bluuebunny/crossref_metadata_2025 huggingface dataset:
Zimmermannella helvola gen. nov., sp. nov., Zimmermannella alba sp. nov., Zimmermannella bifida sp. nov., Zimmermannella faecalis sp. nov. and Leucobacter albus sp. nov., novel members of the family Microbacteriaceae
Authors: Lin Yi-Chueh , Uemori Kazunori , de Briel Dominique A. , Arunpairojana Vallapa , Yokota Akira
Published: September 2004

Seven strains of actinobacteria, isolated from soil, wounds, urine, cow faeces, human blood and butter, were characterized by a polyphasic approach to clarify their taxonomic position. On the basis of chemotaxonomy, 16S rRNA gene analysis and DNA relatedness, strain IAM 14851Tcan be classified within the cluster of the genusLeucobacterand is proposed as a novel species,Leucobacter albussp. nov., with strain IAM 14851T(=TISTR 1515T) as the type strain. The other six strains formed a phylogenetically separate branch in the familyMicrobacteriaceae, having the following characteristics: the major menaquinones are MK-8 to MK-10, the DNA G+C content ranges from 62 to 68 mol%, the diamino acid in the cell wall is diaminobutyric acid and the muramic acid in the peptidoglycan is of the acetyl type. The major fatty acids are 12-methyltetradecanoic acid (anteiso-C15 : 0), hexadecanoic acid (C16 : 0), 14-methyl-pentadecanoic acid (iso-C16 : 0) and 14-methyl-hexadecanoic acid (anteiso-C17 : 0). On the basis of morphological, physiological and chemotaxonomic characteristics, together with DNA–DNA hybridization and 16S rRNA gene sequence comparison, the novel genusZimmermannellagen. nov. is proposed for these six strains. Four novel species are proposed:Zimmermannella helvolasp. nov. (type species; type strain IAM 14726T=NBRC 15775T=DSM 20419T=TISTR 1509T),Zimmermannella albasp. nov. (type strain IAM 14724T=NBRC 15616T=TISTR 1510T),Zimmermannella bifidasp. nov. (type strain IAM 14848T=TISTR 1511T) andZimmermannella faecalissp. nov. (type strain IAM 15030T=NBRC 15706T=ATCC 13722T=TISTR 1514T).
Kocuria marina sp. nov., a novel actinobacterium isolated from marine sediment
Authors: Kim Seung Bum , Nedashkovskaya Olga I. , Mikhailov Valery V. , Han Suk Kyun , Kim Kyoung-Ok , Rhee Moon-Soo , Bae Kyung Sook
Published: September 2004

An actinobacterial strain was isolated from marine sediment taken from the Troitsa Bay of the Gulf of Peter the Great, East Siberian Sea, and subjected to a taxonomic investigation. The isolate, designated KMM 3905T, was Gram-positive, aerobic, non-motile and coccoid. The strain tolerated up to 15 % NaCl in growth media, although its presence was not essential for growth. Chemotaxonomic and phylogenetic properties of the strain were consistent with its classification in the genus Kocuria. The strain formed an independent phylogenetic line in the 16S rRNA gene tree encompassed by members of Kocuria. Comparison of phenotypic characteristics also supported its assignment to a novel species within Kocuria. The name Kocuria marina sp. nov. (type strain KMM 3905T=KCTC 9943T) is proposed for this halotolerant actinobacterium from the marine environment.
Taxonomic variation in the Mycobacterium fortuitum third biovariant complex: description of Mycobacterium boenickei sp. nov., Mycobacterium houstonense sp. nov., Mycobacterium neworleansense sp. nov. and Mycobacterium brisbanense sp. nov. and recognition of Mycobacterium porcinum from human clinical isolates
Authors: Schinsky Mark F. , Morey Roger E. , Steigerwalt Arnold G. , Douglas Michael P. , Wilson Rebecca W. , Floyd Margaret M. , Butler W. Ray , Daneshvar Maryam I. , Brown-Elliott Barbara A. , Wallace Richard J. , McNeil Michael M. , Brenner Don J. , Brown June M.
Published: September 2004

The Mycobacterium fortuitum third biovariant complex (sorbitol-negative and sorbitol-positive) contains unnamed taxa first characterized in 1991. These organisms can cause respiratory infections, a spectrum of soft tissue and skeletal infections, bacteraemia and disseminated disease. To evaluate this group of organisms, clinical reference isolates and the type strains of M. fortuitum third biovariant complex sorbitol-negative (n=21), M. fortuitum third biovariant complex sorbitol-positive (n=3), M. fortuitum (n=3), Mycobacterium peregrinum (pipemidic acid-susceptible) (n=1), Mycobacterium porcinum (n=1), Mycobacterium senegalense (n=2) and Mycobacterium septicum (n=1) were characterized by using conventional phenotypic (morphological, physiological and antimicrobial susceptibilities), chemotaxonomic (HPLC and cellular fatty acids) and genotypic [RFLP of the rRNA gene (ribotyping), PCR-RFLP of a 439 bp segment of the 65 kDa hsp gene (PCR restriction analysis) and 16S rRNA gene sequence] analysis, DNA G+C content and DNA–DNA relatedness analyses. The results of these studies indicated that the strains comprised M. porcinum (n=13), M. septicum (n=1) and four novel closely related genetic groups within the M. fortuitum third biovariant complex: Mycobacterium boenickei sp. nov. (n=6), Mycobacterium houstonense sp. nov. (n=2), Mycobacterium neworleansense sp. nov. (n=1) and Mycobacterium brisbanense sp. nov. (n=1), with type strains ATCC 49935T (=W5998T=DSM 44677T), ATCC 49403T (=W5198T=DSM 44676T) ATCC 49404T (=W6705T=DSM 44679T) and ATCC 49938T (=W6743T=DSM 44680T), respectively.
Reclassification of Agromyces fucosus subsp. hippuratus as Agromyces hippuratus sp. nov., comb. nov. and emended description of Agromyces fucosus
Authors: Ortiz-Martinez A. , Gonzalez J. M. , Evtushenko L. I. , Jurado V. , Laiz L. , Groth I. , Saiz-Jimenez C.
Published: September 2004

