bluuebunny/crossref_metadata_2025 huggingface dataset:
Dactylosporangium luridum sp. nov., Dactylosporangium luteum sp. nov. and Dactylosporangium salmoneum sp. nov., nom. rev., isolated from soil
Authors: Kim Byung-Yong , Stach James E. M. , Weon Hang-Yeon , Kwon Soon-Wo , Goodfellow Michael
Published: November 2009

Forty strains isolated from soil taken from a hay meadow were assigned to the genus Dactylosporangium on the basis of colonial properties. 16S rRNA gene sequence analysis showed that the isolates formed a group that was most closely related to the type strain of Dactylosporangium aurantiacum, but well separated from other Dactylosporangium type strains and from ‘Dactylosporangium salmoneum’ NRRL B-16294. Twelve of 13 representative isolates had identical 16S rRNA gene sequences and formed a subclade that was distinct from corresponding phyletic lines composed of the remaining isolate, strain BK63T, the ‘D. salmoneum’ strain and the type strains of recognized Dactylosporangium species. DNA–DNA relatedness data indicated that representatives of the multi-membered 16S rRNA gene subclade, isolate BK63T and the ‘D. salmoneum’ subclade formed distinct genomic species; all of these organisms had chemotaxonomic and morphological properties consistent with their classification in the genus Dactylosporangium. They were also distinguished from one another and from the type strains of recognized Dactylosporangium species based on a range of phenotypic properties. Combined genotypic and phenotypic data showed that isolate BK63T, isolates BK51T, BK53 and BK69, and strain NRRL B-16294T should be classified in the genus Dactylosporangium as representing novel species. The names proposed for these species are Dactylosporangium luridum sp. nov. (type strain BK63T  = DSM 45324T  = KACC 20933T  = NRRL B-24775T), Dactylosporangium luteum sp. nov. (type strain BK51T  = DSM 45323T  = KACC 20899T  = NRRL B-24774T) and Dactylosporangium salmoneum sp. nov., nom. rev. (type strain NRRL B-16294T  = ATCC 31222T  = DSM 43910T  = JCM 3272T  = NBRC 14103T).
Agaricicola taiwanensis gen. nov., sp. nov., an alphaproteobacterium isolated from the edible mushroom Agaricus blazei
Authors: Chu Jiunn-Nan , Arun A. B. , Chen Wen-Ming , Chou Jui-Hsing , Shen Fo-Ting , Rekha P. D. , Kämpfer P. , Young Li-Sen , Lin Shih-Yao , Young Chiu-Chung
Published: November 2009

A Gram-negative, beige-pigmented, aerobic, motile, club-shaped bacterium, designated strain CC-SBABM117T, was isolated from the stipe of the edible mushroom Agaricus blazei Murrill. 16S rRNA gene sequence analysis demonstrated that the strain shared <93 % similarity with the type strains of species in the genera Pannonibacter, Methylopila, Nesiotobacter and Stappia. The organism was unable to produce acid from carbohydrates, but utilized a number of organic acids and amino acids. Ubiquinone 10 (Q-10) was the major respiratory quinone and C18 : 1
ω7c, C19 : 0 cyclo ω8c, C16 : 0 and C18 : 0 were the predominant fatty acids. The predominant polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content of strain CC-SBABM117T was 62.7 mol%. On the basis of 16S rRNA gene sequence analysis and chemotaxonomic and physiological data, strain CC-SBABM117T is considered to represent a novel species of a new genus, for which the name Agaricicola taiwanensis gen. nov., sp. nov. is proposed. The type strain of Agaricicola taiwanensis is CC-SBABM117T (=BCRC 17964T =CCM 7684T).
Proposal to unify Clostridium orbiscindens Winter et al. 1991 and Eubacterium plautii (Séguin 1928) Hofstad and Aasjord 1982, with description of Flavonifractor plautii gen. nov., comb. nov., and reassignment of Bacteroides capillosus to Pseudoflavonifractor capillosus gen. nov., comb. nov.
Authors: Carlier Jean-Philippe , Bedora-Faure Marie , K'ouas Guylène , Alauzet Corentine , Mory Francine
Published: November 2009

We isolated several strains from various clinical samples (five samples of blood, four of intra-abdominal pus and one of infected soft tissue) that were anaerobic, motile or non-motile and Gram-positive rods. Some of the strains formed spores. Phylogenetic analysis of the 16S rRNA gene sequence showed that these organisms could be placed within clostridial cluster IV as defined by Collinset al.[(1994).Int J Syst Bacteriol44, 812–826] and shared more than 99 % sequence similarity withClostridium orbiscindensDSM 6740TandEubacterium plautiiDSM 4000T. Together, they formed a distinct cluster, withBacteroides capillosusATCC 29799Tbranching off from this line of descent with sequence similarities of 97.1–97.4 %. The next nearest neighbours of these organisms wereClostridium viride,Oscillibacter valericigenes,Papillibacter cinnamivoransandSporobacter termitidis, with sequence similarities to the respective type strains of 93.1–93.4, 91.2–91.4, 89.8–90 and 88.7–89.3 %. On the basis of biochemical properties, phylogenetic position, DNA G+C content and DNA–DNA hybridization, it is proposed to unifyClostridium orbiscindensandEubacterium plautiiin a new genus asFlavonifractor plautiigen. nov., comb. nov., with the type strain Prévot S1T(=ATCC 29863T=VPI 0310T=DSM 4000T), and to reassignBacteroides capillosustoPseudoflavonifractor capillosusgen. nov., comb. nov., with the type strain CCUG 15402AT(=ATCC 29799T=VPI R2-29-1T).
Candida spencermartinsiae sp. nov., Candida taylorii sp. nov. and Pseudozyma abaconensis sp. nov., novel yeasts from mangrove and coral reef ecosystems
Authors: Statzell-Tallman Adele , Scorzetti Gloria , Fell Jack W.
Published: November 2009

