bluuebunny/crossref_metadata_2025 huggingface dataset:
Synchrony in reaction–diffusion models of morphogenesis: applications to curvature-dependent proliferation and zero-diffusion front waves
Authors: Abbas Lamia , Demongeot Jacques , Glade Nicolas
Published: November 2009

The paper presents the classical age-dependent approach of the morphogenesis in the framework of the von Foerster equation, in which we introduce a new constraint and study a new feature: (i) the new constraint concerns cell proliferation along the contour lines of the cell density, depending on the local curvature such as it favours the amplification of the concavities (like in the gastrulation process) and (ii) the new feature consists of considering, on the cell density surface, a remarkable line (the null mean Gaussian curvature line), on which the normal diffusion vanishes, favouring local coexistence of diffusing morphogens, metabolites or cells, and hence the auto-assemblages of these entities. Two applications to biological multi-agents systems are studied, gastrulation and feather morphogenesis.
Machine analysis of facial behaviour: naturalistic and dynamic behaviour
Authors: Pantic Maja
Published: November 2009

This article introduces recent advances in the machine analysis of facial expressions. It describes the problem space, surveys the problem domain and examines the state of the art. Two recent research topics are discussed with particular attention: analysis of facial dynamics and analysis of naturalistic (spontaneously displayed) facial behaviour. Scientific and engineering challenges in the field in general, and in these specific subproblem areas in particular, are discussed and recommendations for accomplishing a better facial expression measurement technology are outlined.
Emotions are emergent processes: they require a dynamic computational architecture
Authors: Scherer Klaus R.
Published: November 2009

Emotion is a cultural and psychobiological adaptation mechanism which allows each individual to react flexibly and dynamically to environmental contingencies. From this claim flows a description of the elements theoretically needed to construct a virtual agent with the ability to display human-like emotions and to respond appropriately to human emotional expression. This article offers a brief survey of the desirable features of emotion theories that make them ideal blueprints for agent models. In particular, the component process model of emotion is described, a theory which postulates emotion-antecedent appraisal on different levels of processing that drive response system patterning predictions. In conclusion, investing seriously in emergent computational modelling of emotion using a nonlinear dynamic systems approach is suggested.
Role of expressive behaviour for robots that learn from people
Authors: Breazeal Cynthia
Published: November 2009

Robotics has traditionally focused on developing intelligent machines that can manipulate and interact with objects. The promise of personal robots, however, challenges researchers to develop socially intelligent robots that can collaboratewithpeople to do things. In the future, robots are envisioned to assist people with a wide range of activities such as domestic chores, helping elders to live independently longer, serving a therapeutic role to help children with autism, assisting people undergoing physical rehabilitation and much more. Many of these activities shall require robots to learn new tasks, skills and individual preferences while ‘on the job’ from people with little expertise in the underlying technology. This paper identifies four key challenges in developing social robots that can learn from natural interpersonal interaction. The author highlights the important role that expressive behaviour plays in this process, drawing on examples from the past 8 years of her research group, the Personal Robots Group at the MIT Media Lab.
The face is not an empty canvas: how facial expressions interact with facial appearance
Authors: Hess Ursula , Adams Reginald B. , Kleck Robert E.
Published: November 2009

Faces are not simply blank canvases upon which facial expressions write their emotional messages. In fact, facial appearance and facial movement are both important social signalling systems in their own right. We here provide multiple lines of evidence for the notion that the social signals derived from facial appearance on the one hand and facial movement on the other interact in a complex manner, sometimes reinforcing and sometimes contradicting one another. Faces provide information on who a person is. Sex, age, ethnicity, personality and other characteristics that can define a person and the social group the person belongs to can all be derived from the face alone. The present article argues that faces interact with the perception of emotion expressions because this information informs a decoder's expectations regarding an expresser's probable emotional reactions. Facial appearance also interacts more directly with the interpretation of facial movement because some of the features that are used to derive personality or sex information are also features that closely resemble certain emotional expressions, thereby enhancing or diluting the perceived strength of particular expressions.
Darwin's contributions to our understanding of emotional expressions
Authors: Ekman Paul
Published: November 2009

Darwin charted the field of emotional expressions with five major contributions. Possible explanations of why he was able to make such important and lasting contributions are proposed. A few of the important questions that he did not consider are described. Two of those questions have been answered at least in part; one remains a major gap in our understanding of emotion.
Halomonas stevensii sp. nov., Halomonas hamiltonii sp. nov. and Halomonas johnsoniae sp. nov., isolated from a renal care centre
Authors: Kim Kwang Kyu , Lee Keun Chul , Oh Hee-Mock , Lee Jung-Sook
Published: November 2009

A total of 14 Halomonas strains were isolated from the blood of two patients and from dialysis machines of a renal care centre. The strains were Gram-negative, halophilic, motile and non-spore-forming rods. They produced cream-coloured colonies and contained Q-9 as the predominant ubiquinone and C18 : 1
ω7c and C16 : 0 as the major fatty acids. Phylogenetic analysis based on 16S rRNA gene sequencing showed that the 14 isolates were most closely related to Halomonas magadiensis 21 MIT with 98.1–98.9 % sequence similarity and that they formed three separate lineages among themselves. Combined phenotypic and DNA–DNA hybridization data support the conclusion that they represent three novel species of the genus Halomonas, for which the names Halomonas stevensii sp. nov. (type strain S18214T=KCTC 22148T=DSM 21198T), Halomonas hamiltonii sp. nov. (type strain W1025T=KCTC 22154T=DSM 21196T) and Halomonas johnsoniae sp. nov. (type strain T68687T=KCTC 22157T=DSM 21197T) are proposed.
Arcobacter marinus sp. nov.
Authors: Kim Hye Min , Hwang Chung Yeon , Cho Byung Cheol
Published: November 2009

