular analysis it became evident that strain BO1T was clearly different from all other Brucella species, and therefore represents a novel species within the genus Brucella. Because of its unexpected isolation, the name Brucella inopinata with the type strain BO1T (=BCCN 09-01T=CPAM 6436T) is proposed.
-
-
-
Kinneretia asaccharophila gen. nov., sp. nov., isolated from a freshwater lake, a member of the Rubrivivax branch of the family Comamonadaceae
More LessA strictly aerobic, Gram-negative bacterium, strain KIN192T, isolated from fresh water from Lake Kinneret, Israel, was examined using a polyphasic approach to characterize and clarify its phylogenetic and taxonomic position. Sequences of the 16S rRNA and gyrB genes and ITS1 revealed close relationships to species of the genera Pelomonas, Mitsuaria and Roseateles, in the Rubrivivax branch of the family Comamonadaceae of the Betaproteobacteria. Physiological and biochemical tests, cellular fatty acid analysis and DNA–DNA hybridizations indicated that this strain should be assigned to a new genus and species in the Rubrivivax phylogenetic branch, for which the name Kinneretia asaccharophila gen. nov., sp. nov., is proposed. The type strain of Kinneretia asaccharophila is strain KIN192T (=CCUG 53117T =CECT 7319T).
-
-
-
Campylobacter subantarcticus sp. nov., isolated from birds in the sub-Antarctic region
More LessSix Gram-stain-negative, spiral-shaped, microaerobic isolates were obtained during a sampling from wild birds in the sub-Antarctic region. Based on initial observations, these isolates were classified as Campylobacter lari-like. The isolates were further characterized by whole-cell protein and amplified fragment length polymorphism (AFLP) analysis, which revealed that they were distinct from C. lari and all other known species of the genus Campylobacter. Here, we present comprehensive phylogenetic, genomic and phenotypic evidence that these isolates represent a novel species within the genus Campylobacter, for which the name Campylobacter subantarcticus sp. nov. is proposed. The type strain is R-3023T (=LMG 24377T =CCUG 38513T).
-
-
-
Gram-negative bacteria associated with brewery yeasts: reclassification of Obesumbacterium proteus biogroup 2 as Shimwellia pseudoproteus gen. nov., sp. nov., and transfer of Escherichia blattae to Shimwellia blattae comb. nov.
More LessPhylogenetic analyses of type and reference strains of Obesumbacterium proteus biogroups 1 and 2 plus a novel isolate of biogroup 2 were carried out based on 16S rRNA gene sequences and partial sequences of four protein-coding genes (fusA, leuS, pyrG and rpoB). Both approaches revealed that O. proteus biogroup 1 strains were closely related to Hafnia alvei. Biogroup 2 strains, however, formed a distinct monophyletic clade of generic status that included Escherichia blattae. Phenotypic tests were consistent with the molecular classification and provided diagnostic features. It is proposed that biogroup 2 strains be placed in a new genus, Shimwellia gen. nov., as Shimwellia pseudoproteus sp. nov., with strain 521T (=DSM 3038T=LMG 24835T=NCIMB 14534T) as the type strain, and that Escherichia blattae be transferred to the genus Shimwellia as Shimwellia blattae comb. nov., with strain ATCC 29907T (=DSM 4481T) as the type strain.
-
-
-
Chelatococcus sambhunathii sp. nov., a moderately thermophilic alphaproteobacterium isolated from hot spring sediment
More LessA moderately thermophilic bacterial strain (HT4T) isolated from a hot spring sediment was characterized phenotypically and phylogenetically. Cells were Gram-negative, aerobic, non-sporulating, rod-shaped and motile by means of a single polar flagellum. Both oxidase and catalase activities were positive. Heterotrophic growth was observed at pH 6.0–8.5 and at 20–50 °C; optimum growth occurred at pH 7.5–8.0 and 37–42 °C. The major cellular fatty acids were C14 : 0 3-OH, C18 : 0 3-OH, C18 : 1 2-OH, C18 : 1 ω7c and C19 : 0 cyclo ω8c. The DNA G+C content of strain HT4T was 67.8 mol%.16S rRNA gene sequence analysis indicated that strain HT4T clustered within the radiation of the genus Chelatococcus and showed 99.0 % similarity with Chelatococcus daeguensis CCUG 54519T and 96 % similarity with Chelatococcus asaccharovorans DSM 6462T. However, levels of DNA–DNA relatedness between strain HT4T and Chelatococcus daeguensis CCUG 54519T and Chelatococcus asaccharovorans DSM 6462T were 52 and 20 %, respectively. On the basis of the phenotypic, physiological and chemotaxonomic data, 16S rRNA gene sequence analysis and DNA–DNA hybridization results, strain HT4T is considered to represent a novel species of the genus Chelatococcus, for which the name Chelatococcus sambhunathii sp. nov. is proposed. The type strain is HT4T (=DSM 18167T=JCM 14988T).
