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345 records – page 1 of 35.

Abyssivirga alkaniphila gen. nov., sp. nov., an alkane-degrading, anaerobic bacterium from a deep-sea hydrothermal vent system, and emended descriptions of Natranaerovirga pectinivora and Natranaerovirga hydrolytica.

https://arctichealth.org/en/permalink/ahliterature275915
Source
Int J Syst Evol Microbiol. 2016 Apr;66(4):1724-34
Publication Type
Article
Date
Apr-2016
Author
Anders Schouw
Tove Leiknes Eide
Runar Stokke
Rolf Birger Pedersen
Ida Helene Steen
Gunhild Bødtker
Source
Int J Syst Evol Microbiol. 2016 Apr;66(4):1724-34
Date
Apr-2016
Language
English
Publication Type
Article
Keywords
Alkanes - metabolism
Arctic Regions
Bacterial Typing Techniques
Base Composition
Biodegradation, Environmental
Clostridiales - classification - genetics - isolation & purification
DNA, Bacterial - genetics
Fatty Acids - chemistry
Glycolipids - chemistry
Hydrothermal Vents - microbiology
Molecular Sequence Data
Peptidoglycan - chemistry
Phospholipids - chemistry
Phylogeny
RNA, Ribosomal, 16S - genetics
Sequence Analysis, DNA
Abstract
A strictly anaerobic, mesophilic, syntrophic, alkane-degrading strain, L81T, was isolated from a biofilm sampled from a black smoker chimney at the Loki's Castle vent field. Cells were straight, rod-shaped, Gram-positive-staining and motile. Growth was observed at pH?6.2-9.5, 14-42?°C and 0.5-6?% (w/w) NaCl, with optima at pH?7.0-8.2, 37?°C and 3% (w/w) NaCl. Proteinaceous substrates, sugars, organic acids and hydrocarbons were utilized for growth. Thiosulfate was used as an external electron acceptor during growth on crude oil. Strain L81T was capable of syntrophic hydrocarbon degradation when co-cultured with a methanogenic archaeon, designated strain LG6, isolated from the same enrichment. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain L81T is affiliated with the family Lachnospiraceae, and is most closely related to the type strains of Natranaerovirga pectinivora (92?% sequence similarity) and Natranaerovirga hydrolytica (90%). The major cellular fatty acids of strain L81T were C15?:?0, anteiso-C15?:?0 and C16?:?0, and the profile was distinct from those of the species of the genus Natranaerovirga. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, three unidentified phospholipids, four unidentified glycolipids and two unidentified phosphoglycolipids. The G+C content of genomic DNA was determined to be 31.7?mol%. Based on our phenotypic, phylogenetic and chemotaxonomic results, strain L81T is considered to represent a novel species of a new genus of the family Lachnospiraceae, for which we propose the name Abyssivirga alkaniphila gen. nov., sp. nov. The type strain of Abyssivirga alkaniphila is L81T (=DSM 29592T=JCM 30920T). We also provide emended descriptions of Natranaerovirga pectinivora and Natranaerovirga hydrolytica.
PubMed ID
26822139 View in PubMed
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[Activity and structure of the sulfate-reducing bacterial community in the sediments of the southern part of Lake Baikal].

