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16S rDNA sequencing of valve tissue improves microbiological diagnosis in surgically treated patients with infective endocarditis.

https://arctichealth.org/en/permalink/ahliterature134307
Source
J Infect. 2011 Jun;62(6):472-8
Publication Type
Article
Date
Jun-2011
Author
Martin Vondracek
Ulrik Sartipy
Ewa Aufwerber
Inger Julander
Dan Lindblom
Katarina Westling
Author Affiliation
Department of Clinical Microbiology, Karolinska University Hospital and Department of Clinical Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
Source
J Infect. 2011 Jun;62(6):472-8
Date
Jun-2011
Language
English
Publication Type
Article
Keywords
Adult
Aged
Bacteria - classification - genetics - isolation & purification
Bacteriological Techniques - methods
DNA, Bacterial - chemistry - genetics
DNA, Ribosomal - chemistry - genetics
Endocarditis - diagnosis - microbiology - surgery
Female
Heart Valves - microbiology
Humans
Male
Middle Aged
RNA, Ribosomal, 16S - genetics
Sensitivity and specificity
Sequence Analysis, DNA - methods
Sweden
Abstract
The aim was to evaluate 16S rDNA sequencing in heart valves in patients with infective endocarditis undergoing surgery.
Fifty-seven patients with infective endocarditis were examined in this prospective study by analysing heart valves with 16S rDNA sequencing and culturing methods and comparing the results to blood cultures. As controls, heart valves from 61 patients without any signs of endocarditis were examined.
All together 77% of the endocarditis patients were positive for 16S rDNA, 84% had positive blood cultures and 23% had positive cultures from heart valves, whereas only 16% of the cultures from heart valves were concordant with results from blood cultures or 16S rDNA. Concordant results between 16S rDNA sequencing and blood cultures were found in 75% patients. All controls were negative for 16S rDNA. In 4 out of 9 patients with negative blood cultures, the aetiology was established by 16S rDNA alone, i.e. viridans group streptococci.
In this Swedish study, 16S rDNA sequencing of valve material was shown to be a valuable addition in blood culture-negative cases. The value of heart valve culture was low. Molecular diagnosis using 16S rDNA sequencing should be recommended in patients undergoing valve replacement for infective endocarditis.
PubMed ID
21601285 View in PubMed
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Aeromonas aquatica sp. nov., Aeromonas finlandiensis sp. nov. and Aeromonas lacus sp. nov. isolated from Finnish waters associated with cyanobacterial blooms.

https://arctichealth.org/en/permalink/ahliterature269272
Source
Syst Appl Microbiol. 2015 May;38(3):161-8
Publication Type
Article
Date
May-2015
Author
R. Beaz-Hidalgo
F. Latif-Eugenín
M J Hossain
K. Berg
R M Niemi
J. Rapala
C. Lyra
M R Liles
M J Figueras
Source
Syst Appl Microbiol. 2015 May;38(3):161-8
Date
May-2015
Language
English
Publication Type
Article
Keywords
Aeromonas - classification - isolation & purification
Cluster analysis
DNA, Ribosomal - chemistry - genetics
DNA-Directed RNA Polymerases
Finland
Genes, Bacterial - genetics
Lakes - microbiology
Molecular Sequence Data
Multilocus Sequence Typing
Phylogeny
RNA, Ribosomal, 16S - genetics
Abstract
Three groups of Aeromonas strains isolated from Finland lakes experiencing cyanobacterial blooms could not be assigned to any known species of this genus on the basis of 16S rRNA and rpoD gene sequences. The Multilocus Phylogenetic Analysis (MLPA) of the concatenated sequence of seven genes (gyrB, rpoD, recA, dnaJ, gyrA, dnaX and atpD; 4093bp) showed that the three groups of strains did not cluster with any known Aeromonas spp. and formed three independent lineages. This was confirmed by performing the analysis with their closest relatives using 15 genes (the latter 7 and cpn60, dnaK, gltA, mdh, radA, rpoB, tsf, zipA; 8751bp). Furthermore, ANI results between the genomes of the type strains of the three potential new species and those of their close relatives were all
PubMed ID
25852023 View in PubMed
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Alloscardovia omnicolens gen. nov., sp. nov., from human clinical samples.

