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Kaya D, Sowers KR, Demirtepe H, Stiell B, Baker JE, Imamoglu I, Kjellerup BV. Assessment of PCB contamination, the potential for in situ microbial dechlorination and natural attenuation in an urban watershed at the East Coast of the United States. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 683:154-165. [PMID: 31129325 DOI: 10.1016/j.scitotenv.2019.05.193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 05/07/2019] [Accepted: 05/14/2019] [Indexed: 06/09/2023]
Abstract
Sediment contamination is a major environmental issue in many urban watersheds and coastal areas due to the potential toxic effects of contaminants on biota and human health. Characterizing and delineating areas of sediment contamination and toxicity are important goals of coastal resource management in terms of ecological and economical perspectives. Core and surficial sediment samples were collected from an industrialized urban watershed at the East Coast of the United Stated and analyzed to evaluate the PCB contamination profile and toxicity resulting from dioxin-like PCBs as well as reductive dechlorination potential of indigenous PCB halorespiring bacteria through dechlorination activity assays. To support the experimental results an anaerobic dechlorination model was applied to identify microbial dechlorination pathways. The total PCB concentration in core samples ranged from 3.9 to 225.6 ng/g·dry weight (dw) decreasing with depth compared to 353.2 to 1213.7 ng/g·dw in surficial samples. The results of this study indicated an increase in PCB contamination over the last century as the industrial activity intensified. The toxicity resulting from dioxin-like PCBs was reduced up to 94% in core samples via 21 pathways resulting from the dechlorination model. Dechlorination rates in surficial sediment were between 1.8 and 13.2 · 10-3 mol% PCB116/day, while lower rates occurred in the core sediment samples. Dechlorination was achieved mainly through meta followed by para dechlorination. However, the rarer ortho dechlorination was also observed. Detection of indigenous PCB dechlorinating bacteria in the sediments and reduction of toxicity indicated potential for natural attenuation when point and nonpoint source PCBs in the urban watershed are controlled and PCB loading reduced.
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Affiliation(s)
- Devrim Kaya
- University of Maryland College Park, Department of Civil and Environmental Engineering, 1146 Glenn L. Martin Hall, College Park, MD 20742, USA
| | - Kevin R Sowers
- University of Maryland Baltimore County, Institute of Marine & Environmental Technology, 701 E. Pratt Street, Baltimore, MD 21202, USA
| | - Hale Demirtepe
- Middle East Technical University, Department of Environmental Engineering, Ankara, Turkey
| | | | - Joel E Baker
- University of Washington Tacoma, The Center for Urban Waters, 1900 Commerce Street, Tacoma, WA 98402-3100, USA
| | - Ipek Imamoglu
- Middle East Technical University, Department of Environmental Engineering, Ankara, Turkey
| | - Birthe V Kjellerup
- University of Maryland College Park, Department of Civil and Environmental Engineering, 1146 Glenn L. Martin Hall, College Park, MD 20742, USA.
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2
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Bian H, Wang P, Wang N, Tian Y, Bai P, Jiang H, Gao J. Dual-model analysis for improving the discrimination performance of human and nonhuman blood based on Raman spectroscopy. BIOMEDICAL OPTICS EXPRESS 2018; 9:3512-3522. [PMID: 30338136 PMCID: PMC6191633 DOI: 10.1364/boe.9.003512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 06/22/2018] [Accepted: 06/25/2018] [Indexed: 05/28/2023]
Abstract
The discrimination accuracy for human and nonhuman blood is important for customs inspection and forensic applications. Recently, Raman spectroscopy has shown effectiveness in analyzing blood droplets and stains with an excitation wavelength of 785 nm. However, the discrimination of liquid whole blood in a vacuum blood tube using Raman spectroscopy, which is a form of noncontact and nondestructive detection, has not been achieved. An excitation wavelength of 532 nm was chosen to avoid the fluorescent background of the blood tube, at the cost of reduced spectroscopic information and discrimination accuracy. To improve the accuracy and true positive rate (TPR) for human blood, a dual-model analysis method is proposed. First, model 1 was used to discriminate human-unlike nonhuman blood. Model 2 was then used to discriminate human-like nonhuman blood from the "human blood" obtained by model 1. A total of 332 Raman spectra from 10 species were used to build and validate the model. A blind test and external validation demonstrated the effectiveness of the model. Compared with the results obtained by the single partial least-squares model, the discrimination performance was improved. The total accuracy and TPR, which are highly important for practical applications, increased to 99.1% and 97.4% from 87.2% and 90.6%, respectively.
