scholarly journals Shewanella gaetbuli sp. nov., a slight halophile isolated from a tidal flat in Korea

2004 ◽  
Vol 54 (2) ◽  
pp. 487-491 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Kook Hee Kang ◽  
Tae-Kwang Oh ◽  
Yong-Ha Park
Keyword(s):  
16S Rdna ◽  
Tidal Flat ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Phenotypic Properties ◽  
16S Rdna Sequence ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Isoprenoid Quinones ◽  
Type Strains

A Gram-negative, motile, non-spore-forming, rod-shaped strain, TF-27T (=KCCM 41648T=JCM 11814T), was isolated from a tidal flat in Korea. This organism grew well at 25–35 °C, with optimum growth at 30 °C. Strain TF-27T grew optimally in the presence of 2 % NaCl; it did not grow without NaCl or in the presence of >8 % NaCl. Strain TF-27T simultaneously contained both menaquinones and ubiquinones as isoprenoid quinones. The predominant menaquinone was MK-7 and the predominant ubiquinones were Q-7 and Q-8. The major fatty acids in strain TF-27T were iso-C15 : 0 (20·6 %) and iso-C15 : 0 2-OH and/or C16 : 1 ω7c (21·1 %). The DNA G+C content of strain TF-27T was 42 mol%. Phylogenetic analyses based on 16S rDNA sequences showed that strain TF-27T falls within the radiation of the cluster that is encompassed by the genus Shewanella. Levels of 16S rDNA sequence similarity between strain TF-27T and the type strains of Shewanella species were 93·2–96·8 %. On the basis of phenotypic properties and phylogenetic data, strain TF-27T should be placed in the genus Shewanella as a novel species, for which the name Shewanella gaetbuli sp. nov. is proposed.

scholarly journals Herbaspirillum chlorophenolicum sp. nov., a 4-chlorophenol-degrading bacterium

2004 ◽  
Vol 54 (3) ◽  
pp. 851-855 ◽  
Author(s):  
Wan-Taek Im ◽  
Hee-Sung Bae ◽  
Akira Yokota ◽  
Sung Taik Lee
Keyword(s):  
16S Rdna ◽  
Sequence Similarity ◽  
Rdna Sequence ◽  
The Novel ◽  
Comamonas Testosteroni ◽  
16S Rdna Sequence ◽  
Rdna Sequences ◽  
Degrading Bacterium ◽  
16S Rdna Sequences ◽  
Type Strains

A 4-chlorophenol-degrading bacterial strain, formerly designated as a strain of Comamonas testosteroni, was reclassified as a member of the genus Herbaspirillum based on its phenotypic and chemotaxonomic characteristics, as well as phylogenetic analysis using 16S rDNA sequences. Phylogenetic inference based on 16S rDNA sequences showed that strain CPW301T clusters in a phylogenetic branch that contains Herbaspirillum species. 16S rDNA sequence similarity of strain CPW301T to species of the genus Herbaspirillum with validly published names is in the range 98·7–98·9 %. Despite the considerably high 16S rDNA sequence similarity, strain CPW301T could be distinguished clearly from type strains of Herbaspirillum species with validly published names by DNA–DNA relatedness values, which were <15·7 %. The genomic DNA G+C content of strain CPW301T is 61·3 mol%. The predominant ubiquinone is Q-8 and the major cellular fatty acids are C16 : 0 and cyclo-C17 : 0. The strain does not fix nitrogen and is not plant-associated. It is an aerobic rod with one unipolar flagellum. On the basis of these characteristics, a novel Herbaspirillum species, Herbaspirillum chlorophenolicum sp. nov., is proposed. The type strain of the novel species is strain CPW301T (=KCTC 12096T=IAM 15024T).

scholarly journals Characterization of a ‘Bacteroidetes’ symbiont in Encarsia wasps (Hymenoptera: Aphelinidae): proposal of ‘Candidatus Cardinium hertigii’

