scholarly journals Burkholderia soli sp. nov., isolated from soil cultivated with Korean ginseng

2007 ◽  
Vol 57 (1) ◽  
pp. 122-125 ◽  
Author(s):  
Seung-Hee Yoo ◽  
Byung-Yong Kim ◽  
Hang-Yeon Weon ◽  
Soon-Wo Kwon ◽  
Seung-Joo Go ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Burkholderia Caryophylli ◽  
The 16S Rrna Gene ◽  
Sequence Similarities ◽  
Korean Ginseng

A polyphasic study was carried out to clarify the taxonomic position of a Gram-negative bacterium isolated from soil cultivated with Korean ginseng in the Eumseong region of Korea. The novel strain, GP25-8T, grew optimally at pH 6–7, 28 °C and 0–1 % NaCl (w/v). The major fatty acids were C18 : 1 ω7c, summed feature 3 (C16 : 1 ω7c/C15 : 0 iso 2-OH) and C16 : 0 (together representing 71.2 % of the total). The 16S rRNA gene sequence similarities between strain GP25-8T and members of the genus Burkholderia ranged from 94.7 to 97.4 %, indicating that this novel strain was phylogenetically related to members of that genus. The novel strain showed the highest sequence similarities to Burkholderia caryophylli ATCC 25418T (97.4 %) and Burkholderia phenazinium LMG 2247T (97.2 %); the levels of DNA–DNA hybridization with these strains were 28 and 12 %, respectively. These results support the conclusion that strain GP25-8T represents a novel species within the genus Burkholderia, for which the name Burkholderia soli sp. nov. is proposed. The type strain is GP25-8T (=KACC 11589T=DSM 18235T).

scholarly journals Bacillus endolithicus sp. nov., isolated from pebbles

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4568-4573 ◽  
Author(s):  
B. Parag ◽  
Ch. Sasikala ◽  
Ch. V. Ramana
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Gram Stain ◽  
Rrna Gene Sequence ◽  
Cellular Fatty Acids ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

Strain JC267T was isolated from pebbles collected from Pingleshwar beach, Gujarat, India. Cells are Gram-stain-positive, facultatively anaerobic, non-motile rods forming sub-terminal endospores in swollen ellipsoidal to oval sporangia. Strain JC267T contains anteiso-C15 : 0, iso-C15 : 0, iso-C14 : 0, iso-C16 : 0, C16 : 0 and anteiso-C17 : 0 as major (>5 %) cellular fatty acids. Polar lipids include phosphatidylglycerol, phospholipids (PL1–3), glycolipids (GL1–2) and an unidentified lipid. Cell-wall amino acids are composed of diagnostic meso-diaminopimelic acid, dl-alanine and a small amount of d-glutamic acid. The genomic DNA G+C content of strain JC267T is 45.5 mol%. The 16S rRNA gene sequence of strain JC267T showed highest sequence similarities of < 98.41 % with all species of the genus Bacillus when subjected to EzTaxon-e blast analysis. The reassociation values based on DNA–DNA hybridization of strain JC267T with Bacillus halosaccharovorans IBRC-M 10095T and Bacillus niabensis JCM 16399T were 26 ± 1 % and 34 ± 3 %, respectively. Based on taxonomic data obtained using a polyphasic approach, strain JC267T represents a novel species of the genus Bacillus, for which the name Bacillus endolithicus sp. nov. is proposed. The type strain is JC267T ( = IBRC-M 10914T = KCTC 33579T).

scholarly journals Kocuria koreensis sp. nov., isolated from fermented seafood

2010 ◽  
Vol 60 (1) ◽  
pp. 140-143 ◽  
Author(s):  
Eun-Jin Park ◽  
Seong Woon Roh ◽  
Min-Soo Kim ◽  
Mi-Ja Jung ◽  
Kee-Sun Shin ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Genomic Dna ◽  
Type Strain ◽  
Phylogenetic Trees ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Cellular Fatty Acids ◽  
The 16S Rrna Gene