Three species of yeasts are taxonomically described for strains isolated from marine environments. Candida spencermartinsiae sp. nov. (type strain CBS 10894T =NRRL Y-48663T) and Candida taylorii sp. nov. (type strain CBS 8508T =NRRL Y-27213T) are anamorphic ascomycetous yeasts in a phylogenetic cluster of marine yeasts in the Debaryomyces/Lodderomyces clade of the Saccharomycetales. The two species were isolated from multiple locations among coral reefs and mangrove habitats. Pseudozyma abaconensis sp. nov. (type strain CBS 8380T =NRRL Y-17380T) is an anamorphic basidiomycete that is related to the smut fungi of the genus Ustilago in the Ustilaginales. P. abaconensis was collected from waters adjacent to a coral reef.
Planotetraspora kaengkrachanensis sp. nov. and Planotetraspora phitsanulokensis sp. nov., isolated from soil
Authors: Suriyachadkun Chanwit , Chunhametha Suwanee , Thawai Chitti , Tamura Tomohiko , Potacharoen Wanchern , Kirtikara Kanyawim , Sanglier Jean-Jacques , Kitpreechavanich Vichien
Published: November 2009

Two novel bacterial strains were isolated from tropical rain forest soil from Thailand. Strains A-T 0875T and A-T 1383T stained Gram-positive and were filamentous bacteria that developed cylindrical sporangia containing four oval- to rod-shaped spores at the ends of short sporangiophores on branched aerial mycelium. The cell-wall peptidoglycan contained meso-diaminopimelic acid, glutamic acid and alanine as cell-wall amino acids; whole-cell hydrolysates contained rhamnose, madurose, glucose, galactose and 3-O-methylmannose as whole-cell sugars. The predominant menaquinone was MK-9(H4). Mycolic acids were not detected. The diagnostic phospholipid was phosphatidylethanolamine. The predominant cellular fatty acids were iso-C16 : 0 and 10-methyl-C17 : 0. For both strains, the G+C content of the genomic DNA was 71 mol%. Phenotypic and chemotaxonomic analyses showed that the characteristics of the two isolates were typical of members of the genus Planotetraspora. Furthermore, 16S rRNA gene sequence analysis also indicated that the strains belonged to the genus Planotetraspora but as representatives of two novel species. Following an evaluation of our phenotypic, chemotaxonomic and genotypic studies, two novel species are proposed, Planotetraspora kaengkrachanensis sp. nov. (type strain A-T 0875T=BCC 24832T=NBRC 104272T) and Planotetraspora phitsanulokensis sp. nov. (type strain A-T 1383T=BCC 26045T=NBRC 104273T).
Prevotella dentasini sp. nov., a black-pigmented species isolated from the oral cavity of donkeys
Authors: Takada Kazuko , Hayashi Kazuhiko , Sato Yutaka , Hirasawa Masatomo
Published: November 2009

Four strains (NUM 1903T, NUM 1904, NUM 1912 and NUM 1925) that were obligately anaerobic, pigmented, Gram-negative-staining rods were isolated from the oral cavity of donkeys. These strains were analysed using the Rapid ID 32A, API 20A and API ZYM systems, by DNA–DNA hybridization with other related species and by 16S rRNA gene sequencing. 16S rRNA gene sequence analysis showed that each of the new isolates was a member of the genus Prevotella and related to Prevotella multiformis PPPA21T, showing about 93 % sequence similarity. Based on phylogenetic and phenotypic evidence, it is proposed that the four strains are representatives of a novel species, for which the name Prevotella dentasini sp. nov. is proposed. The type strain is NUM 1903T (=JCM 15908T=DSM 22229T).
Shewanella fodinae sp. nov., isolated from a coal mine and from a marine lagoon
Authors: Sravan Kumar R. , Sasi Jyothsna T. S. , Sasikala Ch. , Seong C. N. , Lim C. H. , Park S. C. , Ramana Ch. V.
Published: November 2009

Strains JC15T and JC19 were isolated from samples collected from different locations in India, including a coal mine and a marine lagoon. Both strains were Gram-stain-negative rods, motile by means of a single polar flagellum, catalase- and oxidase-positive, and hydrolysed casein, produced H2S and showed β-haemolysis. Strain JC15T grew optimally at pH 6 (range pH 5–8) while strain JC19 grew optimally at pH 7 (range pH 6-9) and both had a growth temperature optimum of 30–37 °C (range 22–40 °C). Both strains could grow chemo-organoheterotrophically and chemolithoautotrophically. Neither strain required NaCl for growth and both could tolerate up to 9 % (w/v) NaCl, with optimum growth at 5 % NaCl. Vitamin B12 was required as a growth factor by both strains. The major fatty acids were iso-C15 : 0, C17 : 1
ω8c and iso-C13 : 0 3-OH. The DNA G+C contents of strains JC15T and JC19 were 53.6 and 54.3 mol%, respectively. A phylogenetic tree based on 16S rRNA gene sequence analysis showed that strains JC15T and JC19 were most closely related to Shewanella haliotis DW01T (approximately 94 % sequence similarity) and to other members of the genus Shewanella. Genomic relatedness (DNA–DNA hybridization) between strains JC15T and JC19 is 88 %. On the basis of phenotypic and molecular genetic evidence, strain JC15T represents a novel species of the genus Shewanella, for which the name Shewanella fodinae sp. nov. is proposed. The type strain is JC15T (=CCUG 57102T =NBRC 105216T =KCTC 22506T).
Reclassification of Bacteroides ureolyticus as Campylobacter ureolyticus comb. nov., and emended description of the genus Campylobacter
Authors: Vandamme P. , Debruyne L. , De Brandt E. , Falsen E.
Published: November 2009