The taxonomic position of Agromyces fucosus subsp. hippuratus is revised on the basis of molecular and phenotypic data. Phylogenetic analysis based on 16S rRNA gene sequences, DNA–DNA relatedness values and differences from other species in phenotypic traits revealed in this and earlier studies suggested reclassification of A. fucosus subsp. hippuratus as a separate species, Agromyces hippuratus sp. nov., comb. nov. The type strain is VKM Ac-1352T (=JCM 9087T). An emended description of Agromyces fucosus is given.
Anoxybacillus ayderensis sp. nov. and Anoxybacillus kestanbolensis sp. nov.
Authors: Dulger Sabriye , Demirbag Zihni , Belduz Ali Osman
Published: September 2004

Two thermophilic bacilli were isolated from mud and water samples of the Ayder and Kestanbol hot springs in the provinces of Rize and Canakkale, respectively, in Turkey. Strains AB04T and K4T were sporulating, Gram-positive, rod-shaped bacteria. These isolates were moderately thermophilic (with an optimum temperature for growth of 50–55 °C), facultative anaerobes able to grow on a wide range of carbon sources including d-glucose, d-raffinose, d-sucrose, d-xylose, d-fructose, l-arabinose, maltose, d-mannose and d-mannitol. Analysis of the 16S rRNA gene sequences showed that these isolates resembled Anoxybacillus flavithermus DSM 2641T and Anoxybacillus gonensis NCIMB 13933T. DNA–DNA hybridization data revealed that thermophilic isolate AB04T has only 51·2 % relatedness to A. flavithermus, 45·1 % relatedness to Anoxybacillus pushchinoensis and 68·6 % relatedness to A. gonensis. Thermophilic isolate K4T showed only 60·4 % relatedness to A. flavithermus, 42·9 % relatedness to A. pushchinoensis and 38·5 % relatedness to A. gonensis. On the basis of the DNA–DNA hybridization data, isolates AB04T and K4T are not related to A. flavithermus DSM 2641T, A. pushchinoensis DSM 12423T or A. gonensis NCIMB 13933T at the species level, but show relatedness to one another of 40·5 %. On the basis of the data presented, it is proposed that strains AB04T (=NCIMB 13972T=NCCB 100050T) and K4T (=NCIMB 13971T=NCCB 100051T) be designated as the type strains of Anoxybacillus ayderensis sp. nov. and Anoxybacillus kestanbolensis sp. nov., respectively.
Emended description of the species Lampropedia hyalina
Authors: Lee Natuschka , Cellamare Carmela Maria , Bastianutti Cristiano , Rosselló-Mora Ramon , Kämpfer Peter , Ludwig Wolfgang , Schleifer Karl Heinz , Stante Loredana
Published: September 2004

Three Lampropedia hyalina strains from different habitats were compared by phenotypic, chemotaxonomic and molecular characteristics. All strains form coccoid cells and have been reported to grow as square tablets of eight to 64 cells. However, two of these strains (ATCC 11041T and ATCC 43383) have apparently lost this ability, and the third strain may temporarily lose this capacity under certain cultivation conditions. The three strains showed only minor differences in metabolic characteristics: the main significant physiological difference was the ability to accumulate polyphosphate under alternating anaerobic–aerobic conditions found for DSM 15336. The three strains showed high similarity in fatty acid composition and only slight differences in the G+C content (63–67 mol%) and DNA–DNA reassociation (90–95 % relatedness). Comparative 16S rRNA gene sequence analyses on these three strains and three Lampropedia hyalina 16S rRNA gene sequences deposited at NCBI showed that they are all very similar (>98·8 %) and that they form a distinct group among the ‘Betaproteobacteria’, showing between 94·6 and 93 % 16S rRNA gene similarity to members of various genera such as Acidovorax, Aquaspirillum, Brachymonas, Comamonas, Delftia and Xenophilus. Fluorescent in situ hybridization with oligonucleotide probes targeting betaproteobacteria on the 16S rRNA and 23S rRNA gene level further supported the conclusion that all investigated strains are members of the ‘Betaproteobacteria’. Two oligonucleotide probes were designed and successfully applied for culture-independent identification of Lampropedia hyalina by means of fluorescent in situ hybridization.
Vagococcus carniphilus sp. nov., isolated from ground beef
Authors: Shewmaker P. Lynn , Steigerwalt Arnold G. , Morey Roger E. , Carvalho Maria da Glória S. , Elliott John A. , Joyce Kevin , Barrett Timothy J. , Teixeira Lucia M. , Facklam Richard R.
Published: September 2004

Nine enterococcus-like strains were referred to the Streptococcus Laboratory at the Centers for Disease Control and Prevention (CDC) for further identification from the National Antimicrobial Resistance Monitoring System Laboratory at the CDC. The cultures were isolated from ground beef purchased from retail in Oregon in 2000. Conventional biochemical testing and analysis of whole-cell protein electrophoretic profiles distinguished these strains from known species of enterococci and vagococci. Comparative 16S rRNA gene sequencing studies revealed that these strains were most closely related to the species Vagococcus fluvialis. DNA–DNA reassociation studies confirmed that these nine strains represented a new taxon. The relative binding ratio was 87 % or greater at the optimal temperature, and the divergence was less than 1 % for strains hybridized against the isolate designated the type strain. DNA–DNA relatedness was 25 % to V. fluvialis and 9 % or less to the other three species of Vagococcus. DNA–DNA relatedness was 33 % or less to the 25 currently described species of Enterococcus. On the basis of this evidence, it is proposed that these strains be classified as Vagococcus carniphilus sp. nov. The type strain of V. carniphilus is 1843-02T (=ATCC BAA-640T=CCUG 46823T). The clinical significance (if any) of these strains is yet to be determined.
Mycobacterium parascrofulaceum sp. nov., novel slowly growing, scotochromogenic clinical isolates related to Mycobacterium simiae
Authors: Turenne C. Y. , Cook V. J. , Burdz T. V. , Pauls R. J. , Thibert L. , Wolfe J. N. , Kabani A.
Published: September 2004

