scholarly journals Marinomonas brasilensis sp. nov., isolated from the coral Mussismilia hispida, and reclassification of Marinomonas basaltis as a later heterotypic synonym of Marinomonas communis

2011 ◽  
Vol 61 (5) ◽  
pp. 1170-1175 ◽  
Author(s):  
Luciane A. Chimetto ◽  
Ilse Cleenwerck ◽  
Marcelo Brocchi ◽  
Anne Willems ◽  
Paul De Vos ◽  
...  
Keyword(s):  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
The Novel ◽  
Pattern Similarity ◽  
Phenotypic Features ◽  
Type Strains ◽  
The 16S Rrna Gene

A Gram-negative, aerobic bacterium, designated strain R-40503T, was isolated from mucus of the reef-builder coral Mussismilia hispida, located in the São Sebastião Channel, São Paulo, Brazil. Phylogenetic analyses revealed that strain R-40503T belongs to the genus Marinomonas. The 16S rRNA gene sequence similarity of R-40503T was above 97 % with the type strains of Marinomonas vaga, M. basaltis, M. communis and M. pontica, and below 97 % with type strains of the other Marinomonas species. Strain R-40503T showed less than 35 % DNA–DNA hybridization (DDH) with the type strains of the phylogenetically closest Marinomonas species, demonstrating that it should be classified into a novel species. Amplified fragment length polymorphism (AFLP), chemotaxonomic and phenotypic analyses provided further evidence for the proposal of a novel species. Concurrently, a close genomic relationship between M. basaltis and M. communis was observed. The type strains of these two species showed 78 % DDH and 63 % AFLP pattern similarity. Their phenotypic features were very similar, and their DNA G+C contents were identical (46.3 mol%). Collectively, these data demonstrate unambiguously that Marinomonas basaltis is a later heterotypic synonym of Marinomonas communis. Several phenotypic features can be used to discriminate between Marinomonas species. The novel strain R-40503T is clearly distinguishable from its neighbours. For instance, it shows oxidase and urease activity, utilizes l-asparagine and has the fatty acid C12 : 1 3-OH but lacks C10 : 0 and C12 : 0. The name Marinomonas brasilensis sp. nov. is proposed, with the type strain R-40503T ( = R-278T  = LMG 25434T  = CAIM 1459T). The DNA G+C content of strain R-40503T is 46.5 mol%.

scholarly journals Thermovibrio ammonificans sp. nov., a thermophilic, chemolithotrophic, nitrate-ammonifying bacterium from deep-sea hydrothermal vents

2004 ◽  
Vol 54 (1) ◽  
pp. 175-181 ◽  
Author(s):  
Costantino Vetriani ◽  
Mark D. Speck ◽  
Susan V. Ellor ◽  
Richard A. Lutz ◽  
Valentin Starovoytov
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vents ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
East Pacific ◽  
Casamino Acids ◽  
The 16S Rrna Gene

A thermophilic, anaerobic, chemolithoautotrophic bacterium was isolated from the walls of an active deep-sea hydrothermal vent chimney on the East Pacific Rise at 9° 50′ N. Cells of the organism were Gram-negative, motile rods that were about 1·0 μm in length and 0·6 μm in width. Growth occurred between 60 and 80 °C (optimum at 75 °C), 0·5 and 4·5 % (w/v) NaCl (optimum at 2 %) and pH 5 and 7 (optimum at 5·5). Generation time under optimal conditions was 1·57 h. Growth occurred under chemolithoautotrophic conditions in the presence of H2 and CO2, with nitrate or sulfur as the electron acceptor and with concomitant formation of ammonium or hydrogen sulfide, respectively. Thiosulfate, sulfite and oxygen were not used as electron acceptors. Acetate, formate, lactate and yeast extract inhibited growth. No chemoorganoheterotrophic growth was observed on peptone, tryptone or Casamino acids. The genomic DNA G+C content was 54·6 mol%. Phylogenetic analyses of the 16S rRNA gene sequence indicated that the organism was a member of the domain Bacteria and formed a deep branch within the phylum Aquificae, with Thermovibrio ruber as its closest relative (94·4 % sequence similarity). On the basis of phylogenetic, physiological and genetic considerations, it is proposed that the organism represents a novel species within the newly described genus Thermovibrio. The type strain is Thermovibrio ammonificans HB-1T (=DSM 15698T=JCM 12110T).

scholarly journals Blastococcus jejuensis sp. nov., an actinomycete from beach sediment, and emended description of the genus Blastococcus Ahrens and Moll 1970

