scholarly journals Nocardioides aquiterrae sp. nov., isolated from groundwater in Korea

2004 ◽  
Vol 54 (1) ◽  
pp. 71-75 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
In-Gi Kim ◽  
Kook Hee Kang ◽  
Tae-Kwang Oh ◽  
Yong-Ha Park
Keyword(s):  
Fatty Acid ◽  
16S Rdna ◽  
Type Strain ◽  
Cellular Fatty Acid ◽  
Major Fatty Acid ◽  
Diaminopimelic Acid ◽  
Phenotypic Characterization ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Diamino Acid

A bacterial strain, GW-9T, which was isolated from groundwater in Korea, was subjected to a polyphasic taxonomic study using phenotypic characterization and phylogenetic and genetic methods. Phylogenetic analysis based on 16S rDNA sequences showed that strain GW-9T forms an evolutionary lineage within the radiation enclosing Nocardioides species and, in particular, a coherent cluster with Nocardioides pyridinolyticus. The cell-wall peptidoglycan type of strain GW-9T was based on ll-diaminopimelic acid as the diamino acid, indicating wall chemotype I. The predominant menaquinone was MK-8(H4). Strain GW-9T had a cellular fatty acid profile containing straight-chain, branched, unsaturated and 10-methyl fatty acids. The major fatty acid was iso-C16 : 0. The DNA G+C content of strain GW-9T was 73 mol%. The 16S rDNA of strain GW-9T was 99·2 % similar to that of the type strain of Nocardioides pyridinolyticus and 94·9–96·0 % similar to sequences of the type strains of other Nocardioides species. Differences in phenotypic characteristics and genetic distinctiveness indicate that strain GW-9T is separate from previously described Nocardioides species. Therefore, on the basis of the data presented, a novel species of the genus Nocardioides, Nocardioides aquiterrae sp. nov., is proposed. The type strain is strain GW-9T (=KCCM 41647T=JCM 11813T).

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 Phenotypic characterization of Astragalus glycyphyllos symbionts and their phylogeny based on the 16S rDNA sequences and RFLP of 16S rRNA gene

2014 ◽  
Vol 105 (6) ◽  
pp. 1033-1048 ◽  
Author(s):  
Sebastian Gnat ◽  
Magdalena Wójcik ◽  
Sylwia Wdowiak-Wróbel ◽  
Michał Kalita ◽  
Aneta Ptaszyńska ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rdna ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Astragalus Glycyphyllos Symbionts

Bacillus hwajinpoensis sp. nov. and an unnamed Bacillus genomospecies, novel members of Bacillus rRNA group 6 isolated from sea water of the East Sea and the Yellow Sea in Korea

2004 ◽  
Vol 54 (3) ◽  
pp. 803-808 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
In-Gi Kim ◽  
Kook Hee Kang ◽  
Tae-Kwang Oh ◽  
Yong-Ha Park
Keyword(s):  
16S Rdna ◽  
Yellow Sea ◽  
Sea Water ◽  
Diaminopimelic Acid ◽  
East Sea ◽  
The Yellow Sea ◽  
Phenotypic Properties ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Group 6

Two Gram-positive or -variable, endospore-forming, slightly halophilic strains (SW-72T and SW-93) were isolated from sea water of the East Sea and the Yellow Sea in Korea, respectively, and subjected to polyphasic taxonomic study. Both strains had cell-wall peptidoglycan that was based on meso-diaminopimelic acid and MK-7 as the predominant menaquinone. The two strains contained large amounts of saturated and branched fatty acids, with anteiso-C15 : 0 as the major fatty acid. The DNA G+C contents of strains SW-72T and SW-93 were 40·9 and 41·0 mol%, respectively. Phylogenetic analysis based on 16S rDNA sequences showed that strains SW-72T and SW-93 fall within the radiation of the cluster that comprises members of the genus Bacillus, particularly Bacillus rRNA group 6. There were five nucleotide differences between the 16S rDNA sequences of strains SW-72T and SW-93. The mean level of DNA–DNA relatedness between strains SW-72T and SW-93 was 21·5 %. Strains SW-72T and SW-93 showed 93·1–95·2 % 16S rDNA sequence similarity to the type strains of Bacillus species that are assigned to rRNA group 6. Strains SW-72T and SW-93 could not be differentiated clearly by using their phenotypic properties. On the basis of phenotypic properties, phylogeny and genomic data, it is proposed that strain SW-72T (=KCCM 41641T=JCM 11807T) should be placed in the genus Bacillus as the type strain of a novel species, Bacillus hwajinpoensis sp. nov., and that strain SW-93 (=KCCM 41640=JCM 11806) should be placed in the genus Bacillus as an unnamed Bacillus genomospecies.

