bluuebunny/crossref_metadata_2025 huggingface dataset:
Mechanism of the defect in gap‐junctional communication by expression of a connexin 26 mutant associated with dominant deafness
Authors: Chen Yongyue , Deng Yanqin , Bao Xiaoyong , Reuss Luis , Altenberg Guillermo A.
Published: July 2005

Gap‐junctional channels (connexin oligomers) are large‐diameter aqueous pores formed by head‐to‐head association of two gap‐junctional hemichannels, one from each of the adjacent cells. Profound hearing loss of genetic origin is common, and mutations of connexin 26 (Cx26) are the most frequent cause of this disorder. The Cx26 R75W mutant has been associated with disruption of cell‐to‐cell communication and profound hearing loss, but the mechanism of the gap‐junctional defect is unknown. Here, we show that Cx26 R75W forms gap‐junctional hemichannels that display altered voltage dependency and reduced permeability, and which cannot form functional gap‐junctional channels between neighboring cells. The R75W phenotype is dominant at the gap‐junction channel but not at the hemichannel level. Therefore, the absence of gap‐junctional communication caused by R75W expression is due to defective gap‐junction formation by functional hemichannels.
Novel drug development opportunity for relaxin in acute myocardial infarction: evidences from a swine model
Authors: Perna Avio‐Maria , Masini Emanuela , Nistri Silvia , Briganti Vittorio , Chiappini Laura , Stefano Pierluigi , Bigazzi Mario , Pieroni Cesco , Sacchi Tatiana Bani , Bani Daniele
Published: July 2005

The hormone relaxin has been shown to cause coronary vasodilation and to prevent ischemia/reperfusion‐induced cardiac injury in rodents. This study provides evidence that relaxin, used as an adjunctive drug to coronary reperfusion, reduces the functional, biochemical, and histopathological signs of myocardial injury in an in vivo swine model of heart ischemia/reperfusion, currently used to test cardiotropic drugs for myocardial infarction. Human recombinant relaxin, given at reperfusion at doses of 1.25, 2.5, and 5 µg/kg b.wt. after a 30‐min ischemia, caused a dose‐related reduction of key markers of myocardial damage (serum myoglobin, CK‐MB, troponin T) and cardiomyocyte apoptosis (caspase 3, TUNEL assay), as well as of cardiomyocyte contractile dysfunction (myofibril hypercontraction). Compared with the controls, relaxin also increased the uptake of the viability tracer 201Thallium and improved ventricular performance (cardiac index). Relaxin likely acts by reducing oxygen free radical‐induced myocardial injury (malondialdehyde, tissue calcium overload) and inflammatory leukocyte recruitment (myeloperoxidase). The present findings show that human relaxin, given as a drug to counteract reperfusion‐induced cardiac injury, affords a clear‐cut protection to the heart of swine with induced myocardial infarction. The findings also provide background to future clinical trials with relaxin as adjunctive therapy to catheter‐based coronary angioplasty in patients with acute myocardial infarction.
Transfer of Pectobacterium chrysanthemi (Burkholder et al. 1953) Brenner et al. 1973 and Brenneria paradisiaca to the genus Dickeya gen. nov. as Dickeya chrysanthemi comb. nov. and Dickeya paradisiaca comb. nov. and delineation of four novel species, Dickeya dadantii sp. nov., Dickeya dianthicola sp. nov., Dickeya dieffenbachiae sp. nov. and Dickeya zeae sp. nov.
Authors: Samson Régine , Legendre Jean Bernard , Christen Richard , Saux Marion Fischer-Le , Achouak Wafa , Gardan Louis
Published: July 2005

A collection of 75 strains of Pectobacterium chrysanthemi (including all biovars and pathovars) and the type strains of Brenneria paradisiaca (CFBP 4178T) and Pectobacterium cypripedii (CFBP 3613T) were studied by DNA–DNA hybridization, numerical taxonomy of 121 phenotypic characteristics, serology and 16S rRNA gene-based phylogenetic analyses. From analysis of 16S rRNA gene sequences, it was deduced that P. chrysanthemi strains and B. paradisiaca CFBP 4178T formed a clade distinct from the genera Pectobacterium and Brenneria; therefore, it is proposed to transfer all the strains to a novel genus, Dickeya gen. nov. By DNA–DNA hybridization, the strains of P. chrysanthemi were distributed among six genomic species: genomospecies 1 harbouring 16 strains of biovar 3 and four strains of biovar 8, genomospecies 2 harbouring 16 strains of biovar 3, genomospecies 3 harbouring two strains of biovar 6 and five strains of biovar 5, genomospecies 4 harbouring five strains of biovar 2, genomospecies 5 harbouring six strains of biovar 1, four strains of biovar 7 and five strains of biovar 9 and genomospecies 6 harbouring five strains of biovar 4 and B. paradisiaca CFBP 4178T. Two strains of biovar 3 remained unclustered. Biochemical criteria, deduced from a numerical taxonomic study of phenotypic characteristics, and serological reactions allowed discrimination of the strains belonging to the six genomic species. Thus, it is proposed that the strains clustered in these six genomic species be assigned to the species Dickeya zeae sp. nov. (type strain CFBP 2052T=NCPPB 2538T), Dickeya dadantii sp. nov. (type strain CFBP 1269T=NCPPB 898T), Dickeya chrysanthemi comb. nov. (subdivided into two biovars, bv. chrysanthemi and bv. parthenii), Dickeya dieffenbachiae sp. nov. (type strain CFBP 2051T=NCPPB 2976T), Dickeya dianthicola sp. nov. (type strain CFBP 1200T=NCPPB 453T) and Dickeya paradisiaca comb. nov., respectively.
Roseicyclus mahoneyensis gen. nov., sp. nov., an aerobic phototrophic bacterium isolated from a meromictic lake
Authors: Rathgeber Christopher , Yurkova Natalia , Stackebrandt Erko , Schumann Peter , Beatty J. Thomas , Yurkov Vladimir
Published: July 2005