https://arctichealth.org/en/permalink/ahliterature162515
Source
Int J Syst Evol Microbiol. 2007 Jul;57(Pt 7):1442-6
Publication Type
Article
Date
Jul-2007
Author
Geert Huys
Marc Vancanneyt
Klaas D'Haene
Enevold Falsen
Georges Wauters
Peter Vandamme
Author Affiliation
Laboratory of Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium. geert.huys@UGent.be
Source
Int J Syst Evol Microbiol. 2007 Jul;57(Pt 7):1442-6
Date
Jul-2007
Language
English
Publication Type
Article
Keywords
Actinobacteria - classification - genetics - isolation & purification - metabolism
Aerobiosis
Bacterial Proteins - genetics
Bacterial Typing Techniques
Base Composition
Belgium
Chaperonin 60 - genetics
Cluster analysis
DNA Fingerprinting
DNA, Bacterial - chemistry - genetics
DNA, Ribosomal - chemistry - genetics
Fermentation
Genes, rRNA
Genotype
Gram-Positive Bacterial Infections - microbiology
Humans
Molecular Sequence Data
Norway
Nucleic Acid Hybridization
Phylogeny
Polymerase Chain Reaction
RNA, Bacterial - genetics
RNA, Ribosomal, 16S - genetics
Sequence Analysis, DNA
Sequence Homology, Nucleic Acid
Sweden
Abstract
The taxonomic position of 12 isolates tentatively assigned to the genus Bifidobacterium on the basis of a limited phenotypic characterization was examined. The isolates were collected between 1978 and 2005 in Belgium, Sweden and Norway, and originated from various human clinical samples, including urine, blood, urethra, oral cavity, tonsil, and abscesses of lung and aortic valve. On the basis of band number and clustering analysis, repetitive DNA element-based PCR fingerprinting using the BOXA1R and (GTG)(5) primers indicated that the clinical isolates represented a taxon probably not belonging to the genus Bifidobacterium. Analysis of 16S rRNA gene sequence similarities revealed that the isolates were most closely affiliated to Parascardovia denticolens LMG 18312(T) (93.0-93.2 %), Scardovia inopinata LMG 18313(T) (92.9-93.1 %) and other members of the Bifidobacteriaceae, indicating that the isolates belong to a novel genus within that family. This observation was further substantiated by the results of partial sequencing of the heat-shock protein 60 gene (hsp60) and determination of the DNA G+C contents (47.3-48.3 mol%). Members of the novel taxon can be phenotypically distinguished from S. inopinata, P. denticolens and Gardnerella vaginalis by the ability to grow on agar under aerobic conditions and on the basis of positive reactions for acid production from L-arabinose, raffinose, salicin and D-xylose. Unambiguous phenotypic differentiation from Aeriscardovia aeriphila and Bifidobacterium species may be difficult, so phenotypic analyses should be complemented by molecular methods. The values for DNA-DNA binding among four members of the novel genus were in the range of 89-100 %, indicating that the strains should be considered as a single novel species of a novel genus, for which the name Alloscardovia omnicolens gen. nov., sp. nov. is proposed. The type strain of Alloscardovia omnicolens is CCUG 31649(T) (=LMG 23792(T)).
PubMed ID
17625172 View in PubMed
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An investigation of bacterial contamination on treatment table surfaces of chiropractors in private practice and attitudes and practices concerning table disinfection.

https://arctichealth.org/en/permalink/ahliterature137451
Source
Am J Infect Control. 2011 Feb;39(1):56-63
Publication Type
Article
Date
Feb-2011
Author
Aaron A Puhl
Christine J Reinhart
Nathan J Puhl
L Brent Selinger
H Stephen Injeyan
Author Affiliation
Department of Pathology and Microbiology, Canadian Memorial Chiropractic College, 6100 Leslie Street, Toronto, Ontario, Canada.
