- Volume 57, Issue 12, 2007
Volume 57, Issue 12, 2007
- Notification List
-
-
-
Notification that new names and new combinations have appeared in volume 57, part 9, 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
-
-
Tetrasphaera remsis sp. nov., isolated from the Regenerative Enclosed Life Support Module Simulator (REMS) air system
Two Gram-positive, coccoid, non-spore-forming bacteria (strains 3-M5-R-4T and 3-M5-R-7), cells of which formed diploid, tetrad and cluster arrangements, were isolated from air of the Regenerative Enclosed Life Support Module Simulator system. On the basis of 16S rRNA gene sequence similarity, these strains were shown to belong to the family Intrasporangiaceae and were related to members of the genus Tetrasphaera, with similarities to the seven known species of the genus Tetrasphaera of 96.71–97.76 %. The fatty acid profile supported affiliation of these novel isolates to the genus Tetrasphaera, although larger amounts of octadecanoic acid (C18 : 0) and cis-9-octadecenoic acid (C18 : 1) were observed in the isolates, thus enabling them to be differentiated from other Tetrasphaera species. In addition, DNA–DNA hybridization studies indicated that these strains belonged to a novel species that could be readily distinguished from its nearest neighbour, Tetrasphaera japonica DSM 13192T, which had less than 20 % DNA–DNA relatedness. Physiological and biochemical tests showed few phenotypic differences, but genotypic analysis enabled these gelatin-liquefying strains to be differentiated from the seven Tetrasphaera species. The strains described in this study therefore represent a novel species, for which the name Tetrasphaera remsis sp. nov. is proposed; the type strain is 3-M5-R-4T (=ATCC BAA-1496T =CIP 109413T).
-
-
-
Rhodococcus qingshengii sp. nov., a carbendazim-degrading bacterium
More LessA Gram-positive, aerobic, non-motile, mesophilic strain, djl-6T, able to degrade carbendazim, was isolated from a carbendazim-contaminated soil sample from Jiangsu province, China. The taxonomic position of this isolate was analysed by using a polyphasic approach. Chemotaxonomic analysis including peptidoglycan type, diagnostic sugar composition, fatty acid profile, menaquinones, polar lipids and mycolic acids showed that the characteristics of strain djl-6T were in good agreement with those of the genus Rhodococcus. DNA–DNA hybridization showed that it had low genomic relatedness with Rhodococcus baikonurensis DSM 44587T (31.8 %), Rhodococcus erythropolis DSM 43066T (23.8 %) and Rhodococcus globerulus DSM 43954T (17.7 %), the three type strains to which strain djl-6T was most closely related based on 16S rRNA gene sequence analysis (99.78, 99.25 and 98.91 % similarity, respectively). Based on the phenotypic properties and DNA–DNA hybridization data, strain djl-6T (=CGMCC 1.6580T =KCTC 19205T) is proposed as the type strain of a novel Rhodococcus species, Rhodococcus qingshengii sp. nov.
-
-
-
Proposal of Umezawaea gen. nov., a new genus of the Actinosynnemataceae related to Saccharothrix, and transfer of Saccharothrix tangerinus Kinoshita et al. 2000 as Umezawaea tangerina gen. nov., comb. nov.
More LessIn the course of phylogenetic analyses of the taxa within the suborder Pseudonocardineae, it was observed that Saccharothrix tangerinus MK27-91F2T was misplaced in the genus Saccharothrix. After a detailed examination of nucleotide signatures in the 16S rRNA gene sequence along with the morphological and chemotaxonomic characteristics of this strain, which are different from those of all species of Saccharothrix as well as the other genera within the suborder, it was concluded that this strain represents a new genus, for which the name Umezawaea gen. nov. is proposed. Pseudosporangia are produced on the aerial mycelium, the whole-cell sugar pattern consists of galactose, mannose and ribose, phosphatidylethanolamine, phosphatidylinositol and lyso-phosphatidylethanolamine are the predominant phospholipids and MK-9(H4) is the predominant menaquinone. The type species of the proposed new genus is Umezawaea tangerina gen. nov., comb. nov., with the type strain MK27-91F2T (=NRRL B-24463T =DSM 44720T =FERM P-16053T =JCM 10302T =NBRC 16184T).
-
-
-
Leucobacter chromiireducens subsp. solipictus subsp. nov., a pigmented bacterium isolated from the nematode Caenorhabditis elegans, and emended description of L. chromiireducens
More LessA yellow-pigmented, Gram-positive, aerobic, non-motile, non-spore-forming, irregular rod-shaped bacterium (strain TAN 31504T) was isolated from the bacteriophagous nematode Caenorhabditis elegans. Based on 16S rRNA gene sequence similarity, DNA G+C content of 69.5 mol%, 2,4-diaminobutyric acid in the cell-wall peptidoglycan, major menaquinone MK-11, abundance of anteiso- and iso-fatty acids, polar lipids diphosphatidylglycerol and phosphatidylglycerol and a number of shared biochemical characteristics, strain TAN 31504T was placed in the genus Leucobacter. DNA–DNA hybridization comparisons demonstrated a 91 % DNA–DNA relatedness between strain TAN 31504T and Leucobacter chromiireducens LMG 22506T indicating that these two strains belong to the same species, when the recommended threshold value of 70 % DNA–DNA relatedness for the definition of a bacterial species by the ad hoc committee on reconciliation of approaches to bacterial systematics is considered. Based on distinct differences in morphology, physiology, chemotaxonomic markers and various biochemical characteristics, it is proposed to split the species L. chromiireducens into two novel subspecies, Leucobacter chromiireducens subsp. chromiireducens subsp. nov. (type strain L-1T=CIP 108389T=LMG 22506T) and Leucobacter chromiireducens subsp. solipictus subsp. nov. (type strain TAN 31504T=DSM 18340T=ATCC BAA-1336T).
-
-
-
Lapillicoccus jejuensis gen. nov., sp. nov., a novel actinobacterium of the family Intrasporangiaceae, isolated from stone
More LessA novel, yellow-pigmented actinobacterium was isolated from a small stone collected in Jeju, Republic of Korea. The cells of the organism, designated strain R-Ac013T, were Gram-positive, aerobic, non-motile cocci that occurred singly or in pairs. The strain showed growth at 10–37 °C and pH 4.1–11.1, and tolerated 2 % NaCl. On the basis of the 16S rRNA gene sequence, the organism was phylogenetically related to members of the genera Tetrasphaera (94.6–97.1 % sequence similarity), Terrabacter (96.5 %), Knoellia (96.4 %), Terracoccus (96.4 %), Oryzihumus (96.4 %), Janibacter (96.1–96.4 %) and Intrasporangium (96.2 %). The chemotaxonomic results for the organism were as follows: ll-diaminopimelic acid as the diagnostic diamino acid in the peptidoglycan, acetyl-type murein, MK-8(H4) as the major menaquinone, a DNA G+C content of 74.1 mol%, and a polar lipid profile that comprised diphosphatidylglycerol and phosphatidylinositol. The fatty acid profile consisted of iso- and anteiso-methyl-branched, straight-chain saturated and monounsaturated types, the major components being iso-C16 : 0, C17 : 1 ω8c and iso-C15 : 0. The combination of the phenotypic and phylogenetic data revealed that this strain represents a novel genus and species of the family Intrasporangiaceae, for which the name Lapillicoccus jejuensis gen. nov., sp. nov. is proposed. The type strain is strain R-Ac013T (=KCTC 19200T=DSM 18607T).
