scholarly journals Leucobacter chromiiresistens sp. nov., a chromate-resistant strain

2011 ◽  
Vol 61 (4) ◽  
pp. 956-960 ◽  
Author(s):  
Gunnar Sturm ◽  
Johanna Jacobs ◽  
Cathrin Spröer ◽  
Peter Schumann ◽  
Johannes Gescher
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Alignments ◽  
Flight Mass Spectrometry ◽  
Type Strains

A Gram-positive, irregular rod-shaped, non-motile, yellow-pigmented bacterium, strain JG 31T, was isolated in the course of identifying chromium-resistant soil bacteria. 16S rRNA gene sequence analysis of the isolated bacterium indicated its phylogenetic position within the genus Leucobacter. Binary 16S rRNA gene sequence alignments of the isolated bacterium with the 11 species of the genus recognized at the time of writing revealed sequence similarities of more than 97 % with Leucobacter alluvii (GenBank accession no: AM072820; 99.4 %), Leucobacter iarius (AM040493; 98.2 %), Leucobacter aridicollis (AJ781047; 97.8 %), Leucobacter komagatae (AB007419; 97.4 %), Leucobacter chironomi (EU346911; 97.1 %) and Leucobacter luti (AM072819; 97.1 %). In contrast, DNA–DNA hybridization experiments showed similarity values below 28 % for DNA samples from the most closely related type strains of L. alluvii, L. aridicollis and L. iarius. Protein analysis by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and automated RiboPrinting using the restriction enzyme PvuII differentiated strain JG 31T from all type strains of the genus Leucobacter. The dominant fatty acids of the novel isolate were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0, while the quinone system consisted of menaquinones MK-11, MK-10, MK-9 and MK-8. In a B-type cross-linked peptidoglycan, the cell-wall amino acids were alanine, glycine, threonine, glutamic acid and 2,4-diaminobutyric acid. Strain JG 31T was able to grow in a medium containing up to 300 mM K2CrO4 and showed cellular aggregation in response to chromate stress. From biochemical and genomic analyses, the new strain is considered to represent a novel species of the genus Leucobacter, for which the name Leucobacter chromiiresistens sp. nov. is proposed. The type strain is strain JG 31T ( = DSM 22788T  = CCOS 200T).

scholarly journals Parabacteroides johnsonii sp. nov., isolated from human faeces

2007 ◽  
Vol 57 (2) ◽  
pp. 293-296 ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Maki Kitahara ◽  
Yoshimi Benno
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Human Faeces ◽  
Gene Sequence Analysis

A bacterial strain isolated from human faeces, M-165T, was characterized in terms of its phenotypic and biochemical features, cellular fatty acid profile, menaquinone profile and phylogenetic position (based on 16S rRNA gene sequence analysis). A 16S rRNA gene sequence analysis showed that the isolate was a member of the genus Parabacteroides. Strain M-165T was closely related to Parabacteroides merdae strains, showing 98 % sequence similarity. The strain was obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-negative, rod-shaped and was able to grow on media containing 20 % bile. Although the phenotypic characteristics of the strain M-165T were similar to those of P. merdae, the isolate could be differentiated from P. merdae by means of API 20A tests for l-arabinose and l-rhamnose fermentation. DNA–DNA hybridization experiments revealed the genomic distinctiveness of the novel strain with respect to P. merdae JCM 9497T (⩽60 % DNA–DNA relatedness). The DNA G+C content of the strain is 47.6 mol%. On the basis of these data, strain M-165T represents a novel species of the genus Parabacteroides, for which the name Parabacteroides johnsonii sp. nov. is proposed. The type strain is M-165T (=JCM 13406T=DSM 18315T).

scholarly journals Planococcus salinarum sp. nov., isolated from a marine solar saltern, and emended description of the genus Planococcus