https://arctichealth.org/en/permalink/ahliterature259583
Source
Mikrobiologiia. 2014 Mar-Apr;83(2):180-90
Publication Type
Article
Author
N V Pimenov
E E Zakharova
A L Briukhanov
V A Korneeva
B B Kuznetsov
T P Turova
T V Pogodaeva
G V Kalmychkov
T I Zemskaia
Source
Mikrobiologiia. 2014 Mar-Apr;83(2):180-90
Language
Russian
Publication Type
Article
Keywords
DNA, Bacterial - genetics
Geologic Sediments - microbiology
Lakes - microbiology
Microbial Consortia - physiology
Molecular Sequence Data
Phylogeny
RNA, Ribosomal, 16S
Siberia
Sulfur-Reducing Bacteria - genetics - isolation & purification
Water Microbiology
Abstract
The rates of sulfate reduction (SR) and the diversity of sulfate-reducing bacteria (SRB) were studied in the sediments of the Posol'skaya banka elevation in the southern part of Lake Baikal. SR rates varied from 1.2 to 1641 nmol/(dm3 day), with high rates (> 600 nmol/(dm3 day)) observed at both deep-water stations and in subsurface silts. Integral SR rates calculated for the uppermost 50 cm of the sediments were higher for gas-saturated and gas hydrate-bearing sediments than in those with low methane content. Enrichment SRB cultures were obtained in Widdel medium for freshwater SRB. Analysis of the 16S rRNA gene fragments from clone libraries obtained from the enrichments revealed the presence of SRB belonged to Desulfosporosinus genus, with D. lacus as the most closely related member (capable of sulfate, sulfite, and thiosulfate reduction), as well as members of the order Clostridiales.
PubMed ID
25423722 View in PubMed
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Addressing the diversity of the honeybee gut symbiont Gilliamella: description of Gilliamella apis sp. nov., isolated from the gut of honeybees (Apis mellifera).

https://arctichealth.org/en/permalink/ahliterature291960
Source
Int J Syst Evol Microbiol. 2018 May; 68(5):1762-1770
Publication Type
Journal Article
Date
May-2018
Author
Jane Ludvigsen
Davide Porcellato
Gro V Amdam
Knut Rudi
Author Affiliation
1?Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), Chr. M. Fahlsensvei 1, 1433 Ås, Norway.
Source
Int J Syst Evol Microbiol. 2018 May; 68(5):1762-1770
Date
May-2018
Language
English
Publication Type
Journal Article
Keywords
Animals
Bacterial Typing Techniques
Base Composition
Bees - microbiology
DNA, Bacterial - genetics
Fatty Acids - chemistry
Gammaproteobacteria - classification - genetics - isolation & purification
Gastrointestinal Tract - microbiology
Norway
Phylogeny
RNA, Ribosomal, 16S - genetics
Sequence Analysis, DNA
Symbiosis
Ubiquinone - chemistry
Abstract
The gut microbiota of honeybees (Apis) and bumblebees (Bombus) include the symbiotic bacterial genus Gilliamella. This genus shows a high degree of functional and genomic diversity and separates into distinct lineages. Gilliamella apicola wkB1T, which was isolated from Apis, was the first species to be described. Recently four new species, isolated from Bombus, were identified. In this paper, we compare several genomes/strains from previous studies spanning this diversity, which gives insight into the phylogenetic relationship among different Gilliamella species. We show that one lineage, isolated only from Apis, is different from other gilliamellas described, based on average nucleotide identity calculation (about 80?%) and phenotypic characterizations. We propose the new species name for this lineage: Gilliamella apis sp. nov. We present the characterization of the type strain NO3T (=DSM 105629T=LMG 30293T), a strain isolated from the Western honeybee Apis mellifera, which clusters within this lineage. Cells of strain NO3T grow best in a microaerophilic atmosphere with enhanced CO2 levels at 36?°C and pH 7.0-7.5. Cells also grow well in anaerobic conditions, but not in aerobic conditions. Cells are approximately 1?µm in length and rod-shaped, and the genomic G+C content is 34.7?mol%. Differential characteristics between strain NO3T and the different type strains of Gilliamella were revealed based on API kit tests and genomic content comparisons. The main respiratory quinone of strain NO3T was ubiquinone-8, and the predominant fatty acids were C18?:?1?7c/C18?:?1?6c, C16?:?0, consistent with the genus Gilliamella.
PubMed ID
29624166 View in PubMed
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Algibacter amylolyticus sp. nov., isolated from intertidal sediment.