A group of pigmented, slowly growing mycobacteria identified by 16S rRNA gene sequencing as ‘MCRO 33’ (GenBank accession no. AF152559) have been isolated from several clinical specimens in various laboratories across Canada. Genotypically, the organism is most closely related toMycobacterium simiae. However, it presents with a similar phenotypic profile toMycobacterium scrofulaceum. Several reference strains obtained from ATCC and TMC culture collections, previously identified asM. scrofulaceumorM. simiae, have also been found to possess the MCRO 33 16S rRNA gene sequence. Biochemical testing, susceptibility testing, HPLC,hsp65gene and 16S–23S spacer (ITS1) sequencing were performed on clinical and reference strains to characterize further this unique species. Of the clinical strains, one was isolated from a cervix biopsy whereas all other clinical isolates were obtained from respiratory samples. In one patient, symptoms, imaging and repeat clinical specimens positive on culture for this organism were suggestive of active clinical disease. The description of this species, for which the nameMycobacterium parascrofulaceumsp. nov. is proposed, follows the present trend of a large number of novelMycobacteriumspecies identified due in great part to sequence-based methods. The type strain is HSC68T(=ATCC BAA-614T=DSM 44648T).
Novosphingobium pentaromativorans sp. nov., a high-molecular-mass polycyclic aromatic hydrocarbon-degrading bacterium isolated from estuarine sediment
Authors: Sohn Jae Hak , Kwon Kae Kyoung , Kang Ji-Hyun , Jung Hong-Bae , Kim Sang-Jin
Published: September 2004

A Gram-negative, yellow-pigmented, halophilic bacterial strain US6-1T, which degrades high-molecular-mass polycyclic aromatic hydrocarbons of two to five rings, was isolated from muddy sediment of Ulsan Bay, Republic of Korea. The 16S rRNA gene of the isolate showed high sequence similarity toNovosphingobium subarcticum(96·23 %) andSphingopyxis alaskensis(96·18 %); however, the isolate formed a distinct phyletic line within the genusNovosphingobium. DNA–DNA relatedness between US6-1Tand the closest strainN. subarcticumrevealed that strain US6-1Twas independent from this species. Isolate US6-1Thad ubiquinone 10 and a DNA G+C ratio of 61·1 mol%. Major fatty acids were octadecanoic acid (18 : 1ω7), hexadecanoic acid (16 : 1ω7) and 2-hydroxy-myristic acid (14 : 0 2-OH). On the basis of polyphasic taxonomic evidence, strain US6-1Tis proposed to represent a novel species in the genusNovosphingobiumfor which the nameNovosphingobium pentaromativoranssp. nov. is proposed. The type strain is US6-1T(=KCTC 10454T=JCM 12182T).
Methylobacillus pratensis sp. nov., a novel non-pigmented, aerobic, obligately methylotrophic bacterium isolated from meadow grass
Authors: Doronina Nina V. , Trotsenko Yuri A. , Kolganova Tatjana V. , Tourova Tatjana P. , Salkinoja-Salonen Mirja S.
Published: September 2004

Strain F31T was isolated from meadow grass (Poa trivialis L.) sampled from the city park in Helsinki. Analysis of phenotypic and genotypic properties showed the strain to be related to the group of obligately methylotrophic non-methane utilizing bacteria (methylobacteria) with the ribulose monophosphate pathway of formaldehyde assimilation. Phylogenetic analysis showed the strain to be closely related to the genus Methylobacillus, and analysis of fatty acid composition confirmed this association. Thus, on the basis of its genotypic and phenotypic properties, the isolate is proposed as a novel species of the genus Methylobacillus, Methylobacillus pratensis sp. nov., with F31T as the type strain (=VKM B-2247T=NCIMB 13994T).
Comparison of 16S rRNA, nifD, recA, gyrB, rpoB and fusA genes within the family Geobacteraceae fam. nov.
Authors: Holmes Dawn E. , Nevin Kelly P. , Lovley Derek R.
Published: September 2004

The sequences of five conserved genes, in addition to the 16S rRNA gene, were investigated in 30 members of the Geobacteraceae fam. nov. All members of the Geobacteraceae examined contained nifD, suggesting that they are capable of nitrogen fixation, which may explain their ability to compete effectively in nitrogen-poor subsurface environments undergoing remediation for petroleum or metal contamination. The phylogenies predicted from rpoB, gyrB, fusA, recA and nifD were generally in agreement with the phylogeny predicted from 16S rRNA gene sequences. Furthermore, phylogenetic analysis of concatemers constructed from all five protein-coding genes corresponded closely with the 16S rRNA gene-based phylogeny. This study demonstrated that the Geobacteraceae is a phylogenetically coherent family within the δ-subclass of the Proteobacteria that is composed of three distinct phylogenetic clusters: Geobacter, Desulfuromonas and Desulfuromusa. The sequence data provided here will make it possible to discriminate better between physiologically distinct members of the Geobacteraceae, such as Pelobacter propionicus and Geobacter species, in geobacteraceae-dominated microbial communities and greatly expands the potential to identify geobacteraceae sequences in libraries of environmental genomic DNA.
Oceanithermus desulfurans sp. nov., a novel thermophilic, sulfur-reducing bacterium isolated from a sulfide chimney in Suiyo Seamount
Authors: Mori Koji , Kakegawa Takeshi , Higashi Yowsuke , Nakamura Ko-ichi , Maruyama Akihiko , Hanada Satoshi
Published: September 2004