2004 ◽  
Vol 54 (3) ◽  
pp. 961-968 ◽  
Author(s):  
Einat Zchori-Fein ◽  
Steve J. Perlman ◽  
Suzanne E. Kelly ◽  
Nurit Katzir ◽  
Martha S. Hunter
Keyword(s):  
Electron Microscopy ◽  
16S Rdna ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rdna Sequence ◽  
Rdna Sequences ◽  
16S Rdna Sequences

Previously, analysis of 16S rDNA sequences placed a newly discovered lineage of bacterial symbionts of arthropods in the ‘Bacteroidetes’. This symbiont lineage is associated with a number of diverse host reproductive manipulations, including induction of parthenogenesis in several Encarsia parasitoid wasps (Hymenoptera: Aphelinidae). In this study, electron microscopy and phylogenetic analysis of the 16S rRNA and gyrB genes of symbionts from Encarsia hispida and Encarsia pergandiella are used to describe and further characterize these bacteria. Phylogenetic analyses based on these two genes showed that the Encarsia symbionts are allied with the Cytophaga aurantiaca lineage within the ‘Bacteroidetes’, with their closest described relative being the acanthamoeba symbiont ‘Candidatus Amoebophilus asiaticus’. The Encarsia symbionts share 97 % 16S rDNA sequence similarity with Brevipalpus mite and Ixodes tick symbionts and 88 % sequence similarity with ‘Candidatus A. asiaticus’. Electron microscopy revealed that many of the bacteria found in the ovaries of the two Encarsia species contained a regular, brush-like array of microfilament-like structures that appear to be characteristic of the symbiont. Finally, the role of this bacterium in parthenogenesis induction in E. hispida was confirmed. Based on phylogenetic analyses and electron microscopy, classification of the symbionts from Encarsia as ‘Candidatus Cardinium hertigii’ is proposed.

scholarly journals Alteromonas litorea sp. nov., a slightly halophilic bacterium isolated from an intertidal sediment of the Yellow Sea in Korea

2004 ◽  
Vol 54 (4) ◽  
pp. 1197-1201 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Soo-Hwan Yeo ◽  
Tae-Kwang Oh ◽  
Yong-Ha Park
Keyword(s):  
16S Rdna ◽  
Phylogenetic Analyses ◽  
Halophilic Bacterium ◽  
The Yellow Sea ◽  
Intertidal Sediment ◽  
Phenotypic Properties ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Slightly Halophilic Bacterium ◽  
Type Strains

A Gram-negative, motile, non-spore-forming, rod-shaped bacterium, designated strain TF-22T, was isolated from an intertidal sediment in Korea. This organism grew optimally at 30–37 °C and in the presence of 2–5 % (w/v) NaCl. It did not grow without NaCl or in the presence of more than 14 % (w/v) NaCl. Strain TF-22T was characterized chemotaxonomically as having ubiquinone-8 as the predominant respiratory lipoquinone and C16 : 0, C16 : 1 ω7c and/or iso-C15 : 0 2-OH and C18 : 1 ω7c as the major fatty acids. The DNA G+C content of strain TF-22T was 46·0 mol%. Phylogenetic analyses based on 16S rDNA sequences showed that strain TF-22T falls within the γ-subclass of the Proteobacteria and forms a coherent cluster with Alteromonas macleodii and Alteromonas marina. Levels of 16S rDNA similarity between strain TF-22T and the type strains of two Alteromonas species were in the range 98·1–98·6 %. The level of DNA–DNA relatedness between strain TF-22T and the type strains of two Alteromonas species was 15·7–18·5 %. Therefore, on the basis of phenotypic properties, phylogeny and genomic distinctiveness, strain TF-22T should be placed in the genus Alteromonas as a novel species, for which the name Alteromonas litorea sp. nov. is proposed. The type strain is TF-22T (=KCCM 41775T=JCM 12188T).