https://arctichealth.org/en/permalink/ahliterature266892
Source
Int J Syst Evol Microbiol. 2015 May;65(Pt 5):1556-60
Publication Type
Article
Date
May-2015
Author
De-Chao Zhang
Jiang Wu
Kathrin Neuner
Jianting Yao
Rosa Margesin
Source
Int J Syst Evol Microbiol. 2015 May;65(Pt 5):1556-60
Date
May-2015
Language
English
Publication Type
Article
Keywords
Bacterial Typing Techniques
Base Composition
DNA, Bacterial - genetics
Fatty Acids - chemistry
Flavobacteriaceae - classification - genetics - isolation & purification
Geologic Sediments - microbiology
Islands
Molecular Sequence Data
Nucleic Acid Hybridization
Phosphatidylethanolamines - chemistry
Phylogeny
Pigmentation
RNA, Ribosomal, 16S - genetics
Russia
Seawater - microbiology
Sequence Analysis, DNA
Vitamin K 2 - analogs & derivatives - chemistry
Abstract
A Gram-reaction-negative, rod-shaped, yellow-pigmented, motile by gliding bacterial strain, designated RU-4-M-4(T), was isolated from intertidal sediment of Sakhalin Island in Russia. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain RU-4-M-4(T) was related to the genus Algibacter and had highest 16S rRNA gene sequence similarity with Algibacter pectinivorans KACC 14153(T) (97.2%). The major cellular fatty acids were iso-C15 : 0 3-OH, C15: 0 and iso-C15 : 1 G. The predominant menaquinone was MK-6. The polar lipid profile contained phosphatidylethanolamine, three unidentified aminolipids and two unidentified lipids. The genomic DNA G+C content of strain RU-4-M-4(T) was 36.4 mol%. Combined data from phenotypic, phylogenetic and DNA-DNA relatedness studies demonstrated that strain RU-4-M-4(T) is a representative of a novel species of the genus Algibacter , for which we propose the name Algibacter amylolyticus sp. nov. (type strain RU-4-M-4(T)?=LMG 28383(T)?=DSM 29199(T)).
PubMed ID
25713044 View in PubMed
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Alkaliphilus namsaraevii sp. nov., an alkaliphilic iron- and sulfur-reducing bacterium isolated from a steppe soda lake.

https://arctichealth.org/en/permalink/ahliterature285198
Source
Int J Syst Evol Microbiol. 2017 Jun;67(6):1990-1995
Publication Type
Article
Date
Jun-2017
Author
Anastasiya Zakharyuk
Lyudmila Kozyreva
Elena Ariskina
Olga Troshina
Dmitry Kopitsyn
Viktoria Shcherbakova
Source
Int J Syst Evol Microbiol. 2017 Jun;67(6):1990-1995
Date
Jun-2017
Language
English
Publication Type
Article
Keywords
Alkalies
Bacterial Typing Techniques
Base Composition
Clostridiales - classification - genetics - isolation & purification
DNA, Bacterial - genetics
Fatty Acids - chemistry
Ferric Compounds - metabolism
Lakes - microbiology
Phylogeny
RNA, Ribosomal, 16S - genetics
Russia
Sequence Analysis, DNA
Sulfur
Sulfur-Reducing Bacteria - classification - genetics - isolation & purification
Abstract
A novel alkaliphilic spore-forming bacterium was isolated from the benthic sediments of the highly mineralized steppe Lake Khilganta (Transbaikal Region, Russia). Cells of the strain, designated ?-07-2T, were straight to slightly curved rods, Gram-stain-positive and motile. Strain ?-07-2T grew in the pH range from 7.0 to 10.7 (optimum pH 9.6-10.3). Growth was observed at 25-47?°C (optimum 30?°C) and at an NaCl concentration from 5 to 150?g l-1 with an optimum at 40?g l-1. Strain ?-07-2T was a chemo-organoheterotroph able to reduce amorphous ferric hydroxide, Fe(III) citrate and elemental sulfur in the presence of yeast extract as the electron donor. It used tryptone, peptone and trypticase with Fe(III) citrate as the electron acceptor. The predominant fatty acids in cell walls were C16:1?8, iso-C15:0, C14?:?0 3-OH and C16?:?0. The DNA G+C content was 32.6?mol%. 16S rRNA gene sequence analysis revealed that strain ?-07-2T was related most closely to members of the genus Alkaliphilus within the family Clostridiaceae. The closest relative was Alkaliphilus peptidifermentans Z-7036T (96.4?% similarity). On the basis of the genotypic, chemotaxonomic and phenotypic data, strain ?-07-2T represents a novel species in the genus Alkaliphilus, for which the name Alkaliphilus namsaraevii sp. nov. is proposed. The type strain is ?-07-2T (=VKM ?-2746?=DSM 26418?).
PubMed ID
28632119 View in PubMed
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Amplification of DNA by the polymerase chain reaction for the efficient diagnosis of pertussis.

