bluuebunny/crossref_metadata_2025 huggingface dataset:
Lysobacter soli sp. nov., isolated from soil of a ginseng field
Authors: Srinivasan Sathiyaraj , Kim Myung Kyum , Sathiyaraj Gayathri , Kim Ho-Bin , Kim Yeon-Ju , Yang Deok-Chun
Published: November 2009

Strain DCY21T, a Gram-negative, gliding and rod-shaped aerobic bacterium was isolated from soil of a ginseng field in the Republic of Korea and characterized using a polyphasic approach in order to determine its taxonomic position. Comparative 16S rRNA gene sequence analysis revealed that strain DCY21T clustered with the species of the genus Lysobacter. It was closely related to Lysobacter gummosus LMG 8763T (97.9 %), Lysobacter capsici YC5194T (97.6 %), Lysobacter antibioticus DSM 2044T (97.5 %), Lysobacter niastensis DSM 18481T (97.2 %) and Lysobacter enzymogenes DSM 2043T (96.9 %). The major cellular fatty acids of strain DCY21T were iso-C15 : 0 (34.3 %), iso-C17 : 1
ω9c (19.5 %) and iso-C17 : 0 (17.2 %) and the major isoprenoid quinone was Q-8. The major polar lipids of strain DCY21T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidyl-N-methylethanolamine. The G+C content of the total DNA was 65.4 mol%. The DNA–DNA relatedness values, and biochemical and physiological characteristics strongly supported the genotypic and phenotypic differentiation of strain DCY21T from species of the genus Lysobacter. Strain DCY21T therefore represents a novel species, for which the name Lysobacter soli sp. nov. is proposed. The type strain is DCY21T (=KCTC 22011T =LMG 24126T).
Vibrio casei sp. nov., isolated from the surfaces of two French red smear soft cheeses
Authors: Bleicher Anne , Neuhaus Klaus , Scherer Siegfried
Published: November 2009

Three Gram-negative, rod-shaped, catalase- and oxidase-positive, facultatively anaerobic and motile bacteria, strains WS 4538, WS 4539Tand WS 4540, were isolated from the surfaces of two fully ripened French red smear soft cheeses. Based on 16S rRNA gene sequence similarity, all three strains were shown to belong to the genusVibrio. They are most closely related toVibrio rumoiensisS-1T(96.3 % similarity) andVibrio litoralisMANO22DT(95.9 %). DNA–DNA hybridization confirmed that all three isolates belong to the same species and clearly separated strain WS 4539TfromV. rumoiensisDSM 19141T(38–42 % relatedness) andV. litoralisDSM 17657T(28–37 %). In contrast to their nearest relatives, the strains exhibitedβ-galactosidase and aesculin hydrolase activities. A 14 bp insertion in the 16S rRNA gene sequence forms an elongated structure at helix 10 in the rRNA molecule and provides a tool for PCR-based identification of the novel species. Partial sequences of the housekeeping genesatpA,recA,rpoAandpyrHsupported the conclusion that the three isolates constitute a separate species within the genusVibrio. The nameVibrio caseisp. nov. is proposed for the novel taxon. Strain WS 4539T(=DSM 22364T=LMG 25240T; DNA G+C content 41.8 mol%) is the type strain and WS 4540 (=DSM 22378 =LMG 25241) is a reference strain.
Kazachstania taianensis sp. nov., a novel ascomycetous yeast species from orchard soil
Authors: Chen Ru , Wei Shao-Chong , Jiang Yuan-Mao , Wang Qi-Ming , Bai Feng-Yan
Published: November 2009

Three teleomorphic ascomycetous yeast isolates (TA11TR-1T, TA11TR-4 and TA11TR-6) from orchard soil from Tai'an, Shandong province, China, were shown to represent a novel species within the genus Kazachstania based on phenotypic characterization and sequence analyses of the 18S rRNA gene, internal transcribed spacer (ITS) regions and 26S rDNA gene D1/D2 domain. The name Kazachstania taianensis sp. nov. (type strain TA11TR-1T =AS 2.4160T =CBS 11405T) is proposed. K. taianensis sp. nov. clustered in a branch together with Kazachstania sinensis, Kazachstania naganishii and the Kazachstania telluris complex with moderate bootstrap support in the neighbour-joining tree reconstructed from combined 18S and D1/D2 sequences. The novel species possessed unusual ITS 1 (338 bp) and ITS 2 (488 bp) sequences. The total length of the ITS–5.8S rDNA gene region of the species was 983 bp, being much longer than those of other ascomycetous yeast species described so far.
Emended description of the genus Actinokineospora Hasegawa 1988 and transfer of Amycolatopsis fastidiosa Henssen et al. 1987 as Actinokineospora fastidiosa comb. nov.
Authors: Labeda D. P. , Price N. P. , Tan G. Y. A. , Goodfellow M. , Klenk H.-P.
Published: November 2009

The species Amycolatopsis fastidiosa (ex Celmer et al. 1977) Henssen et al. 1987 was proposed, based on morphological and chemotaxonomic observations, for a strain originally described as ‘Pseudonocardia fastidiosa’ Celmer et al. 1977 in a US patent. In the course of a phylogenetic study of the taxa with validly published names within the suborder Pseudonocardineae based on 16S rRNA gene sequences, it became apparent that this species was misplaced in the genus Amycolatopsis. After careful evaluation of the phylogeny, morphology, chemotaxonomy and physiology of the type strain, it was concluded that this strain represents a species of the genus Actinokineospora that is unable to produce motile spores. The description of the genus Actinokineospora is therefore emended to accommodate species that do not produce motile spores, and it is proposed that Amycolatopsis fastidiosa be transferred to the genus Actinokineospora as Actinokineospora fastidiosa comb. nov. The type strain is NRRL B-16697T =ATCC 31181T =DSM 43855T =JCM 3276T =NBRC 14105T =VKM Ac-1419T.
Paenalcaligenes hominis gen. nov., sp. nov., a new member of the family Alcaligenaceae
Authors: Kämpfer P. , Falsen E. , Langer S. , Lodders N. , Busse H.-J.
Published: November 2009