-
-
-
Micromonospora lupini sp. nov. and Micromonospora saelicesensis sp. nov., isolated from root nodules of Lupinus angustifolius
A study was conducted to determine the taxonomic status of six actinomycete strains isolated from root nodules of Lupinus angustifolius. The strains were filamentous, Gram-positive and produced single spores at the tip of the hyphae. Phylogenetic, chemotaxonomic and morphological analyses demonstrated that all six strains belonged to the genus Micromonospora. According to the 16S rRNA gene sequence data, the strains were divided into two clusters that are moderately related to Micromonospora mirobrigensis, Micromonospora matsumotoense and Micromonospora purpureochromogenes. Fatty acid patterns also supported the division of the strains, and significant differences between the two groups were found in the amounts of iso-15 : 0, iso-16 : 0, iso-16 : 1 and iso-17 : 0. Furthermore, the two groups showed physiological differences which included utilization of arabinose, trehalose, alanine and sucrose and xylan hydrolysis. Finally, DNA–DNA hybridization and ribotyping studies confirmed that each group represents a novel species. Based on the genotypic and phenotypic data, the novel species Micromonospora lupini sp. nov. (type strain Lupac 14NT =DSM 44874T =LMG 24055T) and Micromonospora saelicesensis sp. nov. (type strain Lupac 09T =DSM 44871T =LMG 24056T) are proposed.
-
-
-
Lechevalieria xinjiangensis sp. nov., a novel actinomycete isolated from radiation-polluted soil in China
A novel actinomycete was isolated from radiation-polluted soil collected from Xinjiang in north-western China. The isolate, strain R24T, was found to have chemical and morphological properties associated with members of the genus Lechevalieria. An almost-complete 16S rRNA gene sequence of the isolate was aligned with corresponding sequences from representatives of the genus Lechevalieria and related taxa, using three tree-making algorithms, and was shown to form a distinct phyletic line in the Lechevalieria phylogenetic tree. DNA–DNA relatedness and phenotypic data served to distinguish strain R24T from members of the three Lechevalieria species with validly published names. The genotypic and phenotypic data show that the isolate should be classified as a novel species within the genus Lechevalieria. The name proposed for this taxon is Lechevalieria xinjiangensis sp. nov. The type strain is R24T (=CGMCC 4.3525T=DSM 45081T).
-
-
-
Knoellia aerolata sp. nov., isolated from an air sample in Korea
An aerobic, Gram-positive, non-motile, non-spore-forming, rod–coccus-shaped bacterium, strain 5317S-21T, was isolated from an air sample from Suwon city, Republic of Korea. The isolate was able to grow within a pH range of 5.0–9.0 and a temperature range of 5–35 °C and it tolerated up to 2 % (w/v) NaCl. The cell-wall peptidoglycan contained meso-diaminopimelic acid as diagnostic diamino acid. The predominant isoprenoid quinone was MK-8(H4). The major polar lipids were phosphatidylinositol, phosphatidylethanolamine and diphosphatidylglycerol; phosphatidylglycerol and several unknown phospholipids were also detected. Mycolic acids were absent. The only whole-cell sugar was glucose. The major cellular fatty acids were iso-C16 : 0, C17 : 1 ω8c and iso-C15 : 0. 16S rRNA gene sequence analysis indicated that strain 5317S-21T was related phylogenetically to members of the genus Knoellia, with 97.4 % sequence similarity to the type strains of Knoellia sinensis and Knoellia subterranea. The G+C content of the genomic DNA of strain 5317S-21T was 73 mol%. Levels of DNA–DNA relatedness between strain 5317S-21T and the type strains of Knoellia sinensis and Knoellia subterranea were 37 and 41 %, respectively. It was concluded that strain 5317S-21T represents a novel species of the genus Knoellia, for which the name Knoellia aerolata sp. nov. is proposed. The type strain is 5317S-21T (=KACC 20583T =DSM 18566T).
-
-
-
Nocardia speluncae sp. nov., isolated from a cave
More LessThe taxonomic status of a mycolic acid-containing actinomycete, isolated from a natural cave on Jeju Island, Republic of Korea, was investigated by means of a polyphasic approach. The isolate, designated strain N2-11T, produced yellow- to orange-coloured vegetative hyphae and white- to pinkish white-coloured aerial mycelia, both of which fragmented into irregular rod-shaped elements. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the organism belonged to the family Nocardiaceae, occupying a distinct position between Nocardia harenae and a Nocardia carnea cluster. The results of chemotaxonomic analyses were consistent with the affiliation of the organism with the genus Nocardia. On the basis of 16S rRNA gene sequence similarities, the closest phylogenetic neighbours were the type strains of N. carnea (98.3 %), Nocardia flavorosea (98.0 %), Nocardia sienata (97.9 %) and Nocardia testacea (97.8 %), but the organism could be clearly distinguished from its phylogenetic relatives with reference to a broad range of physiological markers. On the basis of phenotypic and molecular genetic data presented in this study, strain N2-11T represents a novel species of the genus Nocardia, for which the name Nocardia speluncae sp. nov. is proposed. The type strain is N2-11T (=JBRI 2006T =KCTC 19223T =DSM 45078T).
-
-
-
Nocardioides marinisabuli sp. nov., a novel actinobacterium isolated from beach sand
More LessThe taxonomic position of a novel actinobacterium (designated SBS-12T), which was isolated from beach sand on Jeju Island, Republic of Korea, was determined following a polyphasic taxonomic characterization. Cells of the organism were Gram-positive, catalase-positive, oxidase-negative and non-motile rods. The organism contained ll-diaminopimelic acid in the cell-wall peptidoglycan and MK-8(H4) as predominant menaquinone, and had a polar lipid profile containing phosphatidylglycerol and phosphatidylinositol, iso-C16 : 0 as the major fatty acid and a DNA G+C content of 73.1 mol%. A neighbour-joining tree based on 16S rRNA gene sequences showed that the organism occupies a distinct phylogenetic position within the radiation including representatives of the family Nocardioidaceae. High levels of 16S rRNA gene sequence similarity were found with Nocardioides kribbensis (97.2 %), Nocardioides aquiterrae (96.9 %), Nocardioides pyridinolyticus (96.6 %) and Nocardioides aquaticus (96.3 %). The combination of morphological and chemotaxonomic characteristics was consistent with classification in the genus Nocardioides, but the isolate can be differentiated from all Nocardioides species with validly published names by a range of physiological properties. The name Nocardioides marinisabuli sp. nov. is proposed for this novel organism, with the type strain SBS-12T (=JBRI 2003T=KCCM 42681T=DSM 18965T).
-
- Archaea
-
-
Methermicoccus shengliensis gen. nov., sp. nov., a thermophilic, methylotrophic methanogen isolated from oil-production water, and proposal of Methermicoccaceae fam. nov.
More LessA thermophilic, methylotrophic methanogen, strain ZC-1T, was isolated from the Shengli oilfield, China. Cells of strain ZC-1T were motile cocci, 0.7–1.0 μm in diameter and always occurred in clusters of two to four cells. Lysis-susceptibility experiments and analysis of transmission electron micrographs of strain ZC-1T suggested the presence of a proteinaceous cell wall. Strain ZC-1T used methanol, methylamine and trimethylamine as substrates for methanogenesis. Optimal growth, with a doubling time of around 5 h, occurred at pH 6.0–6.5, 65 °C, 0.3–0.5 M NaCl and 0.05–0.20 M MgCl2. The DNA G+C content of this organism was 56 mol%. Analysis of 16S rRNA gene sequence and the inferred amino acid sequence of the mcrA gene of strain ZC-1T indicated that it is related specifically to members of the family Methanosaetaceae (90.6 and 76.6 % sequence similarity, respectively). However, strain ZC-1T failed to grow with acetate as substrate for methanogenesis, which is a special characteristic of the family Methanosaetaceae. Based on these phenotypic and phylogenic characteristics, strain ZC-1T is proposed to represent a novel genus and species, for which the name Methermicoccus shengliensis gen. nov., sp. nov. is proposed. The type strain is ZC-1T (=CGMCC 1.5056T=DSM 18856T). Methermicoccaceae fam. nov. is also proposed.
