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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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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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Anaerobic microbial Fe(II) oxidation and Fe(III) reduction in coastal marine sediments controlled by organic carbon content.

https://arctichealth.org/en/permalink/ahliterature285578
Source
Environ Microbiol. 2016 Sep;18(9):3159-74
Publication Type
Article
Date
Sep-2016
Author
Katja Laufer
James M Byrne
Clemens Glombitza
Caroline Schmidt
Bo Barker Jørgensen
Andreas Kappler
Source
Environ Microbiol. 2016 Sep;18(9):3159-74
Date
Sep-2016
Language
English
Publication Type
Article
Keywords
Anaerobiosis
Bacteria - classification - genetics - isolation & purification - metabolism
Carbon - analysis - metabolism
Denmark
Ferric Compounds - metabolism
Ferrous Compounds - metabolism
Geologic Sediments - chemistry - microbiology
Nitrates - metabolism
Oxidation-Reduction
Abstract
Coastal marine sediments contain varying concentrations of iron, oxygen, nitrate and organic carbon. It is unknown how organic carbon content influences the activity of nitrate-reducing and phototrophic Fe(II)-oxidizers and microbial Fe-redox cycling in such sediments. Therefore, microcosms were prepared with two coastal marine sediments (Kalø Vig and Norsminde Fjord at Aarhus Bay, Denmark) varying in TOC from 0.4 to 3.0 wt%. The microcosms were incubated under light/dark conditions with/without addition of nitrate and/or Fe(II). Although most probable number (MPN) counts of phototrophic Fe(II)-oxidizers were five times lower in the low-TOC sediment, phototrophic Fe(II) oxidation rates were higher compared with the high-TOC sediment. Fe(III)-amended microcosms showed that this lower net Fe(II) oxidation in the high-TOC sediment is caused by concurrent bacterial Fe(III) reduction. In contrast, MPN counts of nitrate-reducing Fe(II)-oxidizers and net rates of nitrate-reducing Fe(II) oxidation were comparable in low- and high-TOC sediments. However, the ratio of nitratereduced :iron(II)oxidized was higher in the high-TOC sediment, suggesting that a part of the nitrate was reduced by mixotrophic nitrate-reducing Fe(II)-oxidizers and chemoorganoheterotrophic nitrate-reducers. Our results demonstrate that dynamic microbial Fe cycling occurs in these sediments and that the extent of Fe cycling is dependent on organic carbon content.
PubMed ID
27234371 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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The application of amplicon length heterogeneity PCR (LH-PCR) for monitoring the dynamics of soil microbial communities associated with cadaver decomposition.

https://arctichealth.org/en/permalink/ahliterature138769
Source
J Microbiol Methods. 2011 Mar;84(3):388-93
Publication Type
Article
Date
Mar-2011
Author
Lilliana I Moreno
DeEtta Mills
Jill Fetscher
Krista John-Williams
Lee Meadows-Jantz
Bruce McCord
Author Affiliation
International Forensic Research Institute, Florida International University, 11200 SW 8th St. Miami, FL 33199, USA.
Source
J Microbiol Methods. 2011 Mar;84(3):388-93
Date
Mar-2011
Language
English
Publication Type
Article
Keywords
Bacteria - classification - genetics - isolation & purification
Bacteriological Techniques - methods
Biodiversity
Cadaver
Forensic Medicine - methods
Humans
Polymerase Chain Reaction - methods
Soil Microbiology
Time Factors
Abstract
The placement of cadavers in shallow, clandestine graves may alter the microbial and geochemical composition of the underlying and adjacent soils. Using amplicon length heterogeneity-PCR (LH-PCR) the microbial community changes in these soils can be assessed. In this investigation, nine different grave sites were examined over a period of 16weeks. The results indicated that measurable changes occurred in the soil bacterial community during the decomposition process. In this study, amplicons corresponding to anaerobic bacteria, not indigenous to the soil, were shown to produce differences between grave sites and control soils. Among the bacteria linked to these amplicons are those that are most often part of the commensal flora of the intestines, mouth and skin. In addition, over the 16week sampling interval, the level of indicator organisms (i.e., nitrogen fixing bacteria) dropped as the body decomposed and after four weeks of environmental exposure they began to increase again; thus differences in the abundance of nitrogen fixing bacteria were also found to contribute to the variation between controls and grave soils. These results were verified using primers that specifically targeted the nifH gene coding for nitrogenase reductase. LH-PCR provides a fast, robust and reproducible method to measure microbial changes in soil and could be used to determine potential cadaveric contact in a given area. The results obtained with this method could ultimately provide leads to investigators in criminal or missing person scenarios and allow for further analysis using human specific DNA assays to establish the identity of the buried body.
PubMed ID
21138746 View in PubMed
Less detail

Application of molecular genetic methods in diagnostics and epidemiology of food-borne bacterial pathogens.