A beige-pigmented bacterium (strain CCUG 53761AT) was isolated from human blood from an 85-year-old man in Göteborg, Sweden. Comparative analysis of 16S rRNA gene sequences showed that this bacterium displayed <95 % similarity to all described species of the genera of the family Alcaligenaceae. It grouped within the radiation of the genus Alcaligenes, but showed only 93.0–94.8 % similarity to type strains of members of this genus (Alcaligenes faecalis subsp. parafaecalis, 94.8 %; Alcaligenes faecalis subsp. faecalis, 94.2 %; Alcaligenes faecalis subsp. phenolicus, 93.4 %). This discrimination was supported by chemotaxonomic differences. The polyamine pattern consisted of the predominant compound putrescine, moderate amounts of spermidine and minor to trace amounts of spermine and cadaverine; 2-hydroxyputrescine was not detectable. The quinone system was ubiquinone Q-8 with minor amounts of Q-7. The polar lipid profile was composed of the major lipids diphosphatidylglycerol and phosphatidylethanolamine and moderate amounts of phosphatidylglycerol and an unknown phospholipid; minor lipids were also detected. The fatty acid profile, with large amounts of C16 : 0 and C17 : 0 cyclo and the absence of C12 : 0 2-OH as hydroxylated fatty acid, also differed significantly from those reported for Alcaligenes species. On the basis of these data, it is proposed that strain CCUG 53761AT represents a novel genus and species, for which the name Paenalcaligenes hominis gen. nov., sp. nov. is proposed. The type strain of Paenalcaligenes hominis is CCUG 53761AT =CCM 7698T.
Caldithrix palaeochoryensis sp. nov., a thermophilic, anaerobic, chemo-organotrophic bacterium from a geothermally heated sediment, and emended description of the genus Caldithrix
Authors: Miroshnichenko Margarita L. , Kolganova Tatyana V. , Spring Stefan , Chernyh Nikolay , Bonch-Osmolovskaya Elizaveta A.
Published: November 2009

A novel thermophilic, strictly anaerobic, chemo-organotrophic bacterium, designated MCT, was isolated from a geothermally heated sediment of a marine hydrothermal system at Palaeochory Bay, Milos, Greece. Cells of strain MCTwere rods of variable length (4–12 μm) and width (0.2–0.3 μm), occurring as single cells or forming large aggregates that were visible as flocs. Strain MCTgrew optimally at pH 7.0 and 60 °C and with 3 % (w/v) NaCl. Strain MCTgrew chemo-organoheterotrophically and fermented peptides and di- and polysaccharides in the presence of 0.1 g yeast extract l−1. The DNA G+C content of strain MCTwas 43.3 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed strain MCTwithin the genusCaldithrix. However, strain MCTpossessed certain phenotypic features that differentiated it from the type strain of the only species of the genusCaldithrixdescribed to date. On the basis of phylogenetic and phenotypic characteristics, it is proposed that strain MCTrepresents a novel species,Caldithrix palaeochoryensissp. nov. The type strain is MCT(=DSM 21940T=VKM B-2536T). In addition, an emended description of the genusCaldithrixis presented.
Slackia equolifaciens sp. nov., a human intestinal bacterium capable of producing equol
Authors: Jin Jong-Sik , Kitahara Maki , Sakamoto Mitsuo , Hattori Masao , Benno Yoshimi
Published: November 2009

An equol-producing bacterium, strain DZET, which was isolated from human faeces, was characterized by morphological, biochemical and molecular methods. The isolate was Gram-positive, obligately anaerobic, non-spore-forming, asaccharolytic and rod-shaped. 16S rRNA gene sequence analysis showed 92.8, 91.0, 91.1 and 90.6 % similarities withSlackia faecicanis,Slackia exigua,Slackia heliotrinireducensandSlackia isoflavoniconvertens, respectively. Based on these data, we propose a novel species of the genusSlackia,Slackia equolifacienssp. nov. The major cellular fatty acids are C14 : 0, C18 : 1ω9cand C18 : 1ω9cDMA (dimethyl acetal). The DNA G+C content of the strain is 60.8 mol%. The type strain ofS.equolifacienssp. nov. is DZET(=JCM 16059T=CCUG 58231T).
Cohnella luojiensis sp. nov., isolated from soil of a Euphrates poplar forest
Authors: Cai Feng , Wang Yang , Qi Huan , Dai Jun , Yu Bo , An Hongli , Rahman Erkin , Fang Chengxiang
Published: November 2009

A novel strain, HY-22RT, was isolated from soil of a Euphrates poplar forest in Xinjiang, China. The cells were Gram-positive-staining, rod-shaped and motile by means of peritrichous flagella. Growth occurred at 10–37 °C (optimum 30 °C), at pH 7.0–8.0 (optimum pH 7.0) and with 0–1 % NaCl. A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain HY-22RT was closely related to Cohnella phaseoli GSPC1T (96.3 % sequence similarity). The major respiratory quinone was MK-7 and the predominant fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 49.6 mol%. On the basis of the phylogenetic, physiological and chemotaxonomic data, strain HY-22RT represents a novel species in the genus Cohnella, for which the name Cohnella luojiensis sp. nov. is proposed. The type strain is HY-22RT (=CCTCC AB 208254T =NRRL B-59213T).
Gracilibacillus ureilyticus sp. nov., a halotolerant bacterium from a saline–alkaline soil
Authors: Huo Ying-Yi , Xu Xue-Wei , Cui Heng-Lin , Wu Min
Published: November 2009