A novel thermophilic, microaerophilic, sulfur-reducing bacterium designated strain St55BTwas isolated from a sulfide chimney in the hydrothermal field of Suiyo Seamount (Izu-Bonin Arc, Western Pacific). Cells of the isolate were rod-shaped and tended to form a chain-link circular structure (a rotund body) at exponential phase under good growth conditions. The isolate was a chemoheterotroph requiring yeast extract for growth. Although strain St55BTused oxygen as an electron acceptor, it could not form colonies in an oxygen concentration of more than 5 % (v/v). The isolate also used nitrate, nitrite or elemental sulfur in the absence of oxygen. A phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was closely related toOceanithermus profundus, belonging to the phylum ‘Deinococcus–Thermus’ (sequence similarity 99·5 %). However, strain St55BTdiffered fromO. profundusin terms of usage of electron donors, cellular fatty acid profile and DNA G+C content. In addition, a DNA–DNA hybridization test indicated low relatedness between the isolate andO. profundus. For the reasons given above, the nameOceanithermus desulfuranssp. nov. is proposed for strain St55BT(=NBRC 100063T=DSM 15757T).
Phylogenetic relationships among marine Alteromonas-like proteobacteria: emended description of the family Alteromonadaceae and proposal of Pseudoalteromonadaceae fam. nov., Colwelliaceae fam. nov., Shewanellaceae fam. nov., Moritellaceae fam. nov., Ferrimonadaceae fam. nov., Idiomarinaceae fam. nov. and Psychromonadaceae fam. nov.
Authors: Ivanova Elena P. , Flavier Sébastien , Christen Richard
Published: September 2004

The phylogenetic relationships among marineAlteromonas-like bacteria of the generaAlteromonas,Pseudoalteromonas,Glaciecola,Thalassomonas,Colwellia,Idiomarina,Oceanimonas,Oceanisphaera,Shewanella,Moritella,Ferrimonas,Psychromonasand several other genera of the ‘Gammaproteobacteria’ were studied. Results of 16S rRNA gene sequence analyses revealed that some members of these genera formed several coherent groups at the family level. Characteristic signature oligonucleotides for studied taxa were defined. Signature positions are divided into three classes: (i) single compensatory mutations, (ii) double compensatory mutations and (iii) mutations affecting nucleotides not paired in the secondary structure. The 16S rRNA gene sequence similarity level within genera was 93 % or above. This value can be a useful additional criterion for genus discrimination. On the basis of this work and previous polyphasic taxonomic studies, the circumscription of the familyAlteromonadaceaeis limited to the generaAlteromonasandGlaciecolaand the creation is proposed of the familiesPseudoalteromonadaceaefam. nov. to accommodate bacteria of the generaPseudoalteromonasandAlgicolagen. nov. (formerlyPseudoalteromonas bacteriolytica) andColwelliaceaefam. nov. to accommodate bacteria of the generaColwelliaandThalassomonas. Bacteria of the generaOceanimonasandOceanisphaeraformed a robust cluster and shared common signature oligonucleotides. Because of deep branching and lack of association with any other genus, the following families are proposed that include single genera:Idiomarinaceaefam. nov.,Psychromonadaceaefam. nov.,Moritellaceaefam. nov.,Ferrimonadaceaefam. nov. andShewanellaceaefam. nov. Finally, this study also revealed that [Hyphomicrobium]indicumshould be reclassified asPhotobacterium indicumcomb. nov.
Mycobacterium canariasense sp. nov.
Authors: Jiménez M. Soledad , Campos-Herrero M. Isolina , García Diana , Luquin Marina , Herrera Laura , García María J.
Published: September 2004

A novel rapidly growing, non-pigmented mycobacterium was isolated from blood samples obtained from 17 patients with febrile syndrome. Bacterial growth occurred at 30 and 37 °C on Löwenstein–Jensen medium and also on MacConkey agar without crystal violet. Strains contained α- and α′-mycolates in their cell wall. Sequence analysis of the hsp65 and 16S rRNA genes identified the isolates as rapidly growing mycobacteria. Sequences of both genes were unique within the mycobacteria. DNA–DNA hybridization showed that the isolates had less than 15 % reassociation with 13 other recognized rapidly growing mycobacteria. The name Mycobacterium canariasense sp. nov. is proposed for this novel opportunistic pathogen, which is most closely related to Mycobacterium diernhoferi. The type strain is 502329T (=CIP 107998T=CCUG 47953T).
Alicyclobacillus vulcanalis sp. nov., a thermophilic, acidophilic bacterium isolated from Coso Hot Springs, California, USA
Authors: Simbahan Jessica , Drijber Rhae , Blum Paul
Published: September 2004

A thermo-acidophilic Gram-positive bacterium, strain CsHg2T, which grows aerobically at 35–65 °C (optimum 55 °C) and at pH 2·0–6·0 (optimum 4·0), was isolated from a geothermal pool located in Coso Hot Springs in the Mojave Desert, California, USA. Phylogenetic analysis of 16S rRNA gene sequences showed that this bacterium was most closely related to the type strains ofAlicyclobacillus acidocaldarius(97·8 % identity) andAlicyclobacillus sendaiensis(96·9 %), three Japanese strains denoted as UZ-1, KHA-31 and MIH 332 (96·1–96·5 %) andAlicyclobacillusgenomic species FR-6 (96·3 %). Phenotypic characteristics including temperature and pH optima, G+C composition, acid production from a variety of carbon sources and sensitivity to different metal salts distinguished CsHg2TfromA. acidocaldarius,A. sendaiensisand FR-6. The cell lipid membrane was composed mainly ofω-cyclohexyl fatty acid, consistent with membranes from otherAlicyclobacillusspecies. Very low DNA–DNA hybridization values between CsHg2Tand the type strains ofAlicyclobacillusindicate that CsHg2Trepresents a distinct species. On the basis of these results, the nameAlicyclobacillus vulcanalissp. nov. is proposed for this organism. The type strain is CsHg2T(ATCC BAA-915T=DSM 16176T).
Comparative phylogenies of the housekeeping genes atpD, infB and rpoB and the 16S rRNA gene within the Pasteurellaceae
Authors: Christensen Henrik , Kuhnert Peter , Olsen John Elmerdahl , Bisgaard Magne
Published: September 2004

