scholarly journals Sediminicola luteus gen. nov., sp. nov., a novel member of the family Flavobacteriaceae

2006 ◽  
Vol 56 (4) ◽  
pp. 841-845 ◽  
Author(s):  
Shams Tabrez Khan ◽  
Yasuyoshi Nakagawa ◽  
Shigeaki Harayama
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
Golden Yellow ◽  
The Family

The taxonomic position of four Gram-negative, rod-shaped, golden-yellow-coloured bacteria isolated from marine sediments was determined. Analysis of the almost complete 16S rRNA gene sequences indicated that these isolates belong to the family Flavobacteriaceae. An unclassified bacterium, NBRC 15975, was found to be the closest relative, showing 16S rRNA gene sequence similarity of 93 %; other related genera shared only 87·9–90·5 % similarity. In contrast, the four isolates shared high levels of 16S rRNA gene sequence similarity (99·3–99·7 %) and high DNA–DNA reassociation values (93–104 %). The isolates could be differentiated phenotypically from other genera by the abilities to reduce nitrate and to degrade gelatin, casein and starch. The only respiratory quinone was MK-6, and the major fatty acids were iso-C15 : 0, iso-C15 : 1, anteiso-C15 : 0, iso-C17 : 1 ω9c and iso-C17 : 0 3-OH. The DNA G+C content was 38–40 mol%. Differentiating phenotypic characteristics and large phylogenetic distances between the isolates and previously published genera indicated that the isolates constitute a novel genus, for which the name Sediminicola gen. nov. is proposed. The type species is Sediminicola luteus sp. nov. (type strain CNI-3T=NBRC 100966T=LMG 23246T).

scholarly journals Hydromonas duriensis gen. nov., sp. nov., isolated from freshwater

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 4134-4139 ◽  
Author(s):  
Ivone Vaz-Moreira ◽  
Carlos Narciso-da-Rocha ◽  
Evie De Brandt ◽  
Peter Vandamme ◽  
A. C. Silva Ferreira ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
The Family ◽  
Major Respiratory Quinone

An aerobic, Gram-stain-negative rod, designated strain A2P5T, was isolated from the Douro river, in Porto, Portugal. Cells were catalase- and oxidase-positive. Growth occurred at 15–30 °C, at pH 6–8 and in the presence of 1 % (w/v) NaCl. The major respiratory quinone was Q8, the genomic DNA had a G+C content of 47 ± 1 mol%, and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol were amongst the major polar lipids. On the basis of 16S rRNA gene sequence analysis, strain A2P5T was observed to be a member of the family Burkholderiaceae, but could not be identified as a member of any validly named genus. The low levels of 16S rRNA gene sequence similarity to other recognized taxa ( < 91 %), together with the comparative analysis of phenotypic and chemotaxonomic characteristics, supported the proposal of a novel species of a new genus within the family Burkholderiaceae. The name Hydromonas duriensis gen. nov., sp. nov. is proposed. The type strain of Hydromonas duriensis is A2P5T ( = LMG 28428T = CCUG 66137T).

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).

Sandarakinotalea sediminis gen. nov., sp. nov., a novel member of the family Flavobacteriaceae

2006 ◽  
Vol 56 (5) ◽  
pp. 959-963 ◽  
Author(s):  
Shams Tabrez Khan ◽  
Yasuyoshi Nakagawa ◽  
Shigeaki Harayama
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Heterotrophic Bacteria ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
The Family

Four Gram-negative, orange-coloured, aerobic, heterotrophic bacteria were isolated from sediment samples collected on the Pacific coast of Japan near the cities of Toyohashi and Katsuura. 16S rRNA gene sequence analysis indicated that these strains form a distinct lineage within the family Flavobacteriaceae. The four isolates shared 99.9–100 % 16S rRNA gene sequence similarity with each other and showed 88–90.9 % similarity with their neighbours in the family Flavobacteriaceae. The four strains also shared high DNA–DNA reassociation values of 67–99 % with each other. All the strains grew at 37 °C but not at 4 °C, and degraded gelatin, starch and DNA. The major fatty acids were i-C15 : 0, a-C15 : 0, i-C16 : 0 and i-C17 : 0 3-OH. However, two common fatty acids of members of the Flavobacteriaceae, i-C15 : 1 and a-C15 : 1, were absent in these strains. The DNA G+C contents of the four strains were in the range 35–37 mol%. On the basis of the polyphasic evidence, it was concluded that these strains should be classified as a novel genus and a novel species in the family Flavobacteriaceae, for which the name Sandarakinotalea sediminis gen. nov., sp. nov. is proposed. The type strain of Sandarakinotalea sediminis is CKA-5T (=NBRC 100970T=LMG 23247T).