A Gram-stain-positive, halotolerant, neutrophilic, rod-shaped bacterium, strain MF38T, was isolated from a saline–alkaline soil in China and subjected to a polyphasic taxonomic characterization. The isolate grew in the presence of 0–15 % (w/v) NaCl and at pH 6.5–8.5; optimum growth was observed with 3.0 % (w/v) NaCl and at pH 7.0. Chemotaxonomic analysis showed menaquinone MK-7 as the predominant respiratory quinone and anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0, C17 : 0 and C16 : 0 as major fatty acids. The genomic DNA G+C content was 35.3 mol%. 16S rRNA gene sequence similarities of strain MF38T with type strains of described Gracilibacillus species ranged from 95.3 to 97.7 %. Strain MF38T exhibited the closest phylogenetic affinity to the type strain of Gracilibacillus dipsosauri, with 97.7 % 16S rRNA gene sequence similarity. The DNA–DNA reassociation between strain MF38T and G. dipsosauri DSM 11125T was 45 %. On the basis of phenotypic and genotypic data, strain MF38T represents a novel species of the genus Gracilibacillus, for which the name Gracilibacillus ureilyticus sp. nov. (type strain MF38T =CGMCC 1.7727T =JCM 15711T) is proposed.
Chryseobacterium arthrosphaerae sp. nov., isolated from the faeces of the pill millipede Arthrosphaera magna Attems
Authors: Kämpfer Peter , Arun A. B. , Young Chiu-Chung , Chen Wen-Ming , Sridhar K. R. , Rekha P. D.
Published: November 2009

A bacterial strain (CC-VM-7T), isolated from the faeces of the pill millipede Arthrosphaera magna Attems collected in India, was studied to determine its taxonomic allocation. Cells stained Gram-negative and were rod-shaped. Comparative analyses of the 16S rRNA gene sequence of the strain with those of the most closely related species clearly suggested allocation to the genus Chryseobacterium, with the highest sequence similarities of 99.2 % to Chryseobacterium gleum CCUG 14555T, 98.6 % to Chryseobacterium indologenes CCUG 14556T and 98.4 % to Chryseobacterium aquifrigidense KCTC 12894T. 16S rRNA gene sequence similarities to all other species of the genus Chryseobacterium were below 98 %. The major whole-cell fatty acids were iso-C15 : 0 and iso-C17 : 1
ω9c. DNA–DNA hybridization resulted in relatedness values of only 29.6 % (reciprocal 31.3 %) to Chryseobacterium gleum CCUG 14555T, 41.2 % (reciprocal 38.8 %) to C. indologenes CCUG 14556T and 35.4 % (reciprocal 38.5 %) to C. aquifrigidense KCTC 12894T. DNA–DNA relatedness, biochemical and chemotaxonomic properties clearly show that strain CC-VM-7T represents a novel species, for which the name Chryseobacterium arthrosphaerae sp. nov. is proposed. The type strain is CC-VM-7T (=CCUG 57618T =CCM 7645T).
Lactobacillus pobuzihii sp. nov., isolated from pobuzihi (fermented cummingcordia)
Authors: Chen Yi-Sheng , Miyashita Mika , Suzuki Ken-ichiro , Sato Hajime , Hsu Jar-Sheng , Yanagida Fujitoshi
Published: November 2009

Twenty-one homofermentative lactic acid bacteria were isolated from fermented cummingcordia (pobuzihi), a traditional food in Taiwan. The isolates had identical 16S rRNA gene sequences that were distinct from those of other lactobacilli, and their closest neighbours in the 16S rRNA gene sequence phylogenetic tree were strains of Lactobacillus acidipiscis. Levels of DNA–DNA relatedness between representative pobuzihi isolates and strains of L. acidipiscis were 17 % and below. Furthermore, the new isolates could be differentiated clearly from L. acidipiscis NBRC 102163T and NBRC 102164 in terms of acid production from l-arabinose, rhamnose, mannitol, lactose and 5-ketogluconate. It was concluded that the new isolates represent a single novel species of the genus Lactobacillus, for which the name Lactobacillus pobuzihii sp. nov. is proposed. The type strain is E100301T (=RIFY 6501T =NBRC 103219T =KCTC 13174T).
Notes on the characterization of prokaryote strains for taxonomic purposes
Authors: Tindall B. J. , Rosselló-Móra R. , Busse H.-J. , Ludwig W. , Kämpfer P.
Published: November 2009

Taxonomy relies on three key elements: characterization, classification and nomenclature. All three elements are dynamic fields, but each step depends on the one which precedes it. Thus, the nomenclature of a group of organisms depends on the way they are classified, and the classification (among other elements) depends on the information gathered as a result of characterization. While nomenclature is governed by the Bacteriological Code, the classification and characterization of prokaryotes is an area that is not formally regulated and one in which numerous changes have taken place in the last 50 years. The purpose of the present article is to outline the key elements in the way that prokaryotes are characterized, with a view to providing an overview of some of the pitfalls commonly encountered in taxonomic papers.
Haliea mediterranea sp. nov., a marine gammaproteobacterium
Authors: Lucena Teresa , Pascual Javier , Garay Esperanza , Arahal David R. , Macián M. Carmen , Pujalte María J.
Published: November 2009

Strain 7SM29T, an aerobic marine gammaproteobacterium isolated from seawater from Castellón, Spain, was characterized by classical phenotyping, chemotaxonomy and 16S rRNA gene sequence analysis. Strain 7SM29T was found to be closely related to strains in the genus Haliea and to Congregibacter litoralis KT71T, with which a genus-level cluster was formed within the NOR5/OM60 clade of the Gammaproteobacteria. Strain 7SM29T was a short, motile rod with a tuft of three polar flagella. The strain grew on marine agar and formed pale-yellow colonies. Strain 7SM29T required NaCl for growth, reduced nitrate to nitrite, degraded several polymers and showed a preference for organic acids and amino acids over carbohydrates as carbon and energy sources. Strain 7SM29T contained Q-8 as the sole respiratory quinone. The DNA G+C content was 62.1 mol%. Phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine were the major polar lipids. The major cellular fatty acids were unsaturated C16–C18 compounds. On the basis of extensive phenotypic and phylogenetic comparative analysis, it is concluded that the strain represents a novel species of the genus Haliea, for which the name Haliea mediterranea sp. nov. is proposed. The type strain is 7SM29T (=CECT 7447T =DSM 21924T).
Arthrobacter alpinus sp. nov., a psychrophilic bacterium isolated from alpine soil
Authors: Zhang De-Chao , Schumann Peter , Liu Hong-Can , Xin Yu-Hua , Zhou Yu-Guang , Schinner Franz , Margesin Rosa
Published: October 2009

