bluuebunny/crossref_metadata_2025 huggingface dataset:
Description of Francisella hispaniensis sp. nov., isolated from human blood, reclassification of Francisella novicida (Larson et al. 1955) Olsufiev et al. 1959 as Francisella tularensis subsp. novicida comb. nov. and emended description of the genus Francisella
Authors: Huber Birgit , Escudero Raquel , Busse Hans-Jürgen , Seibold Erik , Scholz Holger C. , Anda Pedro , Kämpfer Peter , Splettstoesser Wolf D.
Published: November 2009

Strain FhSp1T, isolated from human blood in Spain in 2003, was studied for its taxonomic allocation. By 16S rRNA and recA gene sequencing, the strain was shown to belong to the genus Francisella. In the 16S rRNA gene sequence, Francisella sp. FhSp1T shared similarity of more than 99 % with strains of Francisella tularensis subspecies and Francisella novicida U112T, 98 % with Francisella piscicida GM2212T and 98.4 % with Francisella philomiragia ATCC 25015T. In the recA gene sequence, Francisella sp. FhSp1T exhibited 91.6–91.7 % similarity to strains of F. tularensis subspecies, 91.2 % to F. novicida U112T and 84 % to F. philomiragia ATCC 25017. The genus affiliation was supported by a quinone system typical of Francisella (Q-8 as the major component), a complex polar lipid profile similar to that of F. tularensis with the major components diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unknown aminophospholipid (APL4) and a fatty acid profile consisting mainly of C10 : 0 (17.2 %), C14 : 0 (11.2 %), C16 : 0 (13.1 %), C18 : 0 3-OH (14.2 %) and C18 : 1
ω9c (7.1 %). DNA–DNA hybridization, which showed unambiguously that FhSp1T represents a novel species, and the results of biochemical tests allowed genotypic and phenotypic differentiation of the isolate from all hitherto-described Francisella species. A multiplex PCR developed in the course of this study discriminated FhSp1T from representatives of all other Francisella species and subspecies, clades A.I and A.II of F. tularensis subsp. tularensis and F. tularensis subsp. holarctica biovar japonica and also between these representatives of the genus. Therefore, we propose the name Francisella hispaniensis sp. nov., with the type strain FhSp1T (=FnSp1T =FSC454T =F62T =DSM 22475T =CCUG 58020T). Furthermore, we formally propose the transfer of the species Francisella novicida to the species Francisella tularensis as Francisella tularensis subsp. novicida comb. nov. (type strain ATCC 15482T =CCUG 33449T =CIP 56.12T). We also present an emended description of the genus Francisella.
Litoricola marina sp. nov.
Authors: Choi Ahyoung , Lee Kiyoung , Oh Hyun-Myung , Feng Jing , Cho Jang-Cheon
Published: November 2009

A Gram-negative, non-pigmented, non-motile, chemoheterotrophic marine bacterium, designated strain IMCC2782T, was isolated from a surface seawater sample of the Yellow Sea, Korea. On the basis of 16S rRNA gene sequence analysis and phenotypic and genotypic characterization, strain IMCC2782T is shown to represent a novel species of the genus Litoricola. Strain IMCC2782T grew at 15–37 °C and tolerated 7.5 % NaCl. Based on 16S rRNA gene sequences, strain IMCC2782T was related most closely to the type strain of Litoricola lipolytica (97.1 % similarity) but showed less than 90 % similarity to the type strains of other bacterial species. The predominant fatty acids were mono-unsaturated C18 : 1 and C16 : 1. The G+C content of the DNA of strain IMCC2782T was 59.6 mol%. A low level of DNA–DNA relatedness (28.1 %) together with several phenotypic characteristics, including enzyme activities, served to differentiate strain IMCC2782T from the type strain of L. lipolytica. Therefore, strain IMCC2782T is considered to represent a novel species of the genus Litoricola, for which the name Litoricola marina sp. nov. is proposed. The type strain is IMCC2782T (=KCTC 22683T =NBRC 105824T).
Marinobacterium lutimaris sp. nov., isolated from a tidal flat
Authors: Kim Jeong Myeong , Lee Se Hee , Jung Ji Young , Jeon Che Ok
Published: November 2009

A Gram-staining-negative, moderately halophilic bacterium, designated strain AN9T, was isolated from a tidal flat of the Taean coast in South Korea. Cells were catalase- and oxidase-positive short rods that were motile by means of a single polar flagellum. Growth of strain AN9T was observed at 15–40 °C (optimum, 25–30 °C) and at pH 6.0–8.0 (optimum, pH 6.5–7.5). Strain AN9T contained ubiquinone Q-8 as the predominant isoprenoid quinone and C10 : 0 3-OH (31.7 %), C18 : 1
ω7c (24.8 %), C16 : 0 (14.7 %) and summed feature 3 (comprising C16 : 1
ω7c and/or iso-C15 : 0 2-OH, 10.72 %) as the major fatty acids. The G+C content of the genomic DNA of strain AN9T was 58 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AN9T was related to members of the genus Marinobacterium and was related most closely to Marinobacterium litorale IMCC1877T (96.8 % similarity). On the basis of chemotaxonomic and molecular data, strain AN9T is considered to represent a novel species of the genus Marinobacterium, for which the name Marinobacterium lutimaris sp. nov. is proposed. The type strain is AN9T (=KACC 13703T =DSM 22012T).
Winogradskyella pacifica sp. nov., a marine bacterium of the family Flavobacteriaceae
Authors: Kim Seung Bum , Nedashkovskaya Olga I.
Published: November 2009