Eight strains of Gram-negative bacteria able to form ring-like cells were isolated from Mahoney Lake, a meromictic lake in south-central British Columbia, Canada. All strains were pink–purple and contained bacteriochlorophyll a incorporated into the light-harvesting 1 and 2 and reaction-centre pigment–protein complexes. Growth did not occur anaerobically under illuminated conditions; these strains were obligately aerobic, prompting their designation as members of the aerobic phototrophic bacteria. Physiological characterization revealed that these isolates share a similar tolerance to high levels of salinity and pH, as would be expected of bacteria from a highly saline lake; however, the strains exhibited marked differences in their ability to utilize organic substrates for aerobic heterotrophic growth. 16S rRNA sequence analysis showed that the strains are closely related to members of the non-phototrophic genera Octadecabacter (92·0–92·9 %) and Ketogulonicigenium (92·2–92·6 %), as well as to aerobic phototrophs of the genera Roseivivax (92·2–92·9 %) and Roseovarius (91·7–92·4 %) within the ‘Alphaproteobacteria’. The DNA G+C content was 66·2 mol%. The unusual light-harvesting complex 2, the distinct morphological features and physiological traits of these strains as well as the phylogenetic data support the proposal of the novel genus and species Roseicyclus mahoneyensis gen. nov., sp. nov., with ML6T (=DSM 16097T=VKM B-2346T) as the type strain.
Lactobacillus plantarum subsp. argentoratensis subsp. nov., isolated from vegetable matrices
Authors: Bringel Françoise , Castioni Anna , Olukoya Daniel K. , Felis Giovanna E. , Torriani Sandra , Dellaglio Franco
Published: July 2005

Fourteen strains isolated from vegetable sources and identified as belonging to Lactobacillus plantarum presented an atypical pattern of amplification with a species-specific multiplex-PCR assay. Phylogenetic analysis of two protein-encoding genes, recA (encoding the recombinase A protein) and cpn60 (encoding the GroEL chaperonin), as well as phenotypic and genomic traits revealed a homogeneous group of very closely related strains for which subspecies status is proposed, with the name Lactobacillus plantarum subsp. argentoratensis. The type strain is DKO 22T (=CIP 108320T=DSM 16365T).
Nocardia polyresistens sp. nov.
Authors: Xu Ping , Li Wen-Jun , Tang Shu-Kun , Jiang Yi , Chen Hua-Hong , Xu Li-Hua , Jiang Cheng-Lin
Published: July 2005

A novel actinomycete strain YIM 33361T was isolated from a soil sample collected from Yunnan, China. Comparative 16S rRNA gene sequencing showed that the strain constituted a distinct subclade within the genus Nocardia, displaying more than 3 % sequence divergence from established species. Based on its morphological, chemotaxonomic, phenotypic and genotypic characteristics, strain YIM 33361T (=CCTCC AA 204004T=KCTC 19027T) is proposed as the type strain of a novel species, Nocardia polyresistens sp. nov.
Six novel Arthrobacter species isolated from deteriorated mural paintings
Authors: Heyrman Jeroen , Verbeeren Jens , Schumann Peter , Swings Jean , De Vos Paul
Published: July 2005

A group of 21 bacterial strains was isolated from samples of biofilm formation in the Servilia tomb (necropolis of Carmona, Spain) and the Saint-Catherine chapel (castle at Herberstein, Austria). A polyphasic taxonomic study of these isolates, including morphological, biochemical and chemotaxonomic characterization, rep-PCR fingerprinting, 16S rRNA gene sequence analysis, DNA base ratio and DNA–DNA relatedness studies, allocated them to the genus Arthrobacter. The isolates represent six novel species, for which the names Arthrobacter castelli sp. nov., Arthrobacter monumenti sp. nov., Arthrobacter parietis sp. nov., Arthrobacter pigmenti sp. nov., Arthrobacter tecti sp. nov. and Arthrobacter tumbae sp. nov. are proposed. The respective type strains are LMG 22283T (=DSM 16402T), LMG 19502T (=DSM 16405T), LMG 22281T (=DSM 16404T), LMG 22284T (=DSM 16403T), LMG 22282T (=DSM 16407T) and LMG 19501T (=DSM 16406T).
Treponema berlinense sp. nov. and Treponema porcinum sp. nov., novel spirochaetes isolated from porcine faeces
Authors: Nordhoff Marcel , Taras David , Macha Moritz , Tedin Karsten , Busse Hans-Jürgen , Wieler Lothar H.
Published: July 2005

Limit-dilution procedures were used to isolate seven, helically coiled bacterial strains from faeces of swine that constituted two unidentified taxa. Comparative 16S rRNA gene sequence analysis showed highest similarity values with species of the genusTreponemaindicating that the isolates are members of this genus. Strain 7CPL208T, as well as five further isolates, and 14V28Tdisplayed the highest 16S rRNA gene sequence similarities withTreponema pectinovorumATCC 33768T(92·3 %) andTreponema parvumOMZ 833T(89·9 %), respectively. Polar lipid profiles distinguished 7CPL208Tand 14V28Tfrom each other as well as from related species. Based on their phenotypic and genotypic distinctiveness, strains 7CPL208Tand 14V28Tare suggested to represent two novel species of the genusTreponema, for which the namesTreponema berlinensesp. nov. andTreponema porcinumsp. nov. are proposed. The type strain forTreponema berlinenseis 7CPL208T(=ATCC BAA-909T=CIP 108244T=JCM 12341T) and forTreponema porcinum14V28T(=ATCC BAA-908T=CIP 108245T=JCM 12342T).
Phyllobacterium catacumbae sp. nov., a member of the order ‘Rhizobiales’ isolated from Roman catacombs
Authors: Jurado V. , Laiz L. , Gonzalez J. M. , Hernandez-Marine M. , Valens M. , Saiz-Jimenez C.
Published: July 2005

Two strains were isolated from tuff, a volcanic rock that forms the walls of the Roman Catacombs of Saint Callixtus in Rome, Italy. A polyphasic approach using nutritional and physiological tests, reactions to antibiotics, fatty acid profiles, DNA base ratios, DNA–DNA reassociation and 16S rRNA gene sequence comparisons showed that the two isolates belong to a novel species within the genusPhyllobacterium. The speciesPhyllobacterium catacumbaesp. nov. is proposed. The type strain is CSC19T(=CECT 5680T=LMG 22520T).
Staphylococcus pseudintermedius sp. nov., a coagulase-positive species from animals
Authors: Devriese Luc A. , Vancanneyt Marc , Baele Margo , Vaneechoutte Mario , De Graef Evelyne , Snauwaert Cindy , Cleenwerck Ilse , Dawyndt Peter , Swings Jean , Decostere Annemie , Haesebrouck Freddy
Published: July 2005

