scholarly journals Photobacterium rosenbergii sp. nov. and Enterovibrio coralii sp. nov., vibrios associated with coral bleaching

2005 ◽  
Vol 55 (2) ◽  
pp. 913-917 ◽  
Author(s):  
F. L. Thompson ◽  
C. C. Thompson ◽  
S. Naser ◽  
B. Hoste ◽  
K. Vandemeulebroecke ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Carbon Sources ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence

Six new Vibrio-like isolates originating from different species of bleached and healthy corals around Magnetic Island (Australia) were investigated using a polyphasic approach. Phylogenetic analyses based on 16S rRNA, recA and rpoA gene sequences split the isolates in two new groups. Strains LMG 22223T, LMG 22224, LMG 22225, LMG 22226 and LMG 22227 were phylogenetic neighbours of Photobacterium leiognathi LMG 4228T (95·6 % 16S rRNA gene sequence similarity), whereas strain LMG 22228T was related to Enterovibrio norvegicus LMG 19839T (95·5 % 16S rRNA gene sequence similarity). The two new groups can be distinguished from closely related species on the basis of several phenotypic features, including fermentation of d-mannitol, melibiose and sucrose, and utilization of different compounds as carbon sources, arginine dihydrolase activity, nitrate reduction, resistance to the vibriostatic agent O/129 and the presence of fatty acids 15 : 0 iso and 17 : 0 iso. The names Photobacterium rosenbergii sp. nov. (type strain LMG 22223T=CBMAI 622T=CC1T) and Enterovibrio coralii sp. nov. (type strain LMG 22228T=CBMAI 623T=CC17T) are proposed to accommodate these new isolates. The G+C contents of the DNA of the two type strains are respectively 47·6 and 48·2 mol%.

scholarly journals Exiguobacterium aestuarii sp. nov. and Exiguobacterium marinum sp. nov., isolated from a tidal flat of the Yellow Sea in Korea

2005 ◽  
Vol 55 (2) ◽  
pp. 885-889 ◽  
Author(s):  
In-Gi Kim ◽  
Mi-Hwa Lee ◽  
Seo-Youn Jung ◽  
Jae Jun Song ◽  
Tae-Kwang Oh ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Yellow Sea ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence

Three Gram-variable, rod-shaped bacterial strains, TF-16T, TF-19 and TF-80T, were isolated from a tidal flat of Daepo Beach (Yellow Sea) near Mokpo City, Korea, and their taxonomic positions were investigated by a polyphasic approach. These isolates grew optimally in the presence of 2 % NaCl and at 30 °C. Their peptidoglycan types were based on l-Lys–Gly. The predominant menaquinone detected in the three strains was MK-7. The three strains contained large amounts of the branched fatty acids iso-C17 : 0, anteiso-C13 : 0, iso-C13 : 0 and iso-C15 : 0. The DNA G+C contents of strains TF-16T, TF-19 and TF-80T were 48·6, 48·4 and 48·0 mol%, respectively. The three strains formed a coherent cluster with Exiguobacterium species in a phylogenetic tree based on 16S rRNA gene sequences. They showed closest phylogenetic affiliation to Exiguobacterium aurantiacum, with 16S rRNA gene sequence similarity values of 98·1–98·3 %. The three strains exhibited 16S rRNA gene sequence similarity values of 94·0–94·6 % to the type strains of other Exiguobacterium species. Levels of DNA–DNA relatedness indicated that strains TF-16T and TF-19 and strain TF-80T are members of two species that are separate from E. aurantiacum. On the basis of phenotypic, phylogenetic and genetic data, strains TF-16T and TF-19 and strain TF-80T represent two novel species in the genus Exiguobacterium; the names Exiguobacterium aestuarii sp. nov. (type strain TF-16T=KCTC 19035T=DSM 16306T; reference strain TF-19) and Exiguobacterium marinum sp. nov. (type strain TF-80T=KCTC 19036T=DSM 16307T) are proposed.

scholarly journals Bacillus thermolactis sp. nov., isolated from dairy farms, and emended description of Bacillus thermoamylovorans

2011 ◽  
Vol 61 (8) ◽  
pp. 1954-1961 ◽  
Author(s):  
An Coorevits ◽  
Niall A. Logan ◽  
Anna E. Dinsdale ◽  
Gillian Halket ◽  
Patsy Scheldeman ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Emended Description

