scholarly journals Pannonibacter phragmitetus, described from a Hungarian soda lake in 2003, had been recognized several decades earlier from human blood cultures as Achromobacter groups B and E

2006 ◽  
Vol 56 (12) ◽  
pp. 2945-2948 ◽  
Author(s):  
Barry Holmes ◽  
Paul Segers ◽  
Tom Coenye ◽  
Marc Vancanneyt ◽  
Peter Vandamme
Keyword(s):  
Human Blood ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Soda Lake ◽  
Single Species ◽  
Blood Cultures ◽  
Rrna Gene ◽  
Gene Sequence Analysis ◽  
The Uk ◽  
Human Blood Cultures

We performed a polyphasic taxonomic study on isolates previously tentatively classified as Achromobacter groups B and E in comparison with the type strain of Pannonibacter phragmitetus, LMG 22736T=NCTC 13350T. Comparative 16S rRNA gene sequence analysis suggested that strains of Achromobacter groups B and E belong to P. phragmitetus (similarity levels were higher than 99 %). DNA–DNA hybridization experiments and other genotypic and phenotypic analyses confirmed that the three taxa represent a single species. Whilst P. phragmitetus was described in 2003 from a Hungarian soda lake, it had been observed in human blood cultures in the UK since 1975. We present here the characteristics of the organism to facilitate its recognition in human clinical specimens and hence to determine its clinical significance.

scholarly journals Fuchsiella ferrireducens sp. nov., a novel haloalkaliphilic, lithoautotrophic homoacetogen capable of iron reduction, and emendation of the description of the genus Fuchsiella

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2432-2440 ◽  
Author(s):  
Tatyana N. Zhilina ◽  
Daria G. Zavarzina ◽  
Ekaterina N. Detkova ◽  
Ekaterina O. Patutina ◽  
Boris B. Kuznetsov
Keyword(s):  
Dna Hybridization ◽  
Iron Reduction ◽  
Gene Sequence ◽  
Soda Lake ◽  
Chloride Ions ◽  
Electron Donors ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequence Analysis ◽  
Ph Range

Two strains of haloalkaliphilic homoacetogenic bacteria capable of iron reduction, Z-7101T and Z-7102, were isolated from soda lake Tanatar III (Altai, Russia). Cells of both strains were flexible, motile, Gram-negative, spore-forming rods. The strains were mesophilic and obligately alkaliphilic: the pH range for growth was 8.5–10.2 (pHopt 9.8). Growth depended on carbonate and chloride ions. The strains were able to grow chemolithoautotrophically on H2+CO2, producing acetate as the only metabolic product. In medium with carbonates as the only potential electron acceptor, the following substrates were utilized for chemo-organotrophic growth: pyruvate, lactate, ethanol, 1-propanol, ethylene glycol and 1-butanol. Strain Z-7101T was able to reduce nitrate, selenate, thiosulfate and anthraquinone 2,6-disulfonate with ethanol as an electron donor. It was also able to reduce synthesized ferrihydrite to siderite with molecular hydrogen or organic compounds, including acetate and formate, as electron donors. It was able to reduce S0 with acetate or formate as electron donors. The DNA G+C content of strain Z-7101T was 34.6 mol%. 16S rRNA gene sequence analysis showed that strains Z-7101T and Z-7102 were members of the order Halanaerobiales and family Halobacteroidaceae, clustering with Fuchsiella alkaliacetigena Z-7100T (98.9–98.4 % similarity). DNA–DNA hybridization was 63.0 % between strain Z-7101T and F. alkaliacetigena Z-7100T. Based on morphological and physiological differences from F. alkaliacetigena Z-7100T and the results of phylogenetic analysis and DNA–DNA hybridization, it is proposed to assign strains Z-7101T and Z-7102 ( = DSM 26052 = VKM B-2790) to the novel species Fuchsiella ferrireducens sp. nov. The type strain is strain Z-7101T ( = DSM 26031T = VKM B-2766T).

scholarly journals First Report ofClostridium lavalenseIsolated in Human Blood Cultures