A novel strain, designated KMM 6019T, was isolated from coastal seawater and subjected to taxonomic examination using a polyphasic approach. A comparative analysis of 16S rRNA gene sequences revealed that strain KMM 6019T formed a distinct phyletic line within the genus Winogradskyella, a member of the family Flavobacteriaceae, phylum Bacteroidetes. The 16S rRNA gene sequence similarity between the novel isolate and the type strains of the recognized species of the genus Winogradskyella was 94.0–97.8 %. Winogradskyella thalassocola KMM 3907T was the closest relative, with 97.8 % sequence similarity. The predominant fatty acids of strain KMM 6019T were iso-C15 : 0, iso-C15 : 1, anteiso-C15 : 0, iso-C15 : 0 3-OH, iso-C16 : 0 3-OH, C15 : 0, iso-C17 : 0 3-OH and summed feature 3 comprising iso-C15 : 0 2-OH and/or C16 : 1
ω7c, which are characteristic for members of the genus Winogradskyella. The DNA G+C content was 35.3 mol%. Strain KMM 6019T moved by gliding and grew with 1–5 % NaCl and at 4–30 °C. The novel strain degraded gelatin, casein and starch and produced acid from cellobiose, d-glucose and maltose. Strain KMM 6019T could clearly be differentiated from the other Winogradskyella species by the ability to utilize inositol and sorbitol and to produce hydrogen sulphide. On the basis of phylogenetic and phenotypic findings, strain KMM 6019T is considered to represent a novel species of the genus Winogradskyella, for which the name Winogradskyella pacifica sp. nov. is proposed. The type strain is KMM 6019T (=KCTC 22997T=LMG 22568T).
Prototheca cutis sp. nov., a newly discovered pathogen of protothecosis isolated from inflamed human skin
Authors: Satoh Kazuo , Ooe Kenji , Nagayama Hirotoshi , Makimura Koichi
Published: November 2009

A strain of a novel pathogenic, achlorophyllic alga belonging to the genus Prototheca was isolated from the inflamed skin of a patient with protothecosis in a Japanese hospital. The pathogen was detected and isolated in biopsy specimens by histopathology and culture-based examination. Analyses of the nuclear 18S rDNA gene and 26S rDNA gene D1/D2 domain sequences and chemotaxonomic studies indicated that this strain represents a novel species with a close phylogenetic relationship to Prototheca wickerhamii and Auxenochlorella protothecoides. This strain grew well at 28–30 °C, showed slow and weak growth at 37 °C, and no growth at 40 °C. This strain grew in vitamin-free medium and assimilated acetate (pH 5.1), l-arabinose and soluble starch as a carbon source. The taxonomic description of Prototheca cutis sp. nov. is proposed (type strain JCM 15793T =CBS 11262T =DSM 22084T) as a pathogen of dermatitis.
Psychrobacter aestuarii sp. nov., isolated from a tidal flat sediment
Authors: Baik Keun Sik , Park Seong Chan , Lim Chae Hong , Lee Kang Hyun , Jeon Doo Young , Kim Choong Mo , Seong Chi Nam
Published: November 2009

A Gram-negative-staining, non-motile, non-spore-forming and strictly aerobic bacterial strain, SC35T, was isolated from tidal flat sediment collected from the South Sea, Korea, and subjected to a taxonomic study using a polyphasic approach. The organism grew optimally at 20–30 °C and with 1–2 % (w/v) NaCl. Strain SC35Tcontained ubiquinone-8 as the predominant respiratory lipoquinone and C18 : 1ω9cas the major fatty acid. The DNA G+C content was 48.5 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain SC35Tformed a lineage within the genusPsychrobacter(94.3–96.5 % sequence similarity), forming a distinct branch in a clade also containingPsychrobacter pacificensisNIBH P2K6TandPsychrobacter celerSW-238T. On the basis of phenotypic and phylogenetic data, strain SC35T(=KCTC 22503T=JCM 16343T) was placed in the genusPsychrobacteras the type strain of a novel species, for which the namePsychrobacter aestuariisp. nov. is proposed.
Brevundimonas halotolerans sp. nov., Brevundimonas poindexterae sp. nov. and Brevundimonas staleyi sp. nov., prosthecate bacteria from aquatic habitats
Authors: Abraham Wolf-Rainer , Estrela Andréia B. , Nikitin Dennis I. , Smit John , Vancanneyt Marc
Published: November 2009

Eight strains of Gram-negative, bacteroid-shaped, prosthecate bacteria, isolated from brackish water (MCS24T, MCS17 and MCS35), the marine environment (CM260, CM272 and CM282) and activated sludge (FWC40T and FWC43T), were characterized using a polyphasic approach. Analysis of 16S rRNA gene sequences determined that all strains were affiliated to the alphaproteobacterial genus Brevundimonas, forming three distinct phyletic lineages within the genus. The strains grew best with 5–30 g NaCl l−1 at 20–30 °C. DNA G+C contents for strains MCS24T, FWC40T and FWC43T were between 65 and 67 mol%, in accordance with values reported previously for other species of the genus. Moreover, chemotaxonomic data and physiological and biochemical tests allowed the phenotypic differentiation of three novel species within the genus Brevundimonas, for which the names Brevundimonas halotolerans sp. nov. (type strain MCS24T =LMG 25346T =CCUG 58273T), Brevundimonas poindexterae sp. nov. (type strain FWC40T =LMG 25261T =CCUG 57883T) and Brevundimonas staleyi sp. nov. (type strain FWC43T =LMG 25262T =CCUG 57884T) are proposed.
Yeasts associated with the curculionid beetle Xyloterinus politus: Candida xyloterini sp. nov., Candida palmyrensis sp. nov. and three common ambrosia yeasts
Authors: Suh Sung-Oui , Zhou Jianlong
Published: November 2009

Seven yeast strains were isolated from the body surface and galleries of Xyloterinus politus, the ambrosia beetle that attacks black oak trees. Based on rDNA sequence comparisons and other taxonomic characteristics, five of the strains were identified as members of the species Saccharomycopsis microspora, Wickerhamomyces hampshirensis and Candida mycetangii, which have been reported previously as being associated with insects. The remaining two yeast strains were proposed as representatives of two novel species, Candida xyloterini sp. nov. (type strain ATCC 62898T=CBS 11547T) and Candida palmyrensis sp. nov. (type strain ATCC 62899T=CBS 11546T). C. xyloterini sp. nov. is a close sister taxon to Ogataea dorogensis and assimilates methanol as a sole carbon source but lacks ascospores. On the other hand, C. palmyrensis sp. nov. is phylogenetically distinct from any other ambrosia yeast reported so far. The species was placed near Candida sophiae-reginae and Candida beechii based on DNA sequence analyses, but neither of these were close sister taxa to C. palmyrensis sp. nov.
Saccharomonospora marina sp. nov., isolated from an ocean sediment of the East China Sea
Authors: Liu Zui , Li Yan , Zheng Liu-Qiang , Huang Yao-Jian , Li Wen-Jun
Published: November 2009

