Algoriphagus pacificus sp. nov. and Algoriphagus oliviformis sp. nov., isolated from a mariculture fishpond

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Huibin Lu ◽  
Zhipeng Cai ◽  
Tongchu Deng ◽  
Youfeng Qian ◽  
Meiying Xu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type

Two Gram-stain-negative, catalase-positive, oxidase-negative, rod-shaped, non-flagellated, non-spore-forming and non-motile strains (YJ13CT and H41T) were isolated from a mariculture fishpond in PR China. Comparisons based on 16S rRNA gene sequences indicated that YJ13CT and H41T shared 16S rRNA gene sequences similarities between 92.6 and 99.2 % with species of the genus Algoriphagus . YJ13CT only shared 93.8 % 16S rRNA gene sequence similarity with H41T. The reconstructed phylogenetic and phylogenomic trees indicated that YJ13CT and H41T clustered closely with species of the genus Algoriphagus . The calculated pairwise orthologous average nucleotide identity with usearch (OrthoANIu) values between strains YJ13CT and H41T and other related strains were all less than 79.5 %. The OrthoANIu value between YJ13CT and H41T was only 69.9 %. MK-7 was the predominant respiratory quinone of YJ13CT and H41T and their major cellular fatty acids contained iso-C15 : 0, C16 : 1 ω7c and C17 : 1 ω9c. The polar lipids profiles of YJ13CT and H41T consisted of phosphatidylethanolamine and several kinds of unidentified lipids. Combining the above descriptions, strains YJ13CT and H41T represent two distinct novel species of the genus Algoriphagus , for which the names Algoriphagus pacificus sp. nov. (type strain YJ13CT=GDMCC 1.2178T=KCTC 82450T) and Algoriphagus oliviformis sp. nov. (type strain H41T=GDMCC 1.2179T=KCTC 82451T) are proposed.

scholarly journals Aequorivita sinensis sp. nov., isolated from sediment of the East China Sea, and reclassification of Vitellibacter todarodis as Aequorivita todarodis comb. nov. and Vitellibacter aquimaris as Aequorivita aquimaris comb. nov.

2020 ◽  
Vol 70 (5) ◽  
pp. 3323-3327 ◽  
Author(s):  
Qian Wang ◽  
Sheng-Dong Cai ◽  
Jie Liu ◽  
De-Chao Zhang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type

The Gram-strain-negative, rod-shaped, facultatively anaerobic, non-motile bacterial strain, designated S1-10T, was isolated from marine sediment. Strain S1-10T grew at 4–42 °C (optimally at 30–35 °C), at pH 7.0–10 (optimally at pH 9) and in the presence of 0.5–8 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S1-10T was related to the genus Aequorivita and had highest 16S rRNA gene sequence similarity to Aequorivita viscosa 8-1bT (97.7%). The predominant cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The main respiratory quinone was menaquinone 6 (MK-6). The genomic DNA G+C content of strain S1-10T was 34.6 mol%. The polar lipid profile of strain S1-10T contained phosphatidylethanolamine, two aminolipids, two glycolipids, one phosphoglycolipid and three unidentified polar lipids. In addition, the maximum values of in silico DNA–DNA hybridization (isDDH) and average nucleotide identity (ANI) between strain S1-10T and A. viscosa CGMCC 1.11023T were 15.4 and 75.7 %, respectively. Combined data from phenotypic, phylogenetic, isDDH and ANI analyses demonstrated that strain S1-10T is the representative of a novel species of the genus Aequorivita , for which we propose the name Aequorivita sinensis sp. nov. (type strain S1-10T=CGMCC 1.12579T=JCM 19789T). We also propose that Vitellibacter todarodis and Vitellibacter aquimaris should be transferred into genus Aequorivita and be named Aequorivita todarodis comb. nov. and Aequorivita aquimaris comb. nov., respectively. The type strain of Aequorivita todarodis comb. nov. is MYP2-2T (= KCTC 62141T= NBRC 113025T) and the type strain of Aequorivita aquimaris comb. nov. is D-24T (=KCTC 42708T=DSM 101732T).