The protein profiles, genomic amplified fragment length polymorphism patterns and 16S rRNA and cpn60 gene sequences of a diverse collection of 26 Bacteroides ureolyticus strains, along with published data on their DNA base, respiratory quinone and cellular fatty acid compositions, were used to reassess the taxonomy of this bacterial species. The results demonstrate that this organism is most appropriately allocated in the genus Campylobacter. The presence of much higher amounts of 18 : 1ω7c in its cellular fatty acid profile and its ability to digest gelatin and casein are the characteristics that differentiate it from present species of the genus Campylobacter. Therefore we propose to reclassify this species incertae sedis into the genus Campylobacter as Campylobacter ureolyticus with strain LMG 6451T (=CCUG 7319T =NCTC 10941T) as the type strain.
Catellibacterium aquatile sp. nov., isolated from fresh water, and emended description of the genus Catellibacterium Tanaka et al. 2004
Authors: Liu Ying , Xu Cheng-Jun , Jiang Jia-Tong , Liu Ying-Hao , Song Xue-Feng , Li Hao , Liu Zhi-Pei
Published: November 2009

A Gram-negative, rod-shaped, non-pigmented, non-spore-forming bacterial strain that was motile by a single polar flagellum, designated A1-9T, was isolated from Daqing reservoir in north-east China and its taxonomic position was studied using a polyphasic approach. Strain A1-9Twas non-halophilic, strictly aerobic and heterotrophic and lacked carotenoids, internal membranes and genes for photosynthesis (pufgenes). Strain A1-9Tgrew at 10–40 °C (optimum, 25–30 °C) and pH 5.5–9.0 (optimum, pH 6.0–6.5) and tolerated up to 1.0 % NaCl (w/v). Neither phototrophic nor fermentative growth was observed. The predominant ubiquinone was Q-10 and the major fatty acid was C18 : 1ω7c(70 %). The DNA G+C content was 64.4 mol% (Tm). Phylogenetic analyses based on the 16S rRNA gene sequence revealed that strain A1-9T, together withCatellibacterium nectariphilumAST4T, formed a deep line within the ‘Rhodobacterclade’ of the familyRhodobacteraceaeand strain A1-9Tshowed 94.2 % 16S rRNA gene sequence similarity toC. nectariphilumAST4T. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain A1-9Tis considered to represent a novel species of the genusCatellibacterium, for which the nameCatellibacterium aquatilesp. nov. is proposed. The type strain is A1-9T(=CGMCC 1.7029T=NBRC 104254T).
Cloacibacterium rupense sp. nov., isolated from freshwater lake sediment
Authors: Cao Shu-Juan , Deng Chun-Ping , Li Bao-Zhen , Dong Xiu-Qin , Yuan Hong-Li
Published: November 2009

A Gram-negative, yellow-pigmented bacterium, designated strain R2A-16T, was isolated from sediment of Rupa Lake in Nepal and analysed using a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain R2A-16Tis affiliated to the genusCloacibacteriumof the familyFlavobacteriaceae; 16S rRNA gene sequence similarity between strain R2A-16TandCloacibacterium normanenseCCUG 46293Twas 98.07 %. The isolate contained iso-C15 : 0(35.6 %) as the major fatty acid and menaquinone MK-6 as the predominant respiratory quinone. The G+C content of the genomic DNA was 33.3 mol%. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain R2A-16Trepresents a novel species of the genusCloacibacterium, for which the nameCloacibacterium rupensesp. nov. is proposed; the type strain is R2A-16T(=CGMCC 1.7656T=NBRC 104931T).
Soonwooa buanensis gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from seawater
Authors: Joung Yochan , Song Jaeho , Lee Kiyoung , Oh Hyun-Myung , Joh Kiseong , Cho Jang-Cheon
Published: November 2009

A Gram-negative, non-motile, non-gliding, strictly aerobic, pale yellow colony-forming, rod-shaped bacterial strain, designated HM0024T, was isolated from coastal seawater of the Yellow Sea and subjected to a polyphasic taxonomy study. Based on 16S rRNA gene sequence similarities, strain HM0024Twas most closely related toChryseobacterium balustinumLMG 8329T(94.4 %),Chryseobacterium scophthalmumLMG 13028T(94.4 %),Chryseobacterium pisciumLMG 23089T(94.3 %) andElizabethkingia meningosepticaATCC 13253T(94.0 %) and shared less than 92 % sequence similarity with other members of the familyFlavobacteriaceae. Phylogenetic analyses showed that strain HM0024Tformed an independent phyletic line of descent within the familyFlavobacteriaceae. The DNA G+C content of the strain was 29.6 mol% and its major cellular fatty acids (>10 %) were iso-C15 : 0, iso-C17 : 03-OH, iso-C17 : 1ω7cand summed feature 3 (C16 : 1ω6cand/or C16 : 1ω7c). The major isoprenoid quinone was MK-6 and the major polar lipids were phosphatidylethanolamine and several aminolipids. Strain HM0024Twas differentiated from phylogenetically related members of the family by having lower DNA G+C content, larger proportions of summed feature 3, anteiso-C15 : 0and iso-C16 : 03-OH and particular phenotypic characteristics. On the basis of phenotypic and phylogenetic data, strain HM0024Tis classified as a representative of a novel genus and species, for which the nameSoonwooa buanensisgen. nov., sp. nov. is proposed. The type strain ofSoonwooa buanensisis HM0024T(=KCTC 22689T=CECT 7503T).
Frondihabitans peucedani sp. nov., an actinobacterium isolated from rhizosphere soil, and emended description of the genus Frondihabitans Greene et al. 2009
Authors: Lee Soon Dong
Published: November 2009