A novel, aerobic, Gram-positive actinomycete strain, designated XMU15T, was isolated from an ocean sediment collected from Zhaoan Bay in the East China Sea and was subjected to a polyphasic approach to determine its taxonomic position. The isolate grew optimally at 28 °C and at pH 7.0 in the presence of 3 % (w/v) NaCl on ISP medium 2. Gelatin liquefaction, milk coagulation and nitrate reduction were positive. Cellulose and starch hydrolysis, hydrogen sulfide and melanin production, and catalase, urease and oxidase activities were negative. The predominant menaquinone of the isolate was MK-9 (H4), and meso-diaminopimelic acid was the diagnostic amino acid in the cell wall. The phospholipids of the isolate comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, and a minor amount of phosphatidylethanolamine. The major fatty acids of the strain were iso-C16 : 0 (26.36 %), C17 : 1
ω6c (16.80 %), C15 : 0 (16.2 %), C16 : 0 (8.90 %), C17 : 1
ω8c (7.69 %) and iso-C16 : 1 H (5.95 %). The DNA G+C content of the genomic DNA was 68.1 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that the isolate fell within the evolutionary radiation encompassed by the genus Saccharomonospora and showed the highest 16S rRNA gene sequence similarity (96.7 %) to Saccharomonospora xinjiangensis DSM 44391T. Based on the results of 16S rRNA gene sequence analysis and phenotypic and genotypic characterization, strain XMU15T (=KCTC 19701T =CCTCC AA 209048T) represents a novel species of the genus Saccharomonospora, for which the name Saccharomonospora marina sp. nov. is proposed.
Verrucosispora sediminis sp. nov., a cyclodipeptide-producing actinomycete from deep-sea sediment
Authors: Dai Huan-Qin , Wang Jian , Xin Yu-Hua , Pei Gang , Tang Shu-Kun , Ren Biao , Ward Alan , Ruan Ji-Sheng , Li Wen-Jun , Zhang Li-Xin
Published: November 2009

An actinomycete, designated MS426T, the culture broth of which showed potent antimicrobial activity, was isolated from a deep-sea sediment sample of the South China Sea. An almost-complete sequence of the 16S rRNA gene of strain MS426Twas determined and aligned with those of representatives of the familyMicromonosporaceaeavailable in public databases. Phylogenetic trees were inferred by using three algorithms. Strain MS426Tformed a branch adjacent toVerrucosispora luteaYIM 013Tin a distinct cluster occupied only by strains of the genusVerrucosispora. Strain MS426Twas distinguishable from the type strains of the two describedVerrucosisporaspecies by using a combination of chemical and morphological markers and by DNA–DNA relatedness. On the basis of these genotypic and phenotypic differences, the novel antimicrobial strain with pharmaceutical potential represents a novel species, for which the nameVerrucosispora sediminissp. nov. is proposed. The type strain is MS426T(=CGMCC 4.3550T=JCM 15670T).
Fontibacter flavus gen. nov., sp. nov., a member of the family ‘Cyclobacteriaceae’, isolated from a hot spring
Authors: Kämpfer Peter , Young Chiu-Chung , Chen Wen-Ming , Rekha P. D. , Fallschissel Kerstin , Lodders Nicole , Chou Jui-Hsing , Shen Fo-Ting , Frischmann Alexa , Busse Hans-Jürgen , Arun A. B.
Published: November 2009

The taxonomic position of a bright orange-pigmented bacterial strain, designated CC-GZM-130T, isolated from a water sample of the Guan-zing-ling hot spring, southern Taiwan, was studied. The strain was able to grow on nutrient agar at 25–40 °C and in the presence of 1–3 % (w/v) NaCl. Comparative analyses of the 16S rRNA gene sequence showed that the isolate was grouped in the vicinity of the genus Aquiflexum with the highest sequence similarity of 92.1 % to the type strain of Aquiflexum balticum, followed by sequence similarities of 92.0, 91.6 and 91.5 % to the type strains of Algoriphagus ornithinivorans, Algoriphagus hitonicola and Belliella baltica, respectively. The polyamine pattern showed that the major compound was sym-homospermidine. The quinone system was menaquinone MK-7. The polar lipid profile was composed predominantly of phosphatidylethanolamine, three polar lipids and one aminolipid. Minor amounts of other lipids were also detectable. The main characteristics of the fatty acid profiles of strain CC-GZM-130T, B. baltica and Aquiflexum balticum were similar, with iso-C15 : 0, iso-C17 : 1
ω9c and iso-C17 : 0 3-OH as the major fatty acids, but some qualitative and quantitative differences were observed. The DNA G+C content of the novel strain was 53.2 mol%. The isolate clearly differed genotypically and phenotypically from representatives of the most closely related genera. On the basis of these differences, a novel species in a new genus, Fontibacter flavus gen. nov., sp. nov., is proposed with CC-GZM-130T (=CCUG 57694T=CCM 7650T) as the type strain of the type species.
Marinitoga litoralis sp. nov., a thermophilic, heterotrophic bacterium isolated from a coastal thermal spring on Île Saint-Paul, Southern Indian Ocean
Authors: Postec Anne , Ciobanu Maria , Birrien Jean-Louis , Bienvenu Nadège , Prieur Daniel , Le Romancer Marc
Published: November 2009