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Affiliation(s)
- Haiyi Bian
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
- Schott Glass Technologies (Suzhou) Co., Ltd., Suzhou 215009, China
| | - Peng Wang
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Ning Wang
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Yubing Tian
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Pengli Bai
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Jiangsu 215163, China
| | - Haowen Jiang
- Department of Urology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Jing Gao
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
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Virkajärvi V, Sarlin T, Laitila A. Fusarium Profiling and Barley Malt Gushing Propensity. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-2017-3321-01] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Vertti Virkajärvi
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT, Finland
| | - Tuija Sarlin
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT, Finland
| | - Arja Laitila
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT, Finland
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González-Ferrero C, Sáiz-Abajo MJ. Characterization and stability studies of bioactive compounds and food matrices as evidence in support of health claims. Int J Food Sci Nutr 2016; 66 Suppl 1:S4-S12. [PMID: 26241010 DOI: 10.3109/09637486.2015.1042843] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The characterization and stability evaluation of food and food constituents (chemical active ingredient/microorganism) for which nutrition or health claims want to be requested are essential for the success of an application to EFSA. This work reviews the requirements that must be fulfilled for a full characterization of the active substance, comprising origin, elaboration, or extraction method, and chemical/microbiological composition, using validated analytical methods. The review focuses not only on establishing the specifications of the final active ingredient or food but also on ensuring homogeneity between batches. In addition, the article discusses the methodologies and conditions of the stability studies that need to be performed on food and food constituents to verify that the relevant compounds--chemical and microbiological active ingredients--will get to the consumer in the intended state and concentration to accomplish the claimed health effect over shelf life.
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Affiliation(s)
- Carolina González-Ferrero
- Centro Nacional de Tecnología y Seguridad Alimentaria - CNTA , Food Ingredients - R&D&I, San Adrián , Spain
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Herrmann L, Haase I, Blauhut M, Barz N, Fischer M. DNA-based differentiation of the Ecuadorian cocoa types CCN-51 and Arriba based on sequence differences in the chloroplast genome. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:12118-12127. [PMID: 25404556 DOI: 10.1021/jf504258w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Two cocoa types, Arriba and CCN-51, are being cultivated in Ecuador. With regard to the unique aroma, Arriba is considered a fine cocoa type, while CCN-51 is a bulk cocoa because of its weaker aroma. Because it is being assumed that Arriba is mixed with CCN-51, there is an interest in the analytical differentiation of the two types. Two methods to identify CCN-51 adulterations in Arriba cocoa were developed on the basis of differences in the chloroplast DNA. On the one hand, a different repeat of the sequence TAAAG in the inverted repeat region results in a different length of amplicons for the two cocoa types, which can be detected by agarose gel electrophoresis, capillary gel electrophoresis, and denaturing high-performance liquid chromatography. On the other hand, single nucleotide polymorphisms (SNPs) between the CCN-51 and Arriba sequences represent restriction sites, which can be used for restriction fragment length polymorphism analysis. A semi-quantitative analysis based on these SNPs is feasible. A method for an exact quantitation based on these results is not realizable. These sequence variations were confirmed for a comprehensive cultivar collection of Arriba and CCN-51, for both bean and leaf samples.
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Affiliation(s)
- Luise Herrmann
- Hamburg School of Food Science, Institut für Lebensmittelchemie, Universität Hamburg , Grindelallee 117, 20146 Hamburg, Germany
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Hermet A, Mounier J, Keravec M, Vasseur V, Barbier G, Jany J. Application of capillary electrophoresis single-stranded conformation polymorphism (CE-SSCP) analysis for identification of fungal communities in cheese. Food Microbiol 2014; 41:82-90. [DOI: 10.1016/j.fm.2014.01.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 07/24/2013] [Accepted: 01/21/2014] [Indexed: 10/25/2022]
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7
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Combination of multiplex PCR with denaturing high-performance liquid chromatography for rapid detection of Mycobacterium genus and simultaneous identification of the Mycobacterium tuberculosis complex. Diagn Microbiol Infect Dis 2013; 77:53-7. [DOI: 10.1016/j.diagmicrobio.2013.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 05/22/2013] [Accepted: 06/01/2013] [Indexed: 11/17/2022]
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8
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Skraban J, Dzeroski S, Zenko B, Tusar L, Rupnik M. Changes of poultry faecal microbiota associated with Clostridium difficile colonisation. Vet Microbiol 2013; 165:416-24. [PMID: 23664184 DOI: 10.1016/j.vetmic.2013.04.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 03/04/2013] [Accepted: 04/12/2013] [Indexed: 12/17/2022]
Abstract
Bacterial, fungal and archaeal microbiota was analysed in 143 chicken faecal samples from a single poultry farm. After DHPLC (denaturing high performance liquid chromatography) 15 bacterial groups, 10 fungal groups and a single archaeal species were differentiated. Samples were grouped into two clusters with significantly different frequencies of C. difficile positive and negative samples in each cluster. Acidaminococcus intestini, described here for the first time as a part of poultry faecal microbiota, was significantly more likely present in C. difficile negative samples, while presence/absence of some other microorganisms (Enterococcus cecorum, Lactobacillus galinarum, Moniliella sp. and Trichosporon asahii) was close to significance. Two other groups not reported previously for poultry, Coprobacillus sp. and Turicibacter sp. did not differ significantly between C. difficile positive and negative samples. Differences in microbiota diversity depend on animal age, but not on the presence of C. difficile. With machine learning (WEKA J48) we have defined specific combinations of microbial groups predictive for C. difficile colonisation. Microbial groups associated with C. difficile colonisation in poultry are different than those reported for humans and include bacteria as well as fungi. Also with this approach A. intestini was found to be most strongly related to C. difficile negative samples.