A novel actinobacterium, designated RS-15T, was isolated from rhizosphere soil of a plant (Peucedanum japonicum Thunb.) on Mara Island, Jeju, Republic of Korea. Cells were strictly aerobic, Gram-stain-positive, oxidase-negative, catalase-positive, non-motile, irregular, short rods. The peptidoglycan in the cell wall was of the B2β type with ornithine as the diagnostic diamino acid. The major menaquinone was MK-8; small amounts of MK-9 and MK-7 were also present. The polar lipids contained phosphatidylglycerol, five unknown glycolipids, three unknown phospholipids and two unknown lipids. Mycolic acids were not present. The predominant fatty acids were summed feature 7 (one or more of C18 : 1
ω9c, C18 : 1
ω12t and C18 : 1
ω7c), anteiso-C15 : 0 and C14 : 0 2-OH. The DNA G+C content was 68.3 mol%. 16S rRNA gene sequence analysis showed that strain RS-15T belonged to the family Microbacteriaceae and formed a tight phylogenetic cluster with Frondihabitans australicus E1HC-02T (98.5 % sequence similarity). The DNA–DNA relatedness between strain RS-15T and Frondihabitans australicus DSM 17894T was 17.2 % (17.1 %, duplicate measurements). On the basis of the physiological, chemotaxonomic and DNA–DNA hybridization data, strain RS-15T is considered to represent a novel species of the genus Frondihabitans, for which the name Frondihabitans peucedani sp. nov. is proposed. The type strain is RS-15T (=KCTC 13435T =DSM 22180T). An emended description of the genus Frondihabitans is also presented.
Saccharopolyspora phatthalungensis sp. nov., isolated from rhizosphere soil of Hevea brasiliensis
Authors: Duangmal Kannika , Mingma Ratchanee , Thamchaipenet Arinthip , Matsumoto Atsuko , Takahashi Yoko
Published: November 2009

The taxonomic position of a rhizosphere soil isolate, designated strain SR8.15T, was determined by using a polyphasic approach. Phylogenetic analysis based on an almost-complete 16S rRNA gene sequence of the strain showed that it formed a well-separated sub-branch within the radiation encompassing the genus Saccharopolyspora. Highest levels of 16S rRNA gene sequence similarity were found between strain SR8.15T and Saccharopolyspora shandongensis CGMCC 4.3530T (98.9 %) and Saccharopolyspora spinosa DSM 44228T (98.5 %). However, these strains shared low levels of DNA–DNA relatedness (<26 %). Strain SR8.15T had chemical characteristics consistent with its classification in the genus Saccharopolyspora. It contained meso-diaminopimelic acid as the diagnostic diamino acid. Whole-cell hydrolysates contained arabinose and galactose. The diagnostic phospholipids were phosphatidylcholine, phosphatidylglycerol and phosphatidylinositol. The main menaquinone was MK-9(H4). No mycolic acid was detected. The predominant cellular fatty acid was iso-C16 : 0. The G+C content of the genomic DNA of strain SR8.15T was 70.3 mol%. Strain SR8.15T had a phenotypic profile that readily distinguished it from recognized representatives of the genus Saccharopolyspora. It is evident from its combined genotypic and phenotypic properties that strain SR8.15T represents a novel species of the genus Saccharopolyspora, for which the name Saccharopolyspora phatthalungensis sp. nov. is proposed. The type strain is SR8.15T (=TISTR 1921T=BCC 35844T=NRRL B-24798T).
Burkholderia acidipaludis sp. nov., aluminium-tolerant bacteria isolated from Chinese water chestnut (Eleocharis dulcis) growing in highly acidic swamps in South-East Asia
Authors: Aizawa Tomoko , Bao Ve Nguyen , Vijarnsorn Pisoot , Nakajima Mutsuyasu , Sunairi Michio
Published: November 2009

Two strains of aluminium-tolerant bacteria, SA33T and 7A078, were isolated from Chinese water chestnut (Eleocharis dulcis) growing in highly acidic swamps (pH 2–4) in actual acid sulfate soil areas of Vietnam (SA33T) and Thailand (7A078). The strains were Gram-negative, aerobic, non-spore-forming rods, 0.6–0.7 μm wide and 1.3–1.7 μm long. These strains showed good growth at pH 3.0–8.0 and 17–37 °C. The organisms contained ubiquinone Q-8 as the predominant isoprenoid quinone and C16 : 0, C18 : 1
ω7c and C17 : 0 cyclo as the major fatty acids. Their fatty acid profiles were similar to those reported for other Burkholderia species. The DNA G+C content of these strains was 64 mol%. On the basis of 16S rRNA gene sequence similarity, the strains were shown to belong to the genus Burkholderia. Although the 16S rRNA gene sequence similarity values calculated for strain SA33T to 7A078 and the type strains of Burkholderia kururiensis, B. sacchari and B. tuberum were 100, 97.3, 97.1 and 97.0 %, respectively, strains SA33T and 7A078 formed a group that was distinct in the phylogenetic trees; the DNA–DNA relatedness of strain SA33T to 7A078 and these three type strains were respectively 90, 47, 46 and 45 %. The results of physiological and biochemical tests, including whole-cell protein pattern analysis, allowed phenotypic differentiation of these strains from described Burkholderia species. Therefore, strains SA33T and 7A078 represent a novel species, for which the name Burkholderia acidipaludis sp. nov. is proposed. The type strain is SA33T (=NBRC 101816T =VTCC-D6-6T). Strain 7A078 (=NBRC 103872 =BCC 36999) is a reference strain.
Haloactinobacterium album gen. nov., sp. nov., a halophilic actinobacterium, and proposal of Ruaniaceae fam. nov.
Authors: Tang Shu-Kun , Zhi Xiao-Yang , Wang Yun , Wu Jin-Yuan , Lee Jae-Chan , Kim Chang-Jin , Lou Kai , Xu Li-Hua , Li Wen-Jun
Published: November 2009

