Ruegeria intermedia sp. nov., a moderately thermophilic bacterium isolated from a coastal hot spring

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2538-2544 ◽  
Author(s):  
P. Kämpfer ◽  
A. B. Arun ◽  
P. D. Rekha ◽  
H.-J. Busse ◽  
C.-C. Young ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Gene Sequence ◽  
Hot Spring ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Moderately Thermophilic ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
The 16S Rrna Gene

A cream-coloured, Gram-negative, aerobic, non-motile moderately thermophilic, rod-to-irregular-shaped bacterium, CC-GIMAT-2T, was isolated from a coastal hot spring of Green Island (Lutao), located off Taituang, Taiwan, on marine agar 2216. The 16S rRNA gene sequence analysis and subsequent comparisons showed that it was placed into the genus Ruegeria with 97.4 % similarity to Ruegeria lacuscaerulensis ITI-1157T, and a lower sequence similarity to all other species of the genus Ruegeria . Reconstruction of phylogenetic trees indicated that strain CC-GIMAT-2T clustered within the genus Ruegeria . Robust tree topology for the genus Ruegeria including the new strain was only obtained by including all Rhodobacteraceae type strains but not if the analysis was limited to few selected taxa. The quinone system contained exclusively ubiquinone Q-10 and the fatty acid profile consisted mainly of C18 : 1ω7c, 11-methyl C18 : 1ω7c and C12 : 0 3-OH. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified aminolipid. Other lipids were detected in moderate to minor amounts. The characteristic feature of the polyamine pattern was the predominant triamine spermidine. On the basis of the 16S rRNA gene sequence analysis and of the chemotaxonomic and physiological data, strain CC-GIMAT-2T represents a novel species of the genus Ruegeria , for which the name Ruegeria intermedia sp. nov. is proposed. The type strain is CC-GIMAT-2T ( = CCUG 59209T = LMG 25539T = CCM 7758T).

Patulibacter medicamentivorans sp. nov., isolated from activated sludge of a wastewater treatment plant

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2588-2593 ◽  
Author(s):  
Bárbara Almeida ◽  
Ivone Vaz-Moreira ◽  
Peter Schumann ◽  
Olga C. Nunes ◽  
Gilda Carvalho ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Sequence Analysis ◽  
Type Species ◽  
Gene Sequence ◽  
Treatment Plant ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis

A Gram-positive, aerobic, non-motile, non-endospore-forming rod-shaped bacterium with ibuprofen-degrading capacity, designated strain I11T, was isolated from activated sludge from a wastewater treatment plant. The major respiratory quinone was demethylmenaquinone DMK-7, C18 : 1 cis9 was the predominant fatty acid, phosphatidylglycerol was the predominant polar lipid, the cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid and the G+C content of the genomic DNA was 74.1 mol%. On the basis of 16S rRNA gene sequence analysis, the closest phylogenetic neighbours of strain I11T were Patulibacter ginsengiterrae CECT 7603T (96.8 % similarity), Patulibacter minatonensis DSM 18081T (96.6 %) and Patulibacter americanus DSM 16676T (96.6 %). Phenotypic characterization supports the inclusion of strain I11T within the genus Patulibacter (phylum Actinobacteria) . However, distinctive features and 16S rRNA gene sequence analysis suggest that is represents a novel species, for which the name Patulibacter medicamentivorans sp. nov. is proposed. The type strain is I11T ( = DSM 25962T = CECT 8141T).

scholarly journals Taxonomic revision of the genus Geobacillus : emendation of Geobacillus , G. stearothermophilus , G. jurassicus , G. toebii , G. thermodenitrificans and G. thermoglucosidans (nom. corrig., formerly ‘thermoglucosidasius’); transfer of Bacillus thermantarcticus to the genus as G. thermantarcticus comb. nov.; proposal of Caldibacillus debilis gen. nov., comb. nov.; transfer of G. tepidamans to Anoxybacillus as A. tepidamans comb. nov.; and proposal of Anoxybacillus caldiproteolyticus sp. nov.

