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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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[Abundance and diversity of methanotrophic Gammaproteobacteria in northern wetlands].

https://arctichealth.org/en/permalink/ahliterature259581
Source
Mikrobiologiia. 2014 Mar-Apr;83(2):204-14
Publication Type
Article
Author
O V Danilova
S N Dedysh
Source
Mikrobiologiia. 2014 Mar-Apr;83(2):204-14
Language
Russian
Publication Type
Article
Keywords
Biodiversity
Fresh Water - microbiology
Gammaproteobacteria - genetics - isolation & purification - metabolism
Hydrogen-Ion Concentration
In Situ Hybridization, Fluorescence
Methane - metabolism
Methylococcaceae - genetics
Methylocystaceae - genetics
Molecular Sequence Data
Oxygenases - genetics
Phylogeny
RNA, Ribosomal, 16S
Russia
Wetlands
Abstract
Numeric abundance, identity and pH preferences of methanotrophic Gammaproteobacteria (type I methanotrophs) inhabiting the northern acidic wetlands were studied. The rates of methane oxidation by peat samples from six-wetlands of European Northern Russia (pH 3.9-4.7) varied from 0.04 to 0.60 µg CH4 g(-1) peat h(-1). The number of cells revealed by hybridization with fluorochrome-labeled probes M84 + M705 specific for type I methanotrophs was 0.05-2.16 x 10(5) cells g(-1) dry peat, i.e. 0.4-12.5% of the total number of methanotrophs and 0.004-0.39% of the total number of bacteria. Analysis of the fragments of the pmoA gene encoding particulate methane monooxygenase revealed predominance of the genus Methylocystis (92% of the clones) in the studied sample of acidic peat, while the proportion of the pmoA sequences of type I methanotrophs was insignificant (8%). PCR amplification of the 16S rRNA gene fragments of type I methanotrophs with TypeIF-Type IR primers had low specificity, since only three sequences out of 53 analyzed belonged to methanotrophs and exhibited 93-99% similarity to those of Methylovulum, Methylomonas, and Methylobacter species. Isolates of type I methanotrophs obtained from peat (strains SH10 and 83A5) were identified as members of the species Methylomonaspaludis and Methylovulum miyakonense, respectively. Only Methylomonaspaludum SH10 was capable of growth in acidic media (pH range for growth 3.8-7.2 with the optimum at pH 5.8-6.2), while Methylovulum miyakonense 83A5 exhibited the typical growth characteristics of neutrophilic methanotrophs (pH range for growth 5.5-8.0 with the optimum at pH 6.5-7.5).
PubMed ID
25423724 View in PubMed
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Abundant Trimethylornithine Lipids and Specific Gene Sequences Are Indicative of Planctomycete Importance at the Oxic/Anoxic Interface in Sphagnum-Dominated Northern Wetlands.

https://arctichealth.org/en/permalink/ahliterature273730
Source
Appl Environ Microbiol. 2015 Sep;81(18):6333-44
Publication Type
Article
Date
Sep-2015
Author
Eli K Moore
Laura Villanueva
Ellen C Hopmans
W Irene C Rijpstra
Anchelique Mets
Svetlana N Dedysh
Jaap S Sinninghe Damsté
Source
Appl Environ Microbiol. 2015 Sep;81(18):6333-44
Date
Sep-2015
Language
English
Publication Type
Article
Keywords
Acidobacteria - chemistry - isolation & purification
Bacteria - chemistry - genetics - isolation & purification
High-Throughput Nucleotide Sequencing
In Situ Hybridization, Fluorescence
Lipids - analysis - chemistry
Oxidation-Reduction
Phylogeny
RNA, Bacterial - genetics
RNA, Ribosomal, 16S - genetics
Russia
Soil - chemistry
Soil Microbiology
Sphagnopsida - chemistry - genetics - microbiology
Sweden
Wetlands
Abstract
Northern wetlands make up a substantial terrestrial carbon sink and are often dominated by decay-resistant Sphagnum mosses. Recent studies have shown that planctomycetes appear to be involved in degradation of Sphagnum-derived debris. Novel trimethylornithine (TMO) lipids have recently been characterized as abundant lipids in various Sphagnum wetland planctomycete isolates, but their occurrence in the environment has not yet been confirmed. We applied a combined intact polar lipid (IPL) and molecular analysis of peat cores collected from two northern wetlands (Saxnäs Mosse [Sweden] and Obukhovskoye [Russia]) in order to investigate the preferred niche and abundance of TMO-producing planctomycetes. TMOs were present throughout the profiles of Sphagnum bogs, but their concentration peaked at the oxic/anoxic interface, which coincided with a maximum abundance of planctomycete-specific 16S rRNA gene sequences. The sequences detected at the oxic/anoxic interface were affiliated with the Isosphaera group, while sequences present in the anoxic peat layers were related to an uncultured planctomycete group. Pyrosequencing-based analysis identified Planctomycetes as the major bacterial group at the oxic/anoxic interface at the Obukhovskoye peat (54% of total 16S rRNA gene sequence reads), followed by Acidobacteria (19% reads), while in the Saxnäs Mosse peat, Acidobacteria were dominant (46%), and Planctomycetes contributed to 6% of the total reads. The detection of abundant TMO lipids in planctomycetes isolated from peat bogs and the lack of TMO production by cultures of acidobacteria suggest that planctomycetes are the producers of TMOs in peat bogs. The higher accumulation of TMOs at the oxic/anoxic interface and the change in the planctomycete community with depth suggest that these IPLs could be synthesized as a response to changing redox conditions at the oxic/anoxic interface.
Notes
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PubMed ID
26150465 View in PubMed
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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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The activated sludge ecosystem contains a core community of abundant organisms.