Source
Am J Infect Control. 2011 Feb;39(1):56-63
Date
Feb-2011
Language
English
Publication Type
Article
Keywords
Alberta
Ambulatory Care Facilities
Attitude of Health Personnel
Bacteria - classification - genetics - isolation & purification
Chiropractic
DNA, Bacterial - chemistry - genetics
DNA, Ribosomal - chemistry - genetics
Disinfection - utilization
Environmental Microbiology
Equipment and Supplies - microbiology
Health Services Research
Humans
Private Practice
Questionnaires
RNA, Ribosomal, 16S - genetics
Abstract
The attitudes and behaviors of chiropractors regarding table disinfection have not yet been investigated. The purpose of this study was to evaluate (1) the bacterial contaminants present on treatment tables in private chiropractic clinics, (2) the effectiveness of the paper barrier in preventing bacterial deposition, and (3) chiropractors' attitudes and practices regarding table disinfection.
Defined portions of treatment tables from 14 private clinics in Alberta, Canada were sampled for the presence of bacteria. Growth characteristics and 16S rRNA gene sequencing were used for bacterial identification. In addition, a 12-item survey was administered to southern Alberta chiropractors (n = 79; 81% response rate) inquiring about their attitudes and behaviors regarding table disinfection.
Respondents favored the idea of table disinfection (84%), but only 62% had a routine disinfection protocol. Table sampling revealed the presence of a number of bacteria, including methicillin-resistant Staphylococcus aureus, which were recovered from 3 separate clinics. The paper covering on table headpieces was an effective barrier to bacteria.
Chiropractors have a positive attitude regarding disinfection; however, the risk of infection from treatment tables remains. Modification of the positioning of facial piece paper may be indicated, along with increased emphasis on disinfection.
PubMed ID
21281886 View in PubMed
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Aquatic microbial diversity associated with faecal pollution of Norwegian waterbodies characterized by 16S rRNA gene amplicon deep sequencing.

https://arctichealth.org/en/permalink/ahliterature310310
Source
Microb Biotechnol. 2019 11; 12(6):1487-1491
Publication Type
Journal Article
Date
11-2019
Author
Lisa Paruch
Adam M Paruch
Hans Geir Eiken
Roald Sørheim
Author Affiliation
Division of Environment and Natural Resources, Norwegian Institute of Bioeconomy Research (NIBIO), Fredrik A. Dahls vei 20, 1433, Aas, Norway.
Source
Microb Biotechnol. 2019 11; 12(6):1487-1491
Date
11-2019
Language
English
Publication Type
Journal Article
Keywords
Archaea - classification - genetics
Bacteria - classification - genetics
Cluster analysis
DNA, Archaeal - chemistry - genetics
DNA, Bacterial - chemistry - genetics
DNA, Ribosomal - chemistry - genetics
Feces
Genes, rRNA
High-Throughput Nucleotide Sequencing
Microbiota
Norway
Phylogeny
RNA, Ribosomal, 16S - genetics
Sequence Analysis, DNA
Water Microbiology
Water Pollution
Abstract
Faecal contamination is one of the major factors affecting biological water quality. In this study, we investigated microbial taxonomic diversity of faecally polluted lotic ecosystems in Norway. These ecosystems comprise tributaries of drinking water reservoirs with moderate and high faecal contamination levels, an urban creek exposed to extremely high faecal pollution and a rural creek that was the least faecally polluted. The faecal water contamination had both anthropogenic and zoogenic origins identified through quantitative microbial source tracking applying host-specific Bacteroidales 16S rRNA genetic markers. The microbial community composition revealed that Proteobacteria and Bacteroidetes (70-90% relative abundance) were the most dominant bacterial phyla, followed by Firmicutes, especially in waters exposed to anthropogenic faecal contamination. The core archaeal community consisted of Parvarchaeota (mainly in the tributaries of drinking water reservoirs) and Crenarchaeota (in the rural creek). The aquatic microbial diversity was substantially reduced in water with severe faecal contamination. In addition, the community compositions diverge between waters with dominant anthropogenic or zoogenic pollution origins. These findings present novel interpretations of the effect of anthropo-zoogenic faecal water contamination on microbial diversity in lotic ecosystems.