A Gram-positive, aerobic, non-motile and coccoid actinobacterium, designated P31T, was isolated from a traditional, fermented seafood. The strain was catalase-positive and oxidase-negative. Cells grew in the presence of 0–15.0 % (w/v) NaCl, and at pH 5–10 and 15–37 °C. Major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. Strain P31T contained MK-7 as the predominant menaquinone. The DNA G+C content of the genomic DNA of strain P31T was 65.2 mol%. A phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain P31T was most closely related to Kocuria kristinae DSM 20032T, with 96.9 % similarity, and these two strains clustered together in constructed phylogenetic trees. The DNA–DNA hybridization value between strain P31T and K. kristinae DSM 20032T was 21.1 %. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, it is suggested that strain P31T represents a novel species of the genus Kocuria, for which the name Kocuria koreensis sp. nov. is proposed. The type strain is P31T (=KCTC 19595T=JCM 15915T).

scholarly journals Tetrathiobacter mimigardefordensis sp. nov., isolated from compost, a betaproteobacterium capable of utilizing the organic disulfide 3,3′-dithiodipropionic acid

2006 ◽  
Vol 56 (6) ◽  
pp. 1305-1310 ◽  
Author(s):  
Jan Hendrik Wübbeler ◽  
Tina Lütke-Eversloh ◽  
Stefanie Van Trappen ◽  
Peter Vandamme ◽  
Alexander Steinbüchel
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Alcaligenes Faecalis ◽  
Rrna Gene ◽  
Fatty Acid Profiles ◽  
Rrna Gene Sequence ◽  
Nearest Neighbours ◽  
The 16S Rrna Gene

In this study, a novel betaproteobacterium, strain DPN7T, was isolated under mesophilic conditions from compost because of its capacity to utilize the organic disulfide 3,3′-dithiodipropionic acid. Analysis of the 16S rRNA gene sequence of strain DPN7T revealed 98.5 % similarity to that of Tetrathiobacter kashmirensis LMG 22695T. Values for sequence similarity to members of the genera Alcaligenes, Castellaniella and Taylorella, the nearest neighbours of the genus Tetrathiobacter, were about 95 % or less. The DNA G+C content of strain DPN7T was 55.1 mol%. The level of DNA–DNA hybridization between strain DPN7T and T. kashmirensis LMG 22695T was 41 %, whereas it was much lower between strain DPN7T and Alcaligenes faecalis LMG 1229T (7 %) or Castellaniella defragrans LMG 18538T (5 %). This genotypic divergence was supported by differences in biochemical and chemotaxonomic characteristics. For this reason, and because of the differences in the protein and fatty acid profiles, strain DPN7T should be classified within a novel species of Tetrathiobacter, for which the name Tetrathiobacter mimigardefordensis sp. nov. is proposed. The type strain is strain DPN7T (=DSM 17166T=LMG 22922T).

scholarly journals Agromyces arachidissp. nov. Isolated from a Peanut (Arachis hypogaea) Crop Field

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Chandandeep Kaur ◽  
Anil Kumar Pinnaka ◽  
Nitin Kumar Singh ◽  
Monu Bala ◽  
Shanmugam Mayilraj
Keyword(s):  
Arachis Hypogaea ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Crop Field ◽  
Bacterium Strain ◽  
The 16S Rrna Gene

A Gram-positive, yellowish bacterium strain AK-1Twas isolated from soil sample collected from peanut (Arachis hypogaea) crop field and studied by using a polyphasic approach. The organism had morphological and chemotaxonomic properties consistent with its classification in the genusAgromyces. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain AK-1Twas closely related toAgromyces aurantiacus(98.6%) followed byAgromyces soli(98.3%),Agromyces tropicus(97.6%),Agromyces ulmi(97.3%),Agromyces flavus(97.2%), andAgromyces italicus(97.0%), whereas the sequence similarity values with respect to the otherAgromycesspecies with validly published names were between 95.3 and 96.7 %. However, the DNA-DNA hybridization values obtained between strain AK-1Tand other related strains were well below the threshold that is required for the proposal of a novel species. The DNAG+Ccontent of the strain is 71.8 mol%. The above data in combination with the phenotypic distinctiveness of AK-1Tclearly indicate that the strain represents a novel species, for which the nameAgromyces arachidissp. nov. is proposed. The type strain is AK-1T(=MTCC 10524T= JCM 19251T).

scholarly journals Halorubrum ejinorense sp. nov., isolated from Lake Ejinor, Inner Mongolia, China