2006 ◽  
Vol 56 (10) ◽  
pp. 2391-2396 ◽  
Author(s):  
Soon Dong Lee
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
The Novel ◽  
Separate Species ◽  
Beach Sediment ◽  
Actinomycete Strain ◽  
Type Strains

A novel actinomycete, strain KST3-10T, was isolated from sand sediment of a beach in Jeju, Korea, and was subjected to polyphasic taxonomic characterization. The organism produced circular, smooth, translucent, apricot-coloured colonies comprising coccoid- or rod-shaped cells. Phylogenetic analyses based on 16S rRNA gene sequences showed that the organism belonged to the family Geodermatophilaceae and consistently formed a distinct sub-branch outside the radiation of the genus Blastococcus. The organism showed 16S rRNA gene sequence similarity values of 98.2 % with respect to Blastococcus aggregatus DSM 4725T and 98.1 % with respect to Blastococcus saxobsidens BC444T. The type strains of the two Blastococcus species shared 98.2 % sequence similarity with respect to each other, whereas the levels of sequence similarity between the novel organism and the type strains of the less closely related neighbours, Modestobacter multiseptatus and Geodermatophilus obscurus, were in the range 96.2–96.9 %. The physiological, biochemical and chemotaxonomic data revealed that the novel organism can be readily differentiated from members of the genus Blastococcus and that it merits separate species status. On the basis of the phenotypic and genotypic evidence, strain KST3-10T represents a novel species of the genus Blastococcus, for which the name Blastococcus jejuensis sp. nov. is proposed. The type strain is KST3-10T (=NRRL B-24440T=KCCM 42251T).

scholarly journals Coraliomargarita akajimensis gen. nov., sp. nov., a novel member of the phylum ‘Verrucomicrobia’ isolated from seawater in Japan

2007 ◽  
Vol 57 (5) ◽  
pp. 959-963 ◽  
Author(s):  
Jaewoo Yoon ◽  
Mina Yasumoto-Hirose ◽  
Atsuko Katsuta ◽  
Hiroshi Sekiguchi ◽  
Satoru Matsuda ◽  
...  
Keyword(s):  
Cell Wall ◽  
New Genus ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Hard Coral ◽  
The 16S Rrna Gene

An obligately aerobic, Gram-negative, non-spore-forming, non-motile, spherical bacterium, designated strain 04OKA010-24T, was isolated from seawater surrounding the hard coral Galaxea fascicularis L., collected at Majanohama, Akajima, Japan, and was subjected to a polyphasic taxonomic study. Phylogenetic analyses based on the 16S rRNA gene sequence indicated that the new strain represented a member of the phylum ‘Verrucomicrobia’ and shared 84–95 % sequence similarity with cultivated strains of ‘Verrucomicrobia’ subdivision 4. Amino acid analysis of the cell-wall hydrolysate indicated the absence of muramic acid and diaminopimelic acid, which suggested that the strain did not contain peptidoglycan in the cell wall. The G+C content of the DNA was 53.9 mol%. MK-7 was the major menaquinone and C14 : 0, C18 : 1 ω9c and C18 : 0 were the major fatty acids. On the basis of these data, it was concluded that strain 04OKA010-24T represents a novel species in a new genus in subdivision 4 of the phylum ‘Verrucomicrobia’, for which the name Coraliomargarita akajimensis gen. nov., sp. nov. is proposed. The type strain of Coraliomargarita akajimensis is 04OKA010-24T (=MBIC06463T=IAM 15411T=KCTC 12865T).

Lactobacillus odoratitofui sp. nov., isolated from stinky tofu brine

2010 ◽  
Vol 60 (12) ◽  
pp. 2903-2907 ◽  
Author(s):  
Shiou-Huei Chao ◽  
Masae Sasamoto ◽  
Yuko Kudo ◽  
Junji Fujimoto ◽  
Ying-Chieh Tsai ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Positive Staining ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Dna Reassociation ◽  
Type Strains

Three Gram-positive-staining strains isolated from fermented stinky tofu brine were rod-shaped, non-motile, asporogenous, facultatively anaerobic, heterofermentative and did not exhibit catalase activity. Comparative analyses of 16S rRNA, rpoA and pheS gene sequences demonstrated that the novel strains were members of the genus Lactobacillus. On the basis of 16S rRNA gene sequence similarity, the type strains of Lactobacillus collinoides (98.6 %), Lactobacillus paracollinoides (98.6 %) and Lactobacillus similis (99.6 %) were the closest neighbours. However, DNA–DNA reassociation values with these strains were less than 10 %. The phenotypic and genotypic features demonstrated that these isolates represent a novel species of the genus Lactobacillus, for which the name Lactobacillus odoratitofui sp. nov. is proposed. The type strain is YIT 11304T (=JCM 15043T =BCRC 17810T =DSM 19909T).