A Gram-staining-positive, facultatively anaerobic, non-motile and moderately halophilic actinobacterium, designated YIM 93306T, was isolated from a salt lake in Xinjiang province, north-west China, and subjected to a polyphasic taxonomic study. Strain YIM 93306T grew in the presence of 2–16 % (w/v) NaCl and did not grow without NaCl. The peptidoglycan type was A4α with an l-Lys–l-Glu interpeptide bridge. The whole-cell sugars were glucosamine, arabinose, mannose and two unknown sugars. The predominant menaquinone was MK-8(H4). The major fatty acids were iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, one unknown phosphoglycolipid and one unknown phospholipid. The DNA G+C content was 68.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YIM 93306T fell within the radius of the suborder Micrococcineae. Its closest phylogenetic neighbour was the type strain of Ruania albidiflava (AS 4.3142T; 96.2 % 16S rRNA gene sequence similarity), the sole recognized species of the genus Ruania. Sequence similarities between strain YIM 93306T and members of other genera of the suborder Micrococcineae were <95.2 %. On the basis of phylogenetic analysis, phenotypic characteristics and chemotaxonomic differences, a novel genus and species, Haloactinobacterium album gen. nov., sp. nov., is proposed. The type strain of the species is YIM 93306T (=DSM 21368T =KCTC 19413T =CCTCC AB 208069T). Based on phylogenetic characteristics and 16S rRNA gene signature nucleotide patterns, the genera Ruania and Haloactinobacterium gen. nov. are proposed to belong to a novel family, Ruaniaceae fam. nov.
Halopelagius inordinatus gen. nov., sp. nov., a new member of the family Halobacteriaceae isolated from a marine solar saltern
Authors: Cui Heng-Lin , Li Xin-Yi , Gao Xia , Xu Xue-Wei , Zhou Yu-Guang , Liu Hong-Can , Oren Aharon , Zhou Pei-Jin
Published: November 2009

Two extremely halophilic archaea, strains RO5-2Tand RO5-14, were isolated from Rudong marine solar saltern in Jiangsu, China. Cells of the two strains were pleomorphic, motile and stained Gram-negative. Colonies were red-pigmented. Strains RO5-2Tand RO5-14 were able to grow at 20–50 °C (optimum 37 °C), at 2.6–4.8 M NaCl (optimum 3.4–3.9 M NaCl), at 0.03–0.7 M MgCl2(optimum 0.5 M MgCl2) and at pH 5.5–8.0 (optimum pH 6.5–7.0). Cells lyse in distilled water and the minimal NaCl concentration to prevent cell lysis was 12 % (w/v). The major polar lipids of the two strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and two major glycolipids chromatographically identical to sulfated mannosyl glucosyl diether (S-DGD-1) and mannosyl glucosyl diether (DGD-1). The 16S rRNA gene sequences of strains RO5-2Tand RO5-14 showed 93.4–93.8 % similarity to the closest cultivated relative,Halosarcina pallida. The DNA G+C content of strains RO5-2Tand RO5-14 was 61.0 mol% and 59.9 mol%, respectively. The DNA–DNA relatedness between strains RO5-2Tand RO5-14 was 86.0 %. The phenotypic, chemotaxonomic and phylogenetic properties suggest that strains RO5-2Tand RO5-14 represent a novel species in a new genus within the familyHalobacteriaceae, for which the nameHalopelagius inordinatusgen. nov., sp. nov. is proposed. The type strain is RO5-2T(=CGMCC 1.7739T=JCM 15773T).
Lemierre's syndrome and septicaemia caused solely by Arcanobacterium haemolyticum in a young immunocompetent patient
Authors: Fernández-Suárez Antonio , Aguilar Benítez José Miguel , López Vidal Antonia María , Díaz Iglesias José Miguel
Published: November 2009

We present a case of septicaemia caused by Arcanobacterium haemolyticum in a previously healthy 23-year-old man suffering from acute pharyngotonsillitis, who developed complicated Lemierre's syndrome. Three blood cultures (both aerobic and anaerobic) revealed the exclusive presence of A. haemolyticum. The presence of Fusobacterium necroforum was not essential for the development of this pathology. To our knowledge, this is the first reported case of Lemierre's syndrome caused solely by A. haemolyticum. We confirm that this organism must be considered a potential pathogen in immunocompetent patients.
Development of an indirect ELISA for the detection of serum IgG antibodies against region IV of phase 1 flagellin of Salmonella enterica serovar Brandenburg in sheep
Authors: Perera Kalyani , Murray Alan
Published: November 2009

Region IV of phase 1 flagellin (FliC) of Salmonella enterica serovar Brandenburg (S. Brandenburg) was expressed in Escherichia coli and purified by nickel chelate affinity chromatography. The purified recombinant protein was evaluated for its suitability as an antigen in an indirect ELISA for the detection of antibodies in sheep sera. A cut-off value of 0.1 was calculated using 80 serum samples collected from sheep with no previous history of S. Brandenburg. In the present study we show the results of ELISA with field sera collected from 81 sheep naturally infected with S. Brandenburg. The assay was able to detect antibodies belonging to the IgG class with a sensitivity of 93.8 %. Thus, indirect ELISA might be a suitable screening tool for serological monitoring of sheep flocks infected with S. Brandenburg.
Postoperative spondylodiscitis due to Kytococcus schroeteri in a diabetic woman
Authors: Jacquier H. , Allard A. , Richette P. , Ea H. K. , Sanson-Le Pors M. J. , Berçot B.
Published: November 2009

Kytococcus schroeteri, a Gram-positive coccus, is usually regarded as part of the human skin flora. It has been described in prosthetic valve endocarditis but never as being involved in osteoarticular infections. We report here the first case of a spondylodiscitis due toK. schroeteriidentified by 16S rRNA gene sequencing.
Comparative evaluation of real-time PCR and conventional RT-PCR during a 2 year surveillance for influenza and respiratory syncytial virus among children with acute respiratory infections in Kolkata, India, reveals a distinct seasonality of infection
Authors: Agrawal Anurodh S. , Sarkar Mehuli , Chakrabarti Sekhar , Rajendran K. , Kaur Harpreet , Mishra Akhilesh C. , Chatterjee Mrinal K. , Naik Trailokya N. , Chadha Mandeep S. , Chawla-Sarkar Mamta
Published: November 2009