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Affiliation(s)
- Jure Skraban
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, 1000 Ljubljana, Slovenia
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Gut microbiota patterns associated with colonization of different Clostridium difficile ribotypes. PLoS One 2013; 8:e58005. [PMID: 23469128 PMCID: PMC3585249 DOI: 10.1371/journal.pone.0058005] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 01/29/2013] [Indexed: 12/15/2022] Open
Abstract
C. difficile infection is associated with disturbed gut microbiota and changes in relative frequencies and abundance of individual bacterial taxons have been described. In this study we have analysed bacterial, fungal and archaeal microbiota by denaturing high pressure liquid chromatography (DHPLC) and with machine learning methods in 208 faecal samples from healthy volunteers and in routine samples with requested C. difficile testing. The latter were further divided according to stool consistency, C. difficile presence or absence and C. difficile ribotype (027 or non-027). Lower microbiota diversity was a common trait of all routine samples and not necessarily connected only to C. difficile colonisation. Differences between the healthy donors and C. difficile positive routine samples were detected in bacterial, fungal and archaeal components. Bifidobacterium longum was the single most important species associated with C. difficile negative samples. However, by machine learning approaches we have identified patterns of microbiota composition predictive for C. difficile colonization. Those patterns also differed between samples with C. difficile ribotype 027 and other C. difficile ribotypes. The results indicate that not only the presence of a single species/group is important but that certain combinations of gut microbes are associated with C. difficile carriage and that some ribotypes (027) might be associated with more disturbed microbiota than the others.
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Hutzler M, Geiger E, Jacob F. Use of PCR-DHPLC (Polymerase Chain Reaction-Denaturing High Performance Liquid Chromatography) for the Rapid Differentiation of IndustrialSaccharomyces pastorianusandSaccharomyces cerevisiaeStrains. JOURNAL OF THE INSTITUTE OF BREWING 2012. [DOI: 10.1002/j.2050-0416.2010.tb00798.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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11
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Telleria O, Ezpeleta G, Herrero O, Miranda-Zapico I, Quindós G, Cisterna R. Validation of the PCR–dHPLC method for rapid identification of Candida glabrata phylogenetically related species in different biological matrices. J Chromatogr B Analyt Technol Biomed Life Sci 2012; 893-894:150-6. [DOI: 10.1016/j.jchromb.2012.03.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 02/27/2012] [Accepted: 03/04/2012] [Indexed: 01/31/2023]
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12
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Maurice S, Le Floch G, Le Bras-Quéré M, Barbier G. Improved molecular methods to characterise Serpula lacrymans and other Basidiomycetes involved in wood decay. J Microbiol Methods 2010; 84:208-15. [PMID: 21146565 DOI: 10.1016/j.mimet.2010.11.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 11/15/2010] [Accepted: 11/22/2010] [Indexed: 10/18/2022]
Abstract
Early detection of indoor wood-decay fungi is crucial to prevent building deterioration and thereby avoid considerable economic loss. Due to their increased sensitivity, two reliable DNA-based fingerprinting techniques, capillary electrophoresis single-strand conformation polymorphism (CE-SSCP) and denaturing high-performance liquid chromatography (DHPLC), were used to identify Serpula lacrymans and to profile wood-rot Basidiomycetes in the built environment. Molecular fungal diversity was assessed on 74 environmental samples, collected from 2003 to 2009 from infected buildings in France. S. lacrymans, the most widespread, indoor wood-decay fungus accounted for 64% of total wood-rot Basidiomycetes. A number of other common wood-rot fungi such as Coniophora puteana, Trametes versicolor and Donkioporia expansa were identified. Other Basidiomycetes such as Phlebiopsis gigantea and Scleroderma verrucosum were detected for the first time in the built environment. Reliable diagnostic tools were developed using two PCR-based molecular typing techniques, one for routine diagnosis and another one for community inventories. Together they provided useful data for characterising the complexity of wood-decay ecosystems and helped reveal the coexistence of different wood-decay fungi within the same microbiotope.