A slightly curved, rod-shaped marine bacterium, designated strain CL-S1T, was isolated from near Dokdo, an island in the East Sea, Korea. Cells were Gram-negative and grew well under either aerobic or microaerobic conditions. Analyses of the 16S rRNA and gyrA gene sequences of strain CL-S1T revealed an affiliation with the genus Arcobacter within the class Epsilonproteobacteria. Phylogenetic analyses based on 16S rRNA and gyrA gene sequences showed that strain CL-S1T formed a robust clade with Arcobacter halophilus LA31BT, with sequence similarities of 96.1 and 88.2 %, respectively. DNA–DNA relatedness between strain CL-S1T and A. halophilus DSM 18005T was 44 %, indicating that they represent genomically distinct species. Strain CL-S1T grew optimally at 30–37 °C, at pH 7 and in the presence of 3–5 % NaCl. The dominant cellular fatty acids were iso-C15 : 0 2-OH and/or C16 : 1
ω7c (28.4 %), C16 : 0 (26.2 %) and C18 : 1
ω7c (22.3 %). The DNA G+C content of strain CL-S1T was 28 mol%. Strain CL-S1T differed phenotypically from A. halophilus LA31BT based on its ability to grow aerobically at 10 °C and inability to grow under anaerobic conditions. Based on the data presented, strain CL-S1T is considered to represent a novel species of the genus Arcobacter, for which the name Arcobacter marinus sp. nov. is proposed. The type strain is CL-S1T (=KCCM 90072T =JCM 15502T).
Reclassification of Herbaspirillum putei as a later heterotypic synonym of Herbaspirillum huttiense, with the description of H. huttiense subsp. huttiense subsp. nov. and H. huttiense subsp. putei subsp. nov., comb. nov., and description of Herbaspirillum aquaticum sp. nov.
Authors: Dobritsa Anatoly P. , Reddy M. C. S. , Samadpour Mansour
Published: November 2009

Resequencing of the 16S rRNA gene of the type strain of Herbaspirillum putei Ding and Yokota 2004 revealed 99.9 % sequence similarity to that of the type strain of Herbaspirillum huttiense (Leifson 1962) Ding and Yokota 2004. This high phylogenetic relatedness of H. putei and H. huttiense was confirmed by the results of DNA–DNA hybridization between H. huttiense DSM 10281T and H. putei ATCC BAA-806T (reassociation value 96 %). Therefore, it is proposed to reclassify the type strain of H. putei as a strain of H. huttiense. However, the genome of the type strain of H. putei is about 0.9 Mb larger than that of the H. huttiense type strain. This results in a decrease in the reassociation value in the reciprocal DNA–DNA hybridization to 72 %, a level slightly above the threshold for delineating bacterial species. These data and distinctive phenotypic characteristics indicate that the name Herbaspirillum putei is a later heterotypic synonym of Herbaspirillum huttiense and permit the description of two novel subspecies, Herbaspirillum huttiense subsp. huttiense subsp. nov. (type strain ATCC 14670T =JCM 21423T =DSM 10281T) and Herbaspirillum huttiense subsp. putei subsp. nov., comb. nov. (type strain 7-2T =JCM 21495T =ATCC BAA-806T). Three bacterial strains, IEH 4430T, IEH 4515 and IEH 8757, isolated from water were found to be the closest relatives of these strains. Strain IEH 8757 was classified as a strain of H. huttiense subsp. putei. Studies of genotypic and phenotypic features of strains IEH 4430T and IEH 4515 showed that the strains represent a novel species, which is most closely related to H. huttiense and for which the name Herbaspirillum aquaticum sp. nov. is proposed (type strain IEH 4430T =DSM 21191T =ATCC BAA-1628T).
Sphingobium faniae sp. nov., a pyrethroid-degrading bacterium isolated from activated sludge treating wastewater from pyrethroid manufacture
Authors: Guo Peng , Wang Bao-Zhan , Hang Bao-Jian , Li Lian , Li Shun-Peng , He Jian
Published: November 2009

A bacterial strain capable of degrading pyrethroid, designated JZ-2T, was isolated from activated sludge treating pyrethroid-contaminated wastewater. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JZ-2Tbelongs to the genusSphingobium. It showed the highest levels of 16S rRNA gene sequence similarity toSphingobium cloacaeJCM 10874T(98.3 %) andSphingobium ummarienseCCM 7431T(97.1 %), and 94.8–96.9 % similarity to the type strains of other members of the genusSphingobium. Strain JZ-2Tcontained C18 : 1ω7cas the predominant fatty acid, C14 : 02-OH as the major 2-hydroxy fatty acid, ubiquinone Q-10 as the main respiratory quinone, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine, phosphatidylethanolamine and two sphingoglycolipids as the predominant polar lipids and spermidine as the major polyamine. DNA–DNA hybridization results showed that strain JZ-2Thad low genomic relatedness withS. cloacaeJCM 10874T(34 %) andS. ummarienseCCM 7431T(23 %). Based on the phenotypic, genotypic and phylogenetic data presented, strain JZ-2Tis considered to represent a novel species of the genusSphingobium, for which the nameSphingobium faniaesp. nov. is proposed. The type strain is JZ-2T(=CGMCC 1.7749T=DSM 21829T).
Salsuginibacillus halophilus sp. nov., a halophilic bacterium isolated from a soda lake
Authors: Cao Shu-Juan , Qu Jian-Hang , Yuan Hong-Li , Li Bao-Zhen
Published: November 2009