Four staphylococcal isolates from clinical and necropsy specimens from a cat, a dog, a horse and a parrot (Psittacus erithacus timneh) were found to constitute a distinct taxon. 16S rRNA gene sequence analysis revealed that its closest phylogenetic relatives are Staphylococcus intermedius and Staphylococcus delphini. Growth characteristics, biochemical features and DNA–DNA hybridizations demonstrated that the strains differ from these and other known species and that they represent a single, novel Staphylococcus species for which the name Staphylococcus pseudintermedius sp. nov. is proposed. The novel species is commonly confused with S. intermedius in routine diagnostic veterinary bacteriology. Although the strains described were isolated from lesions and show several characteristics typical of pathogenic staphylococci, such as coagulase, DNase and β-haemolysin production, the pathogenic significance of the novel species remains unclear. The type strain, LMG 22219T (=ON 86T=CCUG 49543T), was isolated from lung tissue of a cat.
Novel chlamydiae in whiteflies and scale insects: endosymbionts ‘Candidatus Fritschea bemisiae’ strain Falk and ‘Candidatus Fritschea eriococci’ strain Elm
Authors: Everett Karin D. E. , Thao MyLo , Horn Matthias , Dyszynski Glen E. , Baumann Paul
Published: July 2005

Bacteria called ‘Fritschea’ are endosymbionts of the plant-feeding whitefly Bemisia tabaci and scale insect Eriococcus spurius. In the gut of B. tabaci, these bacteria live within bacteriocyte cells that are transmitted directly from the parent to oocytes. Whiteflies cause serious economic damage to many agricultural crops; B. tabaci fecundity and host range are less than those of Bemisia argentifolii, possibly due to the presence of this endosymbiont. The B. tabaci endosymbiont has been characterized using electron microscopy and DNA analysis but has not been isolated or propagated outside of insects. The present study compared sequences for 11 endosymbiont genes to genomic data for chlamydial families Parachlamydiaceae, Chlamydiaceae and Simkaniaceae and to 16S rRNA gene signature sequences from 330 chlamydiae. We concluded that it was appropriate to propose ‘Candidatus Fritschea bemisiae’ strain Falk and ‘Candidatus Fritschea eriococci’ strain Elm as members of the family Simkaniaceae in the Chlamydiales.
Novel mycolic acid-containing bacteria in the family Segniliparaceae fam. nov., including the genus Segniliparus gen. nov., with descriptions of Segniliparus rotundus sp. nov. and Segniliparus rugosus sp. nov.
Authors: Butler W. Ray , Floyd Margaret M. , Brown June M. , Toney Sean R. , Daneshvar Maryam I. , Cooksey Robert C. , Carr Janice , Steigerwalt Arnold G. , Charles Nadege
Published: July 2005

Four strains of novel, rapidly growing, acid–alcohol-fast-staining bacteria were characterized with a polyphasic approach. Isolates were received by the Centers for Disease Control and Prevention from domestic health department laboratories for reference testing as unidentifiable, clinical mycobacteria. Bacteria were rod-shaped and produced non-pigmented (white to beige), non-photochromogenic, smooth or wrinkled-rough colonies on Middlebrook 7H10 and 7H11 media at 33 °C. The smooth and wrinkled colony forms were representative of two species with 68·0 and 72·0 mol% DNA G+C content. The cell wall contained meso-diaminopimelic acid and mycolic acids. Species were characterized by cellular fatty acids of C10 : 0, C14 : 0, C16 : 1ω9t, C16 : 0, C18 : 1ω9c and 10-methyl C18 : 0 (tuberculostearic acid). HPLC analysis of mycolic acids produced a novel late-emerging, genus-specific mycolate pattern. TLC analysis demonstrated a novel α
+-mycolate. Species were 98·9 % similar by comparison of 16S rRNA gene sequences; however, the DNA–DNA association was <28 %. Phylogenetic analysis of 16S rRNA gene sequences demonstrated an association with Rhodococcus equi, although a DNA–DNA relatedness value of 2 % did not support a close relationship. PCR analysis of a proposed, selected actinomycete-specific 439 bp fragment of the 65 kDa heat-shock protein was negative for three of the four isolates. The creation of Segniliparaceae fam. nov. is proposed to encompass the genus Segniliparus gen. nov., including two novel species, the type species Segniliparus rotundus sp. nov. and Segniliparus rugosus sp. nov., with the respective type strains CDC 1076T (=ATCC BAA-972T=CIP 108378T) and CDC 945T (=ATCC BAA-974T=CIP 108380T).
Marinobacter maritimus sp. nov., a psychrotolerant strain isolated from sea water off the subantarctic Kerguelen islands
Authors: Shivaji S. , Gupta Pratima , Chaturvedi Preeti , Suresh K. , Delille Daniel
Published: July 2005

A psychrotolerant, Gram-negative, motile bacterium, designated CK 47T, was isolated from sea water off the subantarctic Kerguelen islands (50° 40′ S 68° 25′ E). The isolate grew optimally at 22 °C and minimum and maximum temperature of growth were 4 and 37 °C, respectively. It required Na+for growth and exhibited optimum growth at pH 8·5 and 4 % NaCl. It utilized hexane, heptane and petroleum ether as sole sources of carbon. Strain CK 47Thad Q9 as the major respiratory quinone and C16 : 0(21·7 %), C17 : 0(21·3 %), C18 : 0(5·7 %), C18 : 1ω7c(9·0 %) and C18 : 1ω9c(31·4 %) as predominant fatty acids. The G+C content of the DNA was 58 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that CK 47Tformed a coherent cluster within the genusMarinobacter. It exhibited highest 16S rRNA gene sequence similarity of 96·8 % withMarinobacter lipolyticus. However, the level of DNA–DNA relatedness between strain CK47TandM. lipolyticuswas only 55 %. On the basis of phenotypic characteristics, and phylogenetic and genotypic distinctiveness, strain CK 47Tis considered to represent a novel species of the genusMarinobacter. The nameMarinobacter maritimussp. nov. is proposed, with CK 47T(=JCM 12521T=MTCC 6519T) as the type strain.
Oceanobacillus oncorhynchi sp. nov., a halotolerant obligate alkaliphile isolated from the skin of a rainbow trout (Oncorhynchus mykiss), and emended description of the genus Oceanobacillus
Authors: Yumoto Isao , Hirota Kikue , Nodasaka Yoshinobu , Nakajima Kenji
Published: July 2005