https://arctichealth.org/en/permalink/ahliterature176690
Source
APMIS. 2004 Nov-Dec;112(11-12):908-29
Publication Type
Article
Author
Susanna Lukinmaa
Ulla-Maija Nakari
Marjut Eklund
Anja Siitonen
Author Affiliation
Laboratory of Enteric Pathogens, National Public Health Institute (KTL), Helsinki, Finland.
Source
APMIS. 2004 Nov-Dec;112(11-12):908-29
Language
English
Publication Type
Article
Keywords
Bacteria - classification - genetics - isolation & purification - pathogenicity
Bacterial Typing Techniques - methods
Campylobacter jejuni - genetics - isolation & purification - pathogenicity
Clostridium perfringens - genetics - isolation & purification - pathogenicity
Databases, Genetic
Electrophoresis, Gel, Pulsed-Field - methods
Enterobacteriaceae - genetics - isolation & purification - pathogenicity
Finland - epidemiology
Food Microbiology
Foodborne Diseases - diagnosis - epidemiology - microbiology
Genotype
Humans
Listeria monocytogenes - genetics - isolation & purification - pathogenicity
Molecular Biology - methods
Molecular Epidemiology - methods
Phenotype
Polymerase Chain Reaction - methods
Salmonella enterica - genetics - isolation & purification - pathogenicity
Yersinia - genetics - isolation & purification - pathogenicity
Abstract
Salmonella enterica, Campylobacter and Yersinia species, Shiga toxin-producing Escherichia coli (STEC), Listeria monocytogenes and Clostridium perfringens are the bacterial pathogens constituting the greatest burden of food-borne disease in Finland. Several molecular genetic methods have been applied to diagnose, discriminate and survey these bacteria. PCR, PCR-RFLP and PFGE are the most widely and successfully used. However, these methods are unable to replace conventional and internationally standardised phenotyping. Electronic database libraries of the different genomic profiles will enable continuous surveillance of infections and detection of possible infection clusters at an early stage. Furthermore, whole-genome sequence data have opened up new insights into epidemiological surveillance. Laboratory-based surveillance performed in a timely manner and exploiting adequate methods, and co-operation at local, national and international levels are among the key elements in preventing food-borne diseases. This paper reviews different applications of molecular genetic methods for investigating enteric bacterial pathogens and gives examples of the methods successfully used in diagnostics and epidemiological studies in Finland.
PubMed ID
15638843 View in PubMed
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Application of the filter plate microbial trap (FPMT), for cultivating thermophilic bacteria from thermal springs in Barguzin area, eastern Baikal, Russia.

https://arctichealth.org/en/permalink/ahliterature295596
Source
Biosci Biotechnol Biochem. 2018 Sep; 82(9):1624-1632
Publication Type
Journal Article
Date
Sep-2018
Author
Dawoon Jung
Eun-Young Seo
Jeffrey S Owen
Yoshiteru Aoi
Seungcheon Yong
Elena V Lavrentyeva
Tae Seok Ahn
Author Affiliation
a Department of Environmental Science , Kangwon National University , Chuncheon , Republic of Korea.
Source
Biosci Biotechnol Biochem. 2018 Sep; 82(9):1624-1632
Date
Sep-2018
Language
English
Publication Type
Journal Article
Keywords
Bacteria - classification - genetics - isolation & purification
Hot Springs - microbiology
Phylogeny
RNA, Ribosomal, 16S - genetics
Siberia
Water Microbiology
Abstract
Hot springs are regarded as treasury of valuable thermophiles. Like other bacteria, thermophiles are not easily cultivated using conventional culture methods. We used an advanced cultivation method, the filter plate microbial trap (FPMT), to isolate bacteria from thermal springs. In total, 184 isolates were obtained from five thermal springs using the FPMT and standard agar plate method, and their 16S rRNA gene sequences were analyzed. FPMT allowed us to obtain a culture collection that was larger, richer, and more novel than that obtained by standard cultivation. Seven novel species were obtained using the FPMT technique, whereas only one was isolated using a standard cultivation. We also found clear differences in the patterns of phylogenetic diversity and physiological properties between isolates from two cultivation methods. The results have encouraged us to apply the FPMT method in other extreme environments and offer further support for fostering the development of new cultivation methods.
PubMed ID
29882485 View in PubMed
Less detail

Bacterial Communities Associated with Atherosclerotic Plaques from Russian Individuals with Atherosclerosis.