https://arctichealth.org/en/permalink/ahliterature36891
Source
Scand J Infect Dis. 1992;24(3):339-45
Publication Type
Article
Date
1992
Author
P. Olcén
A. Bäckman
B. Johansson
E. Esbjörner
E. Törnqvist
J. Bygraves
W L McPheat
Author Affiliation
Department of Clinical Microbiology and Immunology, Orebro Medical Center Hospital, Sweden.
Source
Scand J Infect Dis. 1992;24(3):339-45
Date
1992
Language
English
Publication Type
Article
Keywords
Base Sequence
Bordetella pertussis - genetics - isolation & purification
Child
Child, Preschool
DNA, Bacterial - genetics
Female
Humans
Infant
Male
Molecular Sequence Data
Polymerase Chain Reaction
Research Support, Non-U.S. Gov't
Sweden
Whooping Cough - diagnosis
Abstract
The standard diagnostic methods for pertussis have several shortcomings. With the increased knowledge of the Bordetella pertussis genome a specific and conserved DNA sequence, present in about 70-80 copies in each genome, was selected for amplification with the polymerase chain reaction (PCR) technique in order to evaluate its diagnostic potential in children with suspected pertussis. The 400 basepair DNA sequence chosen was present and amplified in all 112 B. pertussis strains and in no other bacterial species examined. The specificity of the amplified material was documented by restriction enzyme cleavage. In nasopharyngeal aspirates a B. pertussis specific PCR product was visualized in 19/25 culture positive and in 5/50 culture negative children. In conclusion the present PCR assay for B. pertussis can be clinically useful and permit a specific diagnosis within 1 day after sampling. Further studies are requested to document its sensitivity, specificity and predictive value for positive and negative results.
PubMed ID
1509238 View in PubMed
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An abbreviated MLVA identifies Escherichia coli ST131 as the major extended-spectrum ß-lactamase-producing lineage in the Copenhagen area.