-
-
-
Desulfovibrio africanus subsp. uniflagellum subsp. nov., a sulfate-reducing bacterium from a uranium-contaminated subsurface aquifer
More LessThe bacterial strain SR-1T was isolated from subsurface sediments of a uranium-contaminated site in Shiprock, New Mexico, USA. Cells are vibrioid and motile by means of a single polar flagellum. Strain SR-1T grows on sulfate, oxidizing formate, lactate and H2, but not malate, and ferments pyruvate. The DNA sequences of the 16S rRNA gene and the 16S–23S internal transcribed spacer of strain SR-1T showed 99.9 and 99.4 % similarity, respectively, to those of the type strain Desulfovibrio africanus DSM 2603T. The DNA sequence of the ITS region is 300 bases in length and contains two tRNA genes (tRNAIle, tRNAAla). The partial DNA sequence of the dsrAB gene showed 94.6 % amino acid sequence similarity to that of D. africanus. The DNA G+C content of strain SR-1T was 62.4 mol% and it showed 72 % DNA–DNA similarity to D. africanus. DNA typing methods that target gene clusters and whole genomes revealed characteristic genomic fingerprints for strain SR-1T. A small plasmid was detected by gel electrophoresis. On the basis of distinct phenotypic and genotypic characteristics, strain SR-1T represents a novel subspecies of D. africanus, for which the name Desulfovibrio africanus subsp. uniflagellum subsp. nov. is proposed. The type strain is SR-1T (=JCM 15510T =LS KCTC 5649T).
-
-
-
Acinetobacter bereziniae sp. nov. and Acinetobacter guillouiae sp. nov., to accommodate Acinetobacter genomic species 10 and 11, respectively
Acinetobacter genospecies (genomic species) 10 and 11 were described by Bouvet and Grimont in 1986 on the basis of DNA–DNA reassociation studies and comprehensive phenotypic analysis. In the present study, the names Acinetobacter bereziniae sp. nov. and Acinetobacter guillouiae sp. nov., respectively, are proposed for these genomic species based on the congruence of results of polyphasic analysis of 33 strains (16 and 17 strains of genomic species 10 and 11, respectively). All strains were investigated by selective restriction fragment amplification (i.e. AFLP) analysis rpoB sequence analysis, amplified rDNA restriction analysis and tDNA intergenic length polymorphism analysis, and their nutritional and physiological properties were determined. Subsets of the strains were studied by 16S rRNA gene sequence analysis and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS or had been classified previously by DNA–DNA reassociation. Results indicate that A. bereziniae and A. guillouiae represent two phenetically and phylogenetically distinct groups within the genus Acinetobacter. Based on the comparative analysis of housekeeping genes (16S rRNA and rpoB genes), these species together represent a monophyletic branch within the genus. Despite their overall phenotypic similarity, the ability to oxidize d-glucose and to grow at 38 °C can be used in the presumptive differentiation of these two species from each other: with the exception of three strains that were positive for only one test, A. bereziniae strains were positive for both tests, whereas A. guillouiae strains were negative in these tests. The strains of A. bereziniae originated mainly from human clinical specimens, whereas A. guillouiae strains were isolated from different environmental sources in addition to human specimens. The type strain of A. bereziniae sp. nov. is LMG 1003T (=CIP 70.12T =ATCC 17924T) and that of A. guillouiae sp. nov. is LMG 988T (=CIP 63.46T =ATCC 11171T =CCUG 2491T).