A halotolerant, obligately alkaliphilic bacterium, R-2T, was isolated from the skin of a rainbow trout (Oncorhynchus mykiss), a freshwater fish. The strain is Gram-positive, ferments several carbohydrates, is rod-shaped and motile by peritrichous flagella and produces ellipsoidal spores. The isolate grows at pH 9–10 but not at pH 7–8. This micro-organism grows in 0–22 % (w/v) NaCl at pH 10. Its major cellular fatty acids are iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0, the major isoprenoid quinone is MK-7 and the DNA G+C content is 38·5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicates that strain R-2T is a member of the genus Oceanobacillus. DNA–DNA hybridization reveals low relatedness between the isolate and Oceanobacillus iheyensis (21·0 %). On the basis of phenotypic characteristics, phylogenetic data and DNA–DNA relatedness data, the isolate should be designated as a novel species, for which the name Oceanobacillus oncorhynchi sp. nov. is proposed. The type strain is R-2T (=JCM 12661T=NCIMB 14022T).
Alkalibacterium iburiense sp. nov., an obligate alkaliphile that reduces an indigo dye
Authors: Nakajima Kenji , Hirota Kikue , Nodasaka Yoshinobu , Yumoto Isao
Published: July 2005

Three indigo-reducing obligately alkaliphilic strains, M3T, 41A and 41C, were isolated. The isolates grew at pH 9–12, but not at pH 7–8. They were Gram-positive, facultatively anaerobic, straight rod-shaped strains with peritrichous flagella. The isolates grew in 0–14 % (w/v) NaCl, with optimum growth at 3–13 %. They grew at temperatures between 10 and 45 °C, with optimum growth at around 30–37 °C. They did not hydrolyse starch or gelatin.dl-lactate was the major end-product fromd-glucose. No quinones could be detected. The peptidoglycan type was A4β, Orn–d-Asp. The major cellular fatty acids were C16 : 0, C16 : 17cand C18 : 19c. The DNA G+C content was 42·6–43·2 mol%. Phylogenetic analysis based on 16S rRNA gene sequence data indicated that the isolates belong to the genusAlkalibacterium. DNA–DNA hybridization revealed low similarity (less than 16 %) of the isolates with respect to the two closest phylogenetically related strains,Alkalibacterium olivapovliticusandAlkalibacterium psychrotolerans. On the basis of phenotypic and chemotaxonomic characteristics, phylogenetic data and DNA–DNA relatedness, the isolates merit classification as a novel species of the genusAlkalibacterium, for which the nameAlkalibacterium iburienseis proposed. The type strain is M3T(=JCM 12662T=NCIMB 14024T).
Paracoccus koreensis sp. nov., isolated from anaerobic granules in an upflow anaerobic sludge blanket (UASB) reactor
Authors: La Hyun-Jun , Im Wan-Taek , Ten Leonid N. , Kang Myung Suk , Shin Do-Yun , Lee Sung-Taik
Published: July 2005

A Gram-negative, short rod- to coccus-shaped, non-spore-forming bacterium (Ch05T) was isolated from granules in an upflow anaerobic sludge blanket (UASB) reactor. On the basis of 16S rRNA gene sequence similarity, strain Ch05T was shown to belong to the subclass α-Proteobacteria, being related to Paracoccus solventivorans (97·5 %), Paracoccus alkenifer (96·9 %) and Paracoccus kocurii (96·4 %). The phylogenetic distance from Paracoccus species with validly published names was always less than 96 %. Physiological and chemotaxonomic data (major ubiquinone, Q-10; major fatty acids, C18 : 1 and C18 : 0) supported the affiliation of strain Ch05T to the genus Paracoccus. The results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain Ch05T from the 17 Paracoccus species with validly published names. Ch05T therefore represents a novel species, for which the name Paracoccus koreensis sp. nov. is proposed. The type strain is Ch05T (=KCTC 12238T=IAM 15216T).
Stackebrandtia nassauensis gen. nov., sp. nov. and emended description of the family Glycomycetaceae
Authors: Labeda D. P. , Kroppenstedt R. M.
Published: July 2005

During the course of a 16S rRNA gene sequence phylogenetic evaluation of putative Glycomyces strains, it was noted that strain NRRL B-16338T is phylogenetically nearest to the genus Glycomyces but apparently is not a member of this or any of the other currently described actinomycete genera. The strain was subjected to a polyphasic study using standard methods for chemotaxonomic, morphological and physiological evaluation. The strain exhibited chemotaxonomic characteristics distinct from Glycomyces in spite of having 16S rRNA gene sequence similarity of 92 % with the described species of this genus. The whole-cell sugar pattern of NRRL B-16338T consisted of ribose and inositol, with traces of arabinose and mannose. The phospholipids observed were phosphatidylglycerol and diphosphatidylglycerol and menaquinones consisting of MK-10(H4), MK-10(H6), MK-11(H4) and MK-11(H6). A significant quantity (14·5 %) of 17 : 0 anteiso 2-hydroxy fatty acid was observed in the fatty acid profile of this strain. These characteristics clearly differentiate NRRL B-16338T from members of the genus Glycomyces and it is proposed that the strain represents a new genus within the family Glycomycetaceae to be called Stackebrandtia gen. nov. The description of this family is emended to permit its inclusion. It is proposed that the type species of the genus should be named Stackebrandtia nassauensis. The type strain LLR-40K-21T (=NRRL B-16338T=DSM 44728T) was isolated from a soil sample from Nassau, Bahamas.
Azospirillum oryzae sp. nov., a nitrogen-fixing bacterium isolated from the roots of the rice plant Oryza sativa
Authors: Xie Cheng-Hui , Yokota Akira
Published: July 2005