Albimonas pacifica sp. nov., isolated from seawater of the Pacific, and emended description of the genus Albimonas

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3597-3601 ◽  
Author(s):  
Guo-Wei Li ◽  
Xi-Ying Zhang ◽  
Chun-Sheng Wang ◽  
Yan-Jiao Zhang ◽  
Xue-Wei Xu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Pacific ◽  
Emended Description

A Gram-stain-negative, aerobic, catalase- and oxidase-positive, non-flagellated, rod-shaped bacterium, designated strain P-50-3T, was isolated from seawater of the Pacific. The strain grew at 10–40 °C (optimum at 30 °C) and with 0–12 % (w/v, optimum 2 %) NaCl. It reduced nitrate to nitrite but did not hydrolyse gelatin, starch or Tween 80. Analysis of 16S rRNA gene sequences showed that strain P-50-3T clustered tightly with the genus Albimonas and shared the highest 16S rRNA gene sequence similarity (94.3 %) with the type strain of Albimonas donghaensis . The major respiratory quinone was Q-10 and the major cellular fatty acids were C18 : 1ω7c, C18 : 0, 11-methyl C18 : 1ω7c and C16 : 0. Polar lipids included phosphatidylglycerol (PG), phosphatidylcholine (PC), two unidentified aminolipids and an unidentified lipid. The genomic DNA G+C content of strain P-50-3T was 69.0 mol%. On the basis of the data obtained in this polyphasic study, strain P-50-3T represents a novel species within the genus Albimonas , for which the name Albimonas pacifica sp. nov. is proposed. The type strain of Albimonas pacifica is P-50-3T ( = KACC 16527T = CGMCC 1.11030T). An emended description of the genus Albimonas Lim et al. 2008 is also proposed.

Flammeovirga pacifica sp. nov., isolated from deep-sea sediment

2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 937-941 ◽  
Author(s):  
Hui Xu ◽  
Yuanyuan Fu ◽  
Ning Yang ◽  
Zhixin Ding ◽  
Qiliang Lai ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Chromosomal Dna ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type

Strain WPAGA1T was isolated from marine sediment of the west Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belonged to the genus Flammeovirga . Strain WPAGA1T exhibited highest 16S rRNA gene sequence similarity with Flammeovirga yaeyamensis NBRC 100898T (98.1 %) and lower sequence similarity with Flammeovirga arenaria IFO 15982T (94.6 %) and other members of the genus Flammeovirga (<94.2 %). DNA–DNA relatedness studies showed that strain WPAGA1T was distinct from F. yaeyamensis NBRC 100898T and F. arenaria NBRC 15982T (43±4 % and 32±2 % relatedness values, respectively). Strain WPAGA1T could be distinguished from all known members of the genus Flammeovirga by a number of phenotypic features. However, the dominant fatty acids of strain WPAGA1T (iso-C15 : 0, C16 : 0 and C20 : 4ω6,9,12,15c), the major polyamine (cadaverine) and the G+C content of the chromosomal DNA (32.9 mol%) were consistent with those of members of the genus Flammeovirga . Based on phenotypic and chemotaxonomic features and 16S rRNA gene sequences, strain WPAGA1T can be assigned to the genus Flammeovirga as a representative of a novel species, for which the name Flammeovirga pacifica sp. nov. is proposed; the type strain is WPAGA1T ( = CCTCC AB 2010364T = LMG 26175T = DSM 24597T = MCCC 1A06425T).