scholarly journals Assessment of Molecular Diversity in Chickpea (Cicer arietinum L.) Rhizobia and Structural Analysis of 16S rDNA Sequences from Mesorhizobium ciceri

2013 ◽  
Vol 62 (3) ◽  
pp. 253-262 ◽  
Author(s):  
AKHILESH YADAV ◽  
ASHA LATA SINGH ◽  
GOVIND KUMAR RAI ◽  
MAJOR SINGH
Keyword(s):  
16S Rdna ◽  
Molecular Diversity ◽  
Variable Region ◽  
Phenotypic Characterization ◽  
Rflp Markers ◽  
Evolutionary Mechanisms ◽  
Minimal Free Energy ◽  
Mesorhizobium Ciceri ◽  
Rdna Sequences ◽  
16S Rdna Sequences

Molecular diversity studies of 19 rhizobia isolates from chickpea were conducted using simple sequence repeats (SSR) and 16S rDNA-RFLP markers. Phenotypic characterization with special reference to salinity and pH tolerance was performed. These isolates were identified as different strains of Mesorhizobium, Rhizobium, Bradyrhizobium, and Agrobacterium. Twenty SSR loci of Mesorhizobium ciceri, distributed across the other rhizobial genome, clearly differentiated 19 rhizobial isolates. Analogous clustering supported the results of 16S rDNA sequence-based phylogeny. Analysis of the 16S rDNA sequences from M. ciceri strains revealed that nucleotide variables (signature sites) were located at 20 different positions; most of them were present in the first 820 bp region from 5' terminal. Interestingly, 14 signature sites were located in two main regions, the variable region V1 (nt 527-584), and variable region V2 (nt 754-813). The secondary structure and minimal free energy were determined in these two regions. These results will be useful in characterizing the micro-evolutionary mechanisms of species formation and increase understanding of the symbiotic relationship.

scholarly journals Nocardioides mesophilus sp. nov., isolated from soil

2010 ◽  
Vol 60 (10) ◽  
pp. 2288-2292 ◽  
Author(s):  
Syed G. Dastager ◽  
Jae-Chan Lee ◽  
Ashok Pandey ◽  
Chang-Jin Kim
Keyword(s):  
Fatty Acid ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
Major Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Straight Chain ◽  
Monophyletic Lineage ◽  
Cellular Fatty Acid Profile

A short coccoid- to rod-shaped, motile, mesophilic actinobacterium, strain MSL-22T, was isolated from soil on Bigeum Island, Korea. A polyphasic study was undertaken to establish the taxonomic position of this strain. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain MSL-22T formed an evolutionary lineage within the radiation of the genus Nocardioides. In particular, it formed a monophyletic lineage with Nocardioides jensenii KCTC 9134T with which it shared the highest sequence similarity of about 97.3%. However, DNA–DNA relatedness demonstrated that strain MSL-22T was distinct from its closest phylogenetic neighbours. The cell-wall peptidoglycan of strain MSL-22T contained ll-diaminopimelic acid. The predominant menaquinone was MK-8(H4). Strain MSL-22T had a cellular fatty acid profile containing straight-chain, branched, unsaturated and 10-methyl fatty acids, with iso-C16 : 0 as the major fatty acid. The DNA G+C content of the strain was 68.7 mol%. On the basis of phenotypic and phylogenetic evidence, the strain is separate from previously described members of the genus Nocardioides and represents a novel species in this genus, for which the name Nocardioides mesophilus sp. nov. is proposed. The type strain is MSL-22T (=DSM 19432T=KCTC 19310T).