Human intestinal spirochetosis diagnosed with colonoscopy and analysis of partial 16S rDNA sequences of involved spirochetes

2001 ◽  
Vol 2 (1) ◽  
pp. 111-116 ◽  
Author(s):  
Wolfgang Kraatz ◽  
Ulf Thunberg ◽  
Bertil Pettersson ◽  
Claes Fellström
Keyword(s):  
16S Rdna ◽  
Type Strain ◽  
Sequence Similarity ◽  
Rdna Sequences ◽  
Intestinal Spirochetosis ◽  
16S Rdna Sequences ◽  
Pcr Products ◽  
Human Intestinal Spirochetosis ◽  
Type Strains ◽  
Rrna Sequences

AbstractDNA was extracted from colonic biopsies of 33 patients with and three without evidence of intestinal spirochetosis (IS) in the large bowel. The biopsies were subjected to PCR. A pair of primers, generating a 207 bp fragment, were designed to detect specifically the 16S rDNA gene ofBrachyspira. PCR products of the expected size were obtained from 33 samples with histologic evidence of IS. The PCR amplicons were used for sequencing. The sequences obtained were aligned to the corresponding 16S rRNA sequences of five type strains ofBrachyspira. The sequences of 23 PCR products were 99–100% identical with the correspond-ingB.aalborgitype strain sequence. Two cases showed 99–100% sequence similarity with the type strain ofB.pilosicoliP43/6/78. Six cases could not be referred to any of the known species ofBrachyspira. Two PCR products gave incomplete sequences.

scholarly journals Photobacterium gaetbulicola sp. nov., a lipolytic bacterium isolated from a tidal flat sediment

2010 ◽  
Vol 60 (11) ◽  
pp. 2587-2591 ◽  
Author(s):  
Young-Ok Kim ◽  
Kyung-Kil Kim ◽  
Sooyeon Park ◽  
So-Jung Kang ◽  
Jeong-Ho Lee ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Type Strains

A Gram-negative, motile, non-spore-forming and lipolytic bacterial strain, designated Gung47T, was isolated from a tidal flat on the west coast of Korea. Strain Gung47T grew optimally at 30 °C and with 2−5 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain Gung47T belonged to the genus Photobacterium. Strain Gung47T exhibited 98.1 % 16S rRNA gene sequence similarity with Photobacterium rosenbergii LMG 22223T and 94.3–96.3 % similarity with other type strains of species of the genus Photobacterium. Strain Gung47T exhibited 47 % DNA–DNA relatedness to P. rosenbergii LMG 22223T. Strain Gung47T contained Q-8 as the predominant ubiquinone and C16 : 1 ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C18 : 1 ω7c as the major fatty acids. In this study, two closely related type strains, P. rosenbergii LMG 22223T and Photobacterium halotolerans LMG 22194T, were also found to have Q-8 as the predominant ubiquinone. The DNA G+C content of strain Gung47T was 50.6 mol%. The differential phenotypic properties together with the phylogenetic and genetic distinctiveness of strain Gung47T demonstrated that this strain is distinguishable from recognized Photobacterium species. Therefore, strain Gung47T is considered to represent a novel species of the genus Photobacterium, for which the name Photobacterium gaetbulicola sp. nov. is proposed. The type strain is Gung47T (=KCTC 22804T =CCUG 58399T).

Two Intracellular Symbiotic Bacteria from the Mulberry Psyllid Anomoneura mori (Insecta, Homoptera)

1998 ◽  
Vol 64 (10) ◽  
pp. 3599-3606 ◽  
Author(s):  
Takema Fukatsu ◽  
Naruo Nikoh
Keyword(s):  
In Situ Hybridization ◽  
16S Rdna ◽  
Phylogenetic Analyses ◽  
Symbiotic Bacteria ◽  
Polymorphism Analysis ◽  
16S Rdna Sequence ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Molecular Phylogenetic