PubMed ID
31290258 View in PubMed
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Arbuscular mycorrhizal fungal community divergence within a common host plant in two different soils in a subarctic Aeolian sand area.

https://arctichealth.org/en/permalink/ahliterature263039
Source
Mycorrhiza. 2014 Oct;24(7):539-50
Publication Type
Article
Date
Oct-2014
Author
Gaia Francini
Minna Männistö
Vilhelmiina Alaoja
Minna-Maarit Kytöviita
Source
Mycorrhiza. 2014 Oct;24(7):539-50
Date
Oct-2014
Language
English
Publication Type
Article
Keywords
Arctic Regions
Biota
Cluster analysis
DNA, Fungal - chemistry - genetics
DNA, Plant - chemistry - genetics
DNA, Ribosomal - chemistry - genetics
Lipids - analysis
Molecular Sequence Data
Mycelium - chemistry
Mycorrhizae - classification - genetics - isolation & purification
Phylogeny
Plant Roots - microbiology
Poaceae - microbiology
RNA, Ribosomal, 18S - genetics
Sequence Analysis, DNA
Soil Microbiology
Abstract
There is rising awareness that different arbuscular mycorrhizal (AM) fungi have different autoecology and occupy different soil niches and that the benefits they provide to the host plant are dependent on plant-AM fungus combination. However, the role and community composition of AM fungi in succession are not well known and the northern latitudes remain poorly investigated ecosystems. We studied AM fungal communities in the roots of the grass Deschampsia flexuosa in two different, closely located, successional stages in a northern Aeolian sand area. The AM fungal taxa richness in planta was estimated by cloning and sequencing small subunit ribosomal RNA genes. AM colonization, shoot d (13)C signature, and %N and %C were measured. Soil microbial community structure and AM fungal mycelium abundance were estimated using phospholipid (PLFA) and neutral lipid (NLFA) analyses. The two successional stages were characterized by distinct plant, microbial, and fungal communities. AM fungal species richness was very low in both the early and late successional stages. AM frequency in D. flexuosa roots was higher in the early successional stage than in the late one. The AM fungal taxa retrieved belonged to the genera generally adapted to Arctic or extreme environments. AM fungi seemed to be important in the early stage of the succession, suggesting that AM fungi may help plants to better cope with the harsh environmental conditions, especially in an early successional stage with more extreme environmental fluctuations.
PubMed ID
24687606 View in PubMed
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Archaeal diversity and a gene for ammonia oxidation are coupled to oceanic circulation.

https://arctichealth.org/en/permalink/ahliterature95465
Source
Environ Microbiol. 2009 Apr;11(4):971-80
Publication Type
Article
Date
Apr-2009
Author
Galand Pierre E
Lovejoy Connie
Hamilton Andrew K
Ingram R Grant
Pedneault Estelle
Carmack Eddy C
Author Affiliation
Département de Biologie et Québec-Océan, Université Laval, Québec G1K 7P4, Canada. pgaland@ceab.csic.es
Source
Environ Microbiol. 2009 Apr;11(4):971-80
Date
Apr-2009
Language
English
Publication Type
Article
Keywords
Ammonia - metabolism
Archaea - classification - genetics - isolation & purification
Archaeal Proteins - genetics
Biodiversity
DNA, Archaeal - chemistry - genetics
DNA, Ribosomal - chemistry - genetics
Genes, rRNA
Oxidation-Reduction
Oxidoreductases - genetics
Phylogeny
RNA, Archaeal - genetics
RNA, Ribosomal, 16S - genetics
Seawater - microbiology
Sequence Analysis, DNA
Sequence Homology, Nucleic Acid
Abstract
Evidence of microbial zonation in the open ocean is rapidly accumulating, but while the distribution of communities is often described according to depth, the other physical factors structuring microbial diversity and function remain poorly understood. Here we identify three different water masses in the North Water (eastern Canadian Arctic), defined by distinct temperature and salinity characteristics, and show that they contained distinct archaeal communities. Moreover, we found that one of the water masses contained an increased abundance of the archaeal alpha-subunit of the ammonia monooxygenase gene (amoA) and accounted for 70% of the amoA gene detected overall. This indicates likely differences in putative biogeochemical capacities among different water masses. The ensemble of our results strongly suggest that the widely accepted view of depth stratification did not explain microbial diversity, but rather that parent water masses provide the framework for predicting communities and potential microbial function in an Arctic marine system. Our results emphasize that microbial distributions are strongly influenced by oceanic circulation, implying that shifting currents and water mass boundaries resulting from climate change may well impact patterns of microbial diversity by displacing whole biomes from their historic distributions. This relocation could have the potential to establish a substantially different geography of microbial-driven biogeochemical processes and associated oceanic production.