A polyphasic taxonomic study was performed on 22 thermotolerant, aerobic, endospore-forming bacteria from dairy environments. Seventeen isolates were retrieved from raw milk, one from a filter cloth and four from grass, straw or milking equipment. These latter four isolates (R-6546, R-7499, R-7764 and R-7440) were identified as Bacillus thermoamylovorans based on DNA–DNA hybridizations (values above 70 % with Bacillus thermoamylovorans LMG 18084T) but showed discrepancies in characteristics with the original species description, so an emended description of this species is given. According to 16S rRNA gene sequence analysis and DNA–DNA hybridization experiments, the remaining 18 isolates (R-6488T, R-28193, R-6491, R-6492, R-7336, R-33367, R-6486, R-6770, R-31288, R-28160, R-26358, R-7632, R-26955, R-26950, R-33520, R-6484, R-26954 and R-7165) represented one single species, most closely related to Bacillus thermoamylovorans (93.9 % 16S rRNA gene sequence similarity), for which the name Bacillus thermolactis is proposed. Cells were Gram-stain-positive, facultatively anaerobic, endospore-forming rods that grew optimally at 40–50 °C. The cell wall peptidoglycan type of strain R-6488T, the proposed type strain, was A1γ based on meso-diaminopimelic acid. Major fatty acids of the strains were C16 : 0 (28.0 %), iso-C16 : 0 (12.1 %) and iso-C15 : 0 (12.0 %). MK-7 was the predominant menaquinone, and major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and some unidentified phospholipids. DNA G+C content was 35.0 mol%. Phenotypic properties allowed discrimination from other thermotolerant species of the genus Bacillus and supported the description of the novel species Bacillus thermolactis, with strain R-6488T ( = LMG 25569T  = DSM 23332T) as the proposed type strain.

scholarly journals Paucibacter toxinivorans gen. nov., sp. nov., a bacterium that degrades cyclic cyanobacterial hepatotoxins microcystins and nodularin

2005 ◽  
Vol 55 (4) ◽  
pp. 1563-1568 ◽  
Author(s):  
Jarkko Rapala ◽  
Katri A. Berg ◽  
Christina Lyra ◽  
R. Maarit Niemi ◽  
Werner Manz ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Fatty Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence

Thirteen bacterial isolates from lake sediment, capable of degrading cyanobacterial hepatotoxins microcystins and nodularin, were characterized by phenotypic, genetic and genomic approaches. Cells of these isolates were Gram-negative, motile by means of a single polar flagellum, oxidase-positive, weakly catalase-positive and rod-shaped. According to phenotypic characteristics (carbon utilization, fatty acid and enzyme activity profiles), the G+C content of the genomic DNA (66·1–68·0 mol%) and 16S rRNA gene sequence analysis (98·9–100 % similarity) the strains formed a single microdiverse genospecies that was most closely related to Roseateles depolymerans (95·7–96·3 % 16S rRNA gene sequence similarity). The isolates assimilated only a few carbon sources. Of the 96 carbon sources tested, Tween 40 was the only one used by all strains. The strains were able to mineralize phosphorus from organic compounds, and they had strong leucine arylamidase and chymotrypsin activities. The cellular fatty acids identified from all strains were C16 : 0 (9·8–19 %) and C17 : 1 ω7c (<1–5·8 %). The other predominant fatty acids comprised three groups: summed feature 3 (<1–2·2 %), which included C14 : 0 3-OH and C16 : 1 iso I, summed feature 4 (54–62 %), which included C16 : 1 ω7c and C15 : 0 iso OH, and summed feature 7 (8·5–28 %), which included ω7c, ω9c and ω12t forms of C18 : 1. A more detailed analysis of two strains indicated that C16 : 1 ω7c was the main fatty acid. The phylogenetic and phenotypic features separating our strains from recognized bacteria support the creation of a novel genus and species, for which the name Paucibacter toxinivorans gen. nov., sp. nov. is proposed. The type strain is 2C20T (=DSM 16998T=HAMBI 2767T=VYH 193597T).

scholarly journals Effusibacillus dendaii sp. nov. isolated from farm soil

2021 ◽  
Author(s):  
Tomoyuki Konishi ◽  
Tomohiko Tamura ◽  
Toru Tobita ◽  
Saori Sakai ◽  
Namio Matsuda ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
Genome Analyses