2016 ◽  
Vol 2016 ◽  
pp. 1-3
Author(s):  
Richard Garceau ◽  
Christine Bourque ◽  
Louise Thibault ◽  
Jean-Charles Côté ◽  
Jean Longtin ◽  
...  
Keyword(s):  
Human Blood ◽  
Gene Sequence ◽  
Blood Cultures ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
First Report ◽  
Oral Amoxicillin ◽  
Diagnostic Samples ◽  
Human Blood Cultures

An 88-year-old man was admitted to the hospital with worsening malaise, fever, and weakness. Anaerobic blood culture bottles revealed the presence of an anaerobic, Gram-positive sporulated bacillus. Empirical antibiotherapy with intravenous piperacillin-tazobactam was initiated. The patient defervesced after four days and was switched to oral amoxicillin on his 6th day of antibiotic therapy and later discharged from the hospital. Four months later, he had recovered. The bacterium was initially identified asClostridium butyricumusing anaerobic manual identification panel. 16S rRNA gene sequence and phylogenetic analysis showed the bacterium to beClostridium lavalense, a recently described species with no previously published case of isolation in human diagnostic samples so far. This is the first report ofClostridium lavalenseisolation from human blood cultures. Further studies are needed in order to elucidate the role ofClostridium lavalensein human disease and its virulence factors.

scholarly journals Kaistia terrae sp. nov., isolated from a wetland in Korea

2010 ◽  
Vol 60 (4) ◽  
pp. 949-952 ◽  
Author(s):  
Soo-Jin Kim ◽  
Hang-Yeon Weon ◽  
Yi-Seul Kim ◽  
Rangasamy Anandham ◽  
Seung-Hee Yoo ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

An ivory-coloured bacterium, designated strain 5YN7-3T, was isolated from a wetland, Yongneup, Korea. Cells of the strain were aerobic, Gram-stain-negative, non-motile and short rods. 16S rRNA gene sequence analysis demonstrated that strain 5YN7-3T belongs to the order Rhizobiales of the class Alphaproteobacteria and is closely related to Kaistia soli 5YN9-8T (97.8 %), Kaistia granuli Ko04T (97.6 %) and Kaistia adipata Chj404T (97.4 %). Strain 5YN7-3T showed DNA–DNA hybridization values of 28, 22 and 35 % with K. granuli Ko04T, K. soli 5YN9-8T and K. adipata Chj404T, respectively. The major fatty acids were C18 : 1 ω7c (51.2 %), C19 : 0 cyclo ω8c (25.0 %), C18 : 0 (12.9 %) and C16 : 0 (10.8 %) (>10 % of total fatty acids). Ubiquinone-10 was the major isoprenoid quinone and the DNA G+C content was 66.5 mol%. The phenotypic characteristics in combination with 16S rRNA gene sequence analysis and DNA–DNA hybridization data clearly define strain 5YN7-3T as a novel species of the genus Kaistia, for which the name Kaistia terrae sp. nov. is proposed. The type strain is 5YN7-3T (=KACC 12910T =DSM 21341T).

scholarly journals Lysobacter novalis sp. nov., isolated from fallow farmland soil

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3131-3136 ◽  
Author(s):  
Hina Singh ◽  
Juan Du ◽  
Kyung-Hwa Won ◽  
Jung-Eun Yang ◽  
Shahina Akter ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Gliding Motility ◽  
Rrna Gene ◽  
The Novel ◽  
Respiratory Quinone ◽  
Gene Sequence Analysis ◽  
Farmland Soil ◽  
Major Respiratory Quinone

A novel bacterial strain, designated THG-PC7T, was isolated from fallow farmland soil in Yongin, South Korea. Cells of strain THG-PC7T were Gram-stain-negative, dark yellow, aerobic, rod-shaped and had gliding motility. Strain THG-PC7T grew optimally at 25–35 °C, at pH 7 and in the absence of NaCl. Comparative 16S rRNA gene sequence analysis identified strain THG-PC7T as belonging to the genus Lysobacter, exhibiting highest sequence similarity with Lysobacter ximonensis KCTC 22336T (98.7 %) followed by Lysobacter niastensis KACC 11588T (95.7 %). In DNA–DNA hybridization tests, DNA relatedness between strain THG-PC7T and its closest phylogenetic neighbour L. ximonensis was below 25 %. The DNA G+C content of the novel isolate was determined to be 62.5 mol%. Flexirubin-type pigments were found to be present. The major cellular fatty acids were determined to be iso-C15 : 0, iso-C16 : 0, anteiso-C15 : 0 and iso-C17 : 1ω9c. The major respiratory quinone was identified as ubiquonone-8 (Q8). The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospolipid. On the basis of results from DNA–DNA hybridization and the polyphasic data, strain THG-PC7T represents a novel species of the genus Lysobacter, for which the name Lysobacter novalis sp. nov. is proposed. The type strain is THG-PC7T( = KACC 18276T = CCTCC AB 2014319T).