An aerobic, Gram-reaction-positive, non-motile, psychrophilic bacterium, designated strain S6-3T, was isolated from alpine soil. Cells exhibited a rod–coccus growth cycle and produced a yellow pigment. Growth occurred at 1–25 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S6-3Twas related to members of the genusArthrobacter, sharing highest sequence similarities with the type strains ofArthrobacter psychrolactophilus(97.9 %) andArthrobacter stackebrandtii(97.6 %). Strain S6-3Thad MK-9(H2) as the major menaquinone and anteiso-C15 : 0as the major fatty acid. The cell-wall peptidoglycan was of type A3αl-Lys–l-Thr–Ala3. The predominant cell-wall sugars were galactose and rhamnose. The genomic DNA G+C content of strain S6-3Twas 61.9 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness data, strain S6-3Tis considered to represent a novel species of the genusArthrobacter, for which the nameArthrobacter alpinussp. nov. is proposed. The type strain is S6-3T(=DSM 22274T=CGMCC 1.8950T).
Arenicella xantha gen. nov., sp. nov., a gammaproteobacterium isolated from a marine sandy sediment
Authors: Romanenko Lyudmila A. , Tanaka Naoto , Frolova Galina M. , Mikhailov Valery V.
Published: November 2009

A Gram-negative, aerobic, yellow-pigmented, rod-shaped, non-motile bacterium, strain KMM 3895T, was isolated from a marine sandy sample collected offshore from the Sea of Japan. Phylogenetic analysis based on the 16S rRNA gene sequence placed strain KMM 3895T in the class Gammaproteobacteria, forming a separate branch, sharing 89.5 % sequence similarity with Nitrincola lacisaponensis 4CAT and 88–87 % similarity with the other members of the cluster, including members of Kangiella, Spongiibacter, Alcanivorax and Microbulbifer. The major isoprenoid quinone was Q-8. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, aminophospholipid and an unknown phospholipid. Fatty acid analysis revealed C16 : 1
ω7, iso-C16 : 0, iso-C18 : 0 and C18 : 1
ω7 as dominant components. The DNA G+C content was determined to be 48.1 mol%. Based on its unique phenotypic characteristics and phylogenetic distance, the marine coastal sediment isolate KMM 3895T should be classified as a representative of a novel genus and species, for which the name Arenicella xantha gen. nov., sp. nov. is proposed. The type strain of Arenicella xantha is KMM 3895T (=NRIC 0759T =JCM 16153T).
Dyadobacter psychrophilus sp. nov., a psychrophilic bacterium isolated from soil
Authors: Zhang De-Chao , Liu Hong-Can , Xin Yu-Hua , Zhou Yu-Guang , Schinner Franz , Margesin Rosa
Published: November 2009

A Gram-negative, aerobic bacterium, designated strain BZ26T, was isolated from hydrocarbon-contaminated soil. The strain was psychrophilic, showing good growth over a temperature range of 1–20 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BZ26T was related to members of the genus Dyadobacter and had highest 16S rRNA gene sequence similarity to Dyadobacter alkalitolerans 12116T (98.1 %), Dyadobacter koreensis KCTC 12537T (97.5 %) and Dyadobacter ginsengisoli Gsoil 043T (97.2 %). Strain BZ26T had MK-7 as the major menaquinone and summed feature 3 (C16 : 1
ω7c/iso-C15 : 0 2-OH), C16 : 1
ω5c and iso-C15 : 0 as major fatty acids. The genomic DNA G+C content of strain BZ26T was 48.9 mol%. On the basis of phenotypic characteristics and genotypic analysis, strain BZ26T is considered to represent a novel species of the genus Dyadobacter, for which the name Dyadobacter psychrophilus sp. nov. is proposed. The type strain is BZ26T (=DSM 22270T =CGMCC 1.8951T).
Chryseobacterium treverense sp. nov., isolated from a human clinical source
Authors: Yassin A. F. , Hupfer H. , Siering C. , Busse H.-J.
Published: November 2009

A yellow-pigmented, Gram-reaction-negative bacterium isolated from a human clinical source was investigated using a polyphasic approach in order to clarify its taxonomic status. Comparative 16S rRNA gene sequence analysis showed that the new isolate constituted a distinct phyletic line within the genusChryseobacterium, displaying >2.8 % sequence divergence with recognized species of this genus. The generic assignment was confirmed by chemotaxonomic data which revealed a fatty acid profile consisting of straight-chain saturated, monounsaturated and branched-chain fatty acids of iso-/anteiso-types as well as 3-hydroxylated fatty acids; a menaquinone with six isoprene units (MK-6) as the predominant respiratory quinone andsym-homospermidine as the predominant polyamine. The novel isolate could be distinguished from other members of the genusChryseobacteriumby a set of distinct biochemical properties. On the basis of phenotypic and phylogenetic evidence, it is proposed that the new isolate represents a novel species of the genusChryseobacteriumfor which the nameChryseobacterium treverensesp. nov. is proposed. The type strain is IMMIB L-1519T(=DSM 22251T=CCUG 57657T).
Classification of ‘Anaerocellum thermophilum’ strain DSM 6725 as Caldicellulosiruptor bescii sp. nov.
Authors: Yang Sung-Jae , Kataeva Irina , Wiegel Juergen , Yin Yanbin , Dam Phuongan , Xu Ying , Westpheling Janet , Adams Michael W. W.
Published: November 2009