2010 ◽  
Vol 60 (4) ◽  
pp. 754-758 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Soo-Young Lee ◽  
Ki-Hoon Oh ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Solar Saltern ◽  
Rrna Gene Sequence ◽  
Marine Solar Saltern ◽  
Emended Description ◽  
Type Strains

A Gram-positive, non-motile and coccoid-, short rod- or rod-shaped bacterial strain, ISL-16T, was isolated from a marine solar saltern in Korea and its taxonomic position was investigated using a polyphasic taxonomic approach. Strain ISL-16T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ISL-16T joined the cluster comprising species of the genus Planococcus. Its 16S rRNA gene sequence contained the same signature nucleotides as those defined for the genus Planococcus. Strain ISL-16T exhibited 16S rRNA gene sequence similarity values of 96.9–98.2 % to the type strains of species of the genus Planococcus. Strain ISL-16T contained MK-8 and MK-7 as the predominant menaquinones and anteiso-C15 : 0, C16 : 1 ω7c alcohol and anteiso-C17 : 0 as the major fatty acids. The DNA G+C content was 48.3 mol%. DNA–DNA relatedness values between strain ISL-16T and the type strains of species of the genus Planococcus were 15–28 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, enabled strain ISL-16T to be differentiated from recognized species of the genus Planococcus. On the basis of the data presented, strain ISL-16T is considered to represent a novel species of the genus Planococcus, for which the name Planococcus salinarum sp. nov. is proposed. The type strain is ISL-16T (=KCTC 13584T=CCUG 57753T). An emended description of the genus Planococcus is also given.

scholarly journals Nocardia jejuensis sp. nov., a novel actinomycete isolated from a natural cave on Jeju Island, Republic of Korea

2006 ◽  
Vol 56 (3) ◽  
pp. 559-562 ◽  
Author(s):  
Soon Dong Lee
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Jeju Island ◽  
Republic Of Korea ◽  
16S Rrna Gene Sequence ◽  
Phylogenetic Position ◽  
Dilution Method ◽  
Rrna Gene ◽  
Rrna Gene Sequence

A novel actinomycete, strain N3-2T, was isolated from a natural cave on Jeju Island, Republic of Korea, using a dilution method and was subjected to polyphasic taxonomy. The almost complete 16S rRNA gene sequence was determined by direct sequencing of the purified PCR product and was compared with those of representatives of the genus Nocardia. It was revealed from the phylogenetic analysis that the organism forms a distinct clade between the Nocardia salmonicida cluster and the Nocardia alba branch within the evolutionary radius occupied by the genus Nocardia of the family Nocardiaceae. The organism showed 16S rRNA gene sequence similarity of 97·4 % with its nearest phylogenetic neighbours, namely N. salmonicida and N. alba. The chemotaxonomic properties, such as the principal amino acid of peptidoglycan, predominant menaquinone and polar lipids, supported the classification in the genus Nocardia. The organism was readily differentiated from Nocardia species with validly published names by a broad set of phenotypic properties and its unique phylogenetic position; the name Nocardia jejuensis sp. nov. is proposed, with N3-2T (=JCM 13281T=NRRL B-24430T) as the type strain.

scholarly journals Loktanella atrilutea sp. nov., isolated from seawater in Japan

2007 ◽  
Vol 57 (9) ◽  
pp. 1966-1969 ◽  
Author(s):  
Shoichi Hosoya ◽  
Akira Yokota
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sanriku Coast ◽  
Type Strains

A Gram-negative, rod-shaped bacterium, IG8T, was isolated from seawater off the Sanriku coast, Japan. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IG8T represented a separate lineage within the genus Loktanella; the highest 16S rRNA gene sequence similarity values were found with the type strains of Loktanella salsilacus (98.6 %) and Loktanella fryxellensis (98.4 %). DNA–DNA hybridization values between strain IG8T and the type strains of L. salsilacus (27.9–36.1 %) and L. fryxellensis (11.3–31.0 %) were clearly below 70 %, the generally accepted limit for species delineation. The DNA G+C content of strain IG8T was 66.3 mol%. On the basis of DNA–DNA hybridization, some biochemical characteristics and 16S rRNA gene sequence comparison, it is proposed that the isolate represents a novel species, Loktanella atrilutea sp. nov. The type strain is IG8T (=IAM 15450T=NCIMB 14280T).