Abstract Gram-positive, rod-shaped, spore-forming, thermophilic, acidophilic bacterium, designated strain skT53T, was isolated from farm soil in Tokyo, Japan. The strain grew aerobically at 37–55°C (optimum 50°C) and pH 4.0–6.0 (optimum 5.0). Phylogenetic analysis of the 16S rRNA gene sequence showed that the isolate was most closely related to the type strain of Effusibacillus consociatus (94.3% similarity). The G + C content of the genomic DNA was 48.22 mol%. MK-7 was the predominant respiratory quinone. The major fatty acids were anteiso-C15:0, iso-C15:0, iso-C16:0 and C18:3ω6c. The results of phenotypic and chemotaxonomic, 16S rRNA gene sequence similarity, and whole genome analyses support strain skT53T as representing a novel species of Effusibacillus dendaii sp. nov. is proposed. The type strain is strain skT53T (= NBRC 114101T = TBRC 11241T).

scholarly journals Rarimicrobium hominis gen. nov., sp. nov., representing the fifth genus in the phylum Synergistetes that includes human clinical isolates

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 3965-3970 ◽  
Author(s):  
Estelle Jumas-Bilak ◽  
Philippe Bouvet ◽  
Emma Allen-Vercoe ◽  
Fabien Aujoulat ◽  
Paul A. Lawson ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Clinical Isolates ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Rrna Gene Sequence

Five human clinical isolates of an unknown, strictly anaerobic, slow-growing, Gram-stain-negative, rod-shaped micro-organism were subjected to a polyphasic taxonomic study. Comparative 16S rRNA gene sequence-based phylogeny showed that the isolates grouped in a clade that included members of the genera Pyramidobacter, Jonquetella, and Dethiosulfovibrio; the type strain of Pyramidobacter piscolens was the closest relative with 91.5–91.7 % 16S rRNA gene sequence similarity. The novel strains were mainly asaccharolytic and unreactive in most conventional biochemical tests. Major metabolic end products in trypticase/glucose/yeast extract broth were acetic acid and propionic acid and the major cellular fatty acids were C13 : 0 and C16 : 0, each of which could be used to differentiate the strains from P. piscolens. The DNA G+C content based on whole genome sequencing for the reference strain 22-5-S 12D6FAA was 57 mol%. Based on these data, a new genus, Rarimicrobium gen. nov., is proposed with one novel species, Rarimicrobium hominis sp. nov., named after the exclusive and rare finding of the taxon in human samples. Rarimicrobium is the fifth genus of the 14 currently characterized in the phylum Synergistetes and the third one in subdivision B that includes human isolates. The type strain of Rarimicrobium hominis is ADV70T ( = LMG 28163T = CCUG 65426T).

scholarly journals Corynebacterium tapiri sp. nov. and Corynebacterium nasicanis sp. nov., isolated from a tapir and a dog, respectively

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 3885-3893 ◽  
Author(s):  
Sandra Baumgardt ◽  
Igor Loncaric ◽  
Peter Kämpfer ◽  
Hans-Jürgen Busse
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Established Species

Two Gram-stain-positive bacterial isolates, strain 2385/12T and strain 2673/12T were isolated from a tapir and a dog's nose, respectively. The two strains were rod to coccoid-shaped, catalase-positive and oxidase-negative. The highest 16S rRNA gene sequence similarity identified Corynebacterium singulare CCUG 37330T (96.3 % similarity) as the nearest relative of strain 2385/12T and suggested the isolate represented a novel species. Corynebacterium humireducens DSM 45392T (98.7 % 16S rRNA gene sequence similarity) was identified as the nearest relative of strain 2673/12T. Results from DNA–DNA hybridization with the type strain of C. humireducens demonstrated that strain 2673/12T also represented a novel species. Strain 2385/12T showed a quinone system consisting predominantly of menaquinones MK-8(H2) and MK-9(H2) whereas strain 2673/12T contained only MK-8(H2) as predominant quinone. The polar lipid profiles of the two strains showed the major compounds phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid. Phosphatidylinositol was identified as another major lipid in 2673/12T whereas it was only found in moderate amounts in strain 2385/12T. Furthermore, moderate to minor amounts of phosphatidylinositol-mannoside, β-gentiobiosyl diacylglycerol and variable counts of several unidentified lipids were detected in the two strains. Both strains contained corynemycolic acids. The polyamine patterns were characterized by the major compound putrescine in strain 2385/12T and spermidine in strain 2673/12T. In the fatty acid profiles, predominantly C18 : 1ω9c and C16 : 0 were detected. The two strains are distinguishable from each other and the nearest related established species of the genus Corynebacterium phylogenetically and phenotypically. In conclusion, two novel species of the genus Corynebacterium are proposed, namely Corynebacterium tapiri sp. nov. (type strain, 2385/12T = CCUG 65456T = LMG 28165T) and Corynebacterium nasicanis sp. nov. (type strain, 2673/12T = CCUG 65455T = LMG 28166T).