-
- Bacteroidetes
-
-
Salegentibacter salarius sp. nov., isolated from a marine solar saltern
More LessA Gram-negative, non-motile, rod-shaped bacterium, strain ISL-6T, phenotypically resembling members of the genus Salegentibacter, was isolated from a marine solar saltern of the Yellow Sea in Korea and subjected to a polyphasic taxonomic investigation. Strain ISL-6T grew optimally at pH 7.0–8.0 and 30 °C and in the presence of 8 % (w/v) NaCl. It contained MK-6 as the predominant menaquinone. The major fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The DNA G+C content was 37.5 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain ISL-6T belonged to the genus Salegentibacter. Strain ISL-6T exhibited 16S rRNA gene sequence similarity values of 92.0–98.6 % with respect to the type strains of recognized Salegentibacter species. Low DNA–DNA relatedness values, differential phenotypic properties and phylogenetic distinctiveness demonstrated that strain ISL-6T is distinguishable from the recognized Salegentibacter species. Therefore strain ISL-6T represents a novel species of the genus Salegentibacter, for which the name Salegentibacter salarius sp. nov. is proposed. The type strain is ISL-6T (=KCTC 12974T =CCUG 54355T).
-
-
-
Lewinella agarilytica sp. nov., a novel marine bacterium of the phylum Bacteroidetes, isolated from beach sediment
More LessA Gram-negative, aerobic, light-orange-coloured, marine bacterium (designated SST-19T) was isolated from beach sediment in Jeju, Korea, and its taxonomic position was determined by means of a polyphasic approach. In a neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, strain SST-19T was positioned within the family ‘Saprospiraceae’, class Sphingobacteria, and formed a consistent cluster with Lewinella persica ATCC 23167T (94.7 % sequence similarity). The levels of 16S rRNA gene sequence similarity between the isolate and recognized members of the family ranged from 84 to 89 %, with Lewinella cohaerens ATCC 23123T, Lewinella nigricans ATCC 23147T, Haliscomenobacter hydrossis DSM 1100T and Saprospira grandis ATCC 23119T showing values of 89.0 , 88.4 , 86.4 and 84.1 %, respectively. Strain SST-19T required seawater for growth and its cells were unbranched, flexible rods or filaments with gliding motility. The cellular fatty acids consisted mainly of saturated, unsaturated and iso-branched fatty acids, the major components being C16 : 1 ω7c and/or iso-C15 : 0 2-OH (24.1 %), C18 : 0 (13.5 %), iso-C15 : 0 (11.1 %) and C16 : 0 (10.9 %). The G+C content of the DNA was found to be 51.3 mol%. On the basis of the results from phenotypic and phylogenetic analyses, the isolate represents a novel species of the genus Lewinella, for which the name Lewinella agarilytica sp. nov. is proposed. The type strain is SST-19T (=JBRI 2009T=KCTC 12774T=JCM 14216T).
-
-
-
Maribacter polysiphoniae sp. nov., isolated from a red alga
A novel gliding, heterotrophic, Gram-negative, yellow–orange-pigmented, aerobic, oxidase- and catalase-positive bacterium, designated strain KMM 6151T, was isolated from the Pacific red alga Polysiphonia japonica. Analysis of the 16S rRNA gene sequence of the strain revealed that it formed a distinct lineage within the genus Maribacter, family Flavobacteriaceae, with sequence similarities in the range 94.6–96.9 %. On the basis of phenotypic, genotypic and phylogenetic data, strain KMM 6151T represents a novel species of the genus Maribacter, for which the name Maribacter polysiphoniae sp. nov. is proposed. The type strain is KMM 6151T (=KCTC 22021T=LMG 23671T).
-
-
-
Spirosoma rigui sp. nov., isolated from fresh water
A Gram-negative, yellow-pigmented bacterium capable of gliding motility, designated strain WPCB118T, was isolated from fresh water collected from the Woopo wetland (Republic of Korea). Cells were rod-shaped and sometimes filamentous. The major fatty acids were iso-C15 : 0 2-OH and/or C16 : 1 ω7c (45.6 %), C16 : 1 ω5c (18.5 %), iso-C15 : 0 (9.5 %) and C16 : 0 (8.8 %). The predominant menaquinone and polar lipid were MK-7 and phosphatidylethanolamine, respectively. The DNA G+C content was 53.3 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain WPCB118T had an evolutionary lineage within the radiation encompassing the members of the family ‘Flexibacteraceae’, its closest neighbour being Spirosoma linguale LMG 10896T (93.7 % gene sequence similarity). Data from this polyphasic study indicated that strain WPCB118T could not be assigned to any recognized species. Strain WPCB118T represents a novel species of the genus Spirosoma, for which the name Spirosoma rigui sp. nov. is proposed. The type strain is WPCB118T (=KCTC 12531T=NBRC 101117T).
-
-
-
Sejongia marina sp. nov., isolated from Antarctic seawater
More LessA Gram-negative, psychrotolerant, chemoheterotrophic, aerobic, non-gliding, non-motile, yellow-pigmented bacterium, designated IMCC3228T, was isolated from coastal seawater of the Antarctic. On the basis of 16S rRNA gene sequence comparisons, the strain was most closely related to the genera Sejongia (95.3–96.1 %) and Chryseobacterium (94.2–95.9 %) in the family Flavobacteriaceae. Phylogenetic trees generated using several treeing algorithms based on 16S rRNA gene sequences showed that this Antarctic marine isolate formed a distinct phyletic line within the genus Sejongia. The DNA G+C content of the strain was 35.0 mol% and the major respiratory quinone was MK-6. Several phenotypic and chemotaxonomic characteristics, including temperature and NaCl optima for growth, oxidase activity and the proportions of major cellular fatty acids, served to differentiate the strain from the recognized species of the genus Sejongia. Therefore strain IMCC3228T represents a novel species of the genus Sejongia, for which the name Sejongia marina sp. nov. is proposed. The type strain is IMCC3228T (=KCCM 42689T=NBRC 103143T).
-
-
-
Ulvibacter antarcticus sp. nov., isolated from Antarctic coastal seawater
More LessA seawater bacterium, designated IMCC3101T, was isolated from Antarctic coastal seawater. The strain was Gram-negative, chemoheterotrophic, obligately aerobic, pigmented dark yellow (flexirubin-type pigments) and devoid of gliding and flagellar motility. On the basis of 16S rRNA gene sequence comparisons, the most closely related species was Ulvibacter litoralis (96.6 %). Phylogenetic trees generated by using 16S rRNA gene sequences confirmed that the strain belonged to the genus Ulvibacter in the family Flavobacteriaceae. The DNA G+C content was 37.0 mol% and the major respiratory quinone was MK-6. Several phenotypic characteristics, including cell and colony morphology, the absence of gliding motility and the temperature range for growth, serve to differentiate the strain from the only species in the genus Ulvibacter with a validly published name (U. litoralis). Therefore, strain IMCC3101T represents a novel species of the genus Ulvibacter, for which the name Ulvibacter antarcticus sp. nov. is proposed. The type strain is IMCC3101T (=KCCM 42686T=NBRC 102682T).
-
-
-
Prevotella maculosa sp. nov., isolated from the human oral cavity
More LessThree strains of anaerobic Gram-negative bacilli isolated from human oral sites were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise a homogeneous group. 16S rRNA gene sequence analysis revealed the strains to constitute a novel group within the genus Prevotella, most closely related to Prevotella oris and Prevotella salivae. A novel species, Prevotella maculosa sp. nov., is proposed to accommodate these strains. Prevotella maculosa is saccharolytic and produces acetic and succinic acids as end products of fermentation. The G+C content of the DNA of the type strain is 48 mol%. The type strain of Prevotella maculosa is W1609T (=DSM 19339T =CCUG 54766T).
-
-
-
Emended descriptions of the genus Lewinella and of Lewinella cohaerens, Lewinella nigricans and Lewinella persica, and description of Lewinella lutea sp. nov. and Lewinella marina sp. nov.