scholarly journals Tumebacillus algifaecis sp. nov., isolated from decomposing algal scum

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2194-2198 ◽  
Author(s):  
Yu-Fan Wu ◽  
Bo Zhang ◽  
Peng Xing ◽  
Qing-Long Wu ◽  
Shuang-Jiang Liu
Keyword(s):  
Taihu Lake ◽  
Cellular Fatty Acid ◽  
Diaminopimelic Acid ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Polar Lipid Profile ◽  
Gram Staining ◽  
Optimum Ph ◽  
Diamino Acid

Bacterial strain THMBR28T was isolated from decomposing algal scum that was collected during an algal bloom in Taihu lake, China. Cells of strain THMBR28T were Gram-staining-positive, facultatively anaerobic and rod-shaped. Growth was observed at 20–45 °C (optimum, 30 °C), at pH 5.0–9.5 (optimum, pH 6.5–7.5), and in the presence of 0–1.0  % (w/v) NaCl (optimum, 0.5  %). Strain THMBR28T contained MK-7 as the major menaquinone and iso-C15 : 0 as the major cellular fatty acid. The polar lipid profile contained phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine and six unidentified polar lipids. The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. The DNA G+C content was 57.6 mol% (T m ). Phylogenetic analysis of 16S rRNA gene sequences showed that strain THMBR28T belonged to the genus Tumebacillus, most closely related to Tumebacillus ginsengisoli DSM 18389T (95.0  %) and Tumebacillus permanentifrigoris Eur1 9.5T (93.4  %). Based on phylogenetic and phenotypic characterization, it is concluded that strain THMBR28T represents a novel species of the genus Tumebacillus, for which the name Tumebacillus algifaecis sp. nov. is proposed, with THMBR28T ( = CGMCC 1.10949T = NBRC 108765T) as the type strain.

scholarly journals Saccharothrix algeriensis sp. nov., isolated from Saharan soil

2004 ◽  
Vol 54 (4) ◽  
pp. 1377-1381 ◽  
Author(s):  
A. Zitouni ◽  
L. Lamari ◽  
H. Boudjella ◽  
B. Badji ◽  
N. Sabaou ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Detailed Analysis ◽  
16S Rdna ◽  
Type Strain ◽  
Novel Species ◽  
Morphological Characteristics ◽  
Saharan Soil ◽  
Rdna Sequences ◽  
Soil Isolate ◽  
16S Rdna Sequences

The taxonomic position of a soil isolate, strain SA 233T, recovered from Saharan soil from Algeria was established using a polyphasic approach. This isolate has been previously reported to produce three novel dithiolopyrrolone antibiotics, and preliminary chemotaxonomic and morphological characteristics suggested that it was representative of a member of the genus Saccharothrix. Phylogenetic analysis of the strain from 16S rDNA sequences, along with a detailed analysis of morphological, chemotaxonomic and physiological characteristics, indicates that it belongs to the genus Saccharothrix and represents a novel species that is readily distinguished from all recognized Saccharothrix species. The name Saccharothrix algeriensis sp. nov. is proposed for the isolate, with type strain SA 233T (=NRRL B-24137T=DSM 44581T).

Intraspecific Variation of Unusual Phospholipids from Corynebacterium spp. Containing a Novel Fatty Acid

1998 ◽  
Vol 180 (17) ◽  
pp. 4650-4657 ◽  
Author(s):  
Tanja Niepel ◽  
Holger Meyer ◽  
Victor Wray ◽  
Wolf-Rainer Abraham
Keyword(s):  
Fatty Acid ◽  
16S Rdna ◽  
Intraspecific Variation ◽  
Fatty Acid Pattern ◽  
Octadecenoic Acid ◽  
The Novel ◽  
Rdna Sequences ◽  
Potential Biomarker ◽  
16S Rdna Sequences ◽  
First Time