Phylogenies of housekeeping gene and 16S rRNA gene sequences were compared to improve the classification of the bacterial family Pasteurellaceae and knowledge of the evolutionary relationships of its members. Deduced partial protein sequences of the housekeeping genes atpD, infB and rpoB were compared in 28, 36 and 28 representative taxa of the Pasteurellaceae, respectively. The monophyly of representatives of the genus Gallibacterium was recognized by analysis of all housekeeping genes, while members of Mannheimia, Actinobacillus sensu stricto and the core group of Pasteurella sensu stricto formed monophyletic groups with two out of three housekeeping genes. Representatives of Mannheimia, Actinobacillus sensu stricto, [Haemophilus] ducreyi and [Pasteurella] trehalosi formed a monophyletic unit by analysis of all three housekeeping genes, which was in contrast to the 16S rRNA gene-derived phylogeny, where these taxa occurred at separate positions in the phylogenetic tree. Representatives of the Rodent, Avian and Aphrophilus–Haemophilus 16S rRNA gene groups were weakly supported by phylogenetic analysis of housekeeping genes. Phylogenies derived by comparison of the housekeeping genes diverged significantly from the 16S rRNA gene-derived phylogeny as evaluated by the likelihood ratio test. A low degree of congruence was also observed between the individual housekeeping gene-derived phylogenies. Estimates on speciation derived from 16S rRNA and housekeeping gene sequence comparisons resulted in quite different evolutionary scenarios for members of the Pasteurellaceae. The phylogeny based on the housekeeping genes supported observed host associations between Mannheimia, Actinobacillus sensu stricto and [Pasteurella] trehalosi and animals with paired hooves.
Parvibaculum lavamentivorans gen. nov., sp. nov., a novel heterotroph that initiates catabolism of linear alkylbenzenesulfonate
Authors: Schleheck David , Tindall Brian J. , Rosselló-Mora Ramón , Cook Alasdair M.
Published: September 2004

Strain DS-1T is a small (0·8 μm in length and 0·2 μm in diameter) heterotrophic bacterium able to ω-oxygenate the commercial surfactant linear alkylbenzenesulfonate (LAS) and shorten the side chain by β-oxidation to yield sulfophenylcarboxylates. The morphotype is widespread in cultures able to utilize LAS, and a second organism with similar characteristics, strain AN-8, is now available. Utilization of LAS is concomitant with formation of a biofilm, and cells were non-motile. Many surfactants were utilized. The organisms also grew with acetate or octane, but required no biofilm and were motile. Analysis of the gene encoding 16S rRNA placed the organisms in the α-subclass of the Proteobacteria with a sequence divergence of >8 % from any species whose name has been validly published. 16S rRNA gene sequence comparison with entries in the GenBank database showed 98 % similarity to an α-protobacterial marine isolate, JP57: strain JP57 displayed the same morphotype as strain DS-1T, but it was unable to utilize surfactants or any single source of carbon tested. The lipid components of strains DS-1T and JP57 were virtually identical. The fatty acids contained ester- and putative amide-linked hydroxy fatty acids, in a combination that is currently unique in the α-Proteobacteria. The major respiratory quinone present in both strains was Q11. The polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and two unidentified aminolipids. Data on the 16S rRNA gene sequence and the lipid composition indicated that strains DS-1T and JP57 should be placed in a new genus, for which the name Parvibaculum is proposed. The differences between these strains, supported by DNA hybridizations, lead to the conclusion that strain DS-1T (=DSM 13023T=NCIMB 13966T) is the type strain of a species in the genus Parvibaculum, for which the name Parvibaculum lavamentivorans gen. nov., sp. nov. is proposed.
Pseudomonas psychrotolerans sp. nov.
Authors: Hauser Elke , Kämpfer Peter , Busse Hans-Jürgen
Published: September 2004

Three yellow-pigmented, Gram-negative, rod-shaped, non-spore-forming bacterial strains, C36T, C37 and C39, were isolated in the Medical Clinic for Small Animals and Ungulates at the University for Veterinary Medicine in Vienna, Austria. On the basis of 16S rRNA gene sequence similarity, strain C36Twas shown to belong to the genusPseudomonas;Pseudomonas oleovoransDSM 1045Twas the nearest relative (99·5 % sequence similarity). OtherPseudomonasspecies shared <97 % sequence similarity with strain C36T. The presence of Q-9 as the major ubiquinone, the predominance of putrescine and spermidine in its polyamine patterns and its fatty acid profile [i.e. the predominance of C16 : 0, summed feature 3 (C16 : 1ω7cand/or 2-OH C15 : 0iso), C18 : 1ω7cand the presence of 3-OH C10 : 0, 3-OH C12 : 0and 2-OH C12 : 0] were in agreement with identification of this strain as a member of the genusPseudomonas. Physiological and biochemical characteristics and the results of genomic fingerprinting clearly differentiated strain C36Tfrom its phylogenetic relativeP. oleovoransDSM 1045T. Results from DNA–DNA hybridization showed that strain C36Trepresents a species that is distinct fromP. oleovoransDSM 1045T. These data demonstrate that strain C36Trepresents a novel species of the genusPseudomonas, for which the namePseudomonas psychrotoleranssp. nov. is proposed. The type strain is C36T(=LMG 21977T=DSM 15758T). Additionally, physiological, biochemical, chemotaxonomic and genomic fingerprints indicate thatP. oleovoransATCC 29347 may not be a member of the speciesP. oleovorans sensu stricto.
Jannaschia cystaugens sp. nov., an Alexandrium (Dinophyceae) cyst formation-promoting bacterium from Hiroshima Bay, Japan
Authors: Adachi Masao , Kanno Tsukasa , Okamoto Ryo , Shinozaki Azusa , Fujikawa-Adachi Kiyomi , Nishijima Toshitaka
Published: September 2004