scholarly journals Dyella monticola sp. nov. and Dyella psychrodurans sp. nov., isolated from monsoon evergreen broad-leaved forest soil of Dinghu Mountain, China

2019 ◽  
Vol 69 (4) ◽  
pp. 1016-1023 ◽  
Author(s):  
Xiang-yue Zhou ◽  
Zeng-hong Gao ◽  
Mei-hong Chen ◽  
Mei-qi Jian ◽  
Li-hong Qiu
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Broad Leaved Forest ◽  
Gene Sequence Analysis ◽  
Leaved Forest

Cells of bacterial strains 4 G-K06T and 4MSK11T, isolated from soil samples collected from monsoon evergreen broad-leaved forest of the Dinghushan Mountain (112° 31′ E 23° 10′ N), Guangdong Province, PR China, were Gram-stain-negative, aerobic, non-spore-forming, non-motile and rod-shaped. Strain 4 G-K06T grew at 10–37 °C, pH 3.5–7.5 and 0–3.5 % (w/v) NaCl; while 4MSK11T grew at 4–42 °C, pH 3.5–7.5 and 0–2.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed strain 4 G-K06T formed a clade with Dyella flagellata 4 M-K16T, Dyella acidisoli 4M-Z03T, Dyella humi DHG40T and Dyella nitratireducens DHG59T, while strain 4MSK11T formed a clade with Dyella caseinilytica DHOB09T and Dyella mobilis DHON07T, both within the genus Dyella . The result of the partial atpD, gyrB and lepA gene sequence analysis supported the conclusion based on 16S rRNA gene sequence analysis, which showed that these two strains represent two novel species of Dyella . The average nucleotide identity and digital DNA–DNA hybridization value for the whole genomes were 75.0–79.0 and 20.3–22.6 % between strains 4 G-K06T, 4MSK11T and those described Dyella species with genome sequences; while the DNA–DNA hybridization rates between strains 4 G-K06T, 4MSK11T and closely related Dyella species (without genome sequence) were 29.5–41.8 %. The major cellular fatty acids of these two strains were iso-C15 : 0, iso-C16 : 0 and iso-C17 : 1 ω9c, while the major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several unidentified phospholipids and aminophospholipids. The only ubiquinone of these two strains was ubiquinone-8. The DNA G+C contents of 4 G-K06T and 4MSK11T were 60.4 and 61.3 mol%, respectively. On the basis of the evidence presented here, strains 4 G-K06T and 4MSK11T represent two novel species of the genus Dyella , for which the names Dyella monticola sp. nov. (type strain 4 G-K06T=LMG 30268T=GDMCC 1.1188T) and Dyella psychrodurans sp. nov. (type strain 4MSK11T=KCTC 62280T=GDMCC 1.1185T) are proposed.

scholarly journals Halioglobus maricola sp. nov., isolated from coastal seawater

2020 ◽  
Vol 70 (3) ◽  
pp. 1868-1875 ◽  
Author(s):  
Shan-Hui Li ◽  
Jaeho Song ◽  
Yeonjung Lim ◽  
Yochan Joung ◽  
Ilnam Kang ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
A Genome ◽  
The 16S Rrna Gene