A Gram-stain-positive, rod-shaped, endospore-forming, halophilic, alkalitolerant bacterium, designated halo-1T, was isolated from sediment of Xiarinaoer soda lake, located in the Inner Mongolia Autonomous Region of China. Strain halo-1T grew in the presence of 9–30 % (w/v) NaCl (optimum 19 %) and at pH 5–10 (optimum pH 9). The cell-wall peptidoglycan contained meso-diaminopimelic acid and the major respiratory isoprenoid quinone was MK-7. The predominant cellular fatty acids of the isolate were anteiso-C15 : 0 (58.35 %), anteiso-C17 : 0 (12.89 %) and C16 : 0 (6.52 %). The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, glycolipid and a phospholipid of unknown structure. The DNA G+C content of the strain was 46.4 mol%. On the basis of 16S rRNA gene sequence similarity, strain halo-1T showed the highest similarity (93.9 %) to Salsuginibacillus kocurii CH9dT. Strain halo-1T could be clearly differentiated from its closest phylogenetic relative on the basis of several phenotypic, genotypic and chemotaxonomic features. Therefore, strain halo-1T represents a novel species, for which the name Salsuginibacillus halophilus sp. nov. is proposed, with the type strain halo-1T (=CGMCC 1.7653T =NBRC 104934T).
Leisingera nanhaiensis sp. nov., isolated from marine sediment
Authors: Sun Fengqin , Wang Baojiang , Liu Xiupian , Lai Qiliang , Du Yaping , Li Guangyu , Luo Jie , Shao Zongze
Published: November 2009

An aerobic, Gram-staining-negative, motile, rod-shaped bacterium, strain NH52FT, was isolated from a sandy sediment sample taken from the South China Sea. On M2 agar medium (a complex medium), colonies were beige in colour. The isolate showed highest 16S rRNA gene sequence similarities to members of the generaLeisingera(96.7 % similarity),Phaeobacter(95.4–96.0 %) andMarinovum(94.1 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NH52FTformed a distinct cluster withLeisingera methylohalidivoransMB2TandLeisingera aquimarinaLMG 24366T. Optimal growth was observed at pH 7.0-8.5 and 25 °C and the new isolate required the presence of 1–4 % (w/v) NaCl. The major fatty acids were C18 : 1ω7c, C16 : 02-OH, C10 : 03-OH, C12 : 03-OH, C16 : 0and 11-methyl C18 : 1ω7c. The DNA G+C content was 60.5 mol%. The phylogenetic and chemotaxonomic characteristics of strain NH52FTwere similar to those of the genusLeisingera. However, the differences in phenotypic properties and the 16S rRNA gene similarity values demonstrated that the new isolate differed from recognized species of the genusLeisingera. On the basis of phenotypic, chemotaxonomic and phylogenetic data, this organism should be classified as a representative of a novel species in the genusLeisingera, for which the nameLeisingera nanhaiensissp. nov. is proposed. The type strain is NH52FT(=LMG 24841T=CCTCC AB 208316T=MCCC 1A04178T).
Umboniibacter marinipuniceus gen. nov., sp. nov., a marine gammaproteobacterium isolated from the mollusc Umbonium costatum from the Sea of Japan
Authors: Romanenko Lyudmila A. , Tanaka Naoto , Frolova Galina M.
Published: November 2009

Two bacterial strains, KMM 3891Tand KMM 3892, were isolated from internal tissues of the marine molluscUmbonium costatumcollected from the Sea of Japan. The novel isolates were Gram-negative, aerobic, faint pink–reddish-pigmented, rod-shaped, non-motile, stenohaline and psychrotolerant bacteria that were unable to degrade most tested complex polysaccharides. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Fatty acid analysis revealed C17 : 1ω6c, C17 : 0, C16 : 0and C16 : 1ω7cas the dominant components. The major isoprenoid quinone was Q-7. The DNA G+C content of strain KMM 3891Twas 51.7 mol%. According to phylogenetic analysis of 16S rRNA gene sequences, strains KMM 3891Tand KMM 3892 were positioned within theGammaproteobacteriaas a separate branch, sharing <93 % sequence similarity to their phylogenetic relatives includingSaccharophagus degradans,Microbulbiferspecies,Endozoicomonas elysicola,Simiduia agarivoransandTeredinibacter turnerae. Based on phenotypic characterization and phylogenetic distance, the novel marine isolates KMM 3891Tand KMM 3892 represent a new genus and species, for which the nameUmboniibacter marinipuniceusgen. nov., sp. nov. is proposed. The type strain ofUmboniibacter marinipuniceusis KMM 3891T(=NRIC 0753T=JCM 15738T).
Alloactinosynnema album gen. nov., sp. nov., a member of the family Actinosynnemataceae isolated from soil
Authors: Yuan Li-Jie , Zhang Yu-Qin , Yu Li-Yan , Liu Hong-Yu , Guan Yan , Lee Jae-Chan , Kim Chang-Jin , Zhang Yue-Qin
Published: November 2009

The taxonomic position of a Gram-stain-positive, aerobic strain, designated 03-9939T, isolated from a soil sample collected from Xinjiang Province, China, was established using a polyphasic approach. Whole-cell hydrolysates of strain 03-9939T contained galactose and ribose as diagnostic sugars and meso-diaminopimelic acid as the diamino acid. The predominant menaquinone was MK-9(H4). The phospholipids consisted of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine. The major fatty acids were iso-C16 : 0 (61.5 %) and iso-C16 : 1 H (11.6 %). The genomic DNA G+C content was 68.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 03-9939T should be placed within the family Actinosynnemataceae, in which the strain formed a distinct lineage. Signature nucleotides in the 16S rRNA gene sequence showed that the strain contained a genus-specific diagnostic nucleotide signature pattern. The combination of phylogenetic analysis, phenotypic characteristics and chemotaxonomic data supported the conclusion that strain 03-9939T represents a novel species in a new genus of the family Actinosynnemataceae, for which the name Alloactinosynnema album gen. nov., sp. nov. is proposed. Strain 03-9939T (=DSM 45114T =KCTC 19294T =CCM 7461T) is the type strain of Alloactinosynnema album.
Sphingosinicella vermicomposti sp. nov., isolated from vermicompost, and emended description of the genus Sphingosinicella
Authors: Yasir Muhammad , Aslam Zubair , Song Geun Cheol , Jeon Che Ok , Chung Young Ryun
Published: November 2009