ABSTRACT The novel fatty acid trans-9-methyl-10-octadecenoic acid was isolated from the coryneform bacterial strain LMG 3820 (previously misidentified as Arthrobacter globiformis) and identified by spectroscopic methods and chemical derivatization. This fatty acid is attached to the unusual lipid acyl phosphatidylglycerol. Five different species of this lipid type were identified; their structures were elucidated by tandem mass spectrometry and are reported here for the first time. Additionally, we identified three different cardiolipins, two bearing the novel fatty acid. The characteristic 10-methyl-octadecanoic acid was present only in phosphatidylinositol. Because of the unusual fatty acid pattern of strain LMG 3820, the 16S rDNA sequence was determined and showed regions of identity to sequences of Corynebacterium variabilis DSM 20132T and DSM 20536. All three strains possessed the novel fatty acid, identifying trans-9-methyl-10-octadecenoic acid as a potential biomarker characteristic for this taxon. Surprisingly, the fatty acid and relative abundances of phospholipids ofCorynebacterium sp. strain LMG 3820 were similar to those of the type strain but different from those of Corynebacterium variabilis DSM 20536, although all three strains possessed identical 16S rDNA sequences and strains DSM 20132T and DSM 20536 have 90.5% DNA-DNA homology. This is one of the rare cases wherein different organisms with identical 16S rDNA sequences have been observed to present recognizably different fatty acid and lipid compositions. Since methylation of a fatty acid considerably lowers the transition temperature of the corresponding lipid resulting in a more flexible cell membrane, the intraspecific variation in the lipid composition, coinciding with the morphological and Gram stain reaction variability of this species, probably offers an advantage for this species to inhabit different environmental niches.

scholarly journals The phylogeny of the genusYersiniabased on 16S rDNA sequences

1993 ◽  
Vol 114 (2) ◽  
pp. 173-177 ◽  
Author(s):  
A. Ibrahim ◽  
B.M. Goebel ◽  
W. Liesack ◽  
M. Griffiths ◽  
E. Stackebrandt
Keyword(s):  
16S Rdna ◽  
Rdna Sequences ◽  
16S Rdna Sequences

scholarly journals Mesonia hippocampi sp. nov., isolated from the brood pouch of a diseased Barbour's Seahorse (Hippocampus barbouri)

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2241-2247 ◽  
Author(s):  
Judy Kolberg ◽  
Hans-Jürgen Busse ◽  
Thomas Wilke ◽  
Patrick Schubert ◽  
Peter Kämpfer ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Type Strain ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Brood Pouch ◽  
Diaminopimelic Acid ◽  
Sugar Residue ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Monophyletic Cluster

An orange-pigmented, Gram-staining-negative, rod-shaped bacterium, designated 96_Hippo_TS_3/13T was isolated from the brood pouch of a diseased seahorse male of the species Hippocampus barbouri from the animal facility of the University of Giessen, Germany. Phylogenetic analyses based on the nearly full-length 16S rRNA gene sequence placed strain 96_Hippo_TS_3/13T into the monophyletic cluster of the genus Mesonia within the family Flavobacteriaceae. However, the strain shared only 92.2–93.8 % sequence similarity to type strains of species of the genus Mesonia, with highest sequence similarity to the type strain of Mesonia aquimarina. Cellular fatty acid analysis showed a Mesonia-typical fatty acid profile including several branched and hydroxyl fatty acids with highest amounts of iso-C15 : 0 (40.9 %) followed by iso-C17 : 0 3-OH (14.8 %). In the polyamine pattern, sym-homospermidine was predominant. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. The quinone system contained exclusively menaquinone MK-6. The only identified compound in the polar lipid profile was phosphatidylethanolamine present in major amounts. Additionally, major amounts of an unidentified aminolipid and two unidentified lipids not containing a phosphate group, an amino group or a sugar residue were detected. The genomic G+C content of strain 96_Hippo_TS_3/13T was 30 mol%. Based on genotypic, chemotaxonomic and physiological characterizations we propose a novel species of the genus Mesonia, Mesonia hippocampi sp. nov., with strain 96_Hippo_TS_3/13T ( = CIP 110839T =  LMG 28572T = CCM 8557T) as the type strain. An emended description of the genus Mesonia is also provided.

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