A novel thermophilic, anaerobic and organotrophic bacterium, designated strain MC3T, was isolated from a coastal thermal spring on Île Saint-Paul in the Southern Indian Ocean. Cells of strain MC3Twere motile rods, 0.8–1.0 μm wide and 1.0–2.4 μm long during exponential phase and up to 7.0 μm long during stationary phase. Strain MC3Twas an anaerobic organotroph able to use diverse organic compounds. It was also able to reduce sulfur to sulfide. Growth was observed at temperatures ranging from 45 to 70 °C (optimum at 60 °C), between pH 5.5 and 7.5 (optimum at pH 6) and from 8 to 46 g NaCl l−1(optimum at 26 g l−1). The total G+C content of the genomic DNA was 26.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons indicated that strain MC3Twas affiliated with the genusMarinitogawithin the orderThermotogales. It shared 94.4–95.7 % 16S rRNA gene sequence similarity with strains of otherMarinitogaspecies;Marinitoga hydrogenitoleranswas found to be the most closely related organism. Based on the data from the phylogenetic analysis and the physiological properties of the novel isolate, strain MC3Tshould be classified as a representative of a novel species, for which the nameMarinitoga litoralissp. nov. is proposed; the type strain is MC3T(=DSM 21709T=JCM 15581T).
Pusillimonas ginsengisoli sp. nov., isolated from soil of a ginseng field
Authors: Srinivasan Sathiyaraj , Kim Myung Kyum , Sathiyaraj Gayathri , Kim Yeon-Ju , Yang Deok-Chun
Published: November 2009

Two novel strains of Gram-negative, non-sporulating, short rod-shaped, motile bacteria, designated DCY25T and DCY28, were isolated from soil of a ginseng field in South Korea and characterized in order to determine their taxonomic position. 16S rRNA gene sequence analysis showed that strains DCY25T and DCY28 belonged to the Betaproteobacteria, the highest sequence similarities being found with Pusillimonas noertemannii BN9T (96.9 %), Bordetella trematum DSM 11334T (95.9 %), Achromobacter denitrificans DSM 30026T (95.9 %), Achromobacter insolitus LMG 6003T (95.8 %) and Pigmentiphaga kullae K24T (95.5 %). Chemotaxonomic data revealed that both strains DCY25T and DCY28 possessed ubiquinone Q-8. Fatty acid analysis of strain DCY25T demonstrated the presence of 19 : 0 cyclo ω8c (22.8 %) and 16 : 0 (16.6 %). The polar lipid profiles of strains DCY25T and DCY28 included phosphatidylethanolamine, phosphatidylglycerol, two unknown aminolipids and diphosphatidylglycerol. The G+C contents of strains DCY25T and DCY28 were 57.3 and 57.2 mol%, respectively. DNA–DNA relatedness values, biochemical and physiological characteristics strongly supported the genotypic and phenotypic differentiation of strains DCY25T and DCY28 from Pusillimonas noertemannii. Therefore, strains DCY25T and DCY28 should be classified in a novel species, for which the name Pusillimonas ginsengisoli sp. nov. is proposed. The type strain is DCY25T (=KCTC 22046T =JCM 14767T); strain DCY28 (=KCTC 22047=JCM 14768) is a reference strain.
Haloplanus vescus sp. nov., an extremely halophilic archaeon from a marine solar saltern, and emended description of the genus Haloplanus
Authors: Cui Heng-Lin , Gao Xia , Li Xin-Yi , Xu Xue-Wei , Zhou Yu-Guang , Liu Hong-Can , Zhou Pei-Jin
Published: November 2009

An extremely halophilic archaeon, strain RO5-8T, was isolated from a disused marine solar saltern in China. The cells were pleomorphic and flat. In static liquid medium, cells floated to the surface. Strain RO5-8Tstained Gram-negative and colonies were pink-pigmented. It was able to grow at 30–50 °C (optimum 40 °C), at 2.6–4.3 M NaCl (optimum 3.1 M NaCl), at 0.03–0.5 M MgCl2(optimum 0.03 M MgCl2) and at pH 5.5–7.5 (optimum pH 6.0–6.5). Cells lysed in distilled water and the minimal NaCl concentration to prevent cell lysis was 12 % (w/v). The major polar lipids of strain RO5-8Twere phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and one major glycolipid chromatographically identical to the sulfated mannosyl glucosyl diether S-DGD-1. On the basis of 16S rRNA gene sequence analysis, strain RO5-8Twas closely related to three strains ofHaloplanus natanswith similarities of 97.3–97.6 %. The DNA G+C content of strain RO5-8Twas 62.1 mol%. The DNA–DNA hybridization value between strain RO5-8TandHaloplanus natansJCM 14081Twas 51.6 %. It was concluded that strain RO5-8Trepresents a novel species of the genusHaloplanus, for which the nameHaloplanus vescussp. nov. is proposed. The type strain is RO5-8T(=CGMCC 1.8712T=JCM 16055T).
Castellaniella daejeonensis sp. nov., isolated from soil
Authors: Lee Myungjin , Jung Hae-Min , Woo Sung-Geun , Yoo Soon-Ae , Ten Leonid N.
Published: November 2009