A Gram-stain-negative, rod-shaped bacterium, designated strain YC7378T was isolated from vermicompost (VC) collected at Masan, Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain YC7378T grew optimally at 30 °C and at pH 6.5–8.5. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YC7378T belongs to the genus Sphingosinicella in the family Sphingomonadaceae. The most closely related strains are Sphingosinicella soli KSL-125T (95.7 %), Sphingosinicella xenopeptidilytica 3-2W4T (95.6 %) and Sphingosinicella microcystinivorans Y2T (95.5 %). Strain YC7378T contained ubiquinone Q-10 as the major respiratory quinone system and sym-homospermidine as the major polyamine. The major fatty acids of strain YC7378T were C18 : 1
ω7c, C16 : 1
ω7c and/or iso-C15 : 0 2-OH, C14 : 0 2-OH and C16 : 0. The major polar lipids were sphingoglycolipid, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The total DNA G+C content was 59.4 mol%. The phenotypic, phylogenetic and chemotaxonomic data showed that strain YC7378T represents a novel species of the genus Sphingosinicella, for which the name Sphingosinicella vermicomposti sp. nov. is proposed. The type strain is YC7378T (=KCTC 22446T =DSM 21593T).
Flavobacterium fluvii sp. nov., isolated from stream sediment
Authors: Lee Se Hee , Kim Jeong Myeong , Lee Jung Ro , Park Woojun , Jeon Che Ok
Published: November 2009

An aerobic, yellow-pigmented, Gram-staining-negative bacterium, designated strain H7T, was isolated from sediment of Gazwa stream in Jinju city, South Korea. Cells of strain H7T were non-motile, straight rods that produced flexirubin pigments and showed catalase- and oxidase activities. Strain H7T contained iso-C15 : 0, anteiso-C15 : 0 and summed feature 3 (comprising C16 : 1
ω7c and/or iso-C15 : 0 2-OH) as the main fatty acids and menaquinone-6 (MK-6) as the major isoprenoid quinone. The DNA G+C content of strain H7T was 37.2 mol%. Comparative 16S rRNA gene sequence analysis showed that strain H7T formed a distinct phyletic line within the genus Flavobacterium. Based on 16S rRNA gene sequence similarities, the novel strain was most closely related to Flavobacterium limicola ST-82T and Flavobacterium resistens BD-b365T with 97.2 % and 97.0 % gene sequence similarities, respectively. The DNA–DNA relatedness of the novel strain with these species was only 18 % and 14 %, respectively. On the basis of phenotypic data and molecular properties, strain H7T represents a novel species within the genus Flavobacterium, for which the name Flavobacterium fluvii sp. nov. is proposed. The type strain is H7T (=KACC 12818T=DSM 19978T).
Psychrobacter piscatorii sp. nov., a psychrotolerant bacterium exhibiting high catalase activity isolated from an oxidative environment
Authors: Yumoto Isao , Hirota Kikue , Kimoto Hideyuki , Nodasaka Yoshinobu , Matsuyama Hidetoshi , Yoshimune Kazuaki
Published: November 2009

A Gram-negative, non-motile, psychrotolerant bacterium exhibiting high catalase activity, designated strain T-3-2T, was isolated from a drain of a fish-processing plant. Its catalase activity was 12 000 U (mg protein)−1, much higher than the activity of the other Psychrobacter strains tested. The strain grew at 0–30 °C and in the presence of 0–12 % NaCl. The predominant isoprenoid quinone was ubiquinone-8 (Q-8), and C16 : 1
ω9c and C18 : 1
ω9c were the predominant cellular fatty acids. The DNA G+C content of strain T-3-2T was 43.9 mol%. 16S rRNA gene sequence phylogeny suggested that strain T-3-2T is a member of the genus Psychrobacter, with the closest relatives being the type strains of Psychrobacter nivimaris (99.2 % similarity), P. aquimaris (98.7 %) and P. proteolyticus (98.5 %). DNA–DNA hybridization showed less than 65 % relatedness with these strains. A phylogenetic tree based on gyrB gene sequences was more reliable, with higher bootstrap values than the 16S rRNA gene sequence-based tree. The result also differentiated the isolate from previously reported Psychrobacter species. Owing to the significant differences in phenotypic and chemotaxonomic characteristics and the phylogenetic and DNA–DNA relatedness data, the isolate merits classification within a novel species, for which the name Psychrobacter piscatorii sp. nov. is proposed. The type strain is T-3-2T (=JCM 15603T =NCIMB 14510T).
Silvimonas iriomotensis sp. nov. and Silvimonas amylolytica sp. nov., new members of the class Betaproteobacteria isolated from the subtropical zone in Japan
Authors: Muramatsu Yuki , Suzuki Ken-ichiro , Nakagawa Yasuyoshi
Published: November 2009

The taxonomic positions of two bacterial strains, ir6-1T and ir6-4T, isolated from soil collected in Iriomote Island in Japan, were determined by using a polyphasic taxonomic approach. The strains were facultatively anaerobic, motile and Gram-stain-negative rods and their optimum pH for growth was pH 4.0. Their major respiratory quinone was ubiquinone-8 and the predominant cellular fatty acids were C14 : 0, C16 : 0, C16 : 1
ω7c and C18 : 1
ω7c. The G+C content of the genomic DNA of ir6-1T and ir6-4T was 59.9 and 57.5 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strains clustered with the genus Silvimonas in the class Betaproteobacteria. DNA–DNA similarities were lower than 53 % among ir6-1T, ir6-4T and Silvimonas terrae NBRC 100961T, and these strains could be differentiated from each other by several phenotypic characters. Based on these results, we propose the emendation of the genus Silvimonas and inclusion of two novel species, Silvimonas iriomotensis sp. nov. (type strain ir6-1T=NBRC 103188T =CGMCC 1.8859T =KCTC 22513T) and Silvimonas amylolytica sp. nov. (ir6-4T =NBRC 103189T =CGMCC 1.8860T =KCTC 22514T).
Campylobacter subantarcticus sp. nov., isolated from birds in the sub-Antarctic region
Authors: Debruyne Lies , Broman Tina , Bergström Sven , Olsen Björn , On Stephen L. W. , Vandamme Peter
Published: November 2009