Amycolatopsis helveola sp. nov. and Amycolatopsis pigmentata sp. nov., isolated from soil

2010 ◽  
Vol 60 (11) ◽  
pp. 2629-2633 ◽  
Author(s):  
Tomohiko Tamura ◽  
Yuumi Ishida ◽  
Misa Otoguro ◽  
Ken-ichiro Suzuki
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Monophyletic Cluster ◽  
The 16S Rrna Gene ◽  
Taxonomical Study

Three short spore chain-forming actinomycete strains were isolated from soil samples collected from subtropical islands in Japan. The cell-wall peptidoglycan of these strains contained meso-diaminopimelic acid (meso-A2pm), glutamic acid and alanine. The major isoprenoid quinone was MK-9(H4), iso-C16 : 0 and 2-OH iso-C16 : 0 were the major cellular fatty acids and phosphatidylethanolamine was a component of the polar lipids. The G+C content of the genomic DNA was 67–69 mol%. Phylogenetic analyses based on the 16S rRNA gene sequences showed that the novel strains consistently formed a monophyletic cluster with Amycolatopsis taiwanensis. On the basis this polyphasic taxonomical study, it is proposed that the two new isolates represent two novel species: Amycolatopsis helveola (type strain TT00-43T=NBRC 103394T=KCTC 19329T) and Amycolatopsis pigmentata (type strain TT99-32T=NBRC 103392T=KCTC 19330T).

scholarly journals Pelagicoccus croceus sp. nov., a novel marine member of the family Puniceicoccaceae within the phylum ‘Verrucomicrobia’ isolated from seagrass

2007 ◽  
Vol 57 (12) ◽  
pp. 2874-2880 ◽  
Author(s):  
Jaewoo Yoon ◽  
Naoya Oku ◽  
Satoru Matsuda ◽  
Hiroaki Kasai ◽  
Akira Yokota
Keyword(s):  
Cell Wall ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
Antibiotic Susceptibility Test ◽  
The Family ◽  
Lactam Antibiotic

An obligately aerobic, spherical, non-motile, pale-yellow pigmented bacterium was isolated from a piece of leaf of seagrass, Enhalus acoroides (L.f.) Royle, grown in Okinawa, Japan and was subjected to a polyphasic taxonomic study. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the novel isolate N5FB36-5T shared approximately 96–98 % sequence similarity with the species of the genus Pelagicoccus of the family Puniceicoccaceae within the phylum ‘Verrucomicrobia’. The DNA–DNA relatedness values of strain N5FB36-5T with Pelagicoccus mobilis 02PA-Ca-133T and Pelagicoccus albus YM14-201T were below 70 %, which is accepted as the phylogenetic definition of a novel species. β-Lactam antibiotic susceptibility test and amino acid analysis of the cell wall hydrolysates indicated the absence of muramic acid and diaminopimelic acid in the cell walls, which suggested that this strain lacks an ordinary Gram-negative type of peptidoglycan in the cell wall. The DNA G+C content of strain N5FB36-5T was 51.6 mol%; MK-7 was the major menaquinone; and the presence of C16 : 0, C16 : 1 ω7c and anteiso-C15 : 0 as the major cellular fatty acids supported the identification of the novel isolate as a member of the genus Pelagicoccus. On the basis of polyphasic taxonomic data, it was concluded that this strain should be classified as a novel species of the genus Pelagicoccus, for which the name Pelagicoccus croceus sp. nov. is proposed. The type strain is N5FB36-5T (=MBIC08282T=KCTC 12903T).

scholarly journals Rheinheimera chironomi sp. nov., isolated from a chironomid (Diptera; Chironomidae) egg mass

2007 ◽  
Vol 57 (8) ◽  
pp. 1872-1875 ◽  
Author(s):  
Malka Halpern ◽  
Yigal Senderovich ◽  
Sagi Snir
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Egg Mass ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties ◽  
Positive Growth ◽  
Type Strains ◽  
The 16S Rrna Gene

A Gram-negative, rod-shaped bacterial strain, designated K19414T, was isolated from a chironomid (Diptera; Chironomidae) egg mass which was sampled from Kishon River in northern Israel. Phylogenetic analysis based on the 16S rRNA gene sequence positioned the novel strain among the genus Rheinheimera, with closest similarity to Rheinheimera pacifica KMM 1406T. The levels of similarity to type strains of Rheinheimera species were lower than 96.5 %. Isolate K19414T is aerobic, motile by means of a single polar flagellum, catalase-negative and oxidase-positive; growth was observed at salinities of 0–2 % NaCl and the temperature for growth ranged from 4 to 40 °C. The major cellular fatty acids are 16 : 0 (14.8 %) and 16 : 1ω7c and/or 15 : 0 iso 2-OH (25.76 %). The DNA G+C content is 49.9 mol%. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain K19414T (=LMG 23818T =DSM 18694T) was classified in the genus Rheinheimera as the type strain of a novel species, for which the name Rheinheimera chironomi sp. nov. is proposed.