The taxonomic position of the free-living diazotrophic strain COC8T isolated from rice was investigated based on phylogenetic analyses. 16S rRNA gene sequence analyses indicated that strain COC8T was closely related to the genus Azospirillum (96 % similarity). Chemotaxonomic characteristics (G+C content of the DNA 66·8 mol%, Q-10 quinone system, 18 : 1ω7c as the major fatty acid and 14 : 0 3-OH and 16 : 0 3-OH as the major hydroxy fatty acids) were also similar to those of the genus Azospirillum. Based on its physiological characteristics, strain COC8T can clearly be differentiated from recognized species of Azospirillum. The name Azospirillum oryzae sp. nov. is proposed to accommodate this bacterial strain; the type strain is COC8T (=IAM 15130T=CCTCC AB204051T).
Novel members of the family Flavobacteriaceae from Antarctic maritime habitats including Subsaximicrobium wynnwilliamsii gen. nov., sp. nov., Subsaximicrobium saxinquilinus sp. nov., Subsaxibacter broadyi gen. nov., sp. nov., Lacinutrix copepodicola gen. nov., sp. nov., and novel species of the genera Bizionia, Gelidibacter and Gillisia
Authors: Bowman John P. , Nichols David S.
Published: July 2005

Several orange- and yellow-pigmented, halophilic, strictly aerobic, chemoheterotrophic, Gram-negative strains were isolated during investigations of maritime Antarctic habitats, including coastal fast sea-ice brine and algae, crustaceans and quartz stone sublithic cyanobacterial biofilms. Isolates investigated in this study belonged to the marine clade of the familyFlavobacteriaceaeand represented lineages that were either distinct from species with validly published names or appeared to be distinct species within existing genera. A polyphasic taxonomic analysis demonstrated the novelty of these strains, and several new taxa are proposed. Strains from quartz stone sublithic communities were grouped into two new genera designatedSubsaximicrobiumgen. nov. andSubsaxibactergen. nov. The genusSubsaximicrobiumincluded the speciesSubsaximicrobium wynnwilliamsiisp. nov. (type species; type strain G#7T=ACAM 1070T=CIP 108525T) andSubsaximicrobium saxinquilinussp. nov. (type strain Y4-5T=ACAM 1063T=CIP 108526T). The genusSubsaxibactercontained a single species designatedSubsaxibacter broadyisp. nov. (type strain P7T=ACAM 1064T=CIP 108527T). A novel bacterial strain isolated from the lake-dwelling, calanoid copepodParalabidocera antarcticawas given the nameLacinutrix copepodicolagen. nov., sp. nov. (type strain DJ3T=ACAM 1055T=CIP 108538T). Four novel species of the genusBizioniawere discovered,Bizionia algoritergicolasp. nov. (type strain APA-1T=ACAM 1056T=CIP 108533T) andBizionia myxarmorumsp. nov. (type strain ADA-4T=ACAM 1058T=CIP 108535T), which were isolated from the carapace surfaces of sea-ice algae-feeding amphipods, andBizionia gelidisalsuginissp. nov. (type strain IC164T=ACAM 1057T=CIP 108536T) andBizionia saleffrenasp. nov. (type strain HFDT=ACAM 1059T=CIP 108534T), which were isolated from sea-ice brines. Several other novel species were also isolated from sea-ice samples, including two novel species of the genusGelidibacter,Gelidibacter gilvussp. nov. (type strain IC158T=ACAM 1054T=CIP 108531T) andGelidibacter salicanalissp. nov. (type strain IC162T=ACAM 1053T=CIP 108532T), as well as three novel species of the genusGillisia,Gillisia illustriluteasp. nov. (type strain IC157T=ACAM 1062T=CIP 108530T),Gillisia sandarakinasp. nov. (type strain IC148T=ACAM 1060T=CIP 108529T) andGillisia hiemivividasp. nov. (type strain IC154T=ACAM 1061T=CIP 108528T).
The phylogenetic position of enteromonads: a challenge for the present models of diplomonad evolution
Authors: Kolisko Martin , Cepicka Ivan , Hampl Vladimír , Kulda Jaroslav , Flegr Jaroslav
Published: July 2005

Unikaryotic enteromonads and diplokaryotic diplomonads have been regarded as closely related protozoan groups. It has been proposed that diplomonads originated within enteromonads in a single event of karyomastigont duplication. This paper presents the first study to address these questions using molecular phylogenetics. The sequences of the small-subunit rRNA genes for three isolates of enteromonads were determined and a tree constructed with available diplomonad, retortamonad and Carpediemonas sequences. The diplomonad sequences formed two main groups, with the genus Giardia on one side and the genera Spironucleus, Hexamita and Trepomonas on the other. The three enteromonad sequences formed a clade robustly situated within the diplomonads, a position inconsistent with the original evolutionary proposal. The topology of the tree indicates either that the diplokaryotic cell of diplomonads arose several times independently, or that the monokaryotic cell of enteromonads originated by secondary reduction from the diplokaryotic state.
Differentiation of Mycobacterium species by analysis of the heat-shock protein 65 gene (hsp65)
Authors: Kim Hong , Kim Sun-Hyun , Shim Tae-Sun , Kim Mi-na , Bai Gill-Han , Park Young-Gil , Lee Sueng-Hyun , Chae Gue-Tae , Cha Chang-Yong , Kook Yoon-Hoh , Kim Bum-Joon
Published: July 2005

The nucleotide sequences (604 bp) of partial heat-shock protein genes (hsp65) from 161 Mycobacterium strains containing 56 reference Mycobacterium species and 105 clinical isolates were determined and compared. hsp65 sequence analysis showed a higher degree of divergence between Mycobacterium species than did 16S rRNA gene analysis. Generally, the topology of the phylogenetic tree based on the hsp65 DNA sequences was similar to that of the 16S rRNA gene, thus revealing natural relationships among Mycobacterium species. When a direct sequencing protocol targeting 422 bp sequences was applied to 70 non-tuberculous mycobacterium (NTM) clinical isolates, all NTMs were clearly identified. In addition, an XhoI PCR restriction fragment length polymorphism analysis method for the differentiation of Mycobacterium tuberculosis complex from NTM strains was developed during this study. The results obtained suggest that 604 bp hsp65 sequences are useful for the phylogenetic analysis and species identification of mycobacteria.
Nocardia elegans sp. nov., a member of the Nocardia vaccinii clade isolated from sputum
Authors: Yassin A. F. , Brenner S.
Published: July 2005