Six Gram-stain-negative, spiral-shaped, microaerobic isolates were obtained during a sampling from wild birds in the sub-Antarctic region. Based on initial observations, these isolates were classified as Campylobacter lari-like. The isolates were further characterized by whole-cell protein and amplified fragment length polymorphism (AFLP) analysis, which revealed that they were distinct from C. lari and all other known species of the genus Campylobacter. Here, we present comprehensive phylogenetic, genomic and phenotypic evidence that these isolates represent a novel species within the genus Campylobacter, for which the name Campylobacter subantarcticus sp. nov. is proposed. The type strain is R-3023T (=LMG 24377T =CCUG 38513T).
Streptococcus porci sp. nov., isolated from swine sources
Authors: Vela A. I. , Perez M. , Zamora L. , Palacios L. , Domínguez L. , Fernández-Garayzábal J. F.
Published: November 2009

Two unidentified Gram-positive, catalase-negative, coccus-shaped organisms were recovered from pigs and subjected to a polyphasic taxonomic analysis. Based on cellular morphology and biochemical criteria, the isolates were tentatively assigned to the genus Streptococcus, although the organisms did not appear to correspond to any recognized species. Comparative 16S rRNA gene sequence studies confirmed this identification and showed that the nearest phylogenetic relatives of the unknown cocci were Streptococcus plurextorum 1956-02T and Streptococcus suis NCTC 10234T (97.9 and 96.0 % 16S rRNA gene sequence similarity, respectively). The new isolates were related most closely to S. suis CIP 103217T based on rpoB gene sequence analysis (<8 % sequence divergence). DNA–DNA pairing studies showed that one of the unidentified strains (2923-03T) displayed DNA relatedness values of 26.6 and 27.2 % with S. plurextorum CECT 7308T and S. suis NCTC 10234T, respectively. On the basis of phenotypic and phylogenetic evidence, it is proposed that the unknown isolates from pigs be classified in the genus Streptococcus as members of Streptococcus porci sp. nov., with the type strain 2923-03T (=CECT 7374T =CCUG 55896T).
Devosia yakushimensis sp. nov., isolated from root nodules of Pueraria lobata (Willd.) Ohwi
Authors: Bautista Vernans V. , Monsalud Rosario G. , Yokota Akira
Published: November 2009

A Gram-negative, strictly aerobic bacterium, comprising non-endospore-forming motile rods (1.2–2.0 μm × 0.4–0.6 μm) with polar flagellae was isolated from root nodules of the leguminous plant Pueraria lobata (Willd.) Ohwi growing on the coast of Yakushima Island, Kagoshima Prefecture, Japan. The novel strain, designated Yak96BT, grew at an optimum pH of 7.0 and an optimum temperature of 28 °C. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the new strain was closely related to Devosia neptuniae J1T and Devosia chinhatensis IPL18T, with sequence similarities of 98.1 % and 97.8 %, respectively. However, the DNA–DNA relatedness values of strain Yak96BT with D. neptuniae LMG 21357T and D. chinhatensis CCM 7426T were 53.6 % and 34 %, respectively. The DNA G+C content of strain Yak96BT was 65.3 mol%, the predominant isoprenoid quinone was Q10 (85 %) and the polar lipids were phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids (>5 %) were 11-methyl C18 : 1
ω7c (35.0 %), C16 : 0 (22.4 %), C18 : 1
ω7c (21.8 %), C19 : 0 cyclo ω8c (6.8 %) and C18 : 0 (5.4 %). The infection/nodulation test was negative and nifH and nodD genes were not detected. Based on its chemotaxonomic and physiological characteristics, strain Yak96BT represents a novel species of the genus Devosia, for which the name Devosia yakushimensis sp. nov. is proposed. The type strain is Yak96BT (=KCTC 22147T=NBRC 103855T=LMG 24299T).
Jannaschia seohaensis sp. nov., isolated from a tidal flat sediment
Authors: Yoon Jung-Hoon , Kang So-Jung , Park Sooyeon , Oh Ki-Hoon , Oh Tae-Kwang
Published: November 2009

A Gram-negative, motile and pleomorphic bacterial strain, SMK-146T, was isolated from a tidal flat sediment of the Yellow Sea, Korea, and its taxonomic position was investigated. Strain SMK-146T grew optimally at pH 7.0–8.0 and 30 °C. It contained Q-10 as the predominant ubiquinone and C18 : 1
ω7c and 11-methyl C18 : 1
ω7c as the major fatty acids. The major polar lipids were phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 68.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SMK-146T belongs to the genus Jannaschia. Strain SMK-146T exhibited 16S rRNA gene sequence similarity values of 95.3–97.0 % to the type strains of the five recognized Jannaschia species. The mean DNA–DNA relatedness value between strain SMK-146T and Jannaschia
seosinensis KCCM 42114T, the closest phylogenetic neighbour, was 17 %. Differential phenotypic properties also revealed that strain SMK-146T differs from the recognized Jannaschia species. On the basis of phenotypic, phylogenetic and genetic data, strain SMK-146T represents a novel species of the genus Jannaschia, for which the name Jannaschia seohaensis sp. nov. is proposed. The type strain is SMK-146T (=KCTC 22172T =CCUG 55326T).
Mesonia phycicola sp. nov., isolated from seaweed, and emended description of the genus Mesonia
Authors: Kang Hye Soon , Lee Soon Dong
Published: November 2009