Acute respiratory tract infections (ARTIs) are one of the most common causes of morbidity and mortality in young children worldwide. Influenza virus and respiratory syncytial virus (RSV) are the predominant aetiological agents during seasonal epidemics, and thus rapid and sensitive molecular tests for screening for such agents and timely identification of epidemics are required. This study compared real-time quantitative PCR (qPCR) with conventional RT-PCR for parallel identification of influenza A virus (IAV) or influenza B virus (IBV) and RSV. A total of 1091 respiratory samples was examined from children with suspected ARTIs between January 2007 and December 2008. Of these, 275 (25.21 %) were positive for either influenza or RSV by qPCR compared with 262 (24 .01%) positive by RT-PCR. Overall, IAV, IBV and RSV were detected in 121 (11.09 %), 59 (5.41 %) and 95 (8.71 %) samples, respectively. In spite of overlapping clinical symptoms, RSV and influenza virus showed distinct seasonal peaks. IAV correlated positively and RSV negatively with rainfall and temperature. No distinct seasonality was observed in IBV infections. This is, to the best of our knowledge, the first report of a systemic surveillance of respiratory viruses with seasonal correlation and prevalence rates from eastern India. This 2 year comparative analysis also confirmed the feasibility of using qPCR in developing countries, which will not only improve the scope for prevention of epidemics, but will also provide crucial epidemiological data from tropical regions.
Helicobacter pylori oipA, vacA and dupA genetic diversity in individual hosts
Authors: Matteo Mario José , Armitano Rita Inés , Granados Gabriela , Wonaga Andrés Dario , Sánches Christian , Olmos Martín , Catalano Mariana
Published: November 2009

Helicobacter pylori putative virulence factors can undergo a continuously evolving mechanism as an approach to bacterial adaptation to the host changing environment during chronic infection. oipA, vacA and dupA genetic diversity among isolates from multiple biopsies (niches) from the antrum and corpus of 40 patients was investigated. A set of 229 isolates was examined. Direct DNA sequence analysis of amplified fragments was used to study oipA ‘on/off’ expression status as well as the presence of C or T insertion in jhp0917 that originates a continuous (jhp0917–jhp0918) dupA gene. vacA alleles were identified by multiplex PCR. Different inter-niches oipA CT repeat patterns were observed in nine patients; in six of these, ‘on’ and ‘off’ mixed patterns were found. In three of these nine patients, different vacA alleles were also observed in a single host. Inter-niche dupA differences involved the absence and presence of jhp0917 and/or jhp0918 or mutations in dupA, including those that may originate a non-functional gene, and they were also present in two patients with mixed oipA CT patterns and in another seven patients. Evidence of mixed infection was observed in two patients only. In conclusion, oipA and dupA genes showed similar inter-niche variability, occurring in approximately 1/4 patients. Conversely, vacA allele microevolution seemed to be a less common event, occurring in approximately 1/10 patients, probably due to the mechanism that this gene evolves ‘in vivo’.
Development of ertapenem resistance in a patient with mediastinitis caused by Klebsiella pneumoniae producing an extended-spectrum β-lactamase
Authors: Skurnik David , Lasocki Sigismond , Bremont Sylvie , Muller-Serieys Claudette , Kitzis Marie Dominique , Courvalin Patrice , Andremont Antoine , Montravers Philippe
Published: November 2009

The aim was to study the clinical and microbiological features associated with a carbapenem-resistant Klebsiella pneumoniae isolate that had been selected in vivo by an ertapenem-containing regimen in a patient with mediastinitis despite high blood and mediastinal levels of ertapenem. Carbapenem resistance was characterized by conjugation, PCR, DNA sequencing and analysis of outer-membrane proteins. The isolates susceptible and resistant to the carbapenems were compared by ribotyping and PFGE. Resistance to all available β-lactams was most probably due to combined production of extended-spectrum β-lactamase (ESBL) CTX-M-15 and loss of OmpK36 porin. The results of ribotyping and PFGE suggest that the carbapenem-resistant strain was a derivative of the original mediastinal isolate rather than a superinfecting isolate. This observation stresses the risk of selection of pan-penem resistant strains of enterobacteria when ertapenem is used for the treatment of severe infections due to ESBL-producing enterobacteria.
Metabolism of azo dyes by human skin microbiota
Authors: Stingley Robin L. , Zou Wen , Heinze Thomas M. , Chen Huizhong , Cerniglia Carl E.
Published: November 2009

Reduction of Methyl Red (MR) and Orange II (Or II) by 26 human skin bacterial species was monitored by a rapid spectrophotometric assay. The analysis indicated that skin bacteria, representing the generaStaphylococcus,Corynebacterium,Micrococcus,DermacoccusandKocuria, were able to reduce MR by 74–100 % in 24 h, with only three species unable to reduce completely the dye in that time. Among the species tested, onlyCorynebacterium xerosiswas unable to reduce Or II to any degree by 24 h, and onlyStaphylococcus delphini,Staphylococcus sciurisubsp.sciuriandPseudomonas aeruginosawere able to reduce completely this dye within 24 h. MR reduction started with early-exponential growth inStaphylococcus aureusandStaphylococcus epidermidis, and around late-exponential/early-stationary growth inP. aeruginosa. Reduction of Or II, Ponceau S and Ponceau BS started during late-exponential/early-stationary growth for all three species. Using liquid chromatography/electrospray ionization mass spectrometry analyses, MR metabolites produced byStaph. aureus,Staph. epidermidisandP. aeruginosawere identified asN,N-dimethyl-p-phenylenediamine and 2-aminobenzoic acid. Searches of available genomic and proteomic data revealed that at least four of the staphylococci in this study,Staphylococcus haemolyticus,Staph. epidermidis,Staphylococcus cohniiandStaphylococcus saprophyticus, have hypothetical genes with 77, 76, 75 and 74 % sequence identity toazo1encoding an azoreductase fromStaph. aureusand hypothetical proteins with 82, 80, 72 and 74 % identity to Azo1, respectively. In addition,Staphylococcus capitishas a protein with 79 % identity to Azo1. Western analysis detected proteins similar to Azo1 in all the staphylococci tested, exceptStaph. delphini,Staph. sciurisubsp.sciuriandStaphylococcus auricularis. The data presented in this report will be useful in the risk assessment process for evaluation of public exposure to products containing these dyes.
Diversity of intestinal Escherichia coli populations in Nicaraguan children with and without diarrhoea
Authors: Reyes Daniel , Vilchez Samuel , Paniagua Margarita , Colque Patricia , Weintraub Andrej , Möllby Roland , Kühn Inger
Published: November 2009