https://arctichealth.org/en/permalink/ahliterature119181
Source
Eur J Clin Microbiol Infect Dis. 2013 Mar;32(3):431-6
Publication Type
Article
Date
Mar-2013
Author
J B Nielsen
A. Albayati
R L Jørgensen
K H Hansen
B. Lundgren
K. Schønning
Author Affiliation
Department of Clinical Microbiology 445, Hvidovre Hospital, Kettegaard Alle 30, 2650 Hvidovre, Denmark. jesper.boye.nielsen@regionh.dk
Source
Eur J Clin Microbiol Infect Dis. 2013 Mar;32(3):431-6
Date
Mar-2013
Language
English
Publication Type
Article
Keywords
Adult
Aged
DNA, Bacterial - genetics
Denmark - epidemiology
Electrophoresis, Capillary - methods
Escherichia coli - classification - enzymology - isolation & purification
Escherichia coli Infections - epidemiology - microbiology
Female
Genotype
Humans
Male
Minisatellite Repeats
Molecular Typing - methods
beta-Lactamases - secretion
Abstract
Rapid bacterial typing is a valuable and necessary tool in the prevention and detection of outbreaks. The purpose of this study was to adapt a multilocus variable number of tandem repeats analysis (MLVA) for analysis on a benchtop capillary electrophoresis instrument and compare the modified assay with multilocus sequence typing (MLST) for typing cefpodoxime-resistant Escherichia coli (E. coli). Further, we identified the causative resistance mechanisms and epidemiological type of infection for isolates producing extended-spectrum ß-lactamases (ESBLs). A collection of E. coli resistant to cefpodoxime was typed by MLST and a modified MLVA assay using a benchtop capillary electrophoresis instrument. Resistance mechanisms were identified by polymerase chain reaction (PCR) and sequencing. Patient history was examined to establish the epidemiological type of infection for ESBL-producing E. coli. MLVA yielded typing results homologous with MLST and it correctly identified E. coli sequence type (ST) 131 that was accounting for 45 % of all ESBL-producing isolates in the sample collection. The majority (76.7 %) of ESBL-producing isolates was healthcare-related and only 23.3 % of the ESBL-producing isolates were community-onset infections (COI), regardless of the ST. Patients with COI were significantly more often of female gender and younger age compared to healthcare-associated infections (HCAI) and hospital-onset infections (HOI). In conclusion, the modified MLVA is a useful tool for the rapid typing of E. coli and it identified ST131 as the predominating ESBL-producing lineage in Copenhagen. Healthcare-related infections were the predominant infection setting of ESBL-producing E. coli and the demographic characteristics differed between patients with COI and healthcare-related infections.
PubMed ID
23129461 View in PubMed
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[Analysis of the Moscow population of Neisseria meningitidis strains by the method of multilocus sequencing-typing].

https://arctichealth.org/en/permalink/ahliterature168921
Source
Zh Mikrobiol Epidemiol Immunobiol. 2006 Mar-Apr;(2):31-6
Publication Type
Article
Author
K O Mironov
A E Platonov
I S Koroleva
G A Shipulin
Source
Zh Mikrobiol Epidemiol Immunobiol. 2006 Mar-Apr;(2):31-6
Language
Russian
Publication Type
Article
Keywords
Cerebrospinal Fluid - microbiology
DNA, Bacterial - genetics
Humans
Meningococcal Infections - microbiology - prevention & control
Molecular Epidemiology
Moscow - epidemiology
Neisseria meningitidis - classification - genetics
Sequence Analysis, DNA
Serotyping
Species Specificity
Abstract
The analysis of meningococcal strains of different serogroups, isolated from the liquor of patients in Moscow, which was carried out with the method of multilocus sequencing-typing (MLST), was presented. At the periods of epidemic morbidity rises in Moscow the prevalence of group A meningococcal strains, belonging to subgroups III with sequence-types 5 (in the 1970s) and 7 (in 1996), was noted, and at a period between epidemics strains of genetic subgroups VI and X were isolated. Meningococcal strains, groups B and C, isolated in 1995 - 2002, had, as a rule, unique sequence-types, differing both one from another and from N. meningitidis sequence-types detected in other countries. Among group B meningococci the prevalence of strains belonging to clonal complex ST-18 was noted, while for group C meningococcci strains belonging to clonal complex ST-41/44 were most typical. Such genetic variability of circulating meningococci was regarded as characteristic of the period between epidemics, observed in Moscow since the end of the 1980s.
PubMed ID
16758895 View in PubMed
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Anaplasma phagocytophilum in questing Ixodes ricinus ticks in southwestern Finland.