A Gram-negative, non-spore-forming, motile, facultatively anaerobic bacterium, designated strain MJ06T, was isolated from oil-contaminated soil and was characterized taxonomically by using a polyphasic approach. Strain MJ06T contained ubiquinone Q-8 as the major respiratory lipoquinone, putrescine as the predominant polyamine and phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol as major polar lipids. The G+C content of the genomic DNA of strain MJ06T was 66.2 mol%. The major fatty acids were summed feature 4 (C16 : 1
ω7c and/or iso-C15 : 0 2-OH; 32.5 %), C16 : 0 (22.8 %) and summed feature 7 (one or more of C18 : 1
ω7c, C18 : 1
ω9t and C18 : 1
ω12t; 14.9 %). Comparative 16S rRNA gene sequence analysis showed that strain MJ06T belonged to the family Alcaligenaceae, class Betaproteobacteria, and joined the evolutionary radiation enclosed by the genus Castellaniella. Levels of 16S rRNA gene sequence similarity between strain MJ06T and its phylogenetically closest relatives, Castellaniella denitrificans NKNTAUT, Castellaniella defragrans 54PinT, Castellaniella ginsengisoli DCY36T and Castellaniella caeni Ho-11T, were 98.6, 98.3, 97.8 and 97.3 %, respectively. Levels of similarity between strain MJ06T and the type strains of all other recognized species in the family Alcaligenaceae were below 95.0 %. Strain MJ06T exhibited relatively low levels of DNA–DNA relatedness with respect to C. defragrans DSM 12141T (52 %), C. denitrificans DSM 11046T (31 %), C. ginsengisoli KCTC 22398T (18 %) and C. caeni KCTC 12197T (15 %). On the basis of its phenotypic and genotypic properties together with phylogenetic distinctiveness, strain MJ06T is considered to represent a novel species of the genus Castellaniella, for which the name Castellaniella daejeonensis sp. nov. is proposed. The type strain is MJ06T (=KCTC 22454T =JCM 16240T).
Fervidicoccus fontis gen. nov., sp. nov., an anaerobic, thermophilic crenarchaeote from terrestrial hot springs, and proposal of Fervidicoccaceae fam. nov. and Fervidicoccales ord. nov.
Authors: Perevalova Anna A. , Bidzhieva Salima Kh. , Kublanov Ilya V. , Hinrichs Kai-Uwe , Liu Xiaolei L. , Mardanov Andrey V. , Lebedinsky Alexander V. , Bonch-Osmolovskaya Elizaveta A.
Published: November 2009

Two novel thermophilic and slightly acidophilic strains, Kam940Tand Kam1507b, which shared 99 % 16S rRNA gene sequence identity, were isolated from terrestrial hot springs of the Uzon caldera on the Kamchatka peninsula. Cells of both strains were non-motile, regular cocci. Growth was observed between 55 and 85 °C, with an optimum at 65–70 °C (doubling time, 6.1 h), and at pH 4.5–7.5, with optimum growth at pH 5.5–6.0. The isolates were strictly anaerobic organotrophs and grew on a narrow spectrum of energy-rich substrates, such as beef extract, gelatin, peptone, pyruvate, sucrose and yeast extract, with yields above 107cells ml−1. Sulfate, sulfite, thiosulfate and nitrate added as potential electron acceptors did not stimulate growth when tested with peptone. H2at 100 % in the gas phase inhibited growth on peptone. Glycerol dibiphytanyl glycerol tetraethers (GDGTs) with zero to four cyclopentyl rings were present in the lipid fraction of isolate Kam940T. The G+C content of the genomic DNA of strain Kam940Twas 37 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolates were archaea of the phylumCrenarchaeota, only distantly related to the cultured members of the classThermoprotei(no more than 89 % identity), and formed an independent lineage adjacent to the ordersDesulfurococcalesandAcidilobalesand clustering only with uncultured clones from hot springs of Yellowstone National Park and Iceland as the closest relatives. On the basis of their phylogenetic position and novel phenotypic features, isolates Kam940Tand Kam1507b are proposed to be assigned to a new genus and species,Fervidicoccus fontisgen. nov., sp. nov. The type strain ofFervidicoccus fontisis strain Kam940T(=DSM 19380T=VKM B-2539T). The phylogenetic data as well as phenotypic properties suggest that the novel crenarchaeotes form the basis of a new family,Fervidicoccaceaefam. nov., and order,Fervidicoccalesord. nov., within the classThermoprotei.
Weissella fabaria sp. nov., from a Ghanaian cocoa fermentation
Authors: De Bruyne Katrien , Camu Nicholas , De Vuyst Luc , Vandamme Peter
Published: November 2009

Two lactic acid bacteria, strains 257Tand 252, were isolated from traditional heap fermentations of Ghanaian cocoa beans. 16S rRNA gene sequence analysis of these strains allocated them to the genusWeissella, showing 99.5 % 16S rRNA gene sequence similarity towardsWeissella ghanensisLMG 24286T. Whole-cell protein electrophoresis, fluorescent amplified fragment length polymorphism fingerprinting of whole genomes and biochemical tests confirmed their unique taxonomic position. DNA–DNA hybridization experiments towards their nearest phylogenetic neighbour demonstrated that the two strains represent a novel species, for which we propose the nameWeissella fabariasp. nov., with strain 257T(=LMG 24289T=DSM 21416T) as the type strain. Additional sequence analysis usingpheSgene sequences proved useful for identification of allWeissella–Leuconostoc–Oenococcusspecies and for the recognition of the novel species.
Report of two unlinked cases of infant botulism in the UK in October 2007
Authors: Grant Kathie A. , Nwarfor Ijeoma , Mpamugo Obioma , Mithani Vina , Lister Paula , Dixon Garth , Nixon Grainne , Planche Timothy , Courtney Max , Morgan Jaime , McLauchlin Jim
Published: November 2009

Infant botulism is a rare disease in the UK, with the first case being recognized in 1978 and only five subsequent cases being reported before 2007. This study reports two unlinked cases of infant botulism, caused by two distinct strains of Clostridium botulinum (toxin types A and B, respectively), that occurred within a single month in the south-east of England in October 2007. The use of real-time PCR to detect C. botulinum neurotoxin genes in clinical specimens to improve the diagnostic procedure and to follow carriage of the causative organism in the infant gut is described. The laboratory investigation of these two cases demonstrated that a combination of the mouse bioassay, real-time PCR assays and conventional microbiological culture can provide rapid confirmation of a clinical diagnosis and affect patient management. Both infants (aged 4 and 8 months) were previously healthy prior to the onset of symptoms, and in both cases, a diagnosis of infant botulism was delayed for at least 10 days after initial admission to hospital. Once diagnosed, one of the infants was the first in the UK to be treated with human-derived botulism immunoglobulin. Real-time PCR was used to demonstrate that C. botulinum was excreted in the infants' faeces for up to 68 and 81 days, respectively. Despite the infrequency of infant botulism in the UK, clinicians should be aware of this rare but serious condition and should seek microbiological advice when presented with young infants with compatible symptomologies.
Structural analysis of a p44/msp2 expression site of Anaplasma phagocytophilum in naturally infected ticks in Japan
Authors: Wuritu  , Ozawa Yutaka , Gaowa  , Kawamori Fumihiko , Masuda Takashi , Masuzawa Toshiyuki , Fujita Hiromi , Ohashi Norio
Published: November 2009