Caenispirillum salinarum sp. nov., a member of the family Rhodospirillaceae isolated from a solar saltern

2012 ◽  
Vol 62 (Pt_7) ◽  
pp. 1698-1702 ◽  
Author(s):  
C. Ritika ◽  
K. Suresh ◽  
P. Anil Kumar
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Solar Saltern ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Family

A novel Gram-negative, vibrio-shaped, motile bacterium, designated strain AK4T, was isolated from a sediment sample collected from a solar saltern at Kakinada, Andhra Pradesh, India. Strain AK4T was positive for oxidase, urease and DNase activities but negative for gelatinase, catalase, ornithine decarboxylase, lysine decarboxylase, nitrate reduction, aesculin, indole and lipase activities. The fatty acids were dominated by unsaturated components, with a high abundance of summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C17 : 1ω6c. Strain AK4T contained Q-10 as the major respiratory quinone and phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine as major polar lipids. The DNA G+C content of strain AK4T was 71.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain AK4T was most closely related to the type strain of Caenispirillum bisanense of the family Rhodospirillaceae (phylum ‘ Proteobacteria ’) (96.6 % sequence similarity). It shared <93.2 % 16S rRNA gene sequence similarity with other members of the family. Based on phenotypic characteristics and phylogenetic inference, strain AK4T is considered to represent a novel species of the genus Caenispirillum , for which the name Caenispirillum salinarum sp. nov. is proposed; the type strain is AK4T ( = MTCC 10963T = JCM 17360T).

scholarly journals Polaromonas glacialis sp. nov. and Polaromonas cryoconiti sp. nov., isolated from alpine glacier cryoconite

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2662-2668 ◽  
Author(s):  
Rosa Margesin ◽  
Cathrin Spröer ◽  
De-Chao Zhang ◽  
Hans-Jürgen Busse
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Alpine Glacier ◽  
Dna Relatedness ◽  
Link Type

The taxonomic positions of two Gram-staining-negative, psychrophilic bacteria, which were isolated from alpine glacier cryoconite and designated strains Cr4-12T and Cr4-35T, were investigated using a polyphasic approach. Both novel strains contained ubiquinone Q-8 as the sole quinone, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0 as the dominant cellular fatty acids, putrescine and 2-hydroxyputrescine as the major polyamines, and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. The genomic DNA G+C contents of strains Cr4-12T and Cr4-35T were 61.3 mol% and 60.7 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two strains belonged to the genus Polaromonas . Although the 16S rRNA gene sequences of strains Cr4-12T and Cr4-35T were very similar (98.7 % sequence similarity), hybridizations indicated a DNA–DNA relatedness value of only 26.9 % between the two novel strains. In pairwise comparisons with the type strains of recognized Polaromonas species, strains Cr4-12T and Cr4-35T showed 16S rRNA gene sequence similarities of 96.4–98.5 % and 96.5–98.4 %, respectively. Based on the phenotypic and phylogenetic evidence and DNA–DNA relatedness data, strains Cr4-12T and Cr4-35T represent two novel species within the genus Polaromonas , for which the names Polaromonas glacialis sp. nov. and Polaromonas cryoconiti sp. nov., respectively, are proposed. The type strain of Polaromonas glacialis sp. nov. is Cr4-12T ( = DSM 24062T  = LMG 26049T  = KACC 15089T) and that of Polaromonas cryoconiti sp. nov. is Cr4-35T ( = DSM 24248T  = LMG 26050T  = KACC 15090T).

Flavobacterium lotistagni sp. nov. and Flavobacterium celericrescens sp. nov., isolated from freshwater habitats

2021 ◽  
Author(s):  
Jia-Hong Wu ◽  
Ya-Xiu You ◽  
Chiu-Chung Young ◽  
Soon-Wo Kwon ◽  
Wen-Ming Chen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Freshwater Habitats