Escherichia coli remains an important aetiological agent of infantile diarrhoea in Nicaragua. However, little is known about whether there is a high prevalence of endemic strains or whether infection is due to the epidemic spread of virulent clones. This study was undertaken to determine the diversity and distribution of clonal groups in a population of intestinal E. coli isolated from the faeces of children from León, Nicaragua, with (n=381) and without (n=145) diarrhoea, between March 2005 and September 2006. All samples had been screened previously for the presence of diarrhoeagenic E. coli (DEC) markers by multiplex PCR. From each sample, 8 E. coli colonies (where available) were analysed by biochemical fingerprinting (PhP-RE system), yielding a total of 4009 tested isolates. On average, three different biochemical phenotypes (BPTs) were found among the eight colonies analysed from each sample. The total diversity, measured as Simpson's diversity index (Di), was 0.97 among all 4009 isolates studied. Cluster analysis of data from all 4009 isolates revealed 24 common BPTs (identified in at least 1 % of the isolates) and 234 less common BPTs. Similar Di values were obtained among isolates from infants with and without diarrhoea, indicating that no widespread outbreak of DEC had occurred. Moreover, among samples that were positive for the DEC types enteroaggregative E. coli, enteropathogenic E. coli and enterotoxigenic E. coli (ETEC) carrying the eltB gene, the diversities were almost as high as among non-DEC samples, whereas samples positive for ETEC carrying estA, enteroinvasive E. coli and enterohaemorrhagic E. coli showed lower diversities, indicating the prevalence of virulent clonal groups among these samples. The PhenePlate patterns of the 24 common BPTs identified here were compared with those obtained from E. coli isolated in a cohort infant study performed in 1991–1992 in the same area. Only 4 % of the isolates from the 1990s were similar to any of the common BPTs found in the present study.
Molecular characterization of a rare G1P[19] rotavirus strain from India: evidence of reassortment between human and porcine rotavirus strains
Authors: Chitambar Shobha D. , Arora Ritu , Chhabra Preeti
Published: November 2009

This study pertains to the characterization of a human rotavirus strain (NIV929893) with a rare specificity of G1P[19]. Three structural genes (VP4, VP6 and VP7) and one non-structural gene (NSP4) of strain NIV929893 were subjected to RT-PCR for amplification of entire coding regions. All of the amplicons were sequenced to carry out phylogenetic analysis. The complete amino acid sequences of the VP7 and VP4 gene products showed clustering of the VP7 gene with G1 strains of human origin and the VP4 gene with P[19] strains of porcine origin. The two viral proteins VP6 and NSP4, described previously as genetically linked proteins, were shown to be subgroup II and genotype B of human and porcine origins, respectively. The findings of this study provide evidence of reassortment between VP7/VP6 genes of humans and VP4/NSP4 genes of porcine species and an independent segregation of VP6 and NSP4 genes in a group A human rotavirus strain with G1P[19] specificity.
Identification of virulence determinants of Mycobacterium avium that impact on the ability to resist host killing mechanisms
Authors: Li Yong-jun , Danelishvili Lia , Wagner Dirk , Petrofsky Mary , Bermudez Luiz E.
Published: November 2009

Mycobacterium aviumis an opportunistic pathogen associated with pulmonary disease in non-AIDS patients and disseminated infection in patients with AIDS. The chief route of infection is by colonization and invasion of the mucosa of the gastrointestinal tract, but infection through the respiratory route also occurs. After crossing the mucosa,M. aviuminfects and replicates within tissue macrophages. To identifyM. aviumgenes required for survivalin vivo, a library of signature-tagged transposon mutants was constructed and screened for clones attenuated in mice. Thirty-two clones were found to be attenuated for their virulence, from which eleven were sequenced and tested further. All the mutants studied grew similarlyin vitroto the wild-type MAC104. Ten mutants were tested individually in mice, confirming the attenuated phenotype. MAV_2450, a polyketide synthase homologue toMycobacterium tuberculosispks12, was identified. STM5 and STM10 genes (encoding two hypothetical proteins MAV_4292 and MAV_4012) were associated with susceptibility to oxidative products. Mutants MAV_2450, MAV_4292, MAV_0385 and MAV_4264 live in macrophage vacuoles with acidic pH (below 6.9). Mutants MAV_4292, MAV_0385 and MAV_4264 were susceptible to nitric oxidein vitro. The study of individual mutants can potentially lead to new knowledge aboutM. aviumpathogenic mechanisms.
Zoonotic transmission of Streptococcus equi subsp. zooepidemicus from a dog to a handler
Authors: Abbott Y. , Acke E. , Khan S. , Muldoon E. G. , Markey B. K. , Pinilla M. , Leonard F. C. , Steward K. , Waller A.
Published: November 2009

This is, to the best of our knowledge, the first case report to describe the apparent transmission ofStreptococcus equisubsp.zooepidemicusfrom an infected dog to a handler who subsequently developed severe systemic infection. Characterization of the haemolytic streptococci isolated from both the patient and the dog, by phenotypic and molecular analysis, confirmed the canine and human isolates were identical.
Detection of Cardiobacterium valvarum in a patient with aortic valve infective endocarditis by broad-range PCR
Authors: Vaněrková Martina , Žaloudíková Barbora , Němcová Eva , Juránková Jana , Pol Jiří , Černý Jan , Němec Petr , Freiberger Tomáš
Published: November 2009