-
-
-
Kistimonas asteriae gen. nov., sp. nov., a gammaproteobacterium isolated from Asterias amurensis
More LessA novel marine bacterium, strain KMD 001T, was isolated from the starfish Asterias amurensis, which inhabits the East Sea of Korea. Strain KMD 001T was aerobic, light-yellow pigmented and Gram-stain-negative. Analyses of the 16S rRNA gene sequence revealed that strain KMD 001T represents a novel lineage within the class Gammaproteobacteria. Strain KMD 001T is closely related to the genera Endozoicomonas and Zooshikella, which belong to the family Hahellaceae and to the order Oceanospirillales. The 16S rRNA gene sequence of strain KMD 001T shows similarities of approximately 91.8–94.6 % with the above-mentioned genera. The DNA G+C content of KMD 001T is 47.6 mol%. It contains Q-9 as the major isoprenoid quinone. The predominant fatty acids were determined to be anteiso-C15 : 0, iso-C15 : 0, iso-C14 : 0 and iso-C16 : 0. Strain KMD 001T should be assigned to a novel bacterial genus within the class Gammaproteobacteria based on its phylogenetic, chemotaxonomic and phenotypic characteristics. The name Kistimonas asteriae gen. nov., sp. nov. is proposed. The type strain is KMD 001T (=KCCM 90076T =JCM 15607T).
-
-
-
Kaistia terrae sp. nov., isolated from a wetland in Korea
An ivory-coloured bacterium, designated strain 5YN7-3T, was isolated from a wetland, Yongneup, Korea. Cells of the strain were aerobic, Gram-stain-negative, non-motile and short rods. 16S rRNA gene sequence analysis demonstrated that strain 5YN7-3T belongs to the order Rhizobiales of the class Alphaproteobacteria and is closely related to Kaistia soli 5YN9-8T (97.8 %), Kaistia granuli Ko04T (97.6 %) and Kaistia adipata Chj404T (97.4 %). Strain 5YN7-3T showed DNA–DNA hybridization values of 28, 22 and 35 % with K. granuli Ko04T, K. soli 5YN9-8T and K. adipata Chj404T, respectively. The major fatty acids were C18 : 1 ω7c (51.2 %), C19 : 0 cyclo ω8c (25.0 %), C18 : 0 (12.9 %) and C16 : 0 (10.8 %) (>10 % of total fatty acids). Ubiquinone-10 was the major isoprenoid quinone and the DNA G+C content was 66.5 mol%. The phenotypic characteristics in combination with 16S rRNA gene sequence analysis and DNA–DNA hybridization data clearly define strain 5YN7-3T as a novel species of the genus Kaistia, for which the name Kaistia terrae sp. nov. is proposed. The type strain is 5YN7-3T (=KACC 12910T =DSM 21341T).
-
-
-
Mameliella alba gen. nov., sp. nov., a marine bacterium of the Roseobacter clade in the order Rhodobacterales
A Gram-negative, non-motile, rod-shaped bacterial strain, JLT354-WT, that accumulates poly-β-hydroxybutyrate granules was isolated from the South China Sea. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain was related to members of the genera Antarctobacter, Sagittula, Oceanicola and Loktanella; levels of similarity between strain JLT354-WT and members of the above genera were less than 92.0 %. The predominant fatty acid of strain JLT354-WT was C18 : 1 ω7c (83.1 %); significant amounts of C18 : 0 (7.9 %) and C12 : 1 3-OH (3.7 %) were also present. The predominant respiratory ubiquinone was Q-10. The DNA G+C content of strain JLT354-WT was 63.7 mol%. The isolate was distinguishable from members of the order Rhodobacterales based on phenotypic and biochemical characteristics. On the basis of the taxonomic data presented, strain JLT354-WT is considered to represent a novel species of a new genus, for which the name Mameliella alba gen. nov., sp. nov. is proposed. The type strain of Mameliella alba is JLT354-WT (=LMG 24665T=CGMCC 1.7290T).
-
-
-
Mesorhizobium alhagi sp. nov., isolated from wild Alhagi sparsifolia in north-western China
More LessEleven strains that formed symbiotic root nodules on Alhagi sparsifolia, designated previously as genospecies II, were identified as a new lineage of Mesorhizobium (Alphaproteobacteria) that could be differentiated from all previously recognized species of the genus Mesorhizobium by using 16S rRNA gene sequences (<97.8 % similarity), DNA–DNA hybridization (<45 %), dnaJ, dnaK, recA, glnA, nifH, nodA and nodC gene sequences, fatty acid profiles (C18 : 1 ω7c, 35 %;11-methyl C18 : 1 ω7c, 30 %) and numerical taxonomy. These strains are therefore considered to represent a novel species, for which the name Mesorhizobium alhagi sp. nov. is proposed, with isolate CCNWXJ12-2T (=ACCC 15461T=HAMBI 3019T) as the type strain.