An aerobic, Gram-reaction-negative, non-motile, catalase- and oxidase-positive bacterium, designated strain MDSW-25T, was isolated from seaweed collected in the vicinity of Mara Island in Jeju province, Republic of Korea. Colonies were smooth, circular and convex with entire edges and yellow in colour. Growth occurred at 10–30 °C, at pH 6.1–9.1 and in the presence of 1–12 % (w/v) NaCl. The major fatty acids were iso-C15 : 0 (25.6 %) and iso-C15 : 1 G (11.3 %), and the major menaquinone was MK-6. The DNA G+C content was 30.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain MDSW-25T belonged to the genus Mesonia, family Flavobacteriaceae. Sequence similarity with Mesonia mobilis and Mesonia algae was 97.5 and 95.4 %, respectively, but DNA relatedness between strain MDSW-25T and M. mobilis KCTC 12708T was only 47 %. A battery of phenotypic data, phylogenetic inference and DNA–DNA hybridization analyses supports the conclusion that strain MDSW-25T (=KCTC 22373T =DSM 21425T) represents a novel species of the genus Mesonia, for which the name Mesonia phycicola sp. nov. is proposed. On the basis of new data obtained in this study, an emended description of the genus Mesonia is also proposed.
Staphylococcus microti sp. nov., isolated from the common vole (Microtus arvalis)
Authors: Nováková Dana , Pantůček Roman , Hubálek Zdeněk , Falsen Enevold , Busse Hans-Jürgen , Schumann Peter , Sedláček Ivo
Published: November 2009

Two strains of Gram-positive cocci were isolated from viscera of common voles (Microtus arvalis Pallas) with generalized Brucella microti infection in the Czech Republic. Biochemical features and phylogenetic analysis based on 16S rRNA gene sequences showed that the strains are representatives of the genus Staphylococcus and assigned Staphylococcus muscae as the nearest relative. A detailed characterization done by ribotyping, rpoB and hsp60 gene sequencing, whole-cell protein analysis and rep-PCR using the (GTG)5 primer differentiated the two strains from all described staphylococci. DNA–DNA hybridization with the type strain of S. muscae demonstrated that the two strains should be considered as members of a novel species (26.8 % reassociation). The two analysed strains were found to be coagulase-negative, novobiocin-susceptible, oxidase-negative cultures, phenotypically close to one another, but showing differences in ribotype profiles. The major fatty acids were iso-C15 : 0, iso-C17 : 0, anteiso-C15 : 0, C18 : 2
ω6,9c/anteiso-C18 : 0, C18 : 0 and C18 : 1
ω9c. MK-7 was the predominant isoprenoid quinone, with minor amounts of MK-6 and MK-8. The polar lipid profile was composed of the major lipids diphosphatidylglycerol and phosphatidylglycerol and several unknown lipids. These results proved that the two isolates represent a novel staphylococcal species. The name proposed for this novel taxon is Staphylococcus microti sp. nov.; the type strain is 4005-LJ(m)T (=CCM 4903T =CCUG 55861T =DSM 22147T).
Thalassobaculum salexigens sp. nov., a new member of the family Rhodospirillaceae from the NW Mediterranean Sea, and emended description of the genus Thalassobaculum
Authors: Urios Laurent , Michotey Valérie , Intertaglia Laurent , Lesongeur Françoise , Lebaron Philippe
Published: November 2009

A novel Gram-negative bacteria, named CZ41_10aT, was isolated from coastal surface waters of the north-western Mediterranean Sea. Cells were motile, pleomorphic rods, 1.6 μm long and 0.7 μm wide and formed cream colonies on marine agar medium. The G+C content of the genomic DNA was 65 mol%. Phylogenetic analysis of 16S rRNA gene sequences placed the new isolate in the genus Thalassobaculum, a member of the family Rhodospirillaceae, class Alphaproteobacteria. Unlike Thalassobaculum litoreum CL-GR58T, its closest relative, strain CZ41_10aT was unable to grow anaerobically and did not exhibit nitrate reductase activity. On the basis of DNA–DNA hybridization, fatty acid content and physiological and biochemical characteristics, this isolate represents a novel species for which the name Thalassobaculum salexigens sp. nov. is proposed. The type strain is CZ41_10aT (=DSM 19539T=CIP 109064T=MOLA 84T). An emended description of the genus Thalassobaculum is also given.
Halomonas xinjiangensis sp. nov., a halotolerant bacterium isolated from a salt lake
Authors: Guan Tong-Wei , Xiao Jing , Zhao Ke , Luo Xiao-Xia , Zhang Xiao-Ping , Zhang Li-Li
Published: November 2009

A novel bacterium, TRM 0175T, belonging to the genusHalomonas, was isolated from a soil sample taken from a salt lake in Xinjiang Province, north-west China. The isolate was Gram-negative, aerobic, rod-shaped and motile by means of peritrichous flagella. It was catalase-positive and oxidase-negative. Growth occurred at NaCl concentrations of 0–20 % (optimum at 10–13 %), at 15–50 °C (optimum at 37 °C) and at pH 6.0–9.0 (optimum at pH 7.0). Metabolism was respiratory with oxygen as terminal electron acceptor. Acid was produced fromd-ribose,d- andl-arabinose,d-xylose,d-galactose,d-mannose,l-rhamnose, cellobiose, maltose, trehalose andd- andl-fucose and was produced weakly from aesculin. The predominant ubiquinone was Q-9. The major fatty acids were C18 : 1ω7cand C19 : 0cycloω8c. The G+C content of the genomic DNA was 60.0 mol%. The affiliation of strain TRM 0175Twith the genusHalomonaswas confirmed by 16S rRNA gene sequence comparisons. The most closely related species wasHalomonas anticariensis; 16S rRNA gene sequence similarity betweenH.anticariensisFP35Tand strain TRM 0175Twas 95.3 %. Phenotypically, some characteristics of TRM 0175Tdiffered from those ofH. anticariensis. On the basis of data from this polyphasic study, strain TRM 0175Trepresents a novel species of the genusHalomonas, for which the nameHalomonas xinjiangensissp. nov. is proposed; the type strain is TRM 0175T(=CCTCC AB 208329T=KCTC 22608T).
Aeromonas fluvialis sp. nov., isolated from a Spanish river
Authors: Alperi Anabel , Martínez-Murcia Antonio J. , Monera Arturo , Saavedra Maria J. , Figueras Maria J.
Published: November 2009