More LessTwo strains, MKG-38T and FYK2402M69T, were isolated from a marine sediment sample and a sea snail, respectively, both collected on the Pacific coast of Japan. Phylogeny of these new isolates based on 16S rRNA gene sequences indicated that they are members of the genus Lewinella. Morphological, physiological and biochemical properties of these two isolates, together with the type strains of the three previously described species of the genus Lewinella, were characterized. The new isolates were Gram-negative, aerobic, rod-shaped, chemo-organotrophic and able to degrade starch and CM-cellulose. A comparative polyphasic study showed that these two isolates represent two novel species of the genus Lewinella, for which the names Lewinella marina sp. nov. (type strain, MKG-38T=NBRC 102633T=NCIMB 14312T) and Lewinella lutea sp. nov. (type strain, FYK2402M69T=NBRC 102634T=NCIMB 14313T) are proposed. Emended descriptions of the genus Lewinella ( Sly et al. 1998 ) and of Lewinella cohaerens, Lewinella nigricans and Lewinella persica are also proposed.
-
- Other Bacteria
-
-
Jonquetella anthropi gen. nov., sp. nov., the first member of the candidate phylum ‘Synergistetes’ isolated from man
Six clinical isolates of a hitherto unknown, strictly anaerobic, Gram-negative rod showing fastidious growth were subjected to a polyphasic taxonomic study, including phenotypic, genomic and phylogenetic feature analyses. 16S rRNA gene sequenced-based phylogeny revealed that the novel strains represent a homogeneous group distant from any recognized species in the candidate phylum ‘Synergistetes’. The novel isolates were most closely related to species of the genus Dethiosulfovibrio, with 88.2–88.7 % 16S rRNA gene sequence similarity. Large-scale chromosome structure and DNA G+C content also differentiated the novel strains from members of the genus Dethiosulfovibrio. The novel strains were asaccharolytic. Major metabolic end products in trypticase/glucose/yeast extract broth were acetic, lactic, succinic and isovaleric acids and the major cellular fatty acids iso-C15 : 0 and C16 : 0. Based on the data presented here, a new genus, Jonquetella gen. nov., is proposed with one novel species, Jonquetella anthropi sp. nov. J. anthropi is the first characterized species of the candidate phylum ‘Synergistetes’ that includes human isolates. The G+C content of the DNA of the type strain of J. anthropi ADV 126T (=AIP 136.05T=CIP 109408T=CCUG 53819T) is 59.4 mol%.
-
-
-
Pelagicoccus croceus sp. nov., a novel marine member of the family Puniceicoccaceae within the phylum ‘Verrucomicrobia’ isolated from seagrass
More LessAn obligately aerobic, spherical, non-motile, pale-yellow pigmented bacterium was isolated from a piece of leaf of seagrass, Enhalus acoroides (L.f.) Royle, grown in Okinawa, Japan and was subjected to a polyphasic taxonomic study. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the novel isolate N5FB36-5T shared approximately 96–98 % sequence similarity with the species of the genus Pelagicoccus of the family Puniceicoccaceae within the phylum ‘Verrucomicrobia’. The DNA–DNA relatedness values of strain N5FB36-5T with Pelagicoccus mobilis 02PA-Ca-133T and Pelagicoccus albus YM14-201T were below 70 %, which is accepted as the phylogenetic definition of a novel species. β-Lactam antibiotic susceptibility test and amino acid analysis of the cell wall hydrolysates indicated the absence of muramic acid and diaminopimelic acid in the cell walls, which suggested that this strain lacks an ordinary Gram-negative type of peptidoglycan in the cell wall. The DNA G+C content of strain N5FB36-5T was 51.6 mol%; MK-7 was the major menaquinone; and the presence of C16 : 0, C16 : 1 ω7c and anteiso-C15 : 0 as the major cellular fatty acids supported the identification of the novel isolate as a member of the genus Pelagicoccus. On the basis of polyphasic taxonomic data, it was concluded that this strain should be classified as a novel species of the genus Pelagicoccus, for which the name Pelagicoccus croceus sp. nov. is proposed. The type strain is N5FB36-5T (=MBIC08282T=KCTC 12903T).
-
- Proteobacteria
-
-
Methylohalomonas lacus gen. nov., sp. nov. and Methylonatrum kenyense gen. nov., sp. nov., methylotrophic gammaproteobacteria from hypersaline lakes
Aerobic enrichment at 4 M NaCl, pH 7.5, with methanol as carbon and energy source from sediments of hypersaline chloride–sulfate lakes in Kulunda Steppe (Altai, Russia) resulted in the isolation of a moderately halophilic and obligately methylotrophic bacterium, strain HMT 1T. The bacterium grew with methanol and methylamine within a pH range of 6.8–8.2 with an optimum at pH 7.5 and at NaCl concentrations of 0.5–4 M with an optimum at 2 M. In addition to methanol and methylamine, it can oxidize ethanol, formate, formaldehyde and dimethylamine. Carbon is assimilated via the serine pathway. The main compatible solute is glycine betaine. 16S rRNA gene sequence analysis placed the isolate as a new lineage in the family Ectothiorhodospiraceae (Gammaproteobacteria). It is proposed, therefore, to accommodate this bacterium within a novel genus and species, Methylohalomonas lacus gen. nov., sp. nov., with HMT 1T (=DSM 15733T =NCCB 100208T =UNIQEM U237T) as the type strain. Two strains were obtained in pure culture from sediments of soda lake Magadi in Kenya and the Kulunda Steppe (Russia) on a mineral medium at pH 10 containing 0.6 M total Na+ using methanol as a substrate. Strain AMT 1T was enriched with methanol, while strain AMT 3 originated from an enrichment culture with CO. The isolates are restricted facultative methylotrophs, capable of growth with methanol, formate and acetate as carbon and energy sources. With methanol, the strains grew within a broad salinity range from 0.3 to 3.5–4 M total Na+, with an optimum at 0.5–1 M. The pH range for growth was between 8.3 and 10.5, with an optimum at pH 9.5, which characterized the soda lake isolates as obligate haloalkaliphiles. Carbon is assimilated autotrophically via the Calvin–Benson cycle. Sequence analysis of the gene coding for the key enzyme RuBisCO demonstrated that strain AMT 1T possessed a single cbbL gene of the ‘green’ form I, clustering with members of the family Ectothiorhodospiraceae. Analysis of the 16S rRNA gene sequence showed that strains AMT 1T and AMT 3 belong to a single species that forms a separate lineage within the family Ectothiorhodospiraceae. On the basis of phenotypic and genetic data, the novel haloalkaliphilic methylotrophs are described as representing a novel genus and species, Methylonatrum kenyense gen. nov., sp. nov. (type strain AMT 1T =DSM 15732T =NCCB 100209T =UNIQEM U238T).
-
-
-
Arenimonas malthae sp. nov., a gammaproteobacterium isolated from an oil-contaminated site
A Gram-negative, rod-shaped bacterium (CC-JY-1T) was isolated on nutrient agar from a soil sample collected from an oil-contaminated site located in Chyai county, Taiwan. 16S rRNA gene sequence analysis demonstrated that this isolate is unique, showing 96.7 % sequence similarity to the type strain of Arenimonas donghaensis and similarities of 93.0–93.8 % to species of the genera Thermomonas, Lysobacter and Silanimonas. The presence of ubiquinone Q-8, a polar lipid profile consisting of the major compounds diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine and the fatty acid profile were in accordance with the phylogenetic affiliation of CC-JY-1T. DNA–DNA reassociation experiments between CC-JY-1T and A. donghaensis KACC 11381T resulted in a mean relatedness value of 32 %, indicating that strain CC-JY1T represents a novel species in the genus Arenimonas, for which we propose the name Arenimonas malthae sp. nov. The type strain is CC-JY-1T (=CCUG 53596T =CIP 109310T).