scholarly journals Marinobacterium halophilum sp. nov., a marine bacterium isolated from the Yellow Sea

2007 ◽  
Vol 57 (1) ◽  
pp. 77-80 ◽  
Author(s):  
Ho-Won Chang ◽  
Young-Do Nam ◽  
Hyuk-Yong Kwon ◽  
Ja Ryeong Park ◽  
Jung-Sook Lee ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
The Yellow Sea ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Type Strains

A moderately halophilic, aerobic, Gram-negative bacterium was isolated from a tidal flat area of Dae-Chun, Chung-Nam, Korea. The strain, designated mano11T, comprised rod-shaped cells that were motile by means of polar flagella. It grew with 3–12 % NaCl and at 4–37 °C and pH 5.3–9.3. The predominant menaquinone present in this strain was MK-7 and diaminopimelic acid was not found in the cell-wall peptidoglycan. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain mano11T belongs to the genus Marinobacterium. Strain mano11T exhibited 92.8–98.3 % 16S rRNA gene sequence similarity when compared with the type strains of three other species of the genus Marinobacterium. DNA–DNA hybridization between strain mano11T and Marinobacterium georgiense DSM 11526T, its closest relative in terms of 16S rRNA gene sequence similarity, was 13 %. On the basis of the phenotypic, genetic and phylogenetic data, strain mano11T represents a novel species of the genus Marinobacterium, for which the name Marinobacterium halophilum sp. nov. is proposed. The type strain is mano11T (=KCTC 12240T=DSM 17586T).

scholarly journals Paracoccus fistulariae sp. nov., a lipolytic bacterium isolated from bluespotted cornetfish, Fistularia commersonii

2010 ◽  
Vol 60 (12) ◽  
pp. 2908-2912 ◽  
Author(s):  
Young-Ok Kim ◽  
Hee Jeong Kong ◽  
Sooyeon Park ◽  
So-Jung Kang ◽  
Kyung-Kil Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
16S Rrna Gene Sequences ◽  
Type Strains

A Gram-stain-negative, non-motile, non-spore-forming and short rod- or rod-shaped bacterial strain, designated 22-5T, was isolated from a bluespotted cornetfish, Fistularia commersonii, and subjected to taxonomic study. Strain 22-5T grew optimally at 30 °C and in the presence of 2–5 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain 22-5T belonged to the genus Paracoccus and joined the cluster comprising Paracoccus homiensis DD-R11T and Paracoccus zeaxanthinifaciens ATCC 21588T, with which strain 22-5T exhibited 97.4 and 96.9 % 16S rRNA gene sequence similarity, respectively. Strain 22-5T exhibited 94.0–96.6 % 16S rRNA gene sequence similarity with the other type strains of species of the genus Paracoccus. Strain 22-5T contained Q-10 as the predominant menaquinone and C18 : 1 ω7c as the predominant fatty acid. In this study, P. zeaxanthinifaciens KCTC 22688T also contained Q-10 as the predominant isoprenoid quinone. The DNA G+C content of strain 22-5T was 63.6 mol%. Strain 22-5T exhibited 44 and 32 % DNA–DNA relatedness to P. homiensis KACC 11518T and P. zeaxanthinifaciens KCTC 22688T, respectively. On the basis of phenotypic, phylogenetic and genetic data, strain 22-5T is considered to represent a novel species of the genus Paracoccus, for which the name Paracoccus fistulariae sp. nov. is proposed. The type strain is 22-5T (=KCTC 22803T =CCUG 58401T).