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 Pseudosphingobacterium domesticum gen. nov., sp. nov., isolated from home-made compost

2007 ◽  
Vol 57 (7) ◽  
pp. 1535-1538 ◽  
Author(s):  
Ivone Vaz-Moreira ◽  
M. Fernanda Nobre ◽  
Olga C. Nunes ◽  
Célia M. Manaia
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Family

A bacterial strain, DC-186T, isolated from home-made compost, was characterized for its phenotypic and phylogenetic properties. The isolate was a Gram-negative rod that was able to grow at 15–36 °C and pH 5.5–8.0. Strain DC-186T was positive in tests for catalase, oxidase and β-galactosidase activities and aesculin hydrolysis. The predominant fatty acids were the summed feature C16 : 1/iso-C15 : 0 2-OH (42 %) and iso-C15 : 0 (26 %), the major respiratory quinone was menaquinone-7 and the genomic DNA G+C content was 42 mol%. 16S rRNA gene sequence analysis and phenetic characterization indicated that this organism belongs to the phylum Bacteroidetes and revealed its affiliation to the family Sphingobacteriaceae. Of recognized taxa, strain DC-186T was most closely related to Sphingobacterium daejeonense (90 % sequence similarity) based on 16S rRNA gene sequence analysis. The low 16S rRNA gene sequence similarity with other recognized taxa and the identification of distinctive phenetic features for this isolate support the definition of a new genus within the family Sphingobacteriaceae. The name Pseudosphingobacterium domesticum gen. nov., sp. nov. is proposed, with strain DC-186T (=CCUG 54353T=LMG 23837T) as the type strain.

scholarly journals Litorimonas taeanensis gen. nov., sp. nov., isolated from a sandy beach

2011 ◽  
Vol 61 (7) ◽  
pp. 1534-1538 ◽  
Author(s):  
Ji Young Jung ◽  
Jeong Myeong Kim ◽  
Hyun Mi Jin ◽  
Sun Young Kim ◽  
Woojun Park ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sandy Beach ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
The Family

A heterotrophic, Gram-negative, prosthecate bacterium, designated strain G5T, was isolated from a sandy beach of Taean in South Korea. Cells of strain G5T were aerobic, catalase- and oxidase-positive, straight to slightly curved motile rods with a single flagellum and formed yellow–orange colonies on agar. Growth occurred at 15–40 °C (optimum 25–30 °C) and pH 6–9 (optimum pH 7–8). The major cellular fatty acids were C18 : 1ω7c, C17 : 0, C16 : 0, 11-methyl C18 : 1ω7c, C17 : 1ω8c and C17 : 1ω6c. The polar lipid pattern indicated the presence of phosphatidylglycerol, monoglycosyldiglyceride, glucuronopyranosyldiglyceride and two unidentified glycolipids. The G+C content of the genomic DNA was 63.6 mol% and the major quinone was Q-10. Comparative 16S rRNA gene sequence analysis showed that strain G5T belonged to the branch containing the genera Hellea, Robiginitomaculum and Hypomonas within the family Hyphomonadaceae. Within this group, strain G5T was most closely related to Hellea balneolensis 26III/A02/215T with 95.8 % 16S rRNA gene sequence similarity. Based on its phylogenetic position and its phenotypic, chemotaxonomic and molecular properties, strain G5T represents a novel species of a novel genus of the family Hyphomonadaceae, for which the name Litorimonas taeanensis gen. nov., sp. nov. is proposed. The type strain is G5T ( = KACC 13701T  = DSM 22008T).

scholarly journals Gracilibacillus ureilyticus sp. nov., a halotolerant bacterium from a saline–alkaline soil

2010 ◽  
Vol 60 (6) ◽  
pp. 1383-1386 ◽  
Author(s):  
Ying-Yi Huo ◽  
Xue-Wei Xu ◽  
Heng-Lin Cui ◽  
Min Wu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Alkaline Soil ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone

A Gram-stain-positive, halotolerant, neutrophilic, rod-shaped bacterium, strain MF38T, was isolated from a saline–alkaline soil in China and subjected to a polyphasic taxonomic characterization. The isolate grew in the presence of 0–15 % (w/v) NaCl and at pH 6.5–8.5; optimum growth was observed with 3.0 % (w/v) NaCl and at pH 7.0. Chemotaxonomic analysis showed menaquinone MK-7 as the predominant respiratory quinone and anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0, C17 : 0 and C16 : 0 as major fatty acids. The genomic DNA G+C content was 35.3 mol%. 16S rRNA gene sequence similarities of strain MF38T with type strains of described Gracilibacillus species ranged from 95.3 to 97.7 %. Strain MF38T exhibited the closest phylogenetic affinity to the type strain of Gracilibacillus dipsosauri, with 97.7 % 16S rRNA gene sequence similarity. The DNA–DNA reassociation between strain MF38T and G. dipsosauri DSM 11125T was 45 %. On the basis of phenotypic and genotypic data, strain MF38T represents a novel species of the genus Gracilibacillus, for which the name Gracilibacillus ureilyticus sp. nov. (type strain MF38T =CGMCC 1.7727T =JCM 15711T) is proposed.

scholarly journals Paenibacillus humicus sp. nov., isolated from poultry litter compost

2007 ◽  
Vol 57 (10) ◽  
pp. 2267-2271 ◽  
Author(s):  
Ivone Vaz-Moreira ◽  
Cátia Faria ◽  
M. Fernanda Nobre ◽  
Peter Schumann ◽  
Olga C. Nunes ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Poultry Litter ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Respiratory Quinone