-
-
-
Azospirillum zeae sp. nov., a diazotrophic bacterium isolated from rhizosphere soil of Zea mays
More LessTwo free-living nitrogen-fixing bacterial strains, N6 and N7T, were isolated from corn rhizosphere. A polyphasic taxonomic approach, including morphological characterization, Biolog analysis, DNA–DNA hybridization, and 16S rRNA, cpn60 and nifH gene sequence analysis, was taken to analyse the two strains. 16S rRNA gene sequence analysis indicated that strains N6 and N7T both belonged to the genus Azospirillum and were closely related to Azospirillum oryzae (98.7 and 98.8 % similarity, respectively) and Azospirillum lipoferum (97.5 and 97.6 % similarity, respectively). DNA–DNA hybridization of strains N6 and N7T showed reassociation values of 48 and 37 %, respectively, with A. oryzae and 43 % with A. lipoferum. Sequences of the nifH and cpn60 genes of both strains showed 99 and ~95 % similarity, respectively, with those of A. oryzae. Chemotaxonomic characteristics (Q-10 as quinone system, 18 : 1ω7c as major fatty acid) and G+C content of the DNA (67.6 mol%) were also similar to those of members of the genus Azospirillum. Gene sequences and Biolog and fatty acid analysis showed that strains N6 and N7T differed from the closely related species A. lipoferum and A. oryzae. On the basis of these results, it is proposed that these nitrogen-fixing strains represent a novel species. The name Azospirillum zeae sp. nov. is suggested, with N7T (=NCCB 100147T=LMG 23989T) as the type strain.
-
-
-
Rhodanobacter ginsengisoli sp. nov. and Rhodanobacter terrae sp. nov., isolated from soil cultivated with Korean ginseng
Two bacterial isolates from ginseng fields in Korea, strains GR17-7T and GP18-1T, were characterized using a polyphasic approach. Phylogenetic analysis of their 16S rRNA gene sequences revealed a clear affiliation with the Gammaproteobacteria, and showed that the closest phylogenetic relationships were with members of the genus Rhodanobacter. The 16S rRNA gene sequence similarity between strains GR17-7T and GP18-1T was 97.2 %. Both strains showed 16S rRNA gene sequence similarities of 95.2–96.9 % to type strains of recognized Rhodanobacter species. The G+C contents of the DNA of strains GR17-7T and GP18-1T were 61.0 and 62.5 mol%, respectively. According to the DNA–DNA hydridization tests, the hybridization value between strains GR17-7T and GP18-1T was 34 %. Strains GR17-7T and GP18-1T showed less than 32 % DNA–DNA relatedness with Rhodanobacter fulvus KCTC 12098T and Rhodanobacter spathiphylli LMG 23181T. Strains GR17-7T and GP18-1T were aerobic, Gram-negative, rod-shaped, and catalase- and oxidase-positive. Major fatty acids of both strains were iso-C17 : 1 ω9c and iso-C16 : 0. Based on the data presented, two novel Rhodanobacter species are proposed, with the names Rhodanobacter ginsengisoli sp. nov. (type strain GR17-7T=KACC 11762T=DSM 18993T) and Rhodanobacter terrae sp. nov. (type strain GP18-1T=KACC 11761T=DSM 19241T).
-
-
-
Reclassification of Vibrio fischeri, Vibrio logei, Vibrio salmonicida and Vibrio wodanis as Aliivibrio fischeri gen. nov., comb. nov., Aliivibrio logei comb. nov., Aliivibrio salmonicida comb. nov. and Aliivibrio wodanis comb. nov.
More LessFour closely related species, Vibrio fischeri, Vibrio logei, Vibrio salmonicida and Vibrio wodanis, form a clade within the family Vibrionaceae; the taxonomic status and phylogenetic position of this clade have remained ambiguous for many years. To resolve this ambiguity, we tested these species against other species of the Vibrionaceae for phylogenetic and phenotypic differences. Sequence identities for the 16S rRNA gene were ≥97.4 % among members of the V. fischeri group, but were ≤95.5 % for members of this group in comparison with type species of other genera of the Vibrionaceae (i.e. Photobacterium and Vibrio, with which they overlap in G+C content, and Enterovibrio, Grimontia and Salinivibrio, with which they do not overlap in G+C content). Combined analysis of the recA, rpoA, pyrH, gyrB and 16S rRNA gene sequences revealed that the species of the V. fischeri group form a tightly clustered clade, distinct from these other genera. Furthermore, phenotypic traits differentiated the V. fischeri group from other genera of the Vibrionaceae, and a panel of 13 biochemical tests discriminated members of the V. fischeri group from type strains of Photobacterium and Vibrio. These results indicate that the four species of the V. fischeri group represent a lineage within the Vibrionaceae that is distinct from other genera. We therefore propose their reclassification in a new genus, Aliivibrio gen. nov. Aliivibrio is composed of four species: Aliivibrio fischeri comb. nov. (the type species) (type strain ATCC 7744T =CAIM 329T =CCUG 13450T =CIP 103206T =DSM 507T =LMG 4414T =NCIMB 1281T), Aliivibrio logei comb. nov. (type strain ATCC 29985T =CCUG 20283T =CIP 104991T =NCIMB 2252T), Aliivibrio salmonicida comb. nov. (type strain ATCC 43839T =CIP 103166T =LMG 14010T =NCIMB 2262T) and Aliivibrio wodanis comb. nov. (type strain ATCC BAA-104T =NCIMB 13582T =LMG 24053T).
-
-
-
Reclassification of Aquaspirillum itersonii and Aquaspirillum peregrinum as Novispirillum itersonii gen. nov., comb. nov. and Insolitispirillum peregrinum gen. nov., comb. nov.
More LessPhylogenetic analysis based on 16S rRNA gene sequences showed that Aquaspirillum itersonii and Aquaspirillum peregrinum form distinct phylogenetic lineages within the Alphaproteobacteria, whereas Aquaspirillum serpens, the type species of the genus Aquaspirillum, belongs to the Betaproteobacteria. A. itersonii and A. peregrinum exhibited 16S rRNA gene sequence similarity values of 82.0–82.4 % to the type strain of A. serpens and of 91.8–92.0 % to each other. A. itersonii and A. peregrinum were clearly distinguishable from A. serpens by differences in ubiquinone types and fatty acid profiles. A. itersonii subsp. itersonii LMG 4337T and A. itersonii subsp. nipponicum LMG 7370T contained Q-10 as the predominant ubiquinone, and A. peregrinum subsp. peregrinum LMG 4340T and A. peregrinum subsp. integrum LMG 5407T contained Q-9 as the predominant ubiquinone, whereas A. serpens LMG 3734T had Q-8 as the predominant ubiquinone. A. itersonii and A. peregrinum were also distinguishable from A. serpens by some differences in the fatty acid composition, including major fatty acids and hydroxy fatty acids. On the basis of these data, A. itersonii and A. peregrinum should be reclassified into two novel genera and species, for which the names Novispirillum itersonii gen. nov., comb. nov. and Insolitispirillum peregrinum gen. nov., comb. nov., respectively, are proposed.
-
-
-
Methylobacterium platani sp. nov., isolated from a leaf of the tree Platanus orientalis
More LessA novel bacterial strain, designated PMB02T, was isolated from a leaf of the tree Platanus orientalis. Colonies grown on TYG agar plates were circular, pink-pigmented and slow-growing, being 0.2–1.5 mm in diameter after 3 days growth. The cells of strain PMB02T were Gram-negative, aerobic, motile rods that possessed oxidase and catalase activities and grew at 20–30 °C, pH 6–8 and in media containing less than 1 % NaCl. The major respiratory quinone was identified as Q-10. A phylogenetic analysis based on 16S rRNA gene sequence comparisons indicated that strain PMB02T was related to members of the genus Methylobacterium. A comparative 16S rRNA gene sequence-based phylogenetic analysis placed the strain in a clade with the species Methylobacterium aquaticum and Methylobacterium variabile, with which it showed sequence similarities of 97.7 and 97.4 %, respectively. The values for DNA–DNA hybridization between strain PMB02T and M. aquaticum CCM 7218T and M. variabile GR3T were less than 32 %. On the basis of the phenotypic characterization, the phylogenetic analysis and the DNA–DNA relatedness data, strain PMB02T is considered to represent a novel species of the genus Methylobacterium, for which the name Methylobacterium platani sp. nov. is proposed. The type strain is PMB02T (=KCTC 12901T=JCM 14648T).