Anaplasma phagocytophilum, an agent of human granulocytic anaplasmosis, infects neutrophils and causes an emerging tickborne febrile disease. The genome of this bacterium contains a large number ofp44/msp2-related genes encoding 44 kDa major outer-membrane proteins, and it is known that a specificp44/msp2gene is predominantly transcribed from a single expression locus. This study successfully characterized the genomic expression site forp44/msp2(3.8 kb) in unculturedA. phagocytophilumfromIxodes persulcatusticks inhabiting a northern part of Japan. Comparative analysis of the sequences revealed that the structures of the expression sites in JapaneseA. phagocytophilumwere similar to those of US strains from human patients and European strains from a dog and sheep, butomp-1N(upstream fromp44/msp2) and a truncatedrecA(downstream fromp44/msp2) in thep44/msp2expression site seemed to share similarities with those of US and European strains. The central hypervariable region sequences of Japanesep44/msp2were found to be quite diverse (24.4–100 % amino acid similarities) and distinct from their closest relatives from US human patients or animal host origins (56.3–97.6 % amino acid similarities) with some exceptions. Thus, this study provides significant information about the molecular characteristics ofA. phagocytophilumin East Asia, as well as the global diversity ofp44/msp2.
Toxic megacolon complicating a Clostridium difficile infection in a pregnant woman
Authors: Candiotto Alberto , Pascoli Irene , Gritti Alessandra , Busato Enrico , Dal Pozzo Giuseppe
Published: November 2009

Clostridium difficile infection (CDI) in non-hospitalized patients has been reported with increased frequency, whereas an association between CDI and pregnancy has not been highlighted. We report a case of toxic megacolon complicating a severe CDI during the second trimester of pregnancy in a patient without traditional risk factors, such as antibiotic use, immunodeficiency, and prolonged and recent hospitalization.
Allelic variability of critical virulence genes (eae, bfpA and perA) in typical and atypical enteropathogenic Escherichia coli in Peruvian children
Authors: Contreras C. A. , Ochoa T. J. , Lacher D. W. , DebRoy C. , Navarro A. , Talledo M. , Donnenberg M. S. , Ecker L. , Gil A. I. , Lanata C. F. , Cleary T. G.
Published: November 2009

Enteropathogenic Escherichia coli (EPEC) is a leading cause of infantile diarrhoea in developing countries. The aim of this study was to describe the allelic diversity of critical EPEC virulence genes and their association with clinical characteristics. One hundred and twenty EPEC strains isolated from a cohort diarrhoea study in Peruvian children were characterized for the allele type of eae (intimin), bfpA (bundlin pilin protein of bundle-forming pilus) and perA (plasmid encoded regulator) genes by PCR-RFLP. Atypical EPEC strains (eae+, bfp−) were the most common pathotype in diarrhoea (54/74, 73 %) and control samples from children without diarrhoea (40/46, 87 %). Overall, there were 13 eae alleles; the most common were beta (34/120, 28 %), theta (24/120, 20 %), kappa (14/120, 12 %) and mu (8/120, 7 %). There were five bfpA alleles; the most common were beta1/7 (10/26), alpha3 (7/26) and beta5 (3/26). There were three perA alleles: beta (8/16), alpha (7/16) and gamma (1/16). The strains belonged to 36 distinct serogroups; O55 was the most frequent. The gamma-intimin allele was more frequently found in diarrhoea episodes of longer duration (>7 days) than those of shorter duration (3/26, 12 % vs 0/48, 0 %, P<0.05). The kappa-intimin allele had the highest clinical severity score in comparison with other alleles (P<0.05). In Peruvian children, the virulence genes of EPEC strains are highly variable. Further studies are needed to evaluate additional virulence markers to determine whether relationships exist between specific variants and clinical features of disease.
Diversity in the cag pathogenicity island of Helicobacter pylori isolates in populations from North and South India
Authors: Kumar Sushil , Kumar Ashok , Dixit Vinod Kumar
Published: November 2009

The cag pathogenicity island (cagPAI) has been reported to be the major virulence determinant in Helicobacter pylori-related diseases. In the present study, the diversity of the cagA gene and the integrity of the cagPAI in 158 H. pylori strains from Varanasi (North India) and Hyderabad (South India) were studied by amplifying the cagA gene (∼3.5 kb), followed by PCR-RFLP analysis. The results revealed significant differences in the cagA gene and the integrity of the cagPAI between North and South Indian isolates. Of 158 isolates, 40 (34.8 %) from Varanasi and 20 (46.5 %) from Hyderabad were found to carry an intact cagPAI. A partially deleted cagPAI was present in 75 (65.2 %) isolates from Varanasi and 23 (53.5 %) from Hyderabad. None of the isolates showed complete deletion of the cagPAI. Differences in the cagA 5′ and 3′ regions were also noted, and 11 isolates (8 from Varanasi and 3 from Hyderabad) that were cagA negative with primers for the 5′ region turned out to be cagA positive with primers for the 3′ variable region. It is tentatively concluded that the 3′ variable region may be a better marker for cagA typing. The results also showed that the majority of the isolates harboured the Western-type EPIYA motif. PCR-RFLP analysis of the cagA gene showed 29 distinguishable digestion patterns, and cluster analysis of RFLP types from a random selection of 32 isolates placed all of the isolates into 5 groups. These results demonstrate that significant differences in the cagPAI occur among isolates from North and South India, and that RFLP of cagA could be employed for elucidating genetic variations among various isolates of H. pylori.
Effect of bile salts on the DNA and membrane integrity of enteric bacteria
Authors: Merritt Megan E. , Donaldson Janet R.
Published: November 2009