-
-
-
Taxonomic study of the genus Salinicola: transfer of Halomonas salaria and Chromohalobacter salarius to the genus Salinicola as Salinicola salarius comb. nov. and Salinicola halophilus nom. nov., respectively
More LessWe have carried out a polyphasic taxonomic characterization of the type strains of the species with the recently validated name Salinicola socius, together with two species that were phylogenetically closely related, Halomonas salaria and Chromohalobacter salarius. 16S rRNA gene sequence analyses showed that they constituted a coherent cluster, with sequence similarities between 98.7 and 97.7 %. We have determined the almost complete 23S rRNA gene sequences of these three type strains, and the percentage of similarity between them was 99.2–97.6 %. Phylogenetic trees based on the 16S rRNA and 23S rRNA gene sequences, obtained by using three different algorithms, were consistent and showed that these three species constituted a cluster separated from the other species of the genera of the family Halomonadaceae, supporting their placement in a single genus. All three species have ubiquinone 9 as the major respiratory quinone, and showed similar fatty acid and polar lipid profiles. The level of DNA–DNA hybridization between Salinicola socius DSM 19940T, Halomonas salaria DSM 18044T and Chromohalobacter salarius CECT 5903T was 41–21 %, indicating that they are different species of the genus Salinicola. A comparative phenotypic study of these strains following the proposed minimal standards for describing new taxa of the family Halomonadaceae has been carried out. The phenotypic data are consistent with the placement of these three species in a single genus and support their differentiation at the species level. On the basis of these data we have emended the description of the species Salinicola socius and we propose to transfer the species Halomonas salaria and Chromohalobacter salarius to the genus Salinicola, as Salinicola salarius comb. nov. (type strain M27T =KCTC 12664T =DSM 18044T) and Salinicola halophilus nom. nov. (type strain CG4.1T =CECT 5903T =LMG 23626T), respectively.
-
-
-
Granulosicoccus coccoides sp. nov., isolated from leaves of seagrass (Zostera marina)
A non-pigmented, motile, Gram-negative bacterium, strain Z 271T, was isolated from the surface of leaves of the seagrass Zostera marina which was collected in Troitza Bay (Sea of Japan, Pacific Ocean). The new isolate grew between 5 °C and 28 °C and was slightly halophilic, tolerating environments containing up to 5 % (w/v) NaCl. Strain Z 271T was able to degrade Tweens 20, 40 and 80 and partially degrade gelatin, but was unable to degrade casein. Phosphatidylethanolamine (36.9 %) and phosphatidylglycerol (63.1 %) were the predominant phospholipids. The major fatty acids included C18 : 1 ω7c (43.7 %), C16 : 1 ω7c (31.1 %) and C16 : 0 (16.8 %). The main respiratory quinone was Q-8. The DNA–DNA relatedness value of strain Z 271T with Granulosicoccus antarcticus IMCC3135T was 35 %. The G+C content of the DNA of strain Z 271T was 60.2 mol%. On the basis of phenotypic and genotypic characteristics and 16S rRNA gene sequence analysis, strain Z 271T represents a novel species of the genus Granulosicoccus for which the name Granulosicoccus coccoides sp. nov. is proposed. The type strain is Z 271T (=KMM 6014T=CIP 109923T).
-
-
-
Rickettsia hoogstraalii sp. nov., isolated from hard- and soft-bodied ticks
A novel spotted fever group Rickettsia was found in Haemaphysalis sulcata ticks collected from sheep and goats in Croatia in 2006. At the same time, a genetically identical organism was co-isolated with the embryonic cell line CCE3 obtained from the soft tick Carios capensis in Georgia, USA. In this study, further phenotypic and genotypic characteristics of the novel rickettsial strain present in H. sulcata ticks were investigated. Based on the cultivation of bacteria in mosquito and Vero cell cultures, the presence of rickettsiae in tick tissues and cell cultures [confirmed by transmission electron microscopy (TEM)] and the amplification and sequencing of five rickettsial genes, it was demonstrated that the novel Rickettsia strain fulfils the criteria to be classified as a novel species. The name Rickettsia hoogstraalii sp. nov. is proposed for the new strain. Rickettsia hoogstraalii sp. nov., an obligately intracellular bacterium, was grown in Vero cells and arthropod CCE3, ISE6 and C6/36 cell lines. The morphology of the cells of the novel species was typical of SFG rickettsiae. The small coccobacillary appearance of the bacteria was apparent with light microscopy. A Gram-negative bacterial cell wall and a cytoplasmic membrane separated by a narrow periplasmic space were visible by TEM. To date, Rickettsia hoogstraalii sp. nov. has been isolated from two species of ticks, H. sulcata and C. capensis. The novel species appears to be geographically widely distributed, having been detected in Croatia, Spain and Georgia, USA. Although no information is available regarding the possible pathogenicity of the novel species for vertebrate hosts, R. hoogstraalii sp. nov. has a cytopathic effect in Vero, CCE3 and ISE6 cells. Sequence analyses of the 16S rRNA, 17 kDa, gltA, ompA and ompB genes indicated that even though R. hoogstraalii sp. nov. was closely related to Rickettsia felis, it represents a separate species within the spotted fever group. The type strain of R. hoogstraalii sp. nov. is strain CroaticaT (=DSM 22243T=UTMB 00003T).