Heterotrophic bacteria isolated from water samples taken from Hiroshima Bay, Japan, and referred to as Alexandrium (Dinophyceae) cyst formation-promoting bacteria, were assigned to the Roseobacter–Sulfitobacter–Silicibacter group within the α-Proteobacteria on the basis of nearly complete 16S rRNA gene sequences. Phylogenetic analyses showed that two strains, CFPB-A9T and CFPB-A5, are closely related to each other and that their closest relative was Jannaschia helgolandensis (95·9 % sequence similarity). These strains were Gram-negative, motile, obligately aerobic rods that required sodium ions and 2–7 % sea salts for growth and did not produce bacteriochlorophyll a. Their optimal growth temperature was 25–30 °C. The strains had Q-10 as the dominant respiratory quinone. Primary cellular fatty acid in both strains was 18 : 1ω7c. The DNA G+C contents of strains CFPB-A9T and CFPB-A5 were 59·1 and 59·2 mol%, respectively. Based on physiological, biological, chemotaxonomic and phylogenetic data, the strains are considered to represent a novel species, Jannaschia cystaugens sp. nov., with type strain CFPB-A9T (=LMG 22015T=NBRC 100362T).
Nocardia pigrifrangens sp. nov., a novel actinomycete isolated from a contaminated agar plate
Authors: Wang Liming , Zhang Yamei , Huang Ying , Maldonado Luis A. , Liu Zhiheng , Goodfellow Michael
Published: September 2004

A polyphasic study was undertaken to establish the taxonomic position of an actinomycete strain isolated from a contaminated agar plate. The strain, designated 7031T, had morphological and chemotaxonomic properties typical of the genus Nocardia. An almost-complete 16S rRNA gene sequence determined for the strain was aligned with available sequences for nocardiae, and phylogenetic trees were inferred using three tree-generating algorithms. Strain 7031T clustered with the type strains of Nocardia carnea and Nocardia flavorosea, showing low 16S rRNA gene sequence similarities to these species (97·2 and 97·5 %, respectively). The strain was also distinguished from the closest species by a range of phenotypic properties. It is proposed that the strain be recognized as a novel species of Nocardia, Nocardia pigrifrangens sp. nov., the type strain of which is 7031T (=AS 4.1808T=JCM 11884T).
Serinicoccus marinus gen. nov., sp. nov., a novel actinomycete with l-ornithine and l-serine in the peptidoglycan
Authors: Yi Hana , Schumann Peter , Sohn Kyounghee , Chun Jongsik
Published: September 2004

A Gram-positive bacterial strain containing l-ornithine as the diagnostic diamino acid was isolated from a sea-water-sample from the East Sea, Korea. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain JC1078T represents a phyletic line within the suborder Micrococcineae of the order Actinomycetales, adjacent to the genus Ornithinimicrobium. The highest sequence similarity values to the isolate were observed against Ornithinimicrobium humiphilum (94·3 %) and Kytococcus sedentarius (94·1 %). The strain was strictly aerobic and moderately halophilic with optimal growth at 2–3 % (w/v) NaCl. Cells were non-motile, non-sporulating and coccoid-shaped. The cell wall contains l-ornithine, glutamic acid, alanine, glycine and serine. The major menaquinone was MK-8(H4). The predominant cellular fatty acids were of the iso- and anteiso-methyl-branched types. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and an unknown glycolipid. The acyl type of the glycan chain of peptidoglycan is acetyl. The DNA G+C content was 72 mol%. The combination of physiological, biochemical and chemotaxonomical data clearly separated the marine isolate from other members of the suborder Micrococcineae. On the basis of polyphasic evidence, it is proposed to classify strain JC1078T in a novel genus and species, for which the name Serinicoccus marinus gen. nov., sp. nov. is proposed. The type strain is JC1078T (=IMSNU 14026T=KCTC 9980T=DSM 15273T).
Sulfurovum lithotrophicum gen. nov., sp. nov., a novel sulfur-oxidizing chemolithoautotroph within the ε-Proteobacteria isolated from Okinawa Trough hydrothermal sediments
Authors: Inagaki Fumio , Takai Ken , Nealson Kenneth H. , Horikoshi Koki
Published: September 2004

A novel mesophilic sulfur- and thiosulfate-oxidizing bacterium, strain 42BKTT, was isolated from the gas-bubbling sediment at the Iheya North hydrothermal system in the mid-Okinawa Trough, Japan. The isolate was a Gram-negative, non-motile and coccoid to oval-shaped bacterium. Growth was observed at 10–40 °C (optimum 28–30 °C) and in the pH range 5·0–9·0 (optimum 6·5–7·0). Strain 42BKTTgrew chemolithoautotrophically with elemental sulfur or thiosulfate as a sole electron donor and oxygen (optimum 5 % in gas phase) or nitrate as an electron acceptor. The G+C content of the genomic DNA was 48·0 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the isolate belonged to the previously uncultivated Group F within theε-Proteobacteria, which includes phylotypes of vent epibiont and environmental sequences from global deep-sea cold seep and hydrothermal vent fields. On the basis of the physiological and molecular characteristics of this isolate, the type species of a novel genus,Sulfurovum lithotrophicumgen. nov., sp. nov., is proposed. The type strain is 42BKTT(=ATCC BAA-797T=JCM 12117T).
Phylogenetic analysis of the genus Aeromonas based on two housekeeping genes
Authors: Soler L. , Yáñez M. A. , Chacon M. R. , Aguilera-Arreola M. G. , Catalán V. , Figueras M. J. , Martínez-Murcia A. J.
Published: September 2004

The phylogenetic relationships of all known species of the genusAeromonas, and especiallyAeromonas bestiarumandAeromonas salmonicida, were investigated on 70 strains using therpoDsequence, which encodes theσ70factor. This analysis was complemented with the sequence ofgyrB, which has already proven useful for determining the phylogenetic relationships in the genus. Nucleotide sequences ofrpoDandgyrBshowed that both genes had similar substitution rates (<2 %) and a similar number of variable positions (34 % forrpoDversus 32 % forgyrB). Strain groupings by analysis ofrpoD,gyrBand a combination of both genes were consistent with the taxonomic organization of allAeromonasspecies described to date. However, the simultaneous analysis of both clocks improved the reliability and the power to differentiate, in particular, closely related taxa. At the inter-species level,gyrBshowed a better resolution for differentiatingAeromonassp. HG11/Aeromonas encheleiaandAeromonas veronii/Aeromonas culicicola/Aeromonas allosaccharophila, whilerpoDmore clearly differentiatedA. salmonicidafromA. bestiarum. The analysis ofrpoDprovided initial evidence for clear phylogenetic divergence between the latter two species.
Oribacterium sinus gen. nov., sp. nov., within the family ‘Lachnospiraceae’ (phylum Firmicutes)
Authors: Carlier Jean-Philippe , K'ouas Guylène , Bonne Isabelle , Lozniewski Alain , Mory Francine
Published: September 2004