PubMed ID
19077007 View in PubMed
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Bacterial communities in ancient permafrost profiles of Svalbard, Arctic.

https://arctichealth.org/en/permalink/ahliterature289236
Source
J Basic Microbiol. 2017 Dec; 57(12):1018-1036
Publication Type
Journal Article
Date
Dec-2017
Author
Purnima Singh
Shiv M Singh
Ram N Singh
Simantini Naik
Utpal Roy
Alok Srivastava
Manfred Bölter
Author Affiliation
Birla Institute of Technology and Science (BITS), Pilani-K.K. Birla Goa Campus, Zuarinagar, Goa, India.
Source
J Basic Microbiol. 2017 Dec; 57(12):1018-1036
Date
Dec-2017
Language
English
Publication Type
Journal Article
Keywords
Arctic Regions
Bacteria - classification - genetics
Bacterial Load
Biota
Cluster analysis
DNA, Bacterial - chemistry - genetics
DNA, Ribosomal - chemistry - genetics
Permafrost - microbiology
Phylogeny
RNA, Ribosomal, 16S - genetics
Sequence Analysis, DNA
Svalbard
Abstract
Permafrost soils are unique habitats in polar environment and are of great ecological relevance. The present study focuses on the characterization of bacterial communities from permafrost profiles of Svalbard, Arctic. Counts of culturable bacteria range from 1.50?×?103 to 2.22?×?105 CFU?g-1 , total bacterial numbers range from 1.14?×?105 to 5.52?×?105 cells?g-1 soil. Bacterial isolates are identified through 16S rRNA gene sequencing. Arthrobacter and Pseudomonas are the most dominant genera, and A. sulfonivorans, A. bergeri, P. mandelii, and P. jessenii as the dominant species. Other species belong to genera Acinetobacter, Bacillus, Enterobacter, Nesterenkonia, Psychrobacter, Rhizobium, Rhodococcus, Sphingobacterium, Sphingopyxis, Stenotrophomonas, and Virgibacillus. To the best of our knowledge, genera Acinetobacter, Enterobacter, Nesterenkonia, Psychrobacter, Rhizobium, Sphingobacterium, Sphingopyxis, Stenotrophomonas, and Virgibacillus are the first northernmost records from Arctic permafrost. The present study fills the knowledge gap of culturable bacterial communities and their chronological characterization from permafrost soils of Ny-Ålesund (79°N), Arctic.
PubMed ID
28940222 View in PubMed
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Bacterial community analysis of drinking water biofilms in southern Sweden.