A Gram-stain-negative, facultatively anaerobic bacterial strain, designated 717T, was isolated from a water sample collected from the Muga river, Girona, north-east Spain. Preliminary analysis of the 16S rRNA gene sequence showed that this strain belonged to the genusAeromonas, the nearest species beingAeromonas veronii(99.5 % similarity, with seven different nucleotides). A polyphasic study based on a multilocus phylogenetic analysis of five housekeeping genes (gyrB,rpoD,recA,dnaJandgyrA; 3684 bp) showed isolate 717Tto be an independent phylogenetic line, withAeromonas sobria,Aeromonas veroniiandAeromonas allosaccharophilaas the closest neighbour species. DNA–DNA reassociation experiments and phenotypic analysis identified that strain 717Trepresents a novel species, for which the nameAeromonas fluvialissp. nov. is proposed, with type strain 717T(=CECT 7401T=LMG 24681T).
Ochrobactrum pituitosum sp. nov., isolated from an industrial environment
Authors: Huber Birgit , Scholz Holger C. , Kämpfer Peter , Falsen Enevold , Langer Stefan , Busse Hans-Jürgen
Published: November 2009

Strain CCUG 50899, a Gram-negative, rod-shaped, non-spore-forming, motile bacterium isolated from industrial environment in Sweden and tentatively assigned to the species Ochrobactrum anthropi, was studied in order to clarify its taxonomic status. 16S rRNA gene sequence similarities placed the strain in the genus Ochrobactrum, sharing highest similarity with the type strains of Ochrobactrum rhizosphaerae (99.3 %), Ochrobactrum thiophenivorans (98.7 %), Ochrobactrum pseudogrignonense (98.6 %) and Ochrobactrum grignonense (98.5 %). The fatty acid profile of [O. anthropi] CCUG 50899 (major fatty acids C18 : 1
ω7c and C19 : 0 cyclo ω8c and presence of C18 : 1 2-OH), the polar lipid profile (diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, two unknown aminolipids and an unknown phospholipid), the presence of the quinone system ubiquinone Q-10 and a polyamine pattern with the major compounds putrescine and spermidine and moderate amounts of sym-homospermidine supported its affiliation to the genus Ochrobactrum. DNA–DNA reassociation experiments with the type strains of its closest relatives O. rhizosphaerae, O. pseudogrignonense, O. thiophenivorans and O. grignonense demonstrated that [O. anthropi] CCUG 50899 should be placed in a novel species, which is distinguishable from related species by a set of biochemical traits. Based on these data, reclassification of [O. anthropi] CCUG 50899 as the type strain of a novel species appears to be justified. Hence, we describe a novel species to accommodate this strain, for which we propose the name Ochrobactrum pituitosum sp. nov. The type strain is CCUG 50899T (=DSM 22207T).
Rhodobacter johrii sp. nov., an endospore-producing cryptic species isolated from semi-arid tropical soils
Authors: Girija K. R. , Sasikala Ch. , Ramana Ch. V. , Spröer C. , Takaichi S. , Thiel V. , Imhoff J. F.
Published: November 2009

An oval to rod-shaped, phototrophic, purple non-sulfur bacterium, strain JA192T, was isolated from an enrichment culture of a pasteurized rhizosphere soil sample from a field cultivated with jowar (sorghum) collected from Godumakunta village near Hyderabad, India. Strain JA192T is Gram-negative, motile and produces endospores. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that the strain JA192T is closely related to Rhodobacter sphaeroides 2.4.1T (99.9 % sequence similarity), Rba. megalophilus JA194T (99.8 %) and Rba. azotoformans KA25T (98.1 %) and clusters with other species of the genus Rhodobacter of the family Rhodobacteraceae. However, DNA–DNA hybridization with Rba. sphaeroides DSM 158T, Rba. megalophilus JA194T and Rba. azotoformans JCM 9340T showed relatedness of only 38–57 % with respect to strain JA192T. On the basis of 16S rRNA gene sequence analysis, DNA–DNA hybridization data and morphological, physiological and chemotaxonomic characters, strain JA192T represents a novel species of the genus Rhodobacter, for which the name Rhodobacter johrii sp. nov. is proposed. The type strain is JA192T (=DSM 18678T =JCM 14543T =MTCC 8172T).
Gracilibacillus thailandensis sp. nov., from fermented fish (pla-ra)
Authors: Chamroensaksri Nitcha , Tanasupawat Somboon , Akaracharanya Ancharida , Visessanguan Wonnop , Kudo Takuji , Itoh Takashi
Published: November 2009

A novel strain, designated TP2-8T, was isolated from fermented fish (pla-ra) in Thailand. It stained Gram-positive and the cells were aerobic, endospore-forming rods. The strain grew at pH 6–8 (optimum pH 7), 15–55 °C (optimum 37 °C) and 1–22 % (w/v) NaCl (optimum 5–10 %). It contained meso-diaminopimelic in the cell-wall peptidoglycan. MK-7 and cellular fatty acids anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0 were major components. Polar lipids diphosphatidylglycerol and phosphatidylglycerol and unidentified lipids were detected. The DNA G+C content was 37.6 mol%. Comparison of the 16S rRNA gene sequence of strain TP2-8T with those of other members of the family Bacillaceae indicated that it was a member of the genus Gracilibacillus (94.9–99.2 % sequence similarity) and was closely related to Gracilibacillus saliphilus YIM 91119T (99.2 % similarity), G. lacisalsi BH312T (98.6 %), G. orientalis XH-63T (97.7 %), ‘G. quinghaiensis’ YIM C229 (97.7 %) and G. boraciitolerans T-16XT (97.2 %). Strain TP2-8T showed low DNA–DNA relatedness (≤49 %) to G. saliphilus YIM 91119T, G. lacisalsi DSM 19029T, G. orientalis CCM 7326T, ‘G. quinghaiensis’ DSM 17858 and G. boraciitolerans JCM 21714T. On the basis of the physiological and biochemical characteristics and molecular data presented, strain TP2-8T is proposed to represent a novel species, Gracilibacillus thailandensis sp. nov. (type strain TP2-8T =JCM 15569T =PCU 304T =TISTR 1881T).
Prauserella muralis sp. nov., from the indoor environment
Authors: Schäfer Jenny , Martin Karin , Kämpfer Peter
Published: November 2009