2007 ◽  
Vol 57 (11) ◽  
pp. 2538-2542 ◽  
Author(s):  
A. M. Castillo ◽  
M. C. Gutiérrez ◽  
M. Kamekura ◽  
Y. Xue ◽  
Y. Ma ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Inner Mongolia ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gram Negative ◽  
Sequence Similarities

A novel halophilic archaeon, strain EJ-32T, was isolated from water from Lake Ejinor in Inner Mongolia, China. The taxonomy of strain EJ-32T was studied by using a polyphasic approach. On the basis of 16S rRNA gene sequence similarities, strain EJ-32T was shown to be phylogenetically related to Halorubrum coriense (97.9 %), Halorubrum trapanicum (97.9 %), Halorubrum sodomense (97.8 %), Halorubrum tebenquichense (97.8 %), Halorubrum xinjiangense (97.6 %), Halorubrum terrestre (97.4 %), Halorubrum distributum (97.1 %) and Halorubrum saccharovorum (96.4 %). Strain EJ-32T was found to be neutrophilic, non-motile and Gram-negative. It grew in medium containing saturation concentrations of NaCl and did not require magnesium for optimal growth. The G+C content of the DNA is 64.0 mol%. Values for DNA–DNA hybridization with respect to phylogenetically related Halorubrum species were ≤49 %, indicating that EJ-32T constitutes a different genospecies. The data show that strain EJ-32T represents a novel species of the genus Halorubrum, for which the name Halorubrum ejinorense sp. nov. is proposed. The type strain is EJ-32T (=CECT 7194T=CGMCC 1.6782T=JCM 14265T).

scholarly journals Mucilaginibacter polysacchareus sp. nov., an exopolysaccharide-producing bacterial species isolated from the rhizoplane of the herb Angelica sinensis

2012 ◽  
Vol 62 (Pt_3) ◽  
pp. 632-637 ◽  
Author(s):  
Song-Ih Han ◽  
Hyo-Jin Lee ◽  
Hae-Ran Lee ◽  
Ki-Kwang Kim ◽  
Kyung-Sook Whang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Bacterial Species ◽  
Angelica Sinensis ◽  
Rrna Gene ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

Three exopolysaccharide-producing bacteria, designated strains DRP28T, DRP29 and DRP31, were isolated from the rhizoplane of Angelica sinensis from the Geumsan, Republic of Korea. Cells were straight rods, Gram reaction-negative, aerobic, non-motile, and catalase- and oxidase- positive. Flexirubin-type pigments were absent. Phylogenetic analysis of the 16S rRNA gene indicated that these bacteria belong to the genus Mucilaginibacter in the phylum Bacteroidetes. 16S rRNA gene sequence similarities to strains of recognized species of the genus Mucilaginibacter were 93.8–97.4 %. The major fatty acids were iso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The strains contained MK-7 as the major isoprenoid quinone. Strains DRP28T, DRP29 and DRP31 formed a single, distinct genomospecies with DNA G+C contents of 41.9–42.7 mol% and DNA hybridization values of 82.6–86.8 %; the strains exhibited DNA–DNA hybridization values of only 20.4–41.3 % with related species of the genus Mucilaginibacter. On the basis of evidence presented in this study, strains DRP28T, DRP29 and DRP31 were considered to represent a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter polysacchareus sp. nov. is proposed. The type strain is DRP28T ( = KACC 15075T  = NBRC 107757T).

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 Microbacterium rhizomatis sp. nov., a β-glucosidase-producing bacterium isolated from rhizome of Korean mountain ginseng

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3196-3202 ◽  
Author(s):  
Van-An Hoang ◽  
Yeon-Ju Kim ◽  
Ngoc Lan Nguyen ◽  
Chang Ho Kang ◽  
Jong-Pyo Kang ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Ginseng Root ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gram Staining ◽  
Gene Sequence Analysis ◽  
The 16S Rrna Gene