2012 ◽  
Vol 62 (Pt_7) ◽  
pp. 1470-1485 ◽  
Author(s):  
An Coorevits ◽  
Anna E. Dinsdale ◽  
Gillian Halket ◽  
Liesbeth Lebbe ◽  
Paul De Vos ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis

Sixty-two strains of thermophilic aerobic endospore-forming bacteria were subjected to polyphasic taxonomic study including 16S rRNA gene sequence analysis, polar lipid and fatty acid analysis, phenotypic characterization, and DNA–DNA hybridization experiments. Distinct clusters of the species Geobacillus stearothermophilus , Geobacillus thermodenitrificans , Geobacillus toebii and Geobacillus thermoglucosidasius were formed, allowing their descriptions to be emended, and the distinctiveness of the poorly represented species Geobacillus jurassicus , Geobacillus subterraneus and Geobacillus caldoxylosilyticus was confirmed. It is proposed that the name Geobacillus thermoglucosidasius be corrected to Geobacillus thermoglucosidans nom. corrig. Bacillus thermantarcticus clustered between Geobacillus species on the basis of 16S rRNA gene sequence analysis, and its transfer to the genus Geobacillus as Geobacillus thermantarcticus comb. nov. (type strain LMG 23032T = DSM 9572T = strain M1T = R-35644T) is proposed. The above-mentioned species, together with Geobacillus thermoleovorans and Geobacillus thermocatenulatus , form a monophyletic cluster representing the genus Geobacillus . The distinctiveness of ‘Geobacillus caldoproteolyticus’ was confirmed and it is proposed that it be accommodated, along with Geobacillus tepidamans , in the genus Anoxybacillus as Anoxybacillus caldiproteolyticus sp. nov. (type strain DSM 15730T = ATCC BAA-818T = LMG 26209T = R-35652T) and Anoxybacillus tepidamans comb. nov. (type strain LMG 26208T = ATCC BAA-942T = DSM 16325T = R-35643T), respectively. The type strain of Geobacillus debilis was not closely related to any members of the genera Anoxybacillus and Geobacillus , and it is proposed that this species be placed in the new genus Caldibacillus as Caldibacillus debilis gen. nov. comb. nov. The type strain of the type species, Caldibacillus debilis, is LMG 23386T ( = DSM 16016T = NCIMB 13995T = TfT = R-35653T).

Genome-based studies indicate that the Enterococcus faecium Clade B strains belong to Enterococcus lactis species and lack of the hospital infection associated markers

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Mireya Viviana Belloso Daza ◽  
Claudia Cortimiglia ◽  
Daniela Bassi ◽  
Pier Sandro Cocconcelli
Keyword(s):  
Sequence Analysis ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Ampicillin Resistance ◽  
Content Type ◽  
Link Type ◽  
Clade B ◽  
Gene Sequence Analysis

Enterococcus lactis and the heterotypic synonym Enterococcus xinjiangensis from dairy origin have recently been identified as a novel species based on 16S rRNA gene sequence analysis. Enterococcus faecium type strain NCTC 7171T was used as the reference genome for determining E. lactis and E. faecium to be separate species. However, this taxonomic classification did not consider the diverse lineages of E. faecium , and the double nature of hospital-associated (clade A) and community-associated (clade B) isolates. Here, we investigated the taxonomic relationship among isolates of E. faecium of different origins and E. lactis , using a genome-based approach. Additional to 16S rRNA gene sequence analysis, we estimated the relatedness among strains and species using phylogenomics based on the core pangenome, multilocus sequence typing, the average nucleotide identity and digital DNA–DNA hybridization. Moreover, following the available safety assessment schemes, we evaluated the virulence profile and the ampicillin resistance of E. lactis and E. faecium clade B strains. Our results confirmed the genetic and evolutionary differences between clade A and the intertwined clade B and E. lactis group. We also confirmed the absence in these strains of virulence gene markers IS16, hylEfm and esp and the lack of the PBP5 allelic profile associated with ampicillin resistance. Taken together, our findings support the reassignment of the strains of E. faecium clade B as E. lactis .