A novel Gram-stain-positive, mycelium-forming actinobacterium (05-Be-005T) isolated from the wall of an indoor environment was studied for its taxonomic position. The isolated strain formed a substrate mycelium that fragmented into rod-shaped cells and showed an aerial mycelium on medium M79. On the basis of 16S rRNA gene sequence similarity studies, strain 05-Be-005T was shown to belong to the genus Prauserella, closely related to Prauserella rugosa DSM 43194T (96.6 % similarity), Prauserella alba YIM 90005T (95.9 %) and Prauserella halophila YIM 90001T (95.4 %). The predominant menaquinone was MK-9(H4); whole-cell hydrolysates contained meso-diaminopimelic acid as the diagnostic diamino acid of the cell wall and arabinose and galactose as the main sugars. Mycolic acids were absent. The polar lipid profile consisted of the lipids diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylinositol, phosphatidylserine and an unknown phospholipid. Major fatty acids C16 : 0 iso, C16 : 0, C17 : 1
ω8c and C17 : 1
ω6c supported the affiliation of strain 05-Be-005T to the genus Prauserella. The results of physiological and biochemical tests allowed clear phenotypic differentiation of strain 05-Be-005T from the three known Prauserella species. Strain 05-Be-005T represents a novel Prauserella species, for which we propose the name Prauserella muralis sp. nov., with the type strain 05-Be-005T (=CCUG 57426T =NRRL B-24780T =CCM 7635T=DSM 45305T).
Mycobacterium paraseoulense sp. nov., a slowly growing, scotochromogenic species related genetically to Mycobacterium seoulense
Authors: Lee Hyung Ki , Lee Seoung-Ae , Lee In-Kyung , Yu Hee-Kyung , Park Young-Gil , Hyun Jin-Won , Kim Kijeong , Kook Yoon-Hoh , Kim Bum-Joon
Published: November 2009

A previously unidentified, slowly growing, scotochromogenic Mycobacterium species, represented by strain 31118T, was discovered during hsp65 sequence-based reidentification of Korean clinical isolates that had been previously identified as Mycobacterium scrofulaceum by conventional biochemical tests. Although the 16S rRNA gene sequence of strain 31118T was identical to that of the recently described Mycobacterium seoulense, phylogenetic analyses based on three independent alternative targets (rpoB, hsp65 and the 16S–23S internal transcribed spacer) showed that it was closely related to M. seoulense but was a distinct phylogenetic entity. Furthermore, the phenetic characteristics of this strain were more similar to those of M. scrofulaceum than to those of M. seoulense. Taken together, these results support the conclusion that this strain represents a novel mycobacterium species, for which the name Mycobacterium paraseoulense sp. nov. is proposed. The type strain is 31118T (=DSM 45000T =KCTC 19145T).
Lutibacter maritimus sp. nov., isolated from a tidal flat sediment
Authors: Park Sooyeon , Kang So-Jung , Oh Tae-Kwang , Yoon Jung-Hoon
Published: November 2009

A Gram-staining-negative, aerobic, non-motile, non-gliding, yellow-pigmented and rod-shaped bacterial strain, designated S7-2T, was isolated from a tidal flat sediment at Saemankum on the west coast of Korea and investigated using a polyphasic taxonomic approach. Strain S7-2T grew optimally at pH 7.0–8.0, at 25–30 °C and in the presence of 2 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain S7-2T clustered with Lutibacter litoralis CF-TF09T, a member of the family Flavobacteriaceae, with which it showed 95.8 % 16S rRNA gene sequence similarity. It contained MK-6 as the predominant menaquinone and iso-C15 : 0 and C15 : 1
ω6c as the major fatty acids. The major polar lipids of strain S7-2T and L. litoralis JCM 13034T were phosphatidylethanolamine and three unidentified lipids. The DNA G+C content was 34.6 mol%. Differential phenotypic properties and phylogenetic distinctiveness suggested that strain S7-2T represents a novel species of the genus Lutibacter, for which the name Lutibacter maritimus sp. nov. is proposed. The type strain is S7-2T (=KCTC 22635T=CCUG 57524T).
Amycolatopsis halophila sp. nov., a halophilic actinomycete isolated from a salt lake
Authors: Tang Shu-Kun , Wang Yun , Guan Tong-Wei , Lee Jae-Chan , Kim Chang-Jin , Li Wen-Jun
Published: November 2009

A novel halophilic actinomycete, designated strain YIM 93223T, was isolated from a salt lake in Xinjiang Province, north-west China, and was subjected to a polyphasic taxonomic study. The isolate grew at 25–45 °C, at pH 6–8 and in the presence of 1–15 % (w/v) NaCl; no growth was observed in the absence of NaCl. Strain YIM 93223T contained meso-diaminopimelic acid, glutamic acid and alanine as cell-wall amino acids, and glucose and galactose as major whole-cell-wall sugars. Major fatty acids were iso-C16 : 0, C16 : 0 and C16 : 1
ω7c/iso-C15 : 0 2-OH. MK-8(H4) was the predominant menaquinone. The genomic DNA G+C content was 66.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 93223T belongs to the genus Amycolatopsis. It shared highest 16S rRNA gene sequence similarity with Amycolatopsis palatopharyngis 1BDZT (96.6 %) and Amycolatopsis marina Ms392AT (96.4 %), but lower values (94.5–96.2 %) with the type strains of other recognized species of the genus Amycolatopsis. On the basis of the data from this polyphasic study, strain YIM 93223T is considered to represent a novel species of the genus Amycolatopsis, for which the name Amycolatopsis halophila sp. nov. is proposed. The type strain is YIM 93223T (=DSM 45216T =KCTC 19403T).