-
-
-
Chitinilyticum aquatile gen. nov., sp. nov., a chitinolytic bacterium isolated from a freshwater pond used for Pacific white shrimp culture
More LessStrain c14T, originally isolated from surface water of a freshwater pond located in Pingtung (southern Taiwan) used for culture of Pacific white shrimp (Litopenaeus vannamei), was subjected to a polyphasic taxonomic approach. The strain exhibited strong chitinolytic activity and was able to grow under aerobic and anaerobic conditions by utilizing chitin exclusively as the carbon, nitrogen and energy source. Phylogenetic analysis of the 16S rRNA gene sequence revealed a clear affiliation of the proposed bacterium to the Betaproteobacteria, most closely related to Chitinibacter tainanensis S1T, Deefgea rivuli WB 3.4-79T and Silvimonas terrae KM-45T, with 94.6, 93.6 and 92.9 % 16S rRNA gene sequence similarity, respectively. The predominant fatty acids detected in cells of strain c14T were C16 : 0, C18 : 1 ω7c and summed feature 3 (C16 : 1 ω7c and/or C15 : 0 iso 2-OH). The G+C content of the genomic DNA was 69.5 (±1.0) mol%. Biochemical, physiological, chemotaxonomic and phylogenetic analyses showed that strain c14T could not be assigned to any known genus of the Betaproteobacteria. Therefore, strain c14T is classified within a novel genus and species, for which the name Chitinilyticum aquatile gen. nov., sp. nov. is proposed. The type strain of Chitinilyticum aquatile is c14T (=LMG 23346T =BCRC 17533T).
-
-
-
Desulfotignum toluenicum sp. nov., a novel toluene-degrading, sulphate-reducing bacterium isolated from an oil-reservoir model column
More LessA Gram-negative, sulphate-reducing bacterium (strain H3T) was isolated from an oil-reservoir model column. The new isolate was able to oxidize toluene coupled to hydrogen sulphide production. For growth, the optimum salt concentration was 1.5 % (w/v), the optimum pH was 7.2 and the optimum temperature was 34 °C. The cells were straight to slightly curved rods, 0.6–1.0 μm in diameter and 1.4–2.5 μm in length. The predominant fatty acids were C16 : 0, C16 : 1 ω7c and C17 : 0 cyclo, and the cells also contained dimethylacetals. Cloning and sequencing of a 1505 bp long fragment of the 16S rRNA gene showed that strain H3T is a member of the Deltaproteobacteria and is related closely to Desulfotignum balticum DSM 7044T. The G+C content of the DNA was 52.0 mol% and the DNA–DNA similarity to D. balticum DSM 7044T was 56.1 %. Based on differences in DNA sequence and the unique property of toluene degradation, it is proposed that strain H3T should be designated a member of a novel species within the genus Desulfotignum, for which the name Desulfotignum toluenicum sp. nov. is proposed. The type strain is H3T (=DSM 18732T=ATCC BAA-1460T).
-
-
-
Shewanella haliotis sp. nov., isolated from the gut microflora of abalone, Haliotis discus hannai
A motile, rod-shaped, pink–orange pigmented bacterium, designated strain DW01T, was isolated from the gut microflora of abalone collected from the South Sea (Republic of Korea). Cells were Gram-negative, facultatively anaerobic, catalase- and oxidase-positive. The major fatty acids were iso-C15 : 0 (17.7 %), C16 : 0 (13.4 %), iso-C15 : 0 2-OH and/or C16 : 1 ω7c (12.5 %) and C17 : 1 ω8c (10.7 %). The DNA G+C content was 53.7 mol%. A phylogenetic tree based on the 16S rRNA gene sequences showed that strain DW01T forms a lineage of the genus Shewanella and is closely related to Shewanella algae ATCC 51192T (98.3 % sequence similarity) and to other members of the genus Shewanella (91.0–94.9 %). The phenotypic characteristics and DNA–DNA hybridization relatedness data indicate that strain DW01T should be distinguished from S. algae ATCC 51192T. On the basis of the data presented in this study, strain DW01T represents a novel species, for which the name Shewanella haliotis sp. nov. is proposed. The type strain is DW01T (=KCTC 12896T=JCM 14758T).
-
- Eukaryotic Micro-Organisms
-
-
Candida flosculorum sp. nov. and Candida floris sp. nov., two yeast species associated with tropical flowers
Two ascomycetous yeast species, Candida flosculorum sp. nov. and Candida floris sp. nov., were isolated from tropical flowers and their associated insects. C. flosculorum was isolated from flower bracts of Heliconia velloziana and Heliconia episcopalis (Heliconiaceae) collected from two Atlantic rain forest sites in Brazil. C. floris was isolated from flowers of Ipomoea sp. (Convolvulaceae) growing on the banks of the river Paraguai in the pantanal ecosystem in Brazil and from an adult of the stingless bee Trigona sp. and a flower of Merremia quinquefolia (Convolvulaceae) in Costa Rica. C. flosculorum belongs to the Metschnikowiaceae clade and C. floris belongs to the Starmerella clade. The type strain of C. flosculorum is UFMG-JL13T (=CBS 10566T=NRRL Y-48258T) and the type strain of C. floris is UWO(PS) 00-226.2T (=CBS 10593T=NRRL Y-48255T).
-
- Other Gram-Positive Bacteria
-
-
Proposal of Viridibacillus gen. nov. and reclassification of Bacillus arvi, Bacillus arenosi and Bacillus neidei as Viridibacillus arvi gen. nov., comb. nov., Viridibacillus arenosi comb. nov. and Viridibacillus neidei comb. nov.
A polyphasic study was undertaken to clarify the taxonomic position of endospore-forming strains 433-D9, 433-E17 and 121-X1. BOX-PCR-generated fingerprints indicated that they may be members of a single species. 16S rRNA gene sequence similarity demonstrated that a representative of this group, 433-D9, is affiliated closely with Bacillus arvi DSM 16317T (100 %), Bacillus arenosi DSM 16319T (99.8 %) and Bacillus neidei NRRL BD-87T (97.1 %). Sequence similarities revealed Bacillus pycnus NRRL NRS-1691T and several Kurthia species as the next nearest relatives. DNA–DNA hybridization results showed that strain 433-D9 is a member of B. arvi. Detection of l-Lys–d-Asp-based peptidoglycan in strain 433-D9, B. arvi DSM 16317T and B. arenosi DSM 16319T was in agreement with their close relationship, but differentiated these strains from B. neidei NRRL BD-87T and B. pycnus NRRL NRS-1691T, for which l-Lys–d-Glu was reported. A similar quinone system was detected in strains 433-D9, 433-E17, 121-X1, B. arvi DSM 16317T, B. arenosi DSM 16319T and B. neidei NRRL BD-87T. This system, unusual for bacilli, consisted of the major compound menaquinone MK-8 (69–80 %) and moderate amounts of MK-7 (19–30 %). This observation was in contrast to the predominance of MK-7 of the closest relative B. pycnus NRRL NRS-1691T, as also reported for representatives of the closely related non-endospore-forming genus Kurthia. Strains 433-D9, B. arvi DSM 16317T and B. arenosi DSM 16319T exhibited homogeneous and discriminative polar lipid profiles and fatty acid profiles consisting of major acids i-C15 : 0 and ai-C15 : 0 and moderate amounts of i-C17 : 1 ω10c and i-C17 : 1 I/ai-C17 : 1 B that discriminated them from closely related strains such as B. neidei NRRL BD-87T. On the basis of clear-cut discriminative chemotaxonomic markers, we propose strains 433-D9, 433-E17 and 121-X1, B. arvi DSM 16317T, B. arenosi DSM 16319T and B. neidei NRRL BD-87T to be reclassified within a separate genus. For this new taxon, we propose the name Viridibacillus gen. nov., and we propose the reclassification of Bacillus arvi, Bacillus arenosi and Bacillus neidei as Viridibacillus arvi gen. nov., comb. nov. (the type species of Viridibacillus, with the type strain DSM 16317T =LMG 22165T), Viridibacillus arenosi comb. nov. (type strain DSM 16319T =LMG 22166T) and Viridibacillus neidei comb. nov. (type strain NRRL BD-87T =DSM 15031T =JCM 11077T).