https://arctichealth.org/en/permalink/ahliterature268301
Source
Microbes Environ. 2015;30(1):99-107
Publication Type
Article
Date
2015
Author
Katharina Lührig
Björn Canbäck
Catherine J Paul
Tomas Johansson
Kenneth M Persson
Peter Rådström
Source
Microbes Environ. 2015;30(1):99-107
Date
2015
Language
English
Publication Type
Article
Keywords
Bacteria - classification - genetics - isolation & purification
Biofilms - growth & development
Biota
Cluster analysis
DNA, Bacterial - chemistry - genetics
DNA, Ribosomal - chemistry - genetics
Drinking Water - microbiology
Molecular Sequence Data
Phylogeny
RNA, Ribosomal, 16S - genetics
Sequence Analysis, DNA
Sweden
Abstract
Next-generation sequencing of the V1-V2 and V3 variable regions of the 16S rRNA gene generated a total of 674,116 reads that described six distinct bacterial biofilm communities from both water meters and pipes. A high degree of reproducibility was demonstrated for the experimental and analytical work-flow by analyzing the communities present in parallel water meters, the rare occurrence of biological replicates within a working drinking water distribution system. The communities observed in water meters from households that did not complain about their drinking water were defined by sequences representing Proteobacteria (82-87%), with 22-40% of all sequences being classified as Sphingomonadaceae. However, a water meter biofilm community from a household with consumer reports of red water and flowing water containing elevated levels of iron and manganese had fewer sequences representing Proteobacteria (44%); only 0.6% of all sequences were classified as Sphingomonadaceae; and, in contrast to the other water meter communities, markedly more sequences represented Nitrospira and Pedomicrobium. The biofilm communities in pipes were distinct from those in water meters, and contained sequences that were identified as Mycobacterium, Nocardia, Desulfovibrio, and Sulfuricurvum. The approach employed in the present study resolved the bacterial diversity present in these biofilm communities as well as the differences that occurred in biofilms within a single distribution system, and suggests that next-generation sequencing of 16S rRNA amplicons can show changes in bacterial biofilm communities associated with different water qualities.
Notes
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PubMed ID
25739379 View in PubMed
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Bacterial Microbiota Associated with the Glacier Ice Worm Is Dominated by Both Worm-Specific and Glacier-Derived Facultative Lineages.

https://arctichealth.org/en/permalink/ahliterature281829
Source
Microbes Environ. 2017 Mar 31;32(1):32-39
Publication Type
Article
Date
Mar-31-2017
Author
Takumi Murakami
Takahiro Segawa
Roman Dial
Nozomu Takeuchi
Shiro Kohshima
Yuichi Hongoh
Source
Microbes Environ. 2017 Mar 31;32(1):32-39
Date
Mar-31-2017
Language
English
Publication Type
Article
Keywords
Alaska
Animals
Bacteria - classification - genetics
Biota
Cluster analysis
DNA, Bacterial - chemistry - genetics
DNA, Ribosomal - chemistry - genetics
Ice Cover - microbiology
Oligochaeta - microbiology
Phylogeny
RNA, Ribosomal, 16S - genetics
Sequence Analysis, DNA
Abstract
The community structure of bacteria associated with the glacier ice worm Mesenchytraeus solifugus was analyzed by amplicon sequencing of 16S rRNA genes and their transcripts. Ice worms were collected from two distinct glaciers in Alaska, Harding Icefield and Byron Glacier, and glacier surfaces were also sampled for comparison. Marked differences were observed in bacterial community structures between the ice worm and glacier surface samples. Several bacterial phylotypes were detected almost exclusively in the ice worms, and these bacteria were phylogenetically affiliated with either animal-associated lineages or, interestingly, clades mostly consisting of glacier-indigenous species. The former included bacteria that belong to Mollicutes, Chlamydiae, Rickettsiales, and Lachnospiraceae, while the latter included Arcicella and Herminiimonas phylotypes. Among these bacteria enriched in ice worm samples, Mollicutes, Arcicella, and Herminiimonas phylotypes were abundantly and consistently detected in the ice worm samples; these phylotypes constituted the core microbiota associated with the ice worm. A fluorescence in situ hybridization analysis showed that Arcicella cells specifically colonized the epidermis of the ice worms. Other bacterial phylotypes detected in the ice worm samples were also abundantly recovered from the respective habitat glaciers; these bacteria may be food for ice worms to digest or temporary residents. Nevertheless, some were overrepresented in the ice worm RNA samples; they may also function as facultative gut bacteria. Our results indicate that the community structure of bacteria associated with ice worms is distinct from that in the associated glacier and includes worm-specific and facultative, glacier-indigenous lineages.
Notes
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PubMed ID
28302989 View in PubMed
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78 records – page 1 of 8.