Enteric bacteria are able to resist the high concentrations of bile encountered throughout the gastrointestinal tract. Here we review the current mechanisms identified in the enteric bacteriaSalmonella,Escherichia coli,Bacillus cereusandListeria monocytogenesto resist the dangerous effects of bile. We describe the role of membrane transport systems, and their connection with DNA repair pathways, in conferring bile resistance to these enterics. We discuss the findings from recent investigations that indicate bile tolerance is dependent upon being able to resist the detergent properties of bile at both the membrane and DNA level.
Pathogenic potential of Aeromonas hydrophila isolated from surface waters in Kolkata, India
Authors: Bhowmik Poulami , Bag Prasanta K. , Hajra Tapas K. , De Rituparna , Sarkar Pradipto , Ramamurthy T.
Published: November 2009

Members of the genusAeromonas(familyAeromonadaceae) are medically important, Gram-negative, rod-shaped micro-organisms and are ubiquitous in aquatic environments.Aeromonasspecies are increasingly recognized as enteric pathogens; they possess several virulence factors associated with human disease, and represent a serious public health concern. In the present study, putative virulence traits ofAeromonas hydrophilaisolates collected from different natural surface waters of Kolkata, India, were compared with a group of clinical isolates from the same geographical area using tissue culture and PCR assays. Enteropathogenic potential was investigated in the mouse model. Of the 21 environmental isolates tested, the majority showed cytotoxicity to HeLa cells (81 %), haemolysin production (71 %) and serum resistance properties (90 %), and they all exhibited multi-drug resistance. Some of the isolates induced fluid accumulation (FA ratio≥100), damage to the gut and an inflammatory reaction in the mouse intestine; these effects were comparable to those of clinical strains ofA. hydrophilaand toxigenicVibrio cholerae. Interestingly, two of the isolates evoked a cell vacuolation effect in HeLa cells, and were also able to induce FA. These findings demonstrate the presence of potentially pathogenic and multi-drug-resistantA. hydrophilain the surface waters, thereby indicating a significant risk to public health. Continuous monitoring of surface waters is important to identify potential water-borne pathogens and to reduce the health risk caused by the genusAeromonas.
Genetic and biochemical analysis of a class C non-specific acid phosphatase (NSAP) of Clostridium perfringens
Authors: Wang Ruoyu , Ohtani Kaori , Wang Yun , Yuan Yonghui , Hassan Sufi , Shimizu Tohru
Published: November 2009

Clostridium perfringens, a Gram-positive anaerobe, is a human pathogen that causes gas gangrene in muscle tissues. Its ability to grow and survive in the host is believed to be due to the production of numerous enzymes that enable the organism to obtain essential nutrients from the host. In this study, CPE0201, a putative acid phosphatase gene deduced by genome analysis, was shown to encode a non-specific acid phosphatase inC. perfringens. Multiple alignments of the amino acid sequence showed that CPE0201 shares two signature motifs that belong to a class C acid phosphatase family. Expression of CPE0201 was shown to be positively regulated by the global VirR/VirS-VR-RNA regulatory cascade at the transcriptional level. To determine the acid phosphatase activity of the CPE0201-encoded protein, cloning, expression, purification and several biochemical characterizations were carried out. The optimum pH for activity of the CPE0201 enzyme was 4.8, and itsVmaxandKmwere 3.08 nmol ml−1min−1and 2.84 mM, respectively, withp-nitrophenyl phosphate (PNPP) as substrate. A CPE0201 mutant did not grow in a minimal medium containing PNPP, while it showed normal growth when Na2HPO4was added to the medium. The enzyme appears to be associated with the surface of the cell, where it may function to acquire inorganic phosphate from organic phosphomonoesters in acidic conditions, which could play an important role in the survival and growth ofC. perfringensin the host tissue.
Defects in flagellin glycosylation affect the virulence of Pseudomonas syringae pv. tabaci 6605
Authors: Taguchi Fumiko , Yamamoto Masanobu , Ohnishi-Kameyama Mayumi , Iwaki Masako , Yoshida Mitsuru , Ishii Tadashi , Konishi Tomoyuki , Ichinose Yuki
Published: November 2009

Flagellar motility and its glycosylation are indispensable for the virulence of Pseudomonas syringae pv. tabaci 6605. Six serine residues of the flagellin protein at positions 143, 164, 176, 183, 193 and 201 are glycosylated, and the glycan structure at 201 was determined to consist of a trisaccharide of two l-rhamnosyl residues and a modified 4-amino-4,6-dideoxyglucosyl (viosamine) residue. To investigate the glycan structures attached to the other serine residues and to identify the glycans important for virulence, Ser/Ala-substituted mutants were generated. Six mutant strains that each retained a single glycosylated serine residue were generated by replacing five of the six serine residues with alanine residues. MALDI-TOF mass analysis of flagellin proteins revealed that the major component of each glycan was a trisaccharide basically similar to that at position 201, but with heterogeneity in glycoform distribution. Swarming motility and amounts of acylhomoserine lactones (AHLs) as quorum-sensing signal molecules were significantly reduced, especially in the S143-5S/A, S164-5S/A and S201-5S/A mutants, whereas tolerance to antibiotics was increased in these three mutants. All the mutants showed lower ability to cause disease on host tobacco plants. These results supported our previous finding that glycosylation of the most externally located sites on the surface of the flagellin molecule, such as S176 and S183, is required for virulence in P. syringae pv. tabaci 6605. Furthermore, it is speculated that flagellum-dependent motility might be correlated with quorum sensing and antibiotic resistance.
The resistance-nodulation-division efflux pump EmhABC influences the production of 2,4-diacetylphloroglucinol in Pseudomonas fluorescens 2P24
Authors: Tian Tao , Wu Xiao-Gang , Duan Hui-Mei , Zhang Li-Qun
Published: November 2009