The thermophilic, cellulolytic, anaerobic bacterium ‘Anaerocellum thermophilum’ strain Z-1320 was isolated from a hot spring almost two decades ago and deposited in the German Collection of Microorganisms and Cell Cultures (DSMZ) as DSM 6725. The organism was classified as representing a new genus, ‘Anaerocellum’, primarily on its growth physiology, cell-wall type and morphology. The results of recent physiological studies and of phylogenetic and genome sequence analyses of strain DSM 6725 of ‘A. thermophilum’ obtained from the DSMZ showed that its properties differed from those originally described for strain Z-1320. In particular, when compared with strain Z-1320, strain DSM 6725 grew at higher temperatures and had an expanded range of growth substrates. Moreover, the 16S rRNA gene sequence of strain DSM 6725 fell within the Caldicellulosiruptor clade. It is therefore suggested that ‘Anaerocellum thermophilum’ should be classified as a member of the genus Caldicellulosiruptor, for which the name Caldicellulosiruptor bescii sp. nov. is proposed (type strain DSM 6725T=ATCC BAA-1888T). C. bescii sp. nov. DSM 6725T is the most thermophilic cellulose-degrading organism known. The strain was able to grow up to 90 °C (pH 7.2) and degraded crystalline cellulose and xylan as well as untreated plant biomass, including potential bioenergy plants such as poplar and switchgrass.
Streptomyces osmaniensis sp. nov., isolated from soil
Authors: Reddy T. V. K. , Mahmood Shaik , Idris M. Mohammed , Ciesielski Slawomir
Published: November 2009

A novel actinomycete, designated strain OU-63T, was isolated from garden soil collected on the campus of Osmania University in Hyderabad, southern India. The strain was found to have morphological and chemotaxonomic characteristics typical of the genusStreptomyces. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belonged to the genusStreptomyces, and was related most closely toStreptomyces chartreusisNBRC 12753T(98.6 % similarity). However, the mean level of DNA–DNA relatedness between the two strains was only 25±1.73 %. Based on DNA–DNA relatedness, morphological and phenotypic data, strain OU-63Tcould be distinguished from the type strains of phylogenetically related species. It is therefore considered to represent a novel species of the genusStreptomyces, for which the nameStreptomyces osmaniensissp. nov. is proposed. The type strain is OU-63T(=CCTCC AA209025T=PCM 2690T).
Neptunomonas antarctica sp. nov., isolated from marine sediment
Authors: Zhang Xi-Ying , Zhang Yan-Jiao , Yu Yong , Li Hui-Juan , Gao Zhao-Ming , Chen Xiu-Lan , Chen Bo , Zhang Yu-Zhong
Published: November 2009

A Gram-negative, motile, oxidase- and catalase-positive and facultatively aerobic bacterium, designated S3-22T, was isolated from marine sediment of the Nella Fjord, Antarctica. Strain S3-22T reduced nitrate to nitrite and grew at pH 6.0–8.0, at 4–25 °C and with 0.5–5 % (w/v) NaCl. It contained Q-8 as the only respiratory quinone and summed feature 3 (C16 : 1
ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C18 : 1
ω7c as the major cellular fatty acids. The genomic DNA G+C content was 45.6 mol%. Phylogenetic analyses of 16S rRNA gene sequences showed that strain S3-22T was affiliated with the genus Neptunomonas, with 97.1 % sequence similarity to Neptunomonas japonica JAMM 0745T and 94.8 % to Neptunomonas naphthovorans NAG-2N-126T, the type strains of the only two recognized Neptunomonas species. DNA–DNA relatedness between strain S3-22T and N. japonica JCM 14595T was 20.4 %. Strain S3-22T could be distinguished from the type strains of Neptunomonas species by several phenotypic properties. Based on the evidence from our polyphasic study, strain S3-22T represents a novel Neptunomonas species, for which the name Neptunomonas antarctica sp. nov. is proposed. The type strain is S3-22T (=CCTCC AB 209086T =KACC 14056T).
Pseudidiomarina aestuarii sp. nov., a marine bacterium isolated from shallow coastal seawater
Authors: Park Seong Chan , Lim Chae Hong , Baik Keun Sik , Lee Kang Hyun , Lee Jung-Sook , Seong Chi Nam
Published: November 2009

A non-motile, rod-shaped and aerobic marine bacterium, designated strain KYW314T, was isolated from seawater collected from the South Sea, Republic of Korea. Cells were Gram-negative, catalase- and oxidase-positive and had proteolytic activity. The major fatty acids were iso-C15 : 0 (17.2 %), C16 : 0 (11.1 %), iso-C17 : 0 (10.5 %) and C18 : 1
ω7c (10.0 %). The DNA G+C content was 56.4 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain KYW314T formed a lineage within the genus Pseudidiomarina (95.4–97.3 % sequence similarity) and a distinct branch within the clade containing Pseudidiomarina taiwanensis PIT1T and Pseudidiomarina
sediminum c121T. Phenotypic characteristics could distinguish strain KYW314T from members of the genus Pseudidiomarina. On the basis of the data presented, strain KYW314T represents a novel species, for which the name Pseudidiomarina aestuarii sp. nov. is proposed. The type strain is KYW314T (=KCTC 22740T =JCM 16344T).
Thermosporothrix hazakensis gen. nov., sp. nov., isolated from compost, description of Thermosporotrichaceae fam. nov. within the class Ktedonobacteria Cavaletti et al. 2007 and emended description of the class Ktedonobacteria
Authors: Yabe Shuhei , Aiba Yoshifumi , Sakai Yasuteru , Hazaka Masaru , Yokota Akira
Published: November 2009