https://arctichealth.org/en/permalink/ahliterature275609
Source
ISME J. 2016 Jan;10(1):11-20
Publication Type
Article
Date
Jan-2016
Author
Aaron M Saunders
Mads Albertsen
Jes Vollertsen
Per H Nielsen
Source
ISME J. 2016 Jan;10(1):11-20
Date
Jan-2016
Language
English
Publication Type
Article
Keywords
Bacteria - classification - genetics - growth & development - isolation & purification
Denmark
Ecosystem
RNA, Ribosomal, 16S - genetics
Sewage - microbiology
Waste Water - microbiology
Abstract
Understanding the microbial ecology of a system requires that the observed population dynamics can be linked to their metabolic functions. However, functional characterization is laborious and the choice of organisms should be prioritized to those that are frequently abundant (core) or transiently abundant, which are therefore putatively make the greatest contribution to carbon turnover in the system. We analyzed the microbial communities in 13 Danish wastewater treatment plants with nutrient removal in consecutive years and a single plant periodically over 6 years, using Illumina sequencing of 16S ribosomal RNA amplicons of the V4 region. The plants contained a core community of 63 abundant genus-level operational taxonomic units (OTUs) that made up 68% of the total reads. A core community consisting of abundant OTUs was also observed within the incoming wastewater to three plants. The net growth rate for individual OTUs was quantified using mass balance, and it was found that 10% of the total reads in the activated sludge were from slow or non-growing OTUs, and that their measured abundance was primarily because of immigration with the wastewater. Transiently abundant organisms were also identified. Among them the genus Nitrotoga (class Betaproteobacteria) was the most abundant putative nitrite oxidizer in a number of activated sludge plants, which challenges previous assumptions that Nitrospira (phylum Nitrospirae) are the primary nitrite-oxidizers in activated sludge systems with nutrient removal.
Notes
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PubMed ID
26262816 View in PubMed
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Active Microbial Communities Inhabit Sulphate-Methane Interphase in Deep Bedrock Fracture Fluids in Olkiluoto, Finland.

https://arctichealth.org/en/permalink/ahliterature274433
Source
Biomed Res Int. 2015;2015:979530
Publication Type
Article
Date
2015
Author
Malin Bomberg
Mari Nyyssönen
Petteri Pitkänen
Anne Lehtinen
Merja Itävaara
Source
Biomed Res Int. 2015;2015:979530
Date
2015
Language
English
Publication Type
Article
Keywords
Bacteria - genetics - metabolism
Base Sequence
Ecosystem
Finland
Geologic Sediments - microbiology
Groundwater - microbiology
High-Throughput Nucleotide Sequencing
Methane - metabolism
Phylogeny
RNA, Messenger - genetics - metabolism
RNA, Ribosomal, 16S - genetics
Sulfates - metabolism
Abstract
Active microbial communities of deep crystalline bedrock fracture water were investigated from seven different boreholes in Olkiluoto (Western Finland) using bacterial and archaeal 16S rRNA, dsrB, and mcrA gene transcript targeted 454 pyrosequencing. Over a depth range of 296-798?m below ground surface the microbial communities changed according to depth, salinity gradient, and sulphate and methane concentrations. The highest bacterial diversity was observed in the sulphate-methane mixing zone (SMMZ) at 250-350?m depth, whereas archaeal diversity was highest in the lowest boundaries of the SMMZ. Sulphide-oxidizing e-proteobacteria (Sulfurimonas sp.) dominated in the SMMZ and ?-proteobacteria (Pseudomonas spp.) below the SMMZ. The active archaeal communities consisted mostly of ANME-2D and Thermoplasmatales groups, although Methermicoccaceae, Methanobacteriaceae, and Thermoplasmatales (SAGMEG, TMG) were more common at 415-559?m depth. Typical indicator microorganisms for sulphate-methane transition zones in marine sediments, such as ANME-1 archaea, a-, ß- and d-proteobacteria, JS1, Actinomycetes, Planctomycetes, Chloroflexi, and MBGB Crenarchaeota were detected at specific depths. DsrB genes were most numerous and most actively transcribed in the SMMZ while the mcrA gene concentration was highest in the deep methane rich groundwater. Our results demonstrate that active and highly diverse but sparse and stratified microbial communities inhabit the Fennoscandian deep bedrock ecosystems.
Notes
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PubMed ID
26425566 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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Aerobic and anaerobic de-epoxydation of mycotoxin deoxynivalenol by bacteria originating from agricultural soil.