This study presents taxonomic descriptions of strains CYK-4T and TWA-26T isolated from freshwater habitats in Taiwan. Both strains were Gram-stain-negative, strictly aerobic, motile by gliding and rod-shaped. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that both strains belonged to the genus Flavobacterium . Analysis of 16S rRNA gene sequences showed that strains CYK-4T and TWA-26T shared 92.7 % sequence similarity and were most closely related to Flavobacterium ovatum W201ET (95.6 %) and Flavobacterium aquaticum JC164T (96.7 %), respectively. Both strains shared common chemotaxonomic characteristics comprising MK-6 as the main isoprenoid quinone, iso-C15 : 0 and iso-C15 : 1 G as the predominant fatty acids, phosphatidylethanolamine as the principal polar lipid, and homospermidine as the major polyamine. The DNA G+C contents of strains CYK-4T and TWA-26T were 41.5 and 31.8 mol%, respectively. The average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values between these two novel isolates and their closest relatives were below the cut-off values of 95–96, 90 and 70 %, respectively, used for species demarcation. On the basis of phenotypic and genotypic properties and phylogenetic inference, both strains should be classified as novel species within the genus Flavobacterium , for which the names Flavobacterium lotistagni sp. nov. (type strain CYK-4T=BCRC 81192T=LMG 31330T) and Flavobacterium celericrescens sp. nov. (type strain TWA-26T=BCRC 81200T=LMG 31333T) are proposed.

Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces

2012 ◽  
Vol 62 (Pt_8) ◽  
pp. 1902-1907 ◽  
Author(s):  
Bédis Dridi ◽  
Marie-Laure Fardeau ◽  
Bernard Ollivier ◽  
Didier Raoult ◽  
Michel Drancourt
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Human Faeces ◽  
Link Type

During attempts to obtain novel, human-associated species of the domain Archaea , a coccoid micro-organism, designated strain B10T, was isolated in pure culture from a sample of human faeces collected in Marseille, France. On the basis of its phenotypic characteristics and 16S rRNA and mcrA gene sequences, the novel strain was classified as a methanogenic archaeon. Cells of the strain were non-motile, Gram-staining-positive cocci that were approximately 850 nm in diameter and showed autofluorescence at 420 nm. Cells were lysed by 0.1 % (w/v) SDS. With hydrogen as the electron donor, strain B10T produced methane by reducing methanol. The novel strain was unable to produce methane when hydrogen or methanol was the sole energy source. In an atmosphere containing CO2, strain B10T could not produce methane from formate, acetate, trimethylamine, 2-butanol, 2-propanol, cyclopentanol, 2-pentanol, ethanol, 1-propanol or 2,3-butanediol. Strain B10T grew optimally with 0.5–1.0 % (w/v) NaCl, at pH 7.6 and at 37 °C. It required tungstate-selenite for growth. The complete genome of the novel strain was sequenced; the size of the genome was estimated to be 2.05 Mb and the genomic DNA G+C content was 59.93 mol%. In phylogenetic analyses based on 16S rRNA gene sequences, the highest sequence similarities (98.0–98.7 %) were seen between strain B10T and several uncultured, methanogenic Archaea that had been collected from the digestive tracts of a cockroach, a chicken and mammals. In the same analysis, the non-methanogenic ‘Candidatus Aciduliprofundum boonei’ DSM 19572 was identified as the cultured micro-organism that was most closely related to strain B10T (83.0 % 16S rRNA gene sequence similarity). Each of the three treeing algorithms used in the analysis of 16S rRNA gene sequences indicated that strain B10T belongs to a novel order that is distinct from the Thermoplasmatales . The novel strain also appeared to be distinct from Methanosphaera stadtmanae DSM 3091T (72.9 % 16S rRNA gene sequence similarity), another methanogenic archaeon that was isolated from human faeces and can use methanol in the presence of hydrogen. Based on the genetic and phenotypic evidence, strain B10T represents a novel species of a new genus for which the name Methanomassiliicoccus luminyensis gen. nov., sp. nov. is proposed. The type strain of the type species is B10T ( = DSM 24529T = CSUR P135T).

scholarly journals Serratia myotis sp. nov. and Serratia vespertilionis sp. nov., isolated from bats hibernating in caves

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 90-94 ◽  
Author(s):  
P. García-Fraile ◽  
M. Chudíčková ◽  
O. Benada ◽  
J. Pikula ◽  
M. Kolařík
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type