We isolated from compost an aerobic, thermophilic, Gram-stain-positive, spore-forming bacterium that formed branched vegetative and aerial mycelia. This strain, designated SK20-1T, grew at 31–58 °C, with optimum growth at 50 °C, while no growth was observed below 28 or above 60 °C. The pH range for growth was 5.4–8.7, with optimum growth at pH 7.0, while no growth was observed below pH 5.0 or above pH 9.1. Strain SK20-1Twas able to hydrolyse polysaccharides such as cellulose, xylan and chitin. The DNA G+C content was 54.0 mol%. The major fatty acid was iso-C17 : 0and the major menaquinone was MK-9(H2). The cell wall contained glutamic acid, serine, alanine and ornithine in a molar ratio of 1.00 : 1.07 : 2.64 : 0.83. The polar lipids consisted of phosphatidylinositol, phosphatidylinositol mannosides, phosphatidylglycerol, diphosphatidylglycerol and an unknown glycolipid. Cell-wall sugars were rhamnose and mannose. Detailed phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SK20-1Tbelongs to the classKtedonobacteria, and that the strain is most closely related toKtedonobacter racemiferSOSP1-21T(88.5 %). On the basis of its phenotypic features and phylogenetic position, we propose that SK20-1Trepresents a novel genus and species,Thermosporothrix hazakensisgen. nov., sp. nov., within the new familyThermosporotrichaceaefam. nov. The type strain ofThermosporothrix hazakensisis strain SK20-1T(=JCM 16142T=ATCC BAA-1881T). In addition, we propose an emended description of the classKtedonobacteriato classify the class in the phylumChloroflexi.
Corynebacterium marinum sp. nov. isolated from coastal sediment
Authors: Du Zong-Jun , Jordan Elizabeth M. , Rooney Alejandro P. , Chen Guan-Jun , Austin Brian
Published: November 2009

A taxonomic study was performed on strain D7015T, which was isolated from coastal sediment close to a coal-fired power station in Qingdao, China. Cells of strain D7015Twere Gram-positive, non-motile, diphtheroid rods that grew in the presence of 0–8 % (w/v) NaCl and at 4–37 °C, with optimum growth at 1 % (w/v) NaCl and 30–32 °C. The DNA G+C content was 65.0 mol%. The major fatty acids were C18 : 1ω9c(56.18 %), C16 : 0(38.02 %), C16 : 1ω7c(4.45 %), C18 : 0(1.0 %) and C14 : 0(0.35 %). On the basis of morphological, physiological and phylogenetic characteristics, strain D7015Twas classified in the genusCorynebacterium. It exhibited a 16S rRNA gene sequence similarity of 95.9 % and a DNA–DNA relatedness value of 20.4 % withCorynebacterium halotoleransDSM 44683T. Strain D7015Twas sufficiently different from recognized species of the genusCorynebacteriumto be considered to represent a novel species. The nameCorynebacterium marinumsp. nov. is proposed, with strain D7015T(=CGMCC 1.6998T=NRRL B-24779T) as the type strain.
Hafnia paralvei sp. nov., formerly known as Hafnia alvei hybridization group 2
Authors: Huys Geert , Cnockaert Margo , Abbott Sharon L. , Janda J. Michael , Vandamme Peter
Published: November 2009

It has been shown previously, based largely on DNA–DNA hybridizations and partial 16S rRNA gene sequencing, that Hafnia alvei is genotypically heterogeneous and consists of at least two DNA hybridization groups (HGs). In the present study, the taxonomic status of H. alvei HGs 1 and 2 was reassessed. A panel of 24 reference strains and isolates previously assigned to one of the two HGs in H. alvei was subjected to (GTG)5-PCR fingerprinting; this resulted in the delineation of two (GTG)5-PCR clusters in perfect accordance with the respective HG designations. Based on full 16S rRNA gene sequencing of a selection of reference strains, H. alvei HGs 1 and 2 showed internal sequence similarities of 99.8 and 99.5 %, respectively. Between the two groups, sequence similarities ranged from 98.8 to 99.1 %. Mean DNA–DNA hybridization values of 74.7–99.9 % were obtained within each of the two HGs, whereas cross-hybridizations between members of H. alvei HG 1 (including ATCC 13337T) and HG 2 revealed only 32.7–48.7 % DNA–DNA hybridization. Previously published and new phenotypic data revealed that a combination of malonate assimilation and β-glucosidase activity enabled correct assignment of Hafnia isolates to one of the two HGs. Collectively, taxonomic data from this study confirm that H. alvei comprises at least two taxa at the species level, of which HG 1 corresponds to H. alvei
sensu
stricto because it includes the type strain ATCC 13337T. Strains formerly classified as members of H. alvei HG 2 represent a novel species, for which the name Hafnia paralvei sp. nov. is proposed; ATCC 29927T (=CDC 4510-73T =LMG 24706T), the former reference strain of H. alvei HG 2, is designated the type strain.
Lachancea nothofagi sp. nov., a yeast associated with Nothofagus species in Patagonia, Argentina
Authors: Mestre M. C. , Ulloa J. R. , Rosa C. A. , Lachance M. A. , Fontenla S.
Published: November 2009

Six strains of a novel yeast species were isolated from Nothofagus species trees in native forests in Patagonia, Argentina. The strains were isolated from bark, fluxes and the ectomycorrhizospheric soil fraction of Nothofagus antarctica, Nothofagus nervosa and Nothofagus pumilio. Analysis of the D1/D2 large-subunit rDNA sequences indicated that the novel species belonged to the genus Lachancea and is closely related to Lachancea meyersii. The name Lachancea nothofagi sp. nov. is proposed to accommodate these strains. The type strain is UWOPS 99-807.3T (=CBS 11611T=NRRL Y-48670T).
Vitellibacter aestuarii sp. nov., isolated from tidal-flat sediment, and an emended description of the genus Vitellibacter
Authors: Kim Bong-Soo , Kim Ok-Sun , Moon Eun Young , Chun Jongsik
Published: November 2009

A Gram-reaction-negative, aerobic, yellowish-orange-pigmented bacterial strain, designated JC2436T, was isolated from tidal-flat sediment of Oi Island in Korea. Comparative 16S rRNA gene sequence analysis indicated its close affiliation to Vitellibacter vladivostokensis, with 96 % sequence similarity to the type strain. Cells grew with 2–6 % NaCl and at 10–41 °C. Orange flexirubin pigments were present. The major isoprenoid quinone was MK-6, the DNA G+C content was 48.7 mol% and the predominant fatty acids (>10 %) were iso-C15 : 0 and iso-C17 : 0 3-OH. The data obtained from this polyphasic study support the classification of this isolate within a novel species in the genus Vitellibacter, for which the name Vitellibacter aestuarii sp. nov. is proposed. The type strain is JC2436T (=IMSNU 14137T =KACC 13727T =KCTC 22361T =JCM 15496T).
Prurigo nodularis due to Mycobacterium tuberculosis
Authors: Saporito Laura , Florena Ada Maria , Colomba Claudia , Pampinella Diego , Di Carlo Paola
Published: November 2009