ABSTRACT We characterized the intracellular symbiotic bacteria of the mulberry psyllid Anomoneura mori by performing a molecular phylogenetic analysis combined with in situ hybridization. In its abdomen, the psyllid has a large, yellow, bilobed mycetome (or bacteriome) which consists of many round uninucleated mycetocytes (or bacteriocytes) enclosing syncytial tissue. The mycetocytes and syncytium harbor specific intracellular bacteria, the X-symbionts and Y-symbionts, respectively. Almost the entire length of the bacterial 16S ribosomal DNA (rDNA) was amplified and cloned from the whole DNA ofA. mori, and two clones, the A-type and B-type clones, were identified by restriction fragment length polymorphism analysis. In situ hybridization with specific oligonucleotide probes demonstrated that the A-type and B-type 16S rDNAs were derived from the X-symbionts and Y-symbionts, respectively. Molecular phylogenetic analyses of the 16S rDNA sequences showed that these symbionts belong to distinct lineages in the γ subdivision of the Proteobacteria. No 16S rDNA sequences in the databases were closely related to the 16S rDNA sequences of the X- and Y-symbionts. However, the sequences that were relatively closely related to them were the sequences of endosymbionts of other insects. The nucleotide compositions of the 16S rDNAs of the X- and Y-symbionts were highly AT biased, and the sequence of the X-symbiont was the most AT-rich bacterial 16S rDNA sequence reported so far.

scholarly journals Muricauda beolgyonensis sp. nov., isolated from a tidal flat

2012 ◽  
Vol 62 (Pt_5) ◽  
pp. 1134-1139 ◽  
Author(s):  
Soo-Young Lee ◽  
Sooyeon Park ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
Tidal Flat ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Type Strains

The taxonomic position of a Gram-staining-negative, non-motile, rod-shaped bacterium, strain BB-My12T, which was isolated from a sediment sample collected from a tidal flat in Korea, was investigated by using a polyphasic approach. Strain BB-My12T grew optimally at 37 °C, at pH 7.0–7.5 and in the presence of 2–3 % (w/v) NaCl. In phylogenetic analyses based on 16S rRNA gene sequences, strain BB-My12T fell within the cluster comprising species of the genus Muricauda and appeared most similar to the type strains of Muricauda aquimarina , Muricauda lutimaris and Muricauda ruestringensis (97.5–97.6 % sequence similarity). The DNA G+C content was 45.0 mol%. Strain BB-My12T contained MK-6 as the predominant menaquinone and iso-C15 : 1, iso-C17 : 0 3-OH and iso-C15 : 0 as the major cellular fatty acids. The polar lipids of strain BB-My12T were phosphatidylethanolamine and four unidentified lipids. The DNA–DNA relatedness values between strain BB-My12T and the type strains of the three species of the genus Muricauda that appeared most closely related were in the range 5–7 %. The genetic distinctiveness and some phenotypic properties indicated that strain BB-My12T did not belong to any established species of the genus Muricauda . Strain BB-My12T is therefore considered to represent a novel species of the genus Muricauda , for which the name Muricauda beolgyonensis sp. nov. is proposed. The type strain is BB-My12T ( = KCTC 23501T  = CCUG 60800T).

scholarly journals Erythrobacter luteolus sp. nov., isolated from a tidal flat of the Yellow Sea in Korea

2005 ◽  
Vol 55 (3) ◽  
pp. 1167-1170 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Kook Hee Kang ◽  
Soo-Hwan Yeo ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Yellow Sea ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Major Fatty Acid ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Phenotypic Properties