A novel Gram-staining-positive, rod-shaped bacterium, designated DCY100T, was isolated from rhizome of mountain ginseng root in Hwacheon mountain, Gangwon province, Republic of Korea. The 16S rRNA gene sequence analysis showed that strain DCY100T belonged to the genus Microbacterium and was most closely related to Microbacterium ginsengisoli KCTC 19189T (97.9 %), Microbacterium lacus JCM 15575T (97.2 %) and Microbacterium invictum DSM 19600T (97.1 %). The major menaquinones were MK-11 and MK-12. The major polar lipids were found to be diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid. The major fatty acids (>10.0 %) were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The cell-wall peptidoglycan contained the amino acids ornithine, alanine, glutamic acid and glycine; whole-cell sugars consisted of glucose, galactose, rhamnose and ribose. The DNA G+C content was 63.6 ± 0.7 mol%. The DNA–DNA hybridization relatedness values between strain DCY100T and Microbacterium ginsengisoli KCTC 19189T, Microbacterium lacus JCM 15575T and Microbacterium invictum DSM 19600T were 36.2 ± 0.4, 22.0 ± 3.0 and 15.3 ± 1.8 %, respectively. On the basis of phenotypic, chemotaxonomic and genotypic analyses, the isolate is classified as a representative of a novel species in the genus Microbacterium, for which the name Microbacterium rhizomatis DCY100T is proposed. The type strain is DCY100T ( = KCTC 39529T = JCM 30598T).

scholarly journals Microbispora bryophytorum sp. nov., an actinomycete isolated from moss (Bryophyta)

2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1274-1279 ◽  
Author(s):  
Chuang Li ◽  
Yuejing Zhang ◽  
Chongxi Liu ◽  
Haiyan Wang ◽  
Junwei Zhao ◽  
...  
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Morphological Characteristics ◽  
Rrna Gene ◽  
The Novel ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

A novel endophytic actinomycete, designated strain NEAU-TX2-2T, was isolated from moss and characterized using a polyphasic approach. The isolate was found to have morphological characteristics typical of the genus Microbispora . The isolate formed longitudinally paired spores on the tips of short sporophores that branched from aerial hyphae. Analysis of the 16S rRNA gene sequence supported the assignment of the novel strain to the genus Microbispora , and strain NEAU-TX2-2T exhibited 99.08 and 98.62 % gene sequence similarities to Microbispora amethystogenes JCM 3021T and Microbispora rosea subsp. rosea JCM 3006T, respectively. However two tree-making algorithms supported the position that strain NEAU-TX2-2T formed a distinct clade with M. rosea subsp. rosea JCM 3006T. A low level of DNA–DNA relatedness allowed the isolate to be differentiated from M. amethystogenes JCM 3021T and M. rosea subsp. rosea JCM 3006T. Moreover, strain NEAU-TX2-2T could also be distinguished from its closest phylogenetic relatives by morphological and physiological characteristics. Therefore, it is proposed that strain NEAU-TX2-2T represents a novel species of the genus Microbispora for which the name Microbispora bryophytorum sp. nov. is proposed. The type strain is NEAU-TX2-2T ( = CGMCC 4.7138T = DSM 46710T).

Lactobacillus gigeriorum sp. nov., isolated from chicken crop

2012 ◽  
Vol 62 (2) ◽  
pp. 330-334 ◽  
Author(s):  
Sylvie Cousin ◽  
Marie-Laure Gulat-Okalla ◽  
Laurence Motreff ◽  
Catherine Gouyette ◽  
Christiane Bouchier ◽  
...  
Keyword(s):  
Lactobacillus Acidophilus ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Metabolic Properties ◽  
Type Strains ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

In the early 1980s, a facultatively anaerobic, non-motile, short rod, designated 202T, was isolated from a chicken crop and identified as a homofermentative lactic acid bacterium. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the strain was affiliated with the genus Lactobacillus, clustering within the Lactobacillus acidophilus–delbrueckii group. In this analysis, strain 202T appeared to be most closely related to the type strains of Lactobacillus intestinalis and Lactobacillus amylolyticus, with gene sequence similarities of 96.1 and 96.2 %, respectively. Strain 202T was found to differ from these two species, however, when investigated by multilocus sequence analysis, and it also differed in terms of some of its metabolic properties. On the basis of these observations, strain 202T is considered to represent a novel species in the genus Lactobacillus, for which the name Lactobacillus gigeriorum sp. nov. is proposed; the type strain is 202T ( = CRBIP 24.85T = DSM 23908T).

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