https://arctichealth.org/en/permalink/ahliterature279945
Source
Exp Appl Acarol. 2016 Dec;70(4):491-500
Publication Type
Article
Date
Dec-2016
Author
Jani J Sormunen
Ritva Penttinen
Tero Klemola
Eero J Vesterinen
Jari Hänninen
Source
Exp Appl Acarol. 2016 Dec;70(4):491-500
Date
Dec-2016
Language
English
Publication Type
Article
Keywords
Anaplasma phagocytophilum - genetics - physiology
Anaplasmosis - microbiology - transmission
Animals
Arachnid Vectors - growth & development - microbiology
DNA, Bacterial - genetics
Ehrlichiosis - microbiology - transmission
Female
Finland
Humans
Ixodes - growth & development - microbiology
Larva - microbiology
Nymph - microbiology
Polymerase Chain Reaction
RNA, Ribosomal, 16S - genetics
Sequence Analysis, DNA
Abstract
Anaplasma phagocytophilum is the causative agent of an emerging tick-borne disease, human granulocytic anaplasmosis. While the bacterium has been reported from questing ticks in neighboring Sweden, Norway and Russia, the few surveys regarding questing ticks in Finland have thus far been negative. In the current study, the prevalence of A. phagocytophilum in Ixodes ricinus populations was evaluated in several study localities around southwestern Finland during 2013-2014. Some of these populations were previously screened and found negative for A. phagocytophilum in 2000. A total of 3158 I. ricinus collected by blanket dragging were screened for Anaplasma spp. using qPCR. Anaplasma were detected in 9.2% of adult ticks (n = 87) and 3.1% of nymphs (n = 979). All larval samples were negative for infection. All Anaplasma-positive samples were identified as A. phagocytophilum by sequencing. This is, to the best of our knowledge, the first report of the pathogen from questing ticks in Finland. Furthermore, the pathogen was detected from several localities found negative during the previous screening 13 years earlier.
PubMed ID
27812829 View in PubMed
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An outbreak of respiratory tularemia caused by diverse clones of Francisella tularensis.

https://arctichealth.org/en/permalink/ahliterature264289
Source
Clin Infect Dis. 2014 Dec 1;59(11):1546-53
Publication Type
Article
Date
Dec-1-2014
Author
Anders Johansson
Adrian Lärkeryd
Micael Widerström
Sara Mörtberg
Kerstin Myrtännäs
Caroline Ohrman
Dawn Birdsell
Paul Keim
David M Wagner
Mats Forsman
Pär Larsson
Source
Clin Infect Dis. 2014 Dec 1;59(11):1546-53
Date
Dec-1-2014
Language
English
Publication Type
Article
Keywords
Adult
Aged
Aged, 80 and over
DNA, Bacterial - genetics
Disease Outbreaks
Female
Francisella tularensis - classification - genetics
Humans
Male
Middle Aged
Phylogeny
Polymorphism, Single Nucleotide
Respiratory Tract Infections - epidemiology - microbiology
Sweden - epidemiology
Tularemia - epidemiology - microbiology
Young Adult
Abstract
The bacterium Francisella tularensis is recognized for its virulence, infectivity, genetic homogeneity, and potential as a bioterrorism agent. Outbreaks of respiratory tularemia, caused by inhalation of this bacterium, are poorly understood. Such outbreaks are exceedingly rare, and F. tularensis is seldom recovered from clinical specimens.
A localized outbreak of tularemia in Sweden was investigated. Sixty-seven humans contracted laboratory-verified respiratory tularemia. F. tularensis subspecies holarctica was isolated from the blood or pleural fluid of 10 individuals from July to September 2010. Using whole-genome sequencing and analysis of single-nucleotide polymorphisms (SNPs), outbreak isolates were compared with 110 archived global isolates.
There were 757 SNPs among the genomes of the 10 outbreak isolates and the 25 most closely related archival isolates (all from Sweden/Finland). Whole genomes of outbreak isolates were >99.9% similar at the nucleotide level and clustered into 3 distinct genetic clades. Unexpectedly, high-sequence similarity grouped some outbreak and archival isolates that originated from patients from different geographic regions and up to 10 years apart. Outbreak and archival genomes frequently differed by only 1-3 of 1 585 229 examined nucleotides.
The outbreak was caused by diverse clones of F. tularensis that occurred concomitantly, were widespread, and apparently persisted in the environment. Multiple independent acquisitions of F. tularensis from the environment over a short time period suggest that natural outbreaks of respiratory tularemia are triggered by environmental cues. The findings additionally caution against interpreting genome sequence identity for this pathogen as proof of a direct epidemiological link.
PubMed ID
25097081 View in PubMed
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345 records – page 1 of 35.