The polyketide metabolite 2,4-diacetylphloroglucinol (2,4-DAPG) plays a major role in the biological control of soil-borne plant diseases by Pseudomonas fluorescens 2P24. Two mutants (PM810 and PM820) with increased extracellular accumulation of 2,4-DAPG were isolated using transposon mutagenesis. The disrupted genes in these two mutants shared >80 % identity with the genes of the EmhR–EmhABC resistance-nodulation-division (RND) efflux system of P. fluorescens cLP6a. The deletion of emhA (PM802), emhB (PM803) or emhC (PM804) genes in strain 2P24 increased the extracellular accumulation of 2,4-DAPG, whereas the deletion of the emhR (PM801) gene decreased the biosynthesis of 2,4-DAPG. The promoter assay confirmed the elevated transcription of emhABC in the EmhR disrupted strain (PM801) and an indirect negative regulation of 2,4-DAPG biosynthetic locus transcription by the EmhABC efflux pump. Induction by exogenous 2,4-DAPG led to remarkable differences in transcription of chromosome-borne phlA : : lacZ fusion in PM901 and PM811 (emhA
−) strains. Additionally, the EmhABC system in strain 2P24 was involved in the resistance to a group of toxic compounds, including ampicillin, chloramphenicol, tetracycline, ethidium bromide and crystal violet. In conclusion, our results suggest that the EmhABC system is an important element that influences the production of antibiotic 2,4-DAPG and enhances resistance to toxic compounds in P. fluorescens 2P24.
Characterization of a virulence-associated and cell-wall-located DNase of Streptococcus pyogenes
Authors: Hasegawa Tadao , Minami Masaaki , Okamoto Akira , Tatsuno Ichiro , Isaka Masanori , Ohta Michio
Published: November 2009

We investigated culture supernatant proteins from the M1 serotype of Streptococcus pyogenes by two-dimensional gel electrophoresis and peptide mass mapping analysis, and characterized the single protein spots. Among them, we analysed the Spy0747 protein. This protein is homologous to the SsnA protein, a cell-wall-located DNase expressed in Streptococcus suis serotype 2. We designated the Spy0747 protein as SpnA. SpnA protein was also detected in the insoluble fraction of whole-cell lysates using shotgun proteomic analysis, suggesting that SpnA is also located in the cell wall. SpnA was expressed as a glutathione S-transferase-fusion protein in Escherichia coli. We confirmed that the recombinant protein had DNase activity that was dependent on Ca2+ and Mg2+, like SsnA. Blood bactericidal assays and mouse infection model experiments showed that the spnA knockout strain was less virulent than the parental strain, thus suggesting that SpnA could play an important role in virulence. Using PCR, we found that the spnA gene was present in all clinical S. pyogenes strains we examined. Our results, together with a previous report identifying Spy0747 as a surface-associated protein, suggest that SpnA is an important cell-wall-located DNase that is generally produced in S. pyogenes and is involved in virulence.
PssA is required for α-amylase secretion in Antarctic Pseudoalteromonas haloplanktis
Authors: Parrilli Ermenegilda , Giuliani Maria , Pezzella Cinzia , Danchin Antoine , Marino Gennaro , Tutino Maria Luisa
Published: November 2009

Extracellular protein secretion is an essential feature in bacterial physiology. The ability to efficiently secrete diverse hydrolytic enzymes represents a key nutritional strategy for all bacteria, including micro-organisms living in extreme and hostile habitats, such as cold environments. However, little is known about protein secretion mechanisms in psychrophilic bacteria. In this study, the recombinant secretion of a cold-adaptedα-amylase in the Antarctic Gram-negativePseudoalteromonas haloplanktisTAC125 was investigated. By a combination of several molecular techniques, the function of thepssAgene was related toα-amylase secretion in this psychrophilic bacterium. Deletion of thepssAgene completely abolished amylase secretion without affecting the extracellular targeting of other substrates mediated by canonical secretion systems. ThepssAgene product, PssA, is a multidomain lipoprotein, predicted to be localized in the bacterial outer membrane, and displaying three TPR (tetratricopeptide repeat) domains and two LysM modules. Based on functional annotation of these domains, combined with the experimental results reported herein, we suggest a role for PssA as a molecular adaptor, in charge of recruiting other cellular components required for specificα-amylase secretion. To the best of our knowledge, no proteins exhibiting the same domain organization have previously been linked to protein secretion.
Volatile antimicrobials from Muscodor crispans, a novel endophytic fungus
Authors: Mitchell Angela M. , Strobel Gary A. , Moore Emily , Robison Richard , Sears Joe
Published: November 2009

Muscodor crispansis a recently described novel endophytic fungus ofAnanas ananassoides(wild pineapple) growing in the Bolivian Amazon Basin. The fungus produces a mixture of volatile organic compounds (VOCs); some of the major components of this mixture, as determined by GC/MS, are propanoic acid, 2-methyl-, methyl ester; propanoic acid, 2-methyl-; 1-butanol, 3-methyl-;1-butanol, 3-methyl-, acetate; propanoic acid, 2-methyl-, 2-methylbutyl ester; and ethanol. The fungus does not, however, produce naphthalene or azulene derivatives as has been observed with many other members of the genusMuscodor. The mixture of VOCs produced byM. crispanscultures possesses antibiotic properties, as does an artificial mixture of a majority of the components. The VOCs of the fungus are effective against a wide range of plant pathogens, including the fungiPythium ultimum,Phytophthora cinnamomi,Sclerotinia sclerotiorumandMycosphaerella fijiensis(the black sigatoka pathogen of bananas), and the serious bacterial pathogen of citrus,Xanthomonas axonopodispv.citri.In addition, the VOCs ofM. crispanskilled several human pathogens, includingYersinia pestis,Mycobacterium tuberculosisandStaphylococcus aureus. Artificial mixtures of the fungal VOCs were both inhibitory and lethal to a number of human and plant pathogens, including three drug-resistant strains ofMycobacterium tuberculosis.The gaseous products ofMuscodor crispanspotentially could prove to be beneficial in the fields of medicine, agriculture, and industry.