A Gram-stain-negative, rod-shaped, aerobic, non-flagellated, chemoheterotrophic bacterium, designated IMCC14385T, was isolated from surface seawater of the East Sea, Republic of Korea. The 16S rRNA gene sequence analysis indicated that IMCC14385T represented a member of the genus Halioglobus sharing 94.6–97.8 % similarities with species of the genus. Whole-genome sequencing of IMCC14385T revealed a genome size of 4.3 Mbp and DNA G+C content of 56.7 mol%. The genome of IMCC14385T shared an average nucleotide identity of 76.6 % and digital DNA–DNA hybridization value of 21.6 % with the genome of Halioglobus japonicus KCTC 23429T. The genome encoded the complete poly-β-hydroxybutyrate biosynthesis pathway. The strain contained summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C17 : 1 ω8c as the predominant cellular fatty acids as well as ubiquinone-8 (Q-8) as the respiratory quinone. The polar lipids detected in the strain were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, five unidentified phospholipids, an unidentified aminolipid, an unidentified aminophospholipid and four unidentified lipids. On the basis of taxonomic data obtained in this study, it is suggested that IMCC14385T represents a novel species of the genus Halioglobus , for which the name Halioglobus maricola sp. nov. is proposed. The type strain is IMCC14385T (=KCTC 72520T=NBRC 114072T).

Isolation and description of Selenomonas timonae sp. nov., a novel Selenomonas species detected in a gingivitis patient

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Angéline Antezack ◽  
Manon Boxberger ◽  
Mariem Ben Khedher ◽  
Bernard La Scola ◽  
Virginie Monnet-Corti
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
A Genome ◽  
Optimum Ph

A Gram-stain-negative bacterium, designated strain Marseille-Q3039T, was isolated from subgingival dental plaque of a woman with gingivitis in Marseille, France. Strain Marseille-Q3039T was found to be an anaerobic, motile and spore-forming crescent-shaped bacterium that grew at 25–41.5 °C (optimum, 37 °C), pH 5.5–8.5 (optimum, pH 7.5) and salinity of 5.0 g l−1 NaCl. The results of 16S rRNA gene sequence analysis revealed that strain Marseille-Q3039T was closely related to Selenomonas infelix ATCC 43532T (98.42 % similarity), Selenomonas dianae ATCC 43527T (97.25 %) and Centipedia periodontii DSM 2778T (97.19 %). The orthologous average nucleotide identity and digital DNA–DNA hybridization relatedness between strain Q3039T and its closest phylogenetic neighbours were respectively 84.57 and 28.2 % for S. infelix ATCC 43532T and 83.93 and 27.2 % for C. periodontii DSM 2778T. The major fatty acids were identified as C13 : 0 (27.7 %), C15 : 0 (24.4 %) and specific C13 : 0 3-OH (12.3 %). Genome sequencing revealed a genome size of 2 351 779 bp and a G+C content of 57.2 mol%. On the basis of the results from phenotypic, chemotaxonomic, genomic and phylogenetic analyses and data, we concluded that strain Marseille-Q3039T represents a novel species of the genus Selenomonas , for which the name Selenomonas timonae sp. nov. is proposed (=CSUR Q3039=CECT 30128).

Terrabacter carboxydivorans sp. nov., a carbon monoxide-oxidizing actinomycete

2011 ◽  
Vol 61 (3) ◽  
pp. 482-486 ◽  
Author(s):  
Sung M. Kim ◽  
Sae W. Park ◽  
Sang T. Park ◽  
Young M. Kim
Keyword(s):  
Carbon Monoxide ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Gene Sequence Analysis ◽  
Diamino Acid ◽  
Type Strains

A bacterial strain, PY2T, capable of oxidizing carbon monoxide, was isolated from a soil sample collected from a roadside at Yonsei University, Seoul, Korea. On the basis of 16S rRNA gene sequence analysis, strain PY2T was shown to belong to the genus Terrabacter and was most closely related to Terrabacter lapilli LR-26T (99.1 % similarity). Strain PY2T was characterized chemotaxonomically as having iso-C15 : 0 as the predominant fatty acid, MK-8(H4) as the major menaquinone, ll-diaminopimelic acid as the diagnostic diamino acid of the cell wall, as possessing a polar lipid profile that included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and unknown amino-containing phosphoglycolipids, and having a DNA G+C content of 75.6 mol%. DNA–DNA relatedness values between strain PY2T and the type strains of T. lapilli, Terrabacter tumescens, Terrabacter terrae and Terrabacter aerolatus were 20.0 %, 22.9 %, 35.9 % and 64.5 %, respectively. Based on the combined evidence from the phylogenetic analyses, chemotaxonomic data and DNA–DNA hybridization experiments, it is proposed that strain PY2T represents a novel species for which the name Terrabacter carboxydivorans sp. nov. is proposed. The type strain is PY2T (=KCCM 42922T=JCM 16259T).