https://arctichealth.org/en/permalink/ahliterature122520
Source
World J Microbiol Biotechnol. 2012 Jan;28(1):7-13
Publication Type
Article
Date
Jan-2012
Author
Rafiqul Islam
Ting Zhou
J Christopher Young
Paul H Goodwin
K Peter Pauls
Author Affiliation
Guelph Food Research Center, Agriculture and Agri-Food Canada, 93 Stone Road West, Guelph, ON, N1G 5C9, Canada. mislam@uoguelph.ca
Source
World J Microbiol Biotechnol. 2012 Jan;28(1):7-13
Date
Jan-2012
Language
English
Publication Type
Article
Keywords
Animals
Bacteria, Aerobic - genetics - isolation & purification - metabolism
Bacteria, Anaerobic - genetics - isolation & purification - metabolism
Biotransformation
Food Contamination - prevention & control
Genes, Bacterial
Humans
Metabolic Detoxication, Drug
Ontario
RNA, Bacterial - genetics
RNA, Ribosomal, 16S - genetics
Soil Microbiology
Trichothecenes - metabolism - toxicity
Abstract
One hundred and fifty soil samples collected from different crop fields in southern Ontario, Canada were screened to obtain microorganisms capable of transforming deoxynivalenol (DON) to de-epoxy DON (dE-DON). Microbial DON to dE-DON transformation (i.e. de-epoxydation) was monitored by using liquid chromatography-ultraviolet-mass spectrometry (LC-UV-MS). The effects of growth substrates, temperature, pH, incubation time and aerobic versus anaerobic conditions on the ability of the microbes to de-epoxydize DON were evaluated. A mixed microbial culture from one composite soil sample showed 100% DON to dE-DON biotransformation in mineral salts broth (MSB) after 144 h of incubation. Treatments of the culture with selective antibiotics followed an elevated temperature (50°C) for 1.5 h considerably reduced the microbial diversity. Partial 16S-rRNA gene sequence analysis of the bacteria in the enriched culture indicated the presence of at least six bacterial genera, namely Serratia, Clostridium, Citrobacter, Enterococcus, Stenotrophomonas and Streptomyces. The enriched culture completely de-epoxydized DON after 60 h of incubation. Bacterial de-epoxydation of DON occurred at pH 6.0-7.5, and a wide array of temperatures (12-40°C). The culture showed rapid de-epoxydation activity under aerobic conditions compared to anaerobic conditions. This is the first report on microbial DON to dE-DON transformation under aerobic conditions and moderate temperatures. The culture could be used to detoxify DON contaminated feed and might be a potential source for gene(s) for DON de-epoxydation.
PubMed ID
22806774 View in PubMed
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Aerobic microbial taxa dominate deep subsurface cores from the Alberta oil sands.

https://arctichealth.org/en/permalink/ahliterature299361
Source
FEMS Microbiol Ecol. 2018 06 01; 94(6):
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Date
06-01-2018
Author
Christina M Ridley
Gerrit Voordouw
Author Affiliation
Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada.
Source
FEMS Microbiol Ecol. 2018 06 01; 94(6):
Date
06-01-2018
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Keywords
Alberta
Bacteria, Aerobic - classification - genetics - isolation & purification
Biodegradation, Environmental
Fungi - classification - genetics - isolation & purification
Hydrocarbons - metabolism
Microbiota - genetics
Oil and Gas Fields - microbiology
RNA, Ribosomal, 16S - genetics
Soil Microbiology
Abstract
Little is known about the microbial ecology of the subsurface oil sands in Northern Alberta, Canada. Biodegradation of low molecular weight hydrocarbons by indigenous microbes has enriched high molecular weight hydrocarbons, resulting in highly viscous bitumen. This extreme subsurface environment is further characterized by low nutrient availability and limited access to water, thus resulting in low microbial biomass. Improved DNA isolation protocols and increasingly sensitive sequencing methods have allowed an in-depth investigation of the microbial ecology of this unique subsurface environmental niche. Community analysis was performed on core samples (n = 62) that were retrieved from two adjacent sites located in the Athabasca Oil Sands at depths from 220 to 320 m below the surface. Microbial communities were dominated by aerobic taxa, including Pseudomonas and Acinetobacter. Only one core sample microbial community was dominated by anaerobic taxa, including the methanogen Methanoculleus, as well as Desulfomicrobium and Thauera. Although the temperature of the bitumen-containing subsurface is low (8°C), two core samples had high fractions of the potentially thermophilic taxon, Thermus. Predominance of aerobic taxa in the subsurface suggests the potential for in situ aerobic hydrocarbon degradation; however, more studies are required to determine the functional role of these taxa within this unique environment.
PubMed ID
29688331 View in PubMed
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