Two bacterial isolates from the sputa of a patient with a pulmonary infection were subjected to a polyphasic taxonomic study. Chemotaxonomic investigations revealed the presence of cell-wall chemotype IV and mycolic acids consistent with the profile for the genus Nocardia. Comparative 16S rRNA gene sequencing showed that these isolates constitute a distinct subline within the genus Nocardia, displaying 99·6–95·5 % sequence similarities with established species. However, DNA–DNA hybridization studies demonstrated unambiguously that the isolates are genealogically distinct from closely related species, namely Nocardia veterana and Nocardia africana, which show high levels of 16S rRNA sequence similarity (99·2 and 99·6 % sequence similarity, respectively). On the basis of both phenotypic and phylogenetic evidence, it is proposed that these isolates be classified as a novel species of the genus Nocardia, for which the name Nocardia elegans sp. nov. is proposed. The type strain is IMMIB N-402T (=CCUG 50200T=CIP 108553T).
Rhodococcus triatomae sp. nov., isolated from a blood-sucking bug
Authors: Yassin A. F.
Published: July 2005

Two bacterial isolates, strains IMMIB RIV-085T and IMMIB RIV-095, isolated from a blood-sucking bug of the genus Triatoma, were characterized by phenotypic and molecular taxonomic methods. Chemotaxonomic investigations revealed the presence of cell-wall chemotype IV and mycolic acids consistent with the genus Rhodococcus. Comparative 16S rRNA gene sequencing showed that the two isolates are genealogically highly related (100 % sequence similarity) and constitute a new subline within the genus Rhodococcus, with Rhodococcus corynebacteroides and Rhodococcus rhodnii as their nearest phylogenetic neighbours (98·4 and 98·3 % sequence similarity, respectively). However, DNA–DNA hybridization experiments demonstrated unambiguously that the isolates are genealogically distinct from R. corynebacteroides and R. rhodnii (32 and 43 % relatedness, respectively). The isolates could be distinguished from their phylogenetic relatives and other members of the genus Rhodococcus by means of biochemical tests. On the basis of both phenotypic and phylogenetic evidence, it is proposed that these isolates be classified as a novel species, Rhodococcus triatomae sp. nov. The type strain is strain IMMIB RIV-085T (=CCUG 50202T=DSM 44892T).
Tetrapisispora namnaonensis sp. nov., a novel ascomycetous yeast species isolated from forest soil of Nam Nao National Park, Thailand
Authors: Sumpradit Tawatchai , Limtong Savitree , Yongmanitchai Wichien , Kawasaki Hiroko , Seki Tatsuji
Published: July 2005

Twenty-one strains of a novel ascomycetous yeast species were isolated from soil collected in three kinds of natural forest, namely a dry dipterocarp forest, a mixed deciduous forest and a pine forest, in Nam Nao National Park, Phetchabun province, Thailand. The strains formed asci containing one to four ovoid to reniform ascospores, assimilated glucose, galactose and glycerol, fermented glucose and galactose vigorously and contained ubiquinone Q-6, indicating that they belonged to the genus Tetrapisispora. A comparative analysis of the small subunit rDNA (SSU rDNA) and the D1/D2 domain of the large subunit rDNA (LSU rDNA) of all available sequences for ascomycetous yeasts confirmed that the strains were phylogenetically related to the genus Tetrapisispora. All strains had identical nucleotide sequences in the D1/D2 domain of the LSU rDNA and differed from the nearest species, Tetrapisispora arboricola IFO 10925T, by 6·4 % nucleotide substitutions. The strains differed from Tetrapisispora arboricola by the ability to assimilate d-gluconic acid, the inability to grow on 50 % glucose medium, the nuclear DNA base composition and deliquescent asci. The strains were differentiated from the other four species of Tetrapisispora on the basis of trehalose assimilation, the ability to grow on 50 % glucose or 10 % NaCl plus 5 % glucose, vitamin requirement, the nuclear DNA base composition and the type of ascus. Based on the characteristics mentioned above, the strains are recognized as a single novel species of the genus Tetrapisispora and the name Tetrapisispora namnaonensis sp. nov. is proposed. The type strain is TN1-01T (=TISTR 5828T=JCM 12664T=CBS 10093T).
Pseudomonas azotifigens sp. nov., a novel nitrogen-fixing bacterium isolated from a compost pile
Authors: Hatayama Kouta , Kawai Satomi , Shoun Hirofumi , Ueda Yasuichi , Nakamura Akira
Published: July 2005

A nitrogen-fixing bacterium, designated strain 6H33bT, was isolated from a compost pile in Japan. The nitrogenase activity of this strain was detected based on its acetylene-reducing activity under low oxygen concentrations (2–4 %). An analysis of the genes responsible for nitrogen fixation in this strain,nifHandnifD, indicated a close relationship to those ofPseudomonas stutzeriA15 (A1501). Sequence similarity searches based on the 16S rRNA gene sequences showed that strain 6H33bTbelongs within the genusPseudomonas sensu stricto; closest similarity was withPseudomonas indica(97·3 %). A comparison of several taxonomic characteristics of 6H33bTwith those ofP. indicaand some type strains of the genusPseudomonas sensu strictoindicated that 6H33bTcould be distinguished fromP. indicabased on the presence of nitrogen fixation ability, the absence of nitrate reduction and denitrification abilities and the utilization of some sugars and organic acids. Phylogenetic analyses and the results of DNA–DNA hybridization experiments also indicated that strain 6H33bTrepresents a species distinct fromP. indica. From these results, it is proposed that strain 6H33bT(=ATCC BAA-1049T=JCM 12708T) is classified as the type strain of a novel species of the genusPseudomonas sensu strictounder the namePseudomonas azotifigenssp. nov.
Pseudomonas panacis sp. nov., isolated from the surface of rusty roots of Korean ginseng
Authors: Park Yoon-Dong , Lee Hyang Burm , Yi Hana , Kim Youngjun , Bae Kyung Sook , Choi Jae-Eul , Jung Hack Sung , Chun Jongsik
Published: July 2005