Cardiobacterium valvarum, a fastidious Gram-negative bacterium, was detected in the aortic valve of a previously healthy 63-year-old man by broad-range PCR and 16S rRNA gene sequencing. In contrast to the patients in five previously published cases, our patient had neither a congenital bicuspid nor a prosthetic aortic valve. Here, we present a case of C. valvarum native tricuspid aortic valve infective endocarditis and a review of the literature.
Escherichia coli and its lipopolysaccharide modulate in vitro Candida biofilm formation
Authors: Bandara H. M. H. N. , Yau J. Y. Y. , Watt R. M. , Jin L. J. , Samaranayake L. P.
Published: November 2009

Demystification of microbial behaviour in mixed biofilms could have a major impact on our understanding of infectious diseases. The objectives of this study were to evaluatein vitrothe interactions of six differentCandidaspecies and a Gram-negative coliform,Escherichia coli, in dual-species biofilms, and to assess the effect ofE. coliLPS onCandidabiofilm formation. A single isolate ofE. coliATCC 25922 and six different species ofCandida,Candida albicansATCC 90028,Candida glabrataATCC 90030,Candida kruseiATCC 6258,Candida tropicalisATCC 13803,Candida parapsilosisATCC 22019 andCandida dubliniensisMYA-646, were studied using a standard biofilm assay. EachCandidaspecies was co-cultured withE. colion a polystyrene surface and biofilm formation was quantified by a c.f.u. assay. The biofilm was then analysed by Live/Dead staining and fluorescence microscopy (confocal laser-scanning microscopy, CLSM), whilst scanning electron microscopy (SEM) was employed to visualize the biofilm architecture. The effect ofE. coliLPS onCandidabiofilm cell activity at defined time intervals was assessed with an XTT reduction assay. A significant quantitative reduction in c.f.u. counts ofC. tropicalis(after 90 min),C. parapsilosis(after 90 min and 24 h),C. krusei(after 24 h) andC. dubliniensis(after 24 and 48 h) was noted on incubation withE. coliin comparison with their monospecies biofilm counterparts (P<0.05). On the other hand, a simultaneous and significant reduction inE. colicell numbers occurred on co-culture withC. albicans(after 90 min), and an elevation ofE. colicell numbers followed co-culture withC. tropicalis(after 24 h) andC. dubliniensis(after 24 h and 48 h) (P<0.05). All quantitative findings were confirmed by SEM and CLSM analyses. By SEM observation, dual-species biofilms demonstrated scanty architecture with reduced visible cell counts at all stages of biofilm development, despite profuse growth and dense colonization in their single-species counterparts. Significantly elevated metabolic activity, as assessed by XTT readings, was observed inE. coliLPS-treatedC. tropicalisandC. parapsilosisbiofilms (after 48 h), whilst this had the opposite effect forC. dubliniensis(after 24 h) (P<0.05). These data indicate thatE. coliandCandidaspecies in a mixed-species environment mutually modulate biofilm development, both quantitatively and qualitatively, and thatE. coliLPS appears to be a key component in mediating these outcomes.
Molecular emm genotyping and antibiotic susceptibility of Streptococcus dysgalactiae subsp. equisimilis isolated from invasive and non-invasive infections
Authors: Sunaoshi Katsuhiko , Murayama Somay Y. , Adachi Keiko , Yagoshi Michiko , Okuzumi Katsuko , Chiba Naoko , Morozumi Miyuki , Ubukata Kimiko
Published: November 2009

To analyse the characteristics of infections caused by Streptococcus dysgalactiae subsp. equisimilis, clinical isolates (n=145) were collected at 11 medical institutions between September 2003 and October 2005. These isolates belonged to Lancefield group A (n=5), group C (n=18) or group G (n=122). Among all isolates, 42 strains were isolated from sterile samples such as blood, synovial fluid and tissue specimens from patients who were mostly over 50 years with invasive infections, and included seven cases of streptococcal toxic shock syndrome and necrotizing fasciitis. In contrast, the remaining 103 were isolated mainly from patients of all age groups with non-invasive infections such as pharyngotonsillitis. These isolates were classified into 25 types based on emm genotyping. A significant difference in emm types was observed between isolates from invasive and non-invasive infections (P<0.001): stG485, stG6792 and stG2078 predominated among isolates from invasive infections. A phylogenetic tree of complete open reading frames of emm genes in this organism showed high homology with those of Streptococcus pyogenes, but not with those of other streptococci. The presence of five different clones was estimated based on DNA profiles of isolates from invasive infections obtained by PFGE. Genes for resistance to macrolides [erm(A), three isolates; erm(B), five isolates; mef(A), seven isolates] and levofloxacin (mutations in gyrA and parC, four isolates) were identified in this organism. These results suggest the need for further nationwide surveillance of invasive infections caused by S. dysgalactiae subsp. equisimilis.
Burkholderia cenocepacia O antigen lipopolysaccharide prevents phagocytosis by macrophages and adhesion to epithelial cells
Authors: Saldías M. Soledad , Ortega Ximena , Valvano Miguel A.
Published: November 2009

Chronic respiratory infections by theBurkholderia cepaciacomplex (Bcc) are of great concern to patients with cystic fibrosis. Bcc isolates may survive intracellularly within amoebae, respiratory epithelial cells and macrophages. The molecular mechanisms facilitating colonization and pathogenesis remain unclear. Given the importance of bacterial adhesion to host surfaces in microbial pathogenesis, we investigated the role of the O antigen LPS in the interaction ofBurkholderia cenocepacia, a member of the Bcc, with macrophages and epithelial cells. Our results demonstrated that the O antigen modulates phagocytosis but does not affect intracellular survival ofB. cenocepacia. Internalization of strains that lack O antigen was significantly increased compared to that of their isogenic smooth counterparts. However, no differences between rough and smooth strains were found in their ability to delay phagosomal maturation. We also found that the O antigen interfered with the ability ofB. cenocepaciato adhere to bronchial epithelial cells, suggesting that this polysaccharide may mask one or more bacterial surface adhesins.