-
-
-
Lactobacillus hayakitensis sp. nov., isolated from intestines of healthy thoroughbreds
Two strains, KBL13T and GBL13, were isolated as one of intestinal lactobacilli from the faecal specimens from different thoroughbreds of the same farm where they were born in Hokkaido, Japan. They were Gram-positive, facultatively anaerobic, catalase-negative, non-spore-forming and non-motile rods. KBL13T and GBL13 homofermentatively metabolize glucose, and produce lactate as the sole final product from glucose. The 16S rRNA gene sequence, DNA–DNA hybridization, DNA G+C content and biochemical characterization indicated that these two strains, KBL13T and GBL13, belong to the same species. In the representative strain, KBL13T, the DNA G+C content was 34.3 mol%. Lactobacillus salivarius JCM 1231T (=ATCC 11741T; AF089108) is the type strain most closely related to the strain KBL13T as shown in the phylogenetic tree, and the 16S rRNA gene sequence identity showed 96.0 % (1425/1484 bp). Comparative 16S rRNA gene sequence analysis of this strain indicated that the two isolated strains belong to the genus Lactobacillus and that they formed a branch distinct from their closest relatives, L. salivarius, Lactobacillus aviarius, Lactobacillus saerimneri and Lactobacillus acidipiscis. DNA–DNA reassociation experiments with L. salivarius and L. aviarius confirmed that KBL13T represents a novel species, for which the name Lactobacillus hayakitensis sp. nov. is proposed. The type strain is KBL13T (=JCM 14209T=DSM 18933T).
-
-
-
Veillonella denticariosi sp. nov., isolated from human carious dentine
More LessSelective culture of human carious dentine for Veillonella strains resulted in the isolation of two strains of a Gram-negative, coccus-shaped bacterium that has not been described previously. Comparative 16S rRNA and dnaK gene sequence analysis indicated that the two strains were homogeneous and comprised a distinct lineage within the genus Veillonella, phylogenetically most closely related to Veillonella rodentium. This was supported by DNA–DNA hybridization, which showed clearly that the two strains were similar and distinct from other Veillonella species, and the production of major cellular fatty acids (C13 : 0 and C17 : 1 ω8), which is consistent with other members of the genus Veillonella. Based on these observations, strains RBV81 and RBV106T represent a novel species, for which the name Veillonella denticariosi sp. nov. is proposed, with the type strain RBV106T (=CIP 109448T =CCUG 54362T =DSM 19009T).
-
-
-
Bacillus plakortidis sp. nov. and Bacillus murimartini sp. nov., novel alkalitolerant members of rRNA group 6
The Gram-positive, alkali- and salt-tolerant marine bacterium strain P203T is described together with its closest phylogenetic neighbour, terrestrial isolate LMG 21005T. Strain P203T was isolated from material from the sponge Plakortis simplex that was obtained from the Sula-Ridge, Norwegian Sea. Strain LMG 21005T was an undescribed strain that was isolated from a church wall mural in Germany. Strains P203T and LMG 21005T were identified as novel alkalitolerant members of the Bacillus rRNA group 6 with a 16S rRNA gene sequence similarity of 99.5 %. The closest described neighbour, Bacillus gibsonii DSM 8722T, showed 99.0 % gene sequence similarity with P203T and 98.8 % similarity with strain LMG 21005T. Despite the high 16S rRNA gene sequence similarity, DNA–DNA cross-hybridization revealed only 25.8–34.1 % similarity amongst the three strains. The DNA G+C contents were 41.1 mol% for strain P203T and 39.6 mol% for strain LMG 21005T. Both strains grew well between pH 7 and pH 11. Strain P203T showed growth at moderate temperatures (from 4 to 30 °C) and in the presence of up to 12 % (w/v) NaCl at pH 9.7, whereas strain LMG 21005T was not salt tolerant (up to 4 % NaCl) and no growth was observed at 4 °C. The major fatty acids of strains P203T, LMG 21005T and the type strain of B. gibsonii were the saturated terminally methyl-branched compounds iso-C15 : 0 (19.8, 15.6 and 28.0 %, respectively) and anteiso-C15 : 0 (57.1, 48.6 and 45.2 %, respectively). Physiological and biochemical tests allowed genotypic and phenotypic differentiation of strains P203T and LMG 21005T from the six related Bacillus species with validly published names and supported the proposal of two novel species, Bacillus plakortidis [type strain P203T (=DSM 19153T=NCIMB 14288T)] and Bacillus murimartini [type strain LMG 21005T (=NCIMB 14102T)].
-
-
-
Cohnella laeviribosi sp. nov., isolated from a volcanic pond
More LessA novel thermophilic and endospore-forming Gram-positive bacterium capable of assimilating and isomerizing l-ribose was isolated from a volcanic area in Likupang, Indonesia. The isolate, RI-39T, was able to grow at high temperatures (37–60 °C); optimum growth was observed at pH 6.5 and 45 °C. The strain contained MK-7 (87 %) as the main respiratory quinone and had a DNA G+C content of 51 mol%. The major cellular fatty acids of the isolate were iso-C16 : 0 and anteiso-C15 : 0 and the predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and lysyl-phosphatidylglycerol. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate represents an evolutionary lineage that is distinct from those of other Cohnella species. Based on morphological, physiological and chemotaxonomic characteristics and 16S rRNA gene sequence comparisons, it is proposed that strain RI-39T represents a novel species, Cohnella laeviribosi sp. nov. The type strain is RI-39T (=KCTC 3987T =KCCM 10653PT =CCUG 52217T).
-
-
-
Ureibacillus composti sp. nov. and Ureibacillus thermophilus sp. nov., isolated from livestock-manure composts
Two Gram-negative, rod-shaped, thermophilic bacterial strains, HC145T and HC148T, were isolated from a compost sample from a compost facility in Ichon, Korea. Sequencing of the 16S rRNA genes of HC145T and HC148T and comparative analyses of the resulting sequences clearly showed that these strains had a phylogenetic affiliation to the genus Ureibacillus. The level of 16S rRNA similarity between the two novel strains was 98.4 % and the levels of sequence similarity between them and existing Ureibacillus species were 97.8–98.1 (HC145T) and 97.4–98.7 % (HC148T). The DNA–DNA reassociation values between the two strains and the type strains of Ureibacillus species ranged from 38 to 51 %. The polar lipid profiles for both isolates consisted of phosphatidylglycerol, diphosphatidylglycerol, phospholipids and glycolipids of unknown composition. The major quinones were MK-8, MK-9 and MK-7, the peptidoglycan type was l-Lys←d-Asp and the main cellular fatty acid was iso-C16 : 0. The DNA G+C contents of strains HC145T and HC148T were 42.4 and 38.5 mol%, respectively. On the basis of the data from this polyphasic study, strains HC145T and HC148T represent members of the genus Ureibacillus, for which the names Ureibacillus composti sp. nov. and Ureibacillus thermophilus sp. nov., respectively, are proposed. The type strain of U. composti is HC145T (=KACC 11361T =DSM 17951T) and the type strain of U. thermophilus is HC148T (=KACC 11362T =DSM 17952T).