A hitherto unknown anaerobic bacillus isolated from sinus pus in a young child (strain AIP 354.02T) was characterized by using phenotypic and genotypic methods. 16S rRNA gene sequence analysis indicated that this strain was phylogenetically affiliated with several sequences of cloned 16S rRNA gene inserts previously deposited in the public databases. According to their 16S rRNA gene sequence similarities, these uncultivated bacteria, together with strain AIP 354.02T, formed a separate subgroup belonging to the family ‘Lachnospiraceae’ within the phylumFirmicutes.Oribacteriumgen. nov. is proposed for this group of organisms andOribacterium sinusgen. nov. sp. nov. for strain AIP 354.02T(=CIP 107991T=CCUG 48084T).
Mycoplasma testudineum sp. nov., from a desert tortoise (Gopherus agassizii) with upper respiratory tract disease
Authors: Brown D. R. , Merritt J. L. , Jacobson E. R. , Klein P. A. , Tully J. G. , Brown M. B.
Published: September 2004

Mycoplasma testudineum sp. nov., first cultured from the upper respiratory tract of a clinically ill tortoise (Gopherus agassizii) in the Mohave Desert, was distinguished from previously described mollicutes serologically and by 16S rRNA gene sequence comparisons. It lacks a cell wall; ferments glucose, mannose, lactose and sucrose; does not produce ‘film and spots’; does not hydrolyse arginine, aesculin or urea; is sensitive to digitonin; and lacks phosphatase activity. The organism causes chronic rhinitis and conjunctivitis of tortoises. The type strain of M. testudineum is BH29T (=ATCC 700618T=MCCM 03231T).
Postgenomic taxonomy of human ureaplasmas – a case study based on multiple gene sequences
Authors: Kong Fanrong , Gilbert Gwendolyn L.
Published: September 2004

In 2000, the full genome sequence of Ureaplasma parvum (previously known as Ureaplasma urealyticum) serovar 3 was released. In 2002, after prolonged debate, it was agreed that the former U. urealyticum should be divided into two species – U. parvum and U. urealyticum. To provide additional support for this decision and improve our understanding of the relationship between these two species, the authors studied four ‘core’ genes or gene clusters in ATCC reference strains of all 14 serovars of U. parvum and U. urealyticum. These ‘core’ regions were the rRNA gene clusters, the EF-Tu genes (tuf), urease gene clusters and multiple-banded antigen genes (mba). The known U. parvum genome sequences (GenBank accession no. NC_002162) were used as reference. DNA insertions and deletions (indels) were found in all of the gene regions studied, except tuf, but they were found only between, not within, the two species. An incidental finding was that there was inter-copy heterogeneity for rRNA gene cluster sequences. Sequence analysis (sequence heterogeneity and especially indels) of all four selected targets consistently supported the separation of human ureaplasmas into two species. Except for multiple-banded antigen, there was less heterogeneity in amino acid sequences of proteins, between species, than in the nucleic acid sequences of the corresponding genes. The degrees of heterogeneity at the 5′ end of the species-specific regions of multiple-banded antigen were almost identical for both amino acid and nucleotide sequences. Analysis of the authors' results provided an interesting case study to help resolve some common problems in the use of sequence data to infer phylogenetic relationships and support taxonomic changes. It is recommended that, to avoid confusion, the new nomenclature be used for human ureaplasmas in future publications.
Helcococcus sueciensis sp. nov., isolated from a human wound
Authors: Collins Matthew D. , Falsen Enevold , Brownlee Kit , Lawson Paul A.
Published: September 2004

A previously undescribed, Gram-positive, catalase-negative, coccus-shaped organism that originated from a human wound was subjected to taxonomic study. On the basis of its cellular morphology and the results of biochemical testing, the unknown organism was identified tentatively as a member of the genus Helcococcus, but it did not correspond to either of the two recognized species of this genus. Comparative 16S rRNA gene sequencing studies confirmed that the bacterium was associated phylogenetically with the genus Helcococcus, with the unidentified organism forming a hitherto unknown subline within the genus. On the basis of biochemical, molecular chemical and molecular phylogenetic evidence, it is proposed that the unknown organism that was recovered from a human wound should be classified as a novel species of the genus Helcococcus, namely Helcococcus sueciensis sp. nov. The type strain is CCUG 47334T (=CIP 108183T).
Paenibacillus antarcticus sp. nov., a novel psychrotolerant organism from the Antarctic environment
Authors: Montes Ma Jesús , Mercadé Elena , Bozal Núria , Guinea Jesús
Published: September 2004

An endospore-forming strain, 20CMT, was isolated from Antarctic sediment and identified as a member of the genus Paenibacillus on the basis of phenotypic and phylogenetic analyses. The organism stained Gram-variable and was facultatively anaerobic. Strain 20CMT was psychrotolerant, growing optimally at 10–15 °C. Like other Paenibacillus species, it contained anteiso-C15 : 0 as the major cellular fatty acid. The DNA G+C content was 40·7 mol%. 16S rRNA gene sequence analysis placed strain 20CMT within the Paenibacillus cluster, with a similarity value of 99·5 % to Paenibacillus macquariensis DSM 2T. DNA–DNA hybridization experiments between the Antarctic isolate and P. macquariensis DSM 2T revealed a reassociation value of 47 %, indicating that strain 20CMT and P. macquariensis DSM 2T belong to different species. Based on evaluation of morphological, physiological, chemotaxonomic and phylogenetic analyses, a novel species, Paenibacillus antarcticus sp. nov., is proposed; the type strain is 20CMT (=LMG 22078T=CECT 5836T).
An updated view of kinetoplastid phylogeny using environmental sequences and a closer outgroup: proposal for a new classification of the class Kinetoplastea
Authors: Moreira David , López-García Purificación , Vickerman Keith
Published: September 2004