During the study of bacteria associated with bats affected by white-nose syndrome hibernating in caves in the Czech Republic, we isolated two facultatively anaerobic, Gram-stain-negative bacteria, designated strains 12T and 52T. Strains 12T and 52T were motile, rod-like bacteria (0.5–0.6 µm in diameter; 1–1.3 µm long), with optimal growth at 20–35 °C and pH 6–8. On the basis of the almost complete sequence of their 16S rRNA genes they should be classified within the genus Serratia ; the closest relatives to strains 12T and 52T were Serratia quinivorans DSM 4597T (99.5 % similarity in 16S rRNA gene sequences) and Serratia ficaria DSM 4569T (99.5 % similarity in 16S rRNA gene sequences), respectively. DNA–DNA relatedness between strain 12T and S. quinivorans DSM 4597T was only 37.1 % and between strain 52T and S. ficaria DSM 4569T was only 56.2 %. Both values are far below the 70 % threshold value for species delineation. In view of these data, we propose the inclusion of the two isolates in the genus Serratia as representatives of Serratia myotis sp. nov. (type strain 12T = CECT 8594T = DSM 28726T) and Serratia vespertilionis sp. nov. (type strain 52T = CECT 8595T = DSM 28727T).

Polaribacter huanghezhanensis sp. nov., isolated from Arctic fjord sediment, and emended description of the genus Polaribacter

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 973-978 ◽  
Author(s):  
Hai Li ◽  
Xi-Ying Zhang ◽  
Chang Liu ◽  
Chao-Yi Lin ◽  
Zhong Xu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Emended Description ◽  
Major Respiratory Quinone

A Gram-negative, orange-colony-forming, aerobic and non-flagellated bacterium, designated strain SM1202T, was isolated from marine sediment of Kongsfjorden, Svalbard. Analysis of 16S rRNA gene sequences revealed that strain SM1202T was phylogenetically closely related to the genus Polaribacter . It shared the highest 16S rRNA gene sequence similarity with the type strain of Polaribacter dokdonensis (94.2 %) and 92.7–93.9 % sequence similarity with type strains of other known species of the genus Polaribacter . The strain grew at 4–35 °C and with 1.0–5.0 % (w/v) NaCl. It contained iso-C15 : 0, iso-C15 : 0 3-OH, iso-C13 : 0, C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH and C15 : 1ω6c as predominant cellular fatty acids and menaquinone-6 (MK-6) as the major respiratory quinone. The polar lipids of strain SM1202T were phosphatidylethanolamine, one unidentified lipid, two unidentified aminophospholipids and one unidentified aminolipid. The genomic DNA G+C content of strain SM1202T was 36.4 mol%. On the basis of the data from this polyphasic taxonomic study, strain SM1202T represents a novel species in the genus Polaribacter of the family Flavobacteriaceae , for which the name Polaribacter huanghezhanensis sp. nov. is proposed. The type strain of Polaribacter huanghezhanensis is SM1202T ( = CCTCC AB 2013148T = KCTC 32516T). An emended description of the genus Polaribacter is also presented.

scholarly journals Luteimonas cucumeris sp. nov., isolated a from cucumber leaf

2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 2916-2920 ◽  
Author(s):  
Zhan-Bin Sun ◽  
Hui Zhang ◽  
Xing-Fang Yuan ◽  
Yin-Xian Wang ◽  
Dong-Mei Feng ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Pr China

A Gram-negative, aerobic and non-motile rod, designated Y4T, was isolated from a cucumber leaf from Pinggu District, east Beijing, PR China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Y4T was most closely related to Luteimonas aquatica RIB1-20T (96.7 % 16S rRNA gene sequence similarity). DNA–DNA relatedness between strain Y4T and L. aquatica RIB1-20T was 42.5±3.9 %. The predominant fatty acids were iso-C15 : 0, iso-C17 : 1ω9c, iso-C16 : 0 and iso-C17 : 0. The major ubiquinone was Q-8. The DNA G+C content of the type strain was 69.9 mol%. Based on the evidence above, strain Y4T represents a novel species of the genus Luteimonas , for which the name Luteimonas cucumeris sp. nov. is proposed. The type strain is Y4T ( = CGMCC 1.10821T = KCTC 23627T).

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