scholarly journals Psychrobacter piscatorii sp. nov., a psychrotolerant bacterium exhibiting high catalase activity isolated from an oxidative environment

2010 ◽  
Vol 60 (1) ◽  
pp. 205-208 ◽  
Author(s):  
Isao Yumoto ◽  
Kikue Hirota ◽  
Hideyuki Kimoto ◽  
Yoshinobu Nodasaka ◽  
Hidetoshi Matsuyama ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Catalase Activity ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Processing Plant ◽  
Rrna Gene Sequence ◽  
Psychrotolerant Bacterium ◽  
Type Strains

A Gram-negative, non-motile, psychrotolerant bacterium exhibiting high catalase activity, designated strain T-3-2T, was isolated from a drain of a fish-processing plant. Its catalase activity was 12 000 U (mg protein)−1, much higher than the activity of the other Psychrobacter strains tested. The strain grew at 0–30 °C and in the presence of 0–12 % NaCl. The predominant isoprenoid quinone was ubiquinone-8 (Q-8), and C16 : 1 ω9c and C18 : 1 ω9c were the predominant cellular fatty acids. The DNA G+C content of strain T-3-2T was 43.9 mol%. 16S rRNA gene sequence phylogeny suggested that strain T-3-2T is a member of the genus Psychrobacter, with the closest relatives being the type strains of Psychrobacter nivimaris (99.2 % similarity), P. aquimaris (98.7 %) and P. proteolyticus (98.5 %). DNA–DNA hybridization showed less than 65 % relatedness with these strains. A phylogenetic tree based on gyrB gene sequences was more reliable, with higher bootstrap values than the 16S rRNA gene sequence-based tree. The result also differentiated the isolate from previously reported Psychrobacter species. Owing to the significant differences in phenotypic and chemotaxonomic characteristics and the phylogenetic and DNA–DNA relatedness data, the isolate merits classification within a novel species, for which the name Psychrobacter piscatorii sp. nov. is proposed. The type strain is T-3-2T (=JCM 15603T =NCIMB 14510T).

Paracoccus caeni sp. nov., isolated from sludge

2011 ◽  
Vol 61 (8) ◽  
pp. 1968-1972 ◽  
Author(s):  
Myungjin Lee ◽  
Song-Geun Woo ◽  
Giho Park ◽  
Myung Kyum Kim
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Type Strains ◽  
Sequence Similarities

A Gram-negative, non-motile bacterium, designated MJ17T, was isolated from sludge at the Daejeon sewage disposal plant in South Korea. Comparative 16S rRNA gene sequence analysis showed that strain MJ17T belonged to the genus Paracoccus in the family Rhodobacteraceae of the class Alphaproteobacteria. 16S rRNA gene sequence similarities between strain MJ17T and type strains of species of the genus Paracoccus were 94.1–97.4 %. The highest similarities were between strain MJ17T and Paracoccus homiensis DD-R11T, Paracoccus zeaxanthinifaciens ATCC 21588T and Paracoccus alcaliphilus JCM 7364T (97.4, 97.2 and 96.3 %, respectively). Strain MJ17T exhibited <22 % DNA–DNA relatedness with P. homiensis KACC 11518T and P. zeaxanthinifaciens JCM 21774T. The G+C content of the genomic DNA was 58.7 mol%. Strain MJ17T contained ubiquinone Q-10. The major fatty acids were C18 : 0 (11.3 %), C16 : 0 (10.2 %) and summed feature 7 (containing one or more of C18 : 1ω7c, C18 : 1ω9c and C18 : 1ω12t; 54.3 %). Poly-β-hydroxybutyrate granules are formed. On the basis of phenotypic and genotypic properties and phylogenetic distinctiveness, strain MJ17T should be classified in a novel species of the genus Paracoccus, for which the name Paracoccus caeni sp. nov. is proposed. The type strain is MJ17T ( = KCTC 22480T  = JCM 16385T  = KEMB 9004-001T).