scholarly journals Flavisolibacter ginsengiterrae gen. nov., sp. nov. and Flavisolibacter ginsengisoli sp. nov., isolated from ginseng cultivating soil

2007 ◽  
Vol 57 (8) ◽  
pp. 1834-1839 ◽  
Author(s):  
Min-Ho Yoon ◽  
Wan-Taek Im
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Separate Species

Two strains (Gsoil 492T and Gsoil 643T) isolated in Pocheon Province, South Korea, from soil used for ginseng cultivation were characterized using a polyphasic approach. Both isolates comprised Gram-negative, aerobic, non-motile, rod-shaped bacteria. They had similar chemotaxonomic characteristics, e.g. containing MK-7 as the major quinone, having a DNA G+C content in the range 42.5–43.3 mol% and possessing iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. A phylogenetic analysis based on 16S rRNA gene sequences indicated that the two isolates formed a tight cluster with several uncultured bacterial clones and with the established genera Terrimonas, Niastella and Chitinophaga in the phylum Bacteroidetes but were clearly separate from these genera. The levels of 16S rRNA gene sequence similarity between the isolates and type strains of related genera ranged from 87.5 to 92.4 %. Furthermore, the results of physiological and biochemical tests allowed phenotypic differentiation of the isolates from phylogenetically closely related species with validly published names. The level of 16S rRNA gene sequence similarity between the two strains was 99.5 %, whereas the DNA–DNA relatedness value was 44 %, indicating that they represent separate species. On the basis of the polyphasic evidence, a novel genus, Flavisolibacter gen. nov., and two novel species, Flavisolibacter ginsengiterrae sp. nov. (type strain Gsoil 492T=KCTC 12656T=DSM 18136T) and Flavisolibacter ginsengisoli sp. nov. (type strain Gsoil 643T=KCTC 12657T=DSM 18119T), are proposed. Flavisolibacter ginsengiterrae is the type species of the genus.

scholarly journals Candidimonas nitroreducens gen. nov., sp. nov. and Candidimonas humi sp. nov., isolated from sewage sludge compost

2011 ◽  
Vol 61 (9) ◽  
pp. 2238-2246 ◽  
Author(s):  
Ivone Vaz-Moreira ◽  
Vânia Figueira ◽  
Ana R. Lopes ◽  
Evie De Brandt ◽  
Peter Vandamme ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sludge Compost ◽  
The Family

Two bacterial strains (SC-089T and SC-092T) isolated from sewage sludge compost were characterized by using a polyphasic approach. The isolates were Gram-negative short rods, catalase- and oxidase-positive, and showed good growth at 30 °C, at pH 7 and with 1 % (w/v) NaCl. Ubiquinone 8 was the major respiratory quinone, and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol were amongst the major polar lipids. On the basis of 16S rRNA gene sequence analysis, the strains were observed to be members of the family Alcaligenaceae, but could not be identified as members of any validly described genus. The low levels of 16S rRNA gene sequence similarity to other recognized taxa, together with comparative analysis of phenotypic traits and chemotaxonomic markers, supported the proposal of a new genus within the family Alcaligenaceae, for which the name Candidimonas gen. nov. is proposed. Strains SC-089T and SC-092T, which shared 99.1 % 16S rRNA gene sequence similarity, could be differentiated at the phenotypic level, and DNA–DNA hybridization results supported their identification as representing distinct species. The names proposed for these novel species are Candidimonas nitroreducens sp. nov. (type strain, SC-089T = LMG 24812T = CCUG 55806T) and Candidimonas humi sp. nov. (type strain, SC-092T = LMG 24813T = CCUG 55807T).

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 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).

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