-
-
-
Bacillus kribbensis sp. nov., isolated from a soil sample in Jeju, Korea
More LessA Gram-positive, endospore-forming bacterium, designated strain BT080T, was isolated from a soil sample in Jeju, Korea. Cells of the isolate were strictly aerobic rods that were motile by means of peritrichous flagella. The strain grew optimally at 30–33 °C and pH 5.5–6.5. Chemotaxonomic data (major isoprenoid quinone, MK-7; DNA G+C content, 43.3 mol%; major fatty acids, anteiso-C15 : 0, iso-C14 : 0, iso-C16 : 0 and iso-C15 : 0) supported the affiliation of the isolate to the genus Bacillus. Comparative 16S rRNA gene sequence analyses showed that strain BT080T formed a distinct phyletic line within the genus Bacillus. The levels of 16S rRNA gene sequence similarity with respect to related Bacillus species were below 96.4 %. On the basis of physiological, biochemical and phylogenetic properties, strain BT080T represents a novel species within the genus Bacillus, for which the name Bacillus kribbensis sp. nov. is proposed. The type strain is BT080T (=KCTC 13934T=DSM 17871T).
-
-
-
Howardella ureilytica gen. nov., sp. nov., a Gram-positive, coccoid-shaped bacterium from a sheep rumen
More LessAn unidentified obligately anaerobic, fastidious, Gram-positive, non-motile, non-spore-forming, non-fermentative coccoid-shaped bacterium (designated strain GPC 589T) was isolated from the rumen fluid of a sheep. The major fatty acid constituents (>5 %) were C16 : 0 (29.2 %), C18 : 0 (40.7 %) and an unidentified compound (19.7 %) with an equivalent chain-length of 13.523. The G+C content of the DNA was 34 mol%. The organism was strongly ureolytic and generated ATP through the hydrolysis of urea. Comparative 16S rRNA gene sequence analysis demonstrated that strain GPC 589T was far removed, phylogenetically, from the ruminococci and related Gram-positive anaerobic cocci but exhibited a phylogenetic association with Clostridium rRNA cluster XIVa [as defined by Collins, M. D., Lawson, P. A., Willems, A., Cordoba, J. J., Fernandez-Garayzabal, J., Garcia, P., Cai, J., Hippe, H. & Farrow, J. A. E. (1994). Int J Syst Bacteriol 44, 812–826]. Sequence divergence values of 12.5 % or more were observed between strain GPC 589T and all other recognized species within this and related rRNA clostridial clusters. Phylogenetic analysis showed that strain GPC 589T represents a new genus within cluster XIVa. On the basis of both phylogenetic and phenotypic evidence, it is proposed that strain GPC 589T should be classified as representing a new genus and novel species, Howardella ureilytica gen. nov., sp. nov. The type strain is strain GPC 589T (=DSM 15118T=JCM 13267T).
-
-
-
Leuconostoc holzapfelii sp. nov., isolated from Ethiopian coffee fermentation and assessment of sequence analysis of housekeeping genes for delineation of Leuconostoc species
A Gram-positive, ovoid lactic acid bacterium, strain LMG 23990T, was isolated from Ethiopian coffee fermentation. 16S rRNA gene sequence analysis indicated that the novel strain belongs to the genus Leuconostoc, with Leuconostoc citreum and Leuconostoc lactis as the closest neighbours (99.6 and 99.0 % 16S rRNA gene sequence similarity, respectively). Genotypic fingerprinting by fluorescent amplified fragment length polymorphism, whole-cell protein electrophoresis, DNA–DNA hybridizations, comparative sequence analysis of pheS, rpoA, atpA, and physiological and biochemical tests allowed us to differentiate strain LMG 23990T from all established Leuconostoc species. Strain LMG 23990T (=CCUG 54536T) therefore represents a novel species, for which the name Leuconostoc holzapfelii sp. nov. is proposed.
-
- Evolution, Phylogeny And Biodiversity
-
-
-
Phylogenetic analysis of Xanthomonas species by comparison of partial gyrase B gene sequences
More LessThe genus Xanthomonas currently comprises 27 species with validly published names that are important crop and horticultural pathogens. We have constructed a phylogram from alignment of gyrase B (gyrB) sequences for all xanthomonad species, both to indicate inter-species relatedness and as an aid for rapid and accurate species-level identification. The phylogeny indicated a monophyletic group, with X. albilineans and X. sacchari as the most ancestral species. Three species, X. hyacinthi, X. translucens and X. theicola, formed an early-branching group. Three clades were supported by high bootstrap values: group 1 comprised X. cucurbitae, X. cassavae and X. codiaei; group 2 comprised X. arboricola, X. campestris, X. populi, X. hortorum, X. gardneri and X. cynarae; group 3 contained the remaining species, within which two further clades, supported by a 100% bootstrap value, were identified. Group 3A comprised X. axonopodis, X. euvesicatoria, X. perforans and X. melonis, together with X. alfalfae, X. citri and X. fuscans, whose names were recently validly published. Group 3B contained the monocot pathogens X. vasicola and X. oryzae. Two recently identified species, X. cynarae and X. gardneri, were poorly discriminated and were related closely to X. hortorum. Three species, X. perforans, X. euvesicatoria and X. alfalfae, had identical gyrB sequences. Partial sequencing of a further five genes from these species found only minor sequence differences that confirmed their close relatedness. Although branch lengths between species varied, indicating different degrees of genetic distinctiveness, the majority (n=21) were well-differentiated, indicating the utility of the method as an identification tool, and we now use this method for routine diagnosis of xanthomonad species.
-
-
-
-
Probable synonymy of the nitrogen-fixing genus Azotobacter and the genus Pseudomonas
More LessThe relationships of the genus Azotobacter, Azomonas macrocytogenes and the genus Pseudomonas were revealed by comparative analysis of partial 16S rRNA and atpD, carA and recA gene sequences and as concatenated nucleotide and peptide sequences. Sequence similarities of Azotobacter species and Azomonas macrocytogenes indicated that these may be considered to be synonyms at the molecular level. In addition, these species show an intimate relationship with species of Pseudomonas, especially P. aeruginosa (the type species of the genus). In terms of the current circumscription of the genus Pseudomonas, Azotobacter and Azomonas macrocytogenes should be considered for amalgamation with Pseudomonas. Azotobacter and Azomonas comprise nitrogen-fixing strains with large pleomorphic cells that form cysts, and peritrichous flagella insertion; characteristics not included in the current circumscription of Pseudomonas. The data are discussed in the light of whether lateral transfer of genes could be involved in the determination of significant morphological characteristics, thus leading to a problem that may be encountered more frequently: how to resolve classification of taxa based on conserved sequences with those based on their phenotype. More fundamentally, the results illuminate problems that will increasingly be encountered: by what criteria can taxa be delineated, what are the most appropriate methods for classification, and what are the proper assumptions of bacterial classification?
-
- Methods
-
-
-
Identification of lactobacilli by pheS and rpoA gene sequence analyses
The aim of this study was to evaluate the use of the phenylalanyl-tRNA synthase alpha subunit (pheS) and the RNA polymerase alpha subunit (rpoA) partial gene sequences for species identification of members of the genus Lactobacillus. Two hundred and one strains representing the 98 species and 17 subspecies were examined. The pheS gene sequence analysis provided an interspecies gap, which in most cases exceeded 10 % divergence, and an intraspecies variation of up to 3 %. The rpoA gene sequences revealed a somewhat lower resolution, with an interspecies gap normally exceeding 5 % and an intraspecies variation of up to 2 %. The combined use of pheS and rpoA gene sequences offers a reliable identification system for nearly all species of the genus Lactobacillus. The pheS and rpoA gene sequences provide a powerful tool for the detection of potential novel Lactobacillus species and synonymous taxa. In conclusion, the pheS and rpoA gene sequences can be used as alternative genomic markers to 16S rRNA gene sequences and have a higher discriminatory power for reliable identification of species of the genus Lactobacillus.
-
-
- International Committee On Systematics Of Prokaryotes
-
- Minutes
- Errata
-
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)