Parabacteroides faecis sp. nov., isolated from human faeces

2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1342-1346 ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Yoshiki Tanaka ◽  
Yoshimi Benno ◽  
Moriya Ohkuma
Keyword(s):  
Sequence Analysis ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Human Faeces ◽  
Link Type ◽  
Gene Sequence Analysis

A bacterial strain, designated 157T, isolated from human faeces was characterized by using a polyphasic taxonomic approach, which included analysis of physiological and biochemical features, cellular fatty acid profiles, menaquinone profiles and its phylogenetic position, based on 16S rRNA gene sequence analysis. The strain was obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-stain-negative rods. The isolate was able to grown on medium containing 20 % (w/v) bile. 16S rRNA gene sequence analysis showed that the strain was a member of the genus Parabacteroides . Strain 157T was closely related to Parabacteroides gordonii JCM 15724T (96 % sequence similarity). The results of hsp60 gene sequence analysis indicated that strain 157T was different from P. gordonii JCM 15724T, with a hsp60 gene sequence similarity of 96.1 %. The major cellular fatty acids of strain 157T were anteiso-C15 : 0, iso-C17 : 0 3-OH, C18 : 1ω9c and anteiso-C17 : 0 3-OH. The major menaquinone of the isolate was MK-9. The DNA G+C content of strain 157T was 41.8 mol%. On the basis of these data, strain 157T represents a novel species of the genus Parabacteroides , for which the name Parabacteroides faecis sp. nov. is proposed; the type strain is 157T ( = JCM 18682T = CCUG 66681T).

Weissella diestrammenae sp. nov., isolated from the gut of a camel cricket (Diestrammena coreana)

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 2951-2956 ◽  
Author(s):  
Sei Joon Oh ◽  
Na-Ri Shin ◽  
Dong-Wook Hyun ◽  
Pil Soo Kim ◽  
Joon Yong Kim ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
The 16S Rrna Gene

A novel, Gram-stain-positive, non-motile, facultatively anaerobic, rod- or coccoid-shaped bacterium, designated strain ORY33T, was isolated from the gut of a camel cricket (Diestrammena coreana). The 16S rRNA gene sequence analysis showed that strain ORY33T belonged to the genus Weissella , with highest sequence similarity to Weissella koreensis S-5623T (97.7 %). The strain grew optimally at 30 °C and pH 7 in the presence of 0 % (w/v) NaCl. Catalase and oxidase activities were negative. The genomic DNA G+C content of strain ORY33T was 45.1 mol%. DNA–DNA hybridization values between strain ORY33T and closely related members of the genus Weissella were less than 27 %. The major fatty acids of strain ORY33T were C18 : 1ω9c, C16 : 0 and C14 : 0. Based on these phenotypic, phylogenetic and genotypic analyses, strain ORY33T represents a novel species belonging to the genus Weissella , for which the name Weissella diestrammenae sp. nov. is proposed. The type strain is ORY33T ( = KACC 16890T = JCM 18559T).

scholarly journals Jhaorihella thermophila gen. nov., sp. nov., a moderately thermophilic bacterium isolated from a coastal hot spring

2011 ◽  
Vol 61 (7) ◽  
pp. 1544-1548 ◽  
Author(s):  
P. D. Rekha ◽  
Chiu-Chung Young ◽  
Peter Kämpfer ◽  
Karin Martin ◽  
A. B. Arun ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Hot Spring ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Moderately Thermophilic ◽  
Gene Sequence Analysis

A beige-coloured, Gram-staining negative, aerobic, non-motile, moderately thermophilic, rod-shaped bacterium, CC-MHSW-1T, was isolated on Marine Agar 2216 from a water sample from a coastal hot spring on Green Island (Lutao), located off Taituang, Taiwan. 16S rRNA gene sequence analysis demonstrated that the novel strain shared <94 % sequence similarity with members of the genera Lutimaribacter, Maritimibacter and Oceanicola. Ubiquinone (Q-10) was the major respiratory quinone and C18 : 1ω7c was the predominant fatty acid. The predominant polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and unidentified phospholipids and aminolipids. The DNA G+C content of strain CC-MHSW-1T was 64.7 mol%. On the basis of 16S rRNA gene sequence analysis and the chemotaxonomic and physiological data, strain CC-MHSW-1T represents a new genus and species in the family Rhodobacteraceae for which the name Jhaorihella thermophila gen. nov., sp. nov., is proposed. The type strain of the type species is CC-MHSW-1T ( = JCM 15068T = CCM 7767T).