https://arctichealth.org/en/permalink/ahliterature282801
Source
PLoS One. 2016;11(10):e0164836
Publication Type
Article
Date
2016
Author
Elvira E Ziganshina
Dilyara M Sharifullina
Andrey P Lozhkin
Rustem N Khayrullin
Igor M Ignatyev
Ayrat M Ziganshin
Source
PLoS One. 2016;11(10):e0164836
Date
2016
Language
English
Publication Type
Article
Keywords
Aged
Atherosclerosis - microbiology - pathology
Bacteria - classification - genetics - isolation & purification
Female
Humans
Male
Middle Aged
Plaque, Atherosclerotic - microbiology
Principal Component Analysis
RNA, Ribosomal, 16S - chemistry - isolation & purification - metabolism
Russia
Sequence Analysis, DNA
Abstract
Atherosclerosis is considered a chronic disease of the arterial wall and is the major cause of severe disease and death among individuals all over the world. Some recent studies have established the presence of bacteria in atherosclerotic plaque samples and suggested their possible contribution to the development of cardiovascular disease. The main objective of this preliminary pilot study was to better understand the bacterial diversity and abundance in human atherosclerotic plaques derived from common carotid arteries of individuals with atherosclerosis (Russian nationwide group) and contribute towards the further identification of a main group of atherosclerotic plaque bacteria by 454 pyrosequencing their 16S ribosomal RNA (16S rRNA) genes. The applied approach enabled the detection of bacterial DNA in all atherosclerotic plaques. We found that distinct members of the order Burkholderiales were present at high levels in all atherosclerotic plaques obtained from patients with atherosclerosis with the genus Curvibacter being predominant in all plaque samples. Moreover, unclassified Burkholderiales as well as members of the genera Propionibacterium and Ralstonia were typically the most significant taxa for all atherosclerotic plaques. Other genera such as Burkholderia, Corynebacterium and Sediminibacterium as well as unclassified Comamonadaceae, Oxalobacteraceae, Rhodospirillaceae, Bradyrhizobiaceae and Burkholderiaceae were always found but at low relative abundances of the total 16S rRNA gene population derived from all samples. Also, we found that some bacteria found in plaque samples correlated with some clinical parameters, including total cholesterol, alanine aminotransferase and fibrinogen levels. Finally, our study indicates that some bacterial agents at least partially may be involved in affecting the development of cardiovascular disease through different mechanisms.
Notes
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PubMed ID
27736997 View in PubMed
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Bacterial Communities in Areas of Oil and Methane Seeps in Pelagic of Lake Baikal.

https://arctichealth.org/en/permalink/ahliterature301934
Source
Microb Ecol. 2019 Aug; 78(2):269-285
Publication Type
Journal Article
Date
Aug-2019
Author
Aleksandra S Zakharenko
Yuriy P Galachyants
Igor V Morozov
Olga V Shubenkova
Alexey A Morozov
Vyacheslav G Ivanov
Nikolay V Pimenov
Andrey Y Krasnopeev
Tamara I Zemskaya
Author Affiliation
Siberian Branch of the Russian Academy of Sciences, Limnological Institute, Ulan-Batorskaya Street 3, 664033, Irkutsk, Russia. zakharenko@lin.irk.ru.
Source
Microb Ecol. 2019 Aug; 78(2):269-285
Date
Aug-2019
Language
English
Publication Type
Journal Article
Keywords
Bacteria - classification - genetics - isolation & purification - metabolism
Bacterial Proteins - genetics - metabolism
DNA, Bacterial - genetics
Geologic Sediments - chemistry - microbiology
Lakes - chemistry - microbiology
Methane - analysis - metabolism
Oils - analysis - metabolism
Oxidation-Reduction
Phylogeny
RNA, Ribosomal, 16S - genetics
Abstract
We have assessed the diversity of bacteria near oil-methane (area I) and methane (area II) seeps in the pelagic zone of Lake Baikal using massive parallel sequencing of 16S rRNA, pmoA, and mxaF gene fragments amplified from total DNA. At depths from the surface to 100 m, sequences belonging to Cyanobacteria dominated. In the communities to a depth of 200 m of the studied areas, Proteobacteria dominated the deeper layers of the water column. Alphaproteobacteria sequences were predominant in the community near the oil-methane seep, while the community near the methane seep was characterized by the prevalence of Alpha- and Gammaproteobacteria. Among representatives of these classes, type I methanotrophs prevailed in the 16S rRNA gene libraries from the near-bottom area, and type II methanotrophs were detected in minor quantities at different depths. In the analysis of the libraries of the pmoA and mxaF functional genes, we observed the different taxonomic composition of methanotrophic bacteria in the surface and deep layers of the water column. All pmoA sequences from area I were type II methanotrophs and were detected at a depth of 300 m, while sequences of type I methanotrophs were the most abundant in deep layers of the water column of area II. All mxaF gene sequences belonged to Methylobacterium representatives. Based on comparative analyses of 16S rRNA, pmoA, and mxaF gene fragment libraries, we suggest that there must be a wider spectrum of functional genes facilitating methane oxidation that were not detected with the primers used.
PubMed ID
30483839 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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