A Gram-negative, non-spore-forming, yellow-pigmented, slightly halophilic bacterial strain, SW-109T, was isolated from a tidal flat of the Yellow Sea in Korea, and subjected to a polyphasic taxonomic study. This isolate did not produce bacteriochlorophyll a and contained ubiquinone-10 as the predominant respiratory lipoquinone and C18 : 1 ω7c as the major fatty acid. The DNA G+C content was 60·3 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SW-109T is phylogenetically affiliated to the genus Erythrobacter of the family Sphingomonadaceae. Strain SW-109T exhibited levels of 16S rRNA gene sequence similarity to the type strains of Erythrobacter species of 94·0–96·3 %, making it possible to categorize strain SW-109T as a species that is separate from previously recognized Erythrobacter species. On the basis of its phenotypic properties and phylogenetic distinctiveness, SW-109T (=KCTC 12311T=JCM 12599T) was classified as the type strain of a novel Erythrobacter species, for which the name Erythrobacter luteolus sp. nov. is proposed.

scholarly journals Ruegeria faecimaris sp. nov., isolated from a tidal flat sediment

2011 ◽  
Vol 61 (5) ◽  
pp. 1182-1188 ◽  
Author(s):  
Ki-Hoon Oh ◽  
Yong-Taek Jung ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Major Fatty Acid ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Phenotypic Properties

A Gram-negative-staining, non-motile and rod-shaped bacterial strain, HD-28T, was isolated from a tidal flat of the Yellow Sea, Korea. Strain HD-28T grew optimally at pH 7.0–8.0 and 30 °C in the presence of 2–3 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain HD-28T was most closely related to species of the genus Ruegeria and exhibited 95.5–96.9 % 16S rRNA gene sequence similarity to the type strains of Ruegeria species. A neighbour-joining phylogenetic tree based on gyrB gene sequences also showed that strain HD-28T fell within the cluster comprising recognized species of the genus Ruegeria, showing 77.5–83.9 % sequence similarity. Strain HD-28T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The major polar lipids detected in strain HD-28T were phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid and two unidentified lipids. The DNA G+C content was 57.9 mol%. Differential phenotypic properties, together with phylogenetic distinctiveness, demonstrated that strain HD-28T could be distinguished from recognized species of the genus Ruegeria. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain HD-28T is considered to represent a novel species of the genus Ruegeria, for which the name Ruegeria faecimaris sp. nov. is proposed. The type strain is HD-28T ( = KCTC 23044T = CCUG 58878T).

Description of Sulfitobacter sediminilitoris sp. nov., isolated from a tidal flat

2020 ◽  
Vol 367 (9) ◽  
Author(s):  
Sooyeon Park ◽  
Siyu Chen ◽  
Jung-Sook Lee ◽  
Wonyong Kim ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Strain ◽  
Sequence Similarity ◽  
Genomic Analysis ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Type Strains

ABSTRACT A Gram-stain-negative bacterial strain, JBTF-M27T, was isolated from a tidal flat from Yellow Sea, Republic of Korea. Neighbor-joining phylogenetic tree of 16S rRNA gene sequences showed that strain JBTF-M27T fell within the clade comprising the type strains of Sulfitobacter species. Strain JBTF-M27T exhibited the highest 16S rRNA gene sequence similarity (98.8%) to the type strain of S. porphyrae. Genomic ANI and dDDH values of strain JBTF-M27T between the type strains of Sulfitobacter species were less than 76.1 and 19.2%, respectively. Mean DNA-DNA relatedness value between strain JBTF-M27T and the type strain of S. porphyrae was 21%. DNA G + C content of strain JBTF-M27T from genome sequence was 57.8% (genomic analysis). Strain JBTF-M27T contained Q-10 as the predominant ubiquinone and C18:1ω7c as the major fatty acid. The major polar lipids of strain JBTF-M27T were phosphatidylcholine, phosphatidylglycerol and one unidentified aminolipid. Distinguished phenotypic properties, along with the phylogenetic and genetic distinctiveness, revealed that strain JBTF-M27T is separated from recognized Sulfitobacter species. On the basis of the data presented, strain JBTF-M27T ( = KACC 21648T = NBRC 114356T) is considered to represent a novel species of the genus Sulfitobacter, for which the name Sulfitobacter sediminilitoris sp. nov. is proposed.

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