Two bacterial strains, PC-142 and PC-147T, isolated from poultry litter compost, were characterized with respect to their phenetic and phylogenetic characteristics. The isolates were endospore-forming rods that were reddish in colour after Gram staining. They were catalase- and oxidase-positive, were able to degrade starch and gelatin and grew at 15–40 °C and pH 5.5–10.0. The predominant fatty acids were anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0, the major respiratory quinone was menaquinone MK-7, the cell-wall peptidoglycan was of the A1γ type and the G+C content of the DNA was 58 mol%. The 16S rRNA gene sequence analysis and phenetic characterization indicated that these organisms belong to the genus Paenibacillus, with Paenibacillus pasadenensis SAFN-007T as the closest phylogenetic neighbour (97.5 %). Strains PC-142, PC-147T and P. pasadenensis SAFN-007T represent a novel lineage within the genus Paenibacillus, characterized by a high DNA G+C content (58–63 mol%). The low levels of 16S rRNA gene sequence similarity with respect to other taxa with validly published names and the identification of distinctive phenetic features in the two isolates indicate that strains PC-142 and PC-147T represent a novel species of the genus Paenibacillus, for which the name Paenibacillus humicus sp. nov. is proposed. The type strain is PC-147T (=DSM 18784T =NBRC 102415T =LMG 23886T).

scholarly journals Limibacillus halophilus gen. nov., sp. nov., a moderately halophilic bacterium in the family Rhodospirillaceae isolated from reclaimed land

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3155-3161 ◽  
Author(s):  
Jong-Hwa Kim ◽  
Maytiya Konkit ◽  
Jung-Hoon Yoon ◽  
Wonyong Kim
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Reclaimed Land ◽  
Moderately Halophilic Bacterium ◽  
The Family

A Gram-stain-negative, aerobic, non-motile, non-spore-forming and short rod-shaped bacterial strain, designated CAU 1121T, was isolated from reclaimed land in the Republic of Korea and its taxonomic position was investigated using a polyphasic approach. The bacterium grew optimally at 37 °C, at pH 6.5 and in the presence of 2 % (w/v) NaCl. Based on 16S rRNA gene sequence similarity, the novel isolate belonged to the family Rhodospirillaceae within the class Alphaproteobacteria and formed an independent lineage within the evolutionary radiation encompassed by the phylum Proteobacteria. Strain CAU 1121T exhibited very low levels of 16S rRNA gene sequence similarity with its phylogenetic neighbours Pelagibius litoralis (similarity, 92.5 %), Fodinicurvata fenggangensis (similarity, 91.4 %), Fodinicurvata sediminis (similarity, 90.7 %) and Tistlia consotensis (similarity, 91.0 %). Strain CAU 1121T contained ubiquinone-10 as the only respiratory quinone and C18 : 1ω7c as the major cellular fatty acid. The DNA G+C content of the strain was 65 mol%. On the basis of phylogenetic inference, and physiological and chemotaxonomic data, it is proposed that strain CAU 1121T represents a novel genus and novel species in the family Rhodospirillaceae, for which the name Limibacillus halophilus gen. nov., sp. nov. is suggested. The type strain is CAU 1121T ( = KCTC 42420T = CECT 8803T = NBRC 110928T).

scholarly journals Alkalimicrobium pacificum gen. nov., sp. nov., a marine bacterium in the family Rhodobacteraceae

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2453-2458 ◽  
Author(s):  
Gaiyun Zhang ◽  
Yanliu Yang ◽  
Shuang Wang ◽  
Zhilei Sun ◽  
Kailin Jiao
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Data ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Unidentified Phospholipid ◽  
The Family

A Gram-stain-negative, aerobic, non-motile, rod-shaped bacterium, designated strain F15T, was isolated from a deep-sea sediment of the western Pacific Ocean. The temperature, pH and NaCl ranges for growth were 4–50 °C, pH 6–11 and 0–10 % (w/v), respectively. Strain F15T showed the highest 16S rRNA gene sequence similarity to Sagittula stellata E-37T (96.4 %), followed by Ponticoccus litoralis CL-GR66T (96.4 %), Antarctobacter heliothermus EL-219T (96.3 %) and Thalassococcus lentus YCS-24T (96.0 %). Phylogenetic analysis based on 16S rRNA gene sequence data showed that strain F15T formed a lineage within the family Rhodobacteraceae of the class Alphaproteobacteria. The polar lipid profile of strain F15T comprised significant amounts of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified glycolipid and one unidentified phospholipid. The predominant cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c, 40.2 %), anteiso-C15 : 0 (30.4 %) and anteiso-C17 : 0 (9.7 %). The genomic DNA G+C content of strain F15T was 60.2 mol% and the major respiratory quinone was Q-10. On the basis of phenotypic, phylogenetic and chemotaxonomic data, strain F15T is considered to represent a novel species of a new genus within the family Rhodobacteraceae, for which the name Alkalimicrobium pacificum gen. nov., sp. nov. is proposed. The type strain is F15T ( = LMG 28107T = JCM 19851T = CGMCC 1.12763T = MCCC 1A09948T).

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