Prurigo nodularis (PN) is a rare chronic skin disorder of unknown origin. Here we describe what is believed to be the first case of PN associated with tuberculosis. For the first time, culture and PCR analysis of skin biopsy confirmed the presence ofMycobacterium tuberculosiscomplex in PN skin lesions. The pruritus and skin lesions resolved following antitubercular therapy. Our case provides further evidence in favour of a link between PN and mycobacterial infection.
MICs and minimum fungicidal concentrations of amphotericin B, itraconazole, posaconazole and terbinafine in Sporothrix schenckii
Authors: Pereira Silveira Carolina , Torres-Rodríguez Josep M. , Alvarado-Ramírez Eidi , Murciano-Gonzalo Francisca , Dolande Maribel , Panizo Mercedes , Reviakina Vera
Published: November 2009

The in vitro susceptibility of 62 isolates of Sporothrix schenckii in its mycelial form, from Latin-American countries (Peru, Venezuela, Brazil and Uruguay) and Spain, to amphotericin B (AB), itraconazole (IZ), posaconazole (PZ) and terbinafine (TB) was determined by measuring the MICs and minimum fungicidal concentrations (MFCs) using a standardized Clinical and Laboratory Standards Institute method. In general, TB was the most active drug, with the lowest geometric mean (GM) MIC and MFC values amongst isolates from the five countries tested. IZ and PZ showed almost the same activity against all strains tested, except for isolates from Uruguay where IZ gave the highest GM MIC (10.68 mg l−1). AB showed the widest MIC range (0.03–16.0 mg l−1); however, this drug was less active against 79 % of isolates (MICs above 1 mg l−1). MFCs were 5 to 20 times higher than the MICs, but the lowest GM MFC and range values were found for TB. IZ and PZ gave the highest GM MFC. MFC may be a better predictor of therapeutic response than MIC, especially in immunosuppressed patients, making the use of IZ and PZ an inappropriate treatment. There were some differences in susceptibility according to the geographical source of the isolates, with the MIC being lower for TB in Venezuelan strains (P=0.066) and the MFC higher for PZ in Peruvian strains (P=0.02). Thus, geographical origin may be important for appropriate treatment, and may relate to the identification of species of the S. schenckii complex.
High prevalence of plasmid-mediated quinolone resistance determinants in commensal members of the Enterobacteriaceae in Ho Chi Minh City, Vietnam
Authors: Minh Vien Le Thi , Baker Stephen , Phuong Thao Le Thi , Phuong Tu Le Thi , Thu Thuy Cao , Thu Nga Tran Thi , Minh Hoang Nguyen Van , Campbell James Iain , Minh Yen Lam , Trong Hieu Nguyen , Vinh Chau Nguyen Van , Farrar Jeremy , Schultsz Constance
Published: November 2009

Antimicrobial-resistant pathogenic members of theEnterobacteriaceaeare a well-defined global problem. We hypothesized that one of the main reservoirs of dissemination of antimicrobial resistance genes in Vietnam is non-pathogenic intestinal flora, and sought to isolate antimicrobial-resistant organisms from hospitalized patients and non-hospitalized healthy individuals in Ho Chi Minh City. The results identified substantial faecal carriage of gentamicin-, ceftazidime- and nalidixic acid-resistant members of theEnterobacteriaceaein both hospitalized patients and non-hospitalized healthy individuals. A high prevalence of quinolone resistance determinants was identified, particularly theqnrSgene, in both community- and hospital-associated strains. Furthermore, the results demonstrated that a combination of quinolone resistance determinants can confer resistance to nalidixic acid and ciprofloxacin, even in the apparent absence of additional chromosomal resistance mutations in wild-type strains and laboratory strains with transferred plasmids. These data suggest that intestinal commensal organisms are a significant reservoir for the dissemination of plasmid-mediated quinolone resistance in Ho Chi Minh City.
Fatal spontaneous bacterial peritonitis and necrotizing fasciitis with bacteraemia caused by Bacillus cereus in a patient with cirrhosis
Authors: Lee Ya-Ling , Shih Sheng-Dong , Weng Yu-Jong , Chen Changhua , Liu Chun-Eng
Published: November 2009

We report a case of spontaneous bacterial peritonitis and necrotizing fasciitis caused by Bacillus cereus in a cirrhotic patient without preceding disruption of skin or symptoms of gastroenteritis. This rapidly fatal infection due to B. cereus adds to the long list of aetiologies of infectious complications among patients with cirrhosis of the liver.
Nocardia cyriacigeorgica: a case of endocarditis with disseminated soft-tissue infection
Authors: Cargill James S. , Boyd Gavin J. , Weightman Nigel C.
Published: November 2009

Nocardia cyriacigeorgica is a common environmental organism. It has been isolated from clinical samples in Europe, Asia and North America, predominantly from respiratory samples but also from samples from several other sites. We present a case report of an 85-year-old female patient in the UK who was found to have a multi-focal soft-tissue infection from which N. cyriacigeorgica was isolated. She had a background history of chronic obstructive pulmonary disease and corticosteroid use for polymyalgia rheumatica. During the course of her treatment echocardiography showed the presence of a mobile heart mass attached to a valve leaflet, a major Dukes criterion for endocarditis. We suggest that in cases of disseminated Nocardia infection, endocarditis should be tested for, particularly in cases failing to respond to treatment. We also review previous reports of both N. cyriacigeorgica infection, and of endocarditis due to Nocardia species and related genera.
Subinhibitory concentrations of moxifloxacin decrease adhesion and biofilm formation of Stenotrophomonas maltophilia from cystic fibrosis
Authors: Pompilio A. , Catavitello C. , Picciani C. , Confalone P. , Piccolomini R. , Savini V. , Fiscarelli E. , D'Antonio D. , Di Bonaventura G.
Published: November 2009