Given their ecological and medical importance, the classification of the kinetoplastid protists (class Kinetoplastea) has attracted much scientific attention for a long time. Morphology-based taxonomic schemes distinguished two major kinetoplastid groups: the strictly parasitic, uniflagellate trypanosomatids and the biflagellate bodonids. Molecular phylogenetic analyses based on 18S rRNA sequence comparison suggested that the trypanosomatids emerged from within the bodonids. However, these analyses revealed a huge evolutionary distance between the kinetoplastids and their closest relatives (euglenids and diplonemids) that makes very difficult the correct inference of the phylogenetic relationships between the different kinetoplastid groups. Using direct PCR amplification of 18S rRNA genes from hydrothermal vent samples, several new kinetoplastid-like sequences have been reported recently. Three of them emerge robustly at the base of the kinetoplastids, breaking the long branch leading to the euglenids and diplonemids. One of these sequences belongs to a close relative of Ichthyobodo necator (a fish parasite) and of the ‘Perkinsiella amoebae’-like endosymbiont of Neoparamoeba spp. amoebae. The authors have studied the reliability of their basal position and used all these slow-evolving basal-emerging sequences as a close outgroup to analyse the phylogeny of the apical kinetoplastids. They thus find a much more stable and resolved kinetoplastid phylogeny, which supports the monophyly of groups that very often emerged as polyphyletic in the trees rooted using the traditional, distant outgroup sequences. A new classification of the class Kinetoplastea is proposed based on the results of the phylogenetic analysis presented. This class is now subdivided into two new subclasses, Prokinetoplastina (accommodating the basal species I. necator and ‘Perkinsiella amoebae’) and Metakinetoplastina (containing the Trypanosomatida together with three additional new orders: Eubodonida, Parabodonida and Neobodonida). The classification of the species formerly included in the genus Bodo is also revised, with the amendment of this genus and the genus Parabodo and the creation of a new genus, Neobodo.
Streptococcus halichoeri sp. nov., isolated from grey seals (Halichoerus grypus)
Authors: Lawson Paul A. , Foster Geoffrey , Falsen Enevold , Davison Nick , Collins Matthew D.
Published: September 2004

Phenotypic and phylogenetic studies were performed on six unidentified, Gram-positive, catalase-negative, chain-forming Streptococcus-like organisms recovered from grey seals. Biochemically the six strains were highly related to each other, but they did not appear to correspond to any recognized species of the genus Streptococcus. Comparative 16S rRNA gene sequencing studies confirmed that phylogenetically the strains were members of the genus Streptococcus, but sequence divergence values of greater than 3 % compared with reference streptococcal species demonstrated that the organisms from seals represent a novel species. SDS-PAGE analysis of whole-cell proteins confirmed the phenotypic distinctiveness of the seal organisms. Based on biochemical criteria and molecular chemical and genetic evidence, it is proposed that the unknown organism from seals be classified as a novel species, Streptococcus halichoeri sp. nov., the type strain of which is CCUG 48324T (=CIP 108195T).
Zobellia amurskyensis sp. nov., Zobellia laminariae sp. nov. and Zobellia russellii sp. nov., novel marine bacteria of the family Flavobacteriaceae
Authors: Nedashkovskaya Olga I. , Suzuki Makoto , Vancanneyt Marc , Cleenwerck Ilse , Lysenko Anatoly M. , Mikhailov Valery V. , Swings Jean
Published: September 2004

The taxonomic position of four newly isolated marine, heterotrophic, gliding, Gram-negative, aerobic, pigmented, agarolytic bacteria was established. 16S rRNA gene sequence analysis indicated affiliation of the isolates to the genusZobelliain the familyFlavobacteriaceae. DNA–DNA hybridization experiments revealed that the strains studied represent three distinct and novel species, for which the namesZobellia amurskyensissp. nov.,Zobellia laminariaesp. nov. andZobellia russelliisp. nov. are proposed, with KMM 3526T(=LMG 22069T=CCUG 47080T), KMM 3676T(=LMG 22070T=CCUG 47083T) and KMM 3677T(=LMG 22071T=CCUG 47084T), respectively, as the type strains.
Bullera cylindrica sp. nov., Bullera hubeiensis sp. nov. and Bullera nakasei sp. nov., ballistoconidium-forming yeast species from plant leaves
Authors: Wang Qi-Ming , Bai Feng-Yan , Lu Hui-Zhong , Jia Jian-Hua , Takashima Masako
Published: September 2004

Among yeasts isolated from plant leaves collected in different regions of China that form whitish or yellowish colonies and symmetrical ballistoconidia, four strains were shown to represent three novel Bullera species by conventional and molecular taxonomic characterization. The novel species are described as Bullera cylindrica sp. nov. (type strain CB 169T=AS 2.2308T=CBS 9744T), Bullera hubeiensis sp. nov. (type strain HX 19.3T=AS 2.2466T=CBS 9747T) and Bullera nakasei sp. nov. (type strain HX 15.5T=AS 2.2435T=CBS 9746T). These three species, and another eight previously described Bullera species represented by Bullera mrakii, formed a strongly supported distinct clade among the hymenomycetous yeasts in each of the phylogenetic trees drawn from the 26S rDNA D1/D2 domain and the internal transcribed spacer region sequences.
Sutterella stercoricanis sp. nov., isolated from canine faeces
Authors: Greetham Hazel L. , Collins Matthew D. , Gibson Glenn R. , Giffard Catriona , Falsen Enevold , Lawson Paul A.
Published: September 2004

Morphological, biochemical and molecular genetic studies were carried out on an unknown non-spore-forming, Gram-negative, rod-shaped bacterium which was isolated from dog faeces. The bacterium grew under anaerobic conditions, was asaccharolytic, resistant to 20 % (v/v) bile and was oxidase- and urease-negative. Phylogenetic analysis based on comparative 16S rRNA gene sequencing showed that the unidentified bacterium clustered withSutterella wadsworthensis, although a sequence divergence of >5 % indicated that the bacterium from dog faeces represented a previously unrecognized subline within the genus. On the basis of the presented findings, a novel species,Sutterella stercoricanissp. nov., is described. The type strain ofSutterella stercoricanisis 5BAC4T(=CCUG 47620T=CIP 108024T).