-
- Eukaryotic Micro-Organisms
-
-
Cryptococcus agrionensis sp. nov., a basidiomycetous yeast of the acidic rock drainage ecoclade, isolated from an acidic aquatic environment of volcanic origin
Seventy-one strains were isolated from the River Agrio–Lake Caviahue acidic aquatic environment in Argentina. Strains were isolated mainly from the most acidic section of the river (pH 1.8–2.7). According to the mini/microsatellite-primed PCR technique and physiological data, these strains are representatives of a single novel species of the genus Cryptococcus. Analysis of the D1/D2 region of the large-subunit rRNA gene showed that the strains belong to the order Filobasidiales of the subphylum Agaricomycotina. The novel isolates formed a phylogenetic group with Cryptococcus ibericus, Cryptococcus aciditolerans and Cryptococcus metallitolerans, the most closely related species. This group, which is phylogenetically related to the Gastricus clade, is considered to be an ecoclade due to its peculiar ecology and physiology. The name Cryptococcus agrionensis sp. nov. is proposed to accommodate these isolates, with strain CRUB 1317T (=CBS 10799T=JCM 15321T) as the type strain.
-
Volumes and issues
-
Volume 74 (2024)
-
Volume 73 (2023)
-
Volume 72 (2022 - 2023)
-
Volume 71 (2020 - 2021)
-
Volume 70 (2020)
-
Volume 69 (2019)
-
Volume 68 (2018)
-
Volume 67 (2017)
-
Volume 66 (2016)
-
Volume 65 (2015)
-
Volume 64 (2014)
-
Volume 63 (2013)
-
Volume 62 (2012)
-
Volume 61 (2011)
-
Volume 60 (2010)
-
Volume 59 (2009)
-
Volume 58 (2008)
-
Volume 57 (2007)
-
Volume 56 (2006)
-
Volume 55 (2005)
-
Volume 54 (2004)
-
Volume 53 (2003)
-
Volume 52 (2002)
-
Volume 51 (2001)
-
Volume 50 (2000)
-
Volume 49 (1999)
-
Volume 48 (1998)
-
Volume 47 (1997)
-
Volume 46 (1996)
-
Volume 45 (1995)
-
Volume 44 (1994)
-
Volume 43 (1993)
-
Volume 42 (1992)
-
Volume 41 (1991)
-
Volume 40 (1990)
-
Volume 39 (1989)
-
Volume 38 (1988)
-
Volume 37 (1987)
-
Volume 36 (1986)
-
Volume 35 (1985)
-
Volume 34 (1984)
-
Volume 33 (1983)
-
Volume 32 (1982)
-
Volume 31 (1981)
-
Volume 30 (1980)
-
Volume 29 (1979)
-
Volume 28 (1978)
-
Volume 27 (1977)
-
Volume 26 (1976)
-
Volume 25 (1975)
-
Volume 24 (1974)
-
Volume 23 (1973)
-
Volume 22 (1972)
-
Volume 21 (1971)
-
Volume 20 (1970)
-
Volume 19 (1969)
-
Volume 18 (1968)
-
Volume 17 (1967)
-
Volume 16 (1966)
-
Volume 15 (1965)
-
Volume 14 (1964)
-
Volume 13 (1963)
-
Volume 12 (1962)
-
Volume 11 (1961)
-
Volume 10 (1960)
-
Volume 9 (1959)
-
Volume 8 (1958)
-
Volume 7 (1957)
-
Volume 6 (1956)
-
Volume 5 (1955)
-
Volume 4 (1954)
-
Volume 3 (1953)
-
Volume 2 (1952)
-
Volume 1 (1951)