A Gram-negative, aerobic bacterium, designated CG20106T, was isolated from the surface tissues of rusty root lesions of Korean ginseng. Phylogenetic analysis of the 16S rRNA gene sequence revealed that this isolate represents a hitherto unknown subline within the genus Pseudomonas. Strain CG20106T was catalase- and oxidase-positive, motile and rod-shaped. The overall phenotypic features of the ginseng isolate were similar to those of Pseudomonas cedrina, Pseudomonas migulae and Pseudomonas azotoformans. However, several physiological and chemotaxonomic properties can be weighted to distinguish the isolate from these organisms. The major fatty acids were C16 : 1
ω7c and/or iso-C15 : 0 2-OH (summed feature 3, 36·4±0·4 %), C16 : 0 (27·5±0·7 %) and C18 : 1
ω7c (19·4±0·2 %). The DNA G+C content was 61·4 mol%. On the basis of the polyphasic results revealed in this study, the name Pseudomonas panacis sp. nov. is proposed for strain CG20106T. The type strain is CG20106T (=IMSNU 14100T=CIP 108524T=KCTC 12330T).
Methylobacterium variabile sp. nov., a methylotrophic bacterium isolated from an aquatic environment
Authors: Gallego Virginia , García Maria Teresa , Ventosa Antonio
Published: July 2005

Strain GR3Twas isolated from drinking water during a screening programme to monitor the bacterial population present in the distribution system of Seville (Spain), and it was studied phenotypically, genotypically and phylogenetically. This pink-pigmented bacterium was identified as aMethylobacteriumsp. Members of this genus are distributed in a wide variety of natural habitats, including soil, dust, air, freshwater and aquatic sediments. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain GR3Twas closely related toMethylobacterium aquaticum(97·4 % sequence similarity), whereas sequence similarity values with respect to the rest of the species belonging to this genus were lower than 96 %. Furthermore, the DNA–DNA hybridization data and its phenotypic characteristics clearly indicate that the isolate represents a novelMethylobacteriumspecies, for which the nameMethylobacterium variabilesp. nov. is proposed. GR3T(=DSM 16961T=CCM 7281T=CECT 7045T) is the type strain; the DNA G+C content of this strain is 69·2 mol%.
Shewanella sediminis sp. nov., a novel Na+-requiring and hexahydro-1,3,5-trinitro-1,3,5-triazine-degrading bacterium from marine sediment
Authors: Zhao Jian-Shen , Manno Dominic , Beaulieu Chantale , Paquet Louise , Hawari Jalal
Published: July 2005

Previously, a psychrophilic rod-shaped marine bacterium (strain HAW-EB3T) isolated from Halifax Harbour sediment was noted for its ability to degrade hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). In the present study phenotypic, chemotaxonomic and genotypic characterization showed that strain HAW-EB3Trepresents a novel species ofShewanella. Strain HAW-EB3Tcontained lysine decarboxylase, which is absent in other knownShewanellaspecies, and distinguished itself from most other species ofShewanellaby the presence of arginine dehydrolase, ornithine decarboxylase and chitinase, and by its ability to oxidize and fermentN-acetyl-d-glucosamine. Strain HAW-EB3Tgrew on several carbon sources (N-acetyl-d-glucosamine, Tween 40, Tween 80, acetate, succinate, butyrate and serine) and showed distinctive fatty acid and quinone compositions. Both phenotypic and 16S rRNA gene phylogenetic cluster analyses demonstrated that HAW-EB3Tbelongs to the Na+-requiring group ofShewanellaspecies. The HAW-EB3T16S rRNA gene sequence displayed ⩽97·4 % similarity to all knownShewanellaspecies and was most similar to those of two bioluminescent species,Shewanella hanedaiandShewanella woodyi. However,gyrBof strain HAW-EB3Twas significantly different from those of otherShewanellaspecies, with similarities less than 85 %. DNA-DNA hybridization showed that its genomic DNA was less than 25 % related to that ofS. hanedaiorS. woodyi. Therefore we proposeShewanella sediminissp. nov., with HAW-EB3T(=NCIMB 14036T=DSM 17055T) as the type strain.
Saccharophagus degradans gen. nov., sp. nov., a versatile marine degrader of complex polysaccharides
Authors: Ekborg Nathan A. , Gonzalez Jose M. , Howard Michael B. , Taylor Larry E. , Hutcheson Steven W. , Weiner Ronald M.
Published: July 2005

Gammaproteobacteria belonging and related to the genusMicrobulbiferare an emerging group of complex carbohydrate-degrading marine bacteria. Previously, all of the representatives were placed withinMicrobulbiferor were unclassified. Recently, a new genus,Teredinibacter, represented by a single species,Teredinibacter turnerae, was formed to include an endosymbiotic branch of these organisms. In this study, based on 16S rRNA gene sequence similarity and phenotypic analyses, a new genus,Saccharophagus, is proposed to accommodate the most versatile marine carbohydrate degrader yet identified,Saccharophagus degradansgen. nov., sp. nov. 2-40T(=ATCC 43961T=DSM 17024T).S. degradansstrain 2-40Tcan degrade 10 tested complex polysaccharides: agar, alginate, chitin, cellulose, fucoidan, laminarin, pectin, pullulan, starch and xylan.S. degradans2-40Tshares 90·5 % 16S rRNA gene sequence similarity with the type strain of theMicrobulbifertype species,Microbulbifer hydrolyticusIRE-31T, and 91·5 % withT. turneraeT7902T, and can be further distinguished from members of these two genera by 16S rRNA gene cluster analysis, the ability to utilize 10 different complex polysaccharides as sole carbon sources, a significantly lower G+C content and differences in fatty acid content. The three genera of complex polysaccharide-degrading, marine bacteria now encompass 20 strains from diverse marine niches.
Nocardioides kribbensis sp. nov., isolated from an alkaline soil
Authors: Yoon Jung-Hoon , Kim In-Gi , Lee Mi-Hwa , Oh Tae-Kwang
Published: July 2005