scholarly journals Chryseobacterium formosense sp. nov., isolated from the rhizosphere of Lactuca sativa L. (garden lettuce)

2005 ◽  
Vol 55 (1) ◽  
pp. 423-426 ◽  
Author(s):  
Chiu-Chung Young ◽  
Peter Kämpfer ◽  
Fo-Ting Shen ◽  
Wei-An Lai ◽  
A. B. Arun
Keyword(s):  
Lactuca Sativa ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Lactuca Sativa L ◽  
Taxonomic Approach ◽  
Type Strains ◽  
The 16S Rrna Gene

A yellow-pigmented bacterial strain (CC-H3-2T), isolated from the rhizosphere of Lactuca sativa L. (garden lettuce) in Taiwan, was investigated using a polyphasic taxonomic approach. The cells were Gram-negative, rod-shaped and non-spore-forming. Phylogenetic analyses using the 16S rRNA gene sequence of the isolate indicated that the organism belongs to the genus Chryseobacterium, with the highest sequence similarity to the type strains of Chryseobacterium indoltheticum (97·7 %), Chryseobacterium scophthalmum (97·5 %), Chryseobacterium joostei (97·2 %) and Chryseobacterium defluvii (97·2 %). The major whole-cell fatty acids were iso-C15 : 0 (52·2 %) and iso-C17 : 0 3-OH. DNA–DNA hybridization experiments revealed levels of only 27·4 % to C. scophthalmum, 27·1 % to C. indoltheticum, 14·1 % to C. joostei and 7·8 % to C. defluvii. DNA–DNA relatedness and biochemical and chemotaxonomic properties demonstrate that strain CC-H3-2 T represents a novel species, for which the name Chryseobacterium formosense sp. nov. is proposed. The type strain is CC-H3-2T (=CCUG 49271T=CIP 108367T).

scholarly journals Polaribacter dokdonensis sp. nov., isolated from seawater

2006 ◽  
Vol 56 (6) ◽  
pp. 1251-1255 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Type Strains ◽  
The 16S Rrna Gene

A Gram-negative, non-motile, non-spore-forming, slightly halophilic bacterial strain, DSW-5T, was isolated from seawater off Dokdo, Korea, and subjected to a polyphasic taxonomic study. It grew optimally at 25–28 °C and in the presence of 2 % (w/v) NaCl. Strain DSW-5T contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C15 : 1 and iso-C15 : 0 3-OH as the major fatty acids. The major polar lipids detected were phosphatidylethanolamine, three unidentified phospholipids and an amino-group-containing lipid. The DNA G+C content was 30.0 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DSW-5T was most closely related to the genus Polaribacter. Similarity values between the 16S rRNA gene sequences of strain DSW-5T and the type strains of recognized Polaribacter species were in the range 96.2–96.8 %. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain DSW-5T (=KCTC 12392T=DSM 17204T) was classified in the genus Polaribacter as the type strain of a novel species, for which the name Polaribacter dokdonensis sp. nov. is proposed.

scholarly journals Algoriphagus terrigena sp. nov., isolated from soil

2006 ◽  
Vol 56 (4) ◽  
pp. 777-780 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Mi-Hwa Lee ◽  
So-Jung Kang ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Type Strains ◽  
The 16S Rrna Gene

A Gram-negative, non-motile, non-spore-forming bacterial strain, DS-44T, was isolated from soil from Dokdo in Korea, and its taxonomic position was investigated by using a polyphasic approach. It grew optimally at 25 °C and in the presence of 2 % (w/v) NaCl. Strain DS-44T contained MK-7 as the predominant menaquinone and iso-C15 : 0 and C16 : 1 ω7c and/or iso-C15 : 0 2-OH as the major fatty acids. The DNA G+C content was 49·0 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DS-44T belongs to the genus Algoriphagus of the phylum Bacteroidetes. Similarity values between the 16S rRNA gene sequences of strain DS-44T and those of the type strains of recognized Algoriphagus species were in the range 93·8–95·7 %, making it possible to categorize strain DS-44T as a species that is separate from previously described Algoriphagus species. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain DS-44T (=KCTC 12545T=CIP 108837T) was classified in the genus Algoriphagus as the type strain of a novel species, for which the name Algoriphagus terrigena sp. nov. is proposed.

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