Lactobacillus heilongjiangensis sp. nov., isolated from Chinese pickle

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4094-4099 ◽  
Author(s):  
Chun Tao Gu ◽  
Chun Yan Li ◽  
Li Jie Yang ◽  
Gui Cheng Huo
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Sequence Similarities

A Gram-stain-positive bacterial strain, S4-3T, was isolated from traditional pickle in Heilongjiang Province, China. The bacterium was characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, pheS gene sequence analysis, rpoA gene sequence analysis, dnaK gene sequence analysis, fatty acid methyl ester (FAME) analysis, determination of DNA G+C content, DNA–DNA hybridization and an analysis of phenotypic features. Strain S4-3T showed 97.9–98.7 % 16S rRNA gene sequence similarities, 84.4–94.1 % pheS gene sequence similarities and 94.4–96.9 % rpoA gene sequence similarities to the type strains of Lactobacillus nantensis , Lactobacillus mindensis , Lactobacillus crustorum , Lactobacillus futsaii , Lactobacillus farciminis and Lactobacillus kimchiensis . dnaK gene sequence similarities between S4-3T and Lactobacillus nantensis LMG 23510T, Lactobacillus mindensis LMG 21932T, Lactobacillus crustorum LMG 23699T, Lactobacillus futsaii JCM 17355T and Lactobacillus farciminis LMG 9200T were 95.4, 91.5, 90.4, 91.7 and 93.1 %, respectively. Based upon the data obtained in the present study, a novel species, Lactobacillus heilongjiangensis sp. nov., is proposed and the type strain is S4-3T ( = LMG 26166T = NCIMB 14701T).

scholarly journals Chelatococcus sambhunathii sp. nov., a moderately thermophilic alphaproteobacterium isolated from hot spring sediment

2010 ◽  
Vol 60 (4) ◽  
pp. 861-865 ◽  
Author(s):  
Digvijay Panday ◽  
Subrata K. Das
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Hot Spring ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Moderately Thermophilic ◽  
Gene Sequence Analysis

A moderately thermophilic bacterial strain (HT4T) isolated from a hot spring sediment was characterized phenotypically and phylogenetically. Cells were Gram-negative, aerobic, non-sporulating, rod-shaped and motile by means of a single polar flagellum. Both oxidase and catalase activities were positive. Heterotrophic growth was observed at pH 6.0–8.5 and at 20–50 °C; optimum growth occurred at pH 7.5–8.0 and 37–42 °C. The major cellular fatty acids were C14 : 0 3-OH, C18 : 0 3-OH, C18 : 1 2-OH, C18 : 1 ω7c and C19 : 0 cyclo ω8c. The DNA G+C content of strain HT4T was 67.8 mol%.16S rRNA gene sequence analysis indicated that strain HT4T clustered within the radiation of the genus Chelatococcus and showed 99.0 % similarity with Chelatococcus daeguensis CCUG 54519T and 96 % similarity with Chelatococcus asaccharovorans DSM 6462T. However, levels of DNA–DNA relatedness between strain HT4T and Chelatococcus daeguensis CCUG 54519T and Chelatococcus asaccharovorans DSM 6462T were 52 and 20 %, respectively. On the basis of the phenotypic, physiological and chemotaxonomic data, 16S rRNA gene sequence analysis and DNA–DNA hybridization results, strain HT4T is considered to represent a novel species of the genus Chelatococcus, for which the name Chelatococcus sambhunathii sp. nov. is proposed. The type strain is HT4T (=DSM 18167T=JCM 14988T).

scholarly journals Enterobacter xiangfangensis sp. nov., isolated from Chinese traditional sourdough, and reclassification of Enterobacter sacchari Zhu et al. 2013 as Kosakonia sacchari comb. nov.