Three Gram-positive, rod- or coccoid-shaped bacterial strains, KSL-2T, KSL-5 and KSL-6, were isolated from an alkaline soil in Korea and subjected to a polyphasic taxonomical analysis. These isolates grew optimally at pH 9·0 and 30 °C. They were characterized chemotaxonomically as having cell wall peptidoglycan based on ll-2,6-diaminopimelic acid, MK-8(H4) as the predominant menaquinone and iso-C16 : 0 as the major fatty acid. The DNA G+C content of the isolates was 73–74 mol%. Strains KSL-2T, KSL-5 and KSL-6 were identical in their 16S rRNA gene sequences and exhibited DNA–DNA relatedness values of 88–93 %. Phylogenetic trees based on 16S rRNA gene sequences showed that the three isolates fell within the evolutionary radiation encompassed by the genus Nocardioides. Levels of 16S rRNA gene sequence similarity between the three strains and the type strains of Nocardioides species ranged from 93·6 % (with Nocardioides albus) to 97·2 % (with Nocardioides aquiterrae). DNA–DNA relatedness levels between the three isolates and N. aquiterrae CJ-14T were 8–15 %. On the basis of phenotypic, phylogenetic and genetic data, strains KSL-2T, KSL-5 and KSL-6 were classified in the genus Nocardioides as members of a novel species for which the name Nocardioides kribbensis sp. nov. is proposed, with KSL-2T (=KCTC 19038T=DSM 16314T) as the type strain.
Prevotella marshii sp. nov. and Prevotella baroniae sp. nov., isolated from the human oral cavity
Authors: Downes Julia , Sutcliffe Iain , Tanner Anne C. R. , Wade William G.
Published: July 2005

Eleven strains of anaerobic Gram-negative bacilli isolated from the human oral cavity were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise two homogeneous groups, designated E2 and E4. 16S rRNA gene sequence analysis revealed that members of both groups belonged to the genus Prevotella but were distinct from any species with validly published names. This distinction was confirmed by DNA–DNA hybridization and phenotypic tests. Two novel species are therefore proposed: Prevotella marshii sp. nov. (group E2) and Prevotella baroniae (group E4). Both species are saccharolytic; the end-products of fermentation for P. marshii are acetic, propionic and succinic acids, while P. baroniae produces acetic and succinic acids with minor amounts of isovaleric and isobutyric acids. The G+C content of the DNA of the type strain of Prevotella marshii is 51 mol% and that of Prevotella baroniae is 52 mol%. The type strain for P. marshii is E9.34T (=DSM 16973T=CCUG 50419T) and that for P. baroniae is E9.33T (=DSM 16972T=CCUG 50418T).
Cellulomonas bogoriensis sp. nov., an alkaliphilic cellulomonad
Authors: Jones Brian E. , Grant William D. , Duckworth A. W. , Schumann Peter , Weiss Norbert , Stackebrandt Erko
Published: July 2005

An alkaliphilic, slightly halotolerant, chemo-organotrophic, Gram-positive, rod-shaped bacterium, strain 69B4T, was isolated from the sediment of the littoral zone of Lake Bogoria, Kenya. Phylogenetically, it is a member of the genusCellulomonas, showing less than 97·5 % sequence similarity to the type strains of otherCellulomonasspecies. The highest level of similarity, albeit moderate, was found with respect toCellulomonas cellaseaDSM 20118T. Chemotaxonomic properties confirm the 16S rRNA gene-based generic affiliation, i.e. a DNA G+C content of 71·5 mol%, anteiso-C15 : 0and C16 : 0as the major fatty acids, MK-9(H4) as the major isoprenoid quinone, a peptidoglycan containingl-ornithine as the diamino acid andd-aspartic acid in the interpeptide bridge and phosphatidylglycerol as the only identified main polar lipid. The strain is aerobic to facultatively anaerobic, being capable of growth under strictly anaerobic conditions. Optimal growth occurs between pH values 9·0 and 10·0. On the basis of its distinct phylogenetic position and metabolic properties, strain 69B4Trepresents a novel species of the genusCellulomonas, for which the nameCellulomonas bogoriensissp. nov. is proposed. The type strain is 69B4T(=DSM 16987T=CIP 108683T).
‘Candidatus Erwinia dacicola’, a coevolved symbiotic bacterium of the olive fly Bactrocera oleae (Gmelin)
Authors: Capuzzo Caterina , Firrao Giuseppe , Mazzon Luca , Squartini Andrea , Girolami Vincenzo
Published: July 2005

The taxonomic identity of the hereditary prokaryotic symbiont of the olive flyBactrocera oleae(Diptera: Tephritidae) was investigated. In order to avoid superficial microbial contaminants and loosely associated saprophytic biota, flies were surface-sterilized at the larval stage and reared under aseptic conditions until adult emergence.B. oleaeflies originating from different geographical locations and collected at different times of the year were tested. Bacterial isolation was undertaken from the cephalic oesophageal bulb, which is known to be a specific site of accumulation for the hosted microsymbionts in the adult insect. Despite evidence of multiplication cycles taking place within the insect, attempts at cultivation of the isolated bacteriaex situwere not productive at any stage, leading to the choice of unculturable status definition. PCR amplification and nucleotide sequencing of the entire 16S rRNA gene consistently yielded a single sequence that displayed marked similarity with enterobacterial lineages, with closest matches (97 %) toErwinia persicinaandErwinia rhapontici. The novel taxon differs from common intestinal bacterial species of fruit flies and from instances of culturable bacteria previously described inB. oleaeraised without sterility precautions, which we also observed as minority occupants or occasional contaminants. The symbiont's identity is also distinct fromPseudomonas savastanoi. In all observations, the numerically dominant inhabitant of the olive fly oesophageal organ was the same unculturable organism, whose presence at later stages was also regularly observed in the midgut. A novel species is proposed, by virtue of its unique properties, under the designation ‘CandidatusErwinia dacicola’.