scholarly journals Pedobacter lentus sp. nov. and Pedobacter terricola sp. nov., isolated from soil

2007 ◽  
Vol 57 (9) ◽  
pp. 2089-2095 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Sooyeon Park ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Type Strains

Two Gram-negative, non-motile, pleomorphic bacterial strains, DS-40T and DS-45T, were isolated from a soil sample collected from Dokdo, Korea, and their exact taxonomic positions were investigated by using a polyphasic approach. Strains DS-40T and DS-45T grew optimally at 25 °C and pH 6.5–7.5 in the presence of 0–1.0 % (w/v) NaCl. They contained MK-7 as the predominant menaquinone and possessed iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH) as the major fatty acids. The DNA G+C contents of strains DS-40T and DS-45T were 36.0 and 36.8 mol%, respectively. Strains DS-40T and DS-45T shared a 16S rRNA gene sequence similarity of 96.7 % and demonstrated a mean DNA–DNA relatedness level of 12 %. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strains DS-40T and DS-45T were most closely phylogenetically affiliated with the genus Pedobacter of the family Sphingobacteriaceae. Strains DS-40T and DS-45T exhibited 16S rRNA gene sequence similarity values of 91.4–93.7 and 89.9–91.6 % with respect to the type strains of Pedobacter and Sphingobacterium species, respectively. Phenotypic and chemotaxonomic properties, together with the phylogenetic data, support the assignment of strains DS-40T and DS-45T as two distinct species within the genus Pedobacter. On the basis of phenotypic, phylogenetic and genetic data, strains DS-40T and DS-45T represent two novel species of the genus Pedobacter, for which the names Pedobacter lentus sp. nov. and Pedobacter terricola sp. nov. are proposed, respectively. The respective type strains are DS-40T (=KCTC 12875T=JCM 14593T) and DS-45T (=KCTC 12876T=JCM 14594T).

scholarly journals Bacillus trypoxylicola sp. nov., xylanase-producing alkaliphilic bacteria isolated from the guts of Japanese horned beetle larvae (Trypoxylus dichotomus septentrionalis)

2010 ◽  
Vol 60 (1) ◽  
pp. 61-66 ◽  
Author(s):  
Tomoko Aizawa ◽  
Makoto Urai ◽  
Noriyuki Iwabuchi ◽  
Mutsuyasu Nakajima ◽  
Michio Sunairi
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Horned Beetle ◽  
Trypoxylus Dichotomus ◽  
Type Strains

Three xylanase-producing alkaliphilic strains, SU1T, 36AC4 and 36AC6, were isolated from the guts of larvae of the Japanese horned beetle (Trypoxylus dichotomus septentrionalis). The isolates stained Gram-positive and were aerobic, spore-forming, non-motile and rod-shaped and grew optimally at 30 °C and pH 9. They contained MK-7 as the major isoprenoid quinone and iso-C15 : 0, anteiso-C15 : 0, anteiso-C17 : 0 and iso-C17 : 0 as the major fatty acids. The DNA G+C contents of the strains were 37.4–37.7 mol%. On the basis of 16S rRNA gene sequence similarity, these strains were shown to belong to the genus Bacillus. Although their 16S rRNA gene sequence similarity to the type strains of the alkaliphilic species Bacillus pseudalcaliphilus and B. alcalophilus was 97 %, the novel isolates formed a distinct group in the phylogenetic trees and DNA–DNA relatedness values to the type strains of these species were less than 30 %. Results of physiological and biochemical tests, including salt preference, enabled these strains to be differentiated phenotypically from described Bacillus species. Therefore, strains SU1T, 36AC4 and 36AC6 represent a novel species for which the name Bacillus trypoxylicola sp. nov. is proposed; the type strain is SU1T (=NBRC 102646T =KCTC 13244T).

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