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2650-2656 ◽  
Author(s):  
Chun Tao Gu ◽  
Chun Yan Li ◽  
Li Jie Yang ◽  
Gui Cheng Huo
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis

A Gram-stain-negative bacterial strain, 10-17T, was isolated from traditional sourdough in Heilongjiang Province, China. The bacterium was characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, RNA polymerase β subunit (rpoB) gene sequence analysis, DNA gyrase (gyrB) gene sequence analysis, initiation translation factor 2 (infB) gene sequence analysis, ATP synthase β subunit (atpD) gene sequence analysis, fatty acid methyl ester analysis, determination of DNA G+C content, DNA–DNA hybridization and an analysis of phenotypic features. Strain 10-17T was phylogenetically related to Enterobacter hormaechei CIP 103441T, Enterobacter cancerogenus LMG 2693T, Enterobacter asburiae JCM 6051T, Enterobacter mori LMG 25706T, Enterobacter ludwigii EN-119T and Leclercia adecarboxylata LMG 2803T, having 99.5 %, 99.3 %, 98.7 %, 98.5 %, 98.4 % and 98.4 % 16S rRNA gene sequence similarity, respectively. On the basis of polyphasic characterization data obtained in the present study, a novel species, Enterobacter xiangfangensis sp. nov., is proposed and the type strain is 10-17T ( = LMG 27195T = NCIMB 14836T = CCUG 62994T). Enterobacter sacchari Zhu et al. 2013 was reclassified as Kosakonia sacchari comb. nov. on the basis of 16S rRNA, rpoB, gyrB, infB and atpD gene sequence analysis and the type strain is strain SP1T( = CGMCC 1.12102T = LMG 26783T).

Description of Noviherbaspirillum malthae gen. nov., sp. nov., isolated from an oil-contaminated soil, and proposal to reclassify Herbaspirillum soli , Herbaspirillum aurantiacum , Herbaspirillum canariense and Herbaspirillum psychrotolerans as Noviherbaspirillum soli comb. nov., Noviherbaspirillum aurantiacum comb. nov., Noviherbaspirillum canariense comb. nov. and Noviherbaspirillum psychrotolerans comb. nov. based on polyphasic analysis

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4100-4107 ◽  
Author(s):  
Shih-Yao Lin ◽  
Asif Hameed ◽  
A. B. Arun ◽  
You-Cheng Liu ◽  
Yi-Han Hsu ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis

An aerobic, Gram-negative, rod-shaped bacterium with polar flagella, strain CC-AFH3T, was isolated from an oil-contaminated site located in Kaohsiung county, Taiwan. Strain CC-AFH3T grew at 20–40 °C, pH 5.0–10.0 and <2 % (w/v) NaCl. 16S rRNA gene sequence analysis indicated that strain CC-AFH3T showed the greatest degree of similarity to Herbaspirillum soli SUEMI10T (96.5 %), H. aurantiacum SUEMI08T (96.3 %), H. canariense SUEMI03T (96.0 %), H. psychrotolerans PB1T (95.4 %) and members of other Herbaspirillum species (94.1–95.2 %), and lower similarity to members of other genera (<94 %). Phylogenetic analyses also positioned the novel strain in the genus Herbaspirillum as an independent lineage. The major fatty acids in strain CC-AFH3T were C10 : 0 3-OH, C12 : 0, C14 : 0 2-OH, C16 : 0, iso-C15 : 0 3-OH, C17 : 0 cyclo, C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c. The major polar lipids of strain CC-AFH3T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. The predominant quinone was ubiquinone 8 (Q-8) and the DNA G+C content was 63.4 mol%. On the basis of 16S rRNA gene sequence analysis in combination with physiological and chemotaxonomic data, strain CC-AFH3T represents a novel species in a new genus, for which we propose the name Noviherbaspirillum malthae gen. nov., sp. nov.; the type strain of Noviherbaspirillum malthae is CC-AFH3T ( = BCRC 80516T = JCM 18414T). We also propose the reclassification of Herbaspirillum soli , Herbaspirillum aurantiacum , Herbaspirillum canariense and ‘Herbaspirillum psychrotolerans’ as Noviherbaspirillum soli comb. nov. (type strain SUEMI10T = LMG 26149T = CECT 7840T), Noviherbaspirillum aurantiacum comb. nov. (type strain SUEMI08T = LMG 26150T = CECT 7839T), Noviherbaspirillum canariense comb. nov. (type strain SUEMI03T = LMG 26151T = CECT 7838T) and Noviherbaspirillum psychrotolerans comb. nov. (type strain PB1T = DSM 26001T = LMG 27282T), respectively. An emended description of Herbaspirillum seropedicae is also presented.

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