scholarly journals Halorubrum aquaticum sp. nov., an archaeon isolated from hypersaline lakes

2011 ◽  
Vol 61 (5) ◽  
pp. 1144-1148 ◽  
Author(s):  
M. C. Gutiérrez ◽  
A. M. Castillo ◽  
P. Corral ◽  
M. Kamekura ◽  
A. Ventosa
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Lipid Analysis ◽  
Halophilic Archaea ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Dna Relatedness ◽  
Gene Sequence Analysis ◽  
Nacl Concentration ◽  
Optimum Ph

Two halophilic archaea, strains EN-2T and SH-4, were isolated from the saline lakes Erliannor and Shangmatala, respectively, in Inner Mongolia, China. Cells were strictly aerobic, motile rods. Colonies were red. Strains EN-2T and SH-4 were able to grow at 25–50 °C (optimum 35–40 °C), with 2.5–5.0 M NaCl (optimum 3.4 M NaCl) and at pH 6.0–9.0 (optimum pH 7.5). MgCl2 was not required for growth. Cells lysed in distilled water and the lowest NaCl concentration that prevented cell lysis was 12 % (w/v). On the basis of 16S rRNA gene sequence analysis, strains EN-2T and SH-4 were closely related to Halorubrum cibi B31T (97.9 and 98.0 % similarity, respectively), Hrr. tibetense 8W8T (97.3 and 97.7 %), Hrr. alkaliphilum DZ-1T (96.8 and 97.1 %), Hrr. luteum CGSA15T (96.8 and 97.0 %) and Hrr. lipolyticum 9-3T (96.8 and 97.0 %). DNA–DNA hybridization showed that strains EN-2T and SH-4 did not belong to the same species as any of these strains (≤45 % DNA–DNA relatedness) but that they are members of the same species (>70 % DNA–DNA relatedness). Polar lipid analysis revealed that strains EN-2T and SH-4 contained phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, sulfated diglycosyl diethers and several unidentified glycolipids. The DNA G+C content of both isolates was 62.1 mol%. It was concluded that strains EN-2T and SH-4 represent a novel species of the genus Halorubrum, for which the name Halorubrum aquaticum sp. nov. is proposed. The type strain is EN-2T ( = CECT 7174T  = CGMCC 1.6377T  = JCM 14031T).

Blastochloris gulmargensis sp. nov., isolated from an epilithic phototrophic biofilm

2011 ◽  
Vol 61 (8) ◽  
pp. 1811-1816 ◽  
Author(s):  
V. Venkata Ramana ◽  
Shivali Kapoor ◽  
E. Shobha ◽  
E. V. V. Ramprasad ◽  
Ch. Sasikala ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phototrophic Biofilm ◽  
Gene Sequence Analysis ◽  
Bacterium Strain ◽  
Blastochloris Viridis

A novel Gram-negative, motile, bacteriochlorophyll b-containing purple non-sulfur bacterium, strain JA248T, was isolated from phototrophic enrichments of a yellow–green epilithic biofilm sample collected from Gulmarg, India. The genomic DNA G+C content of strain JA248T was 63.8 mol%. A phylogenetic tree based on 16S rRNA gene sequence analysis showed that strain JA248T had highest similarity to members of the genus Blastochloris and was closely related to Blastochloris sulfoviridis DSM 729T (98.5 % sequence similarity) and Blastochloris viridis DSM 133T (98.4 %) of the class Alphaproteobacteria. Strain JA248T was characterized based on polyphasic taxonomy, and distinct phenotypic and molecular differences based on DNA–DNA hybridization (relatedness of <46.5 % with the two species of the genus Blastochloris), multilocus sequence analysis, and phenotypic and chemotaxonomic evidence separated strain JA248T from other species of the genus Blastochloris. Strain JA248T therefore represents a novel species in the genus Blastochloris, for which the name Blastochloris gulmargensis sp. nov. is proposed. The type strain is JA248T ( = JCM 14795T  = DSM 19786T).

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