Stenotrophomonas maltophilia is an emerging nosocomial bacterial pathogen that is currently isolated with increasing frequency from the airways of cystic fibrosis (CF) patients. In this study the effect of subinhibitory concentrations (subMICs) of moxifloxacin on adhesion, biofilm formation and cell-surface hydrophobicity of two strains of S. maltophilia isolated from CF patients were evaluated. Adhesion and biofilm formation assays were carried out on polystyrene and quantified by colony counts. Cell-surface hydrophobicity was determined by a test for adhesion to n-hexadecane. Moxifloxacin at 0.03× and 0.06× MIC caused a significant decrease in adhesion and biofilm formation by both strains tested. A significant reduction in cell-surface hydrophobicity following exposure to subMICs of moxifloxacin was observed for one strain only. The results of the present study provide an additional rationale for the use of moxifloxacin in CF patients and more generally in biofilm-related infections involving S. maltophilia.
VopF, a type III effector protein from a non-O1, non-O139 Vibrio cholerae strain, demonstrates toxicity in a Saccharomyces cerevisiae model
Authors: Tripathi Ranjana , Singh Naorem Santa , Dureja Chetna , Haldar Swati , Mondal Alok K. , Raychaudhuri Saumya
Published: November 2009

VopF, a type III effector protein, has been identified as a contributory factor to the intestinal colonization of type III secretion system-positive, non-O1, non-O139 Vibrio cholerae strains. To gain more insight into the function of VopF, a yeast model was developed. Using this model, it was found that ectopic expression of VopF conferred toxicity in yeast.
Identification of Burkholderia cepacia complex bacteria with a lipopolysaccharide-specific monoclonal antibody
Authors: AuCoin David P. , Crump Reva B. , Thorkildson Peter , Nuti Dana E. , LiPuma John J. , Kozel Thomas R.
Published: November 2009

The genus Burkholderia includes many bacteria that cause serious human infections. As is the case with other Gram-negative bacteria, Burkholderia species produce LPS, which is an abundant component of the bacterial cell surface. Burkholderia cepacia complex (Bcc) bacteria (which include at least 17 separate species) produce LPS structures that are quite different. In an attempt to determine the degree of LPS epitope variation among Bcc species, a mAb was produced, designated 5D8, specific for the LPS of B. cepacia. Western blot analysis determined that mAb 5D8 was able to produce the classic ‘ladder pattern’ when used to probe B. cepacia and Burkholderia anthina lysates, although 5D8 did not produce this pattern with the other seven Bcc species tested. mAb 5D8 reacted with varying intensity to most but not all of the additional B. cepacia and B. anthina strains tested. Therefore, there seems to be significant epitope variation among Bcc LPS both between and within species. Additionally, mAb 5D8 reacted with a proteinase-K-sensitive 22 kDa antigen in all Bcc strains and also in a strain of Burkholderia pseudomallei.
A quadruplex real-time PCR assay for rapid detection and differentiation of the Clostridium botulinum toxin genes A, B, E and F
Authors: Satterfield Benjamin A. , Stewart Alvin F. , Lew Cynthia S. , Pickett David O. , Cohen Marissa N. , Moore Emily A. , Luedtke Patrick F. , O'Neill Kim L. , Robison Richard A.
Published: November 2009

Clostridium botulinum is the aetiological agent of botulism, a disease marked by flaccid paralysis that can progress to asphyxiation and death. This species is defined by the production of one of the botulinum neurotoxins (BoNTs), which are the most potent toxins known. Because of their potency, these toxins have the potential to be used as biological weapons, and therefore C. botulinum has been classified as a category A select agent. There are four related but antigenically distinct BoNT types that cause disease in humans, A, B, E and F. The mouse bioassay is the current gold standard by which BoNTs are confirmed. However, this method is expensive, slow and labour-intensive. Although PCR-based assays have been used extensively for the detection of BoNT-producing bacteria in food, animals and faecal samples, and recently to help diagnose disease in humans, no real-time quantitative PCR (qPCR) assay has yet been developed that can identify and differentiate all four BoNTs that cause disease in humans. This report describes the development of a qPCR single-tube assay that uniquely identifies these four BoNTs responsible for human disease. A total of 79 C. botulinum isolates with varying toxin types was evaluated in this study, as well as numerous near-neighbours and other bacterial species. The results showed that this quadruplex assay was capable of detecting any of the four toxin genes in a given sample at a sensitivity of about 130–840 fg genomic DNA and could detect the presence of up to all four BoNT genes simultaneously in a given sample. The assay was also functional in the presence of extraneous organic matter commonly found in various environmental samples.
Mycoplasma salivarium detected in a microbial community with Candida glabrata in the biofilm of an occluded biliary stent
Authors: Henrich Birgit , Schmitt Marcus , Bergmann Nora , Zanger Klaus , Kubitz Ralf , Häussinger Dieter , Pfeffer Klaus
Published: November 2009

Mycoplasma salivarium, preferentially an inhabitant of the human oral cavity, has rarely been found in other locations associated with disease. We describe here, for what is believed to be the first time, the detection of M. salivarium, together with Candida glabrata, in an occluded biliary stent of an icteric, cholestatic patient.
Gemella morbillorum: an underestimated aetiology of central nervous system infection?
Authors: Benedetti Paolo , Rassu Mario , Branscombe Michele , Sefton Armine , Pellizzer Giampietro
Published: November 2009

A case is reported of cerebellar abscess and diffuse cerebritis due toGemella morbillorum. The clinical course was ‘biphasic’, developing with an acute meningeal infection followed shortly afterwards by suppuration in the cerebellar and cerebral parenchyma; this pattern seemed to suggest a latent survival of the aetiological agent, probably within the central nervous system (CNS), despite systemic antibiotic therapy. Based upon a review of cases so far described, infections of the CNS caused byG. morbillorumappear to be an emerging reality.