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Affiliation(s)
- Sundy Maurice
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Université Européenne de Bretagne, ESMISAB, Technopole Brest-Iroise, Plouzané, France.
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13
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Nieguitsila A, Goldenberg O, Deville M, Arné P, Benoît-Valiergue H, Chermette R, Latouche-Cottenot S, Pissard S, Guillot J. Molecular monitoring of fungal communities in air samples by denaturing high-performance liquid chromatography (D-HPLC). J Appl Microbiol 2010; 109:910-7. [DOI: 10.1111/j.1365-2672.2010.04717.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Büchl N, Hutzler M, Mietke-Hofmann H, Wenning M, Scherer S. Differentiation of probiotic and environmental Saccharomyces cerevisiae strains in animal feed. J Appl Microbiol 2010; 109:783-91. [DOI: 10.1111/j.1365-2672.2010.04705.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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15
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Mounier J, Le Blay G, Vasseur V, Le Floch G, Jany JL, Barbier G. Application of denaturing high-performance liquid chromatography (DHPLC) for yeasts identification in red smear cheese surfaces. Lett Appl Microbiol 2010; 51:18-23. [PMID: 20477955 DOI: 10.1111/j.1472-765x.2010.02852.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
AIMS To evaluate and optimize the use of denaturing high-performance liquid chromatography (DHPLC) for yeasts identification in red smear cheese surfaces. METHODS AND RESULTS The resolution of DHPLC was first evaluated and optimized using a mixture of PCR amplicons of the internal transcribed spacer 2 (ITS2) region of 19 yeast reference strains representing 18 species that are common in the cheese microbiota. Sixteen of the 18 yeast species could be resolved by combining runs at temperatures of 57.5 and 59 degrees C. Then, DHPLC was used to investigate the yeast microbiota of pasteurized Maroilles, Munster and Livarot cheese surfaces by comparing their peak profiles with our reference yeast database and by collecting/sequencing of peak fractions. Debaryomyces hansenii and Geotrichum candidum for Munster and Maroilles cheeses, and Candida catenulata, Candida intermedia and G. candidum for Livarot cheese were identified using the reference database and collecting/sequencing of peak fractions. CONCLUSIONS DHPLC technique was found to have good resolution properties and to be useful for investigating the yeast microbiota of red smear cheese surfaces. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first time that DHPLC is applied to study the yeast microbiota of red smear cheese surfaces.
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Affiliation(s)
- J Mounier
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (EA3882), IFR148 ScInBioS, Université Européenne de Bretagne, Université de Brest, ESMISAB, Technopôle de Brest Iroise, Plouzané, France.
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Nazaret S, Assade F, Brothier E, Freydière AM, Bellon G, Cournoyer B. RISA–HPLC analysis of lung bacterial colonizers of cystic fibrosis children. J Microbiol Methods 2009; 76:58-69. [DOI: 10.1016/j.mimet.2008.09.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Revised: 09/05/2008] [Accepted: 09/16/2008] [Indexed: 10/21/2022]
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Huys G, Vanhoutte T, Vandamme P. Application of sequence-dependent electrophoresis fingerprinting in exploring biodiversity and population dynamics of human intestinal microbiota: what can be revealed? Interdiscip Perspect Infect Dis 2008; 2008:597603. [PMID: 19277102 PMCID: PMC2648627 DOI: 10.1155/2008/597603] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2008] [Accepted: 09/22/2008] [Indexed: 01/13/2023] Open
Abstract
Sequence-dependent electrophoresis (SDE) fingerprinting techniques such as denaturing gradient gel electrophoresis (DGGE) have become commonplace in the field of molecular microbial ecology. The success of the SDE technology lays in the fact that it allows visualization of the predominant members of complex microbial ecosystems independent of their culturability and without prior knowledge on the complexity and diversity of the ecosystem. Mainly using the prokaryotic 16S rRNA gene as PCR amplification target, SDE-based community fingerprinting turned into one of the leading molecular tools to unravel the diversity and population dynamics of human intestinal microbiota. The first part of this review covers the methodological concept of SDE fingerprinting and the technical hurdles for analyzing intestinal samples. Subsequently, the current state-of-the-art of DGGE and related techniques to analyze human intestinal microbiota from healthy individuals and from patients with intestinal disorders is surveyed. In addition, the applicability of SDE analysis to monitor intestinal population changes upon nutritional or therapeutic interventions is critically evaluated.
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Affiliation(s)
- Geert Huys
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Tom Vanhoutte
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
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Schweickert B, Goldenberg O, Richter E, Göbel UB, Petrich A, Buchholz P, Moter A. Occurrence and clinical relevance of Mycobacterium chimaera sp. nov., Germany. Emerg Infect Dis 2008; 14:1443-6. [PMID: 18760016 PMCID: PMC2603105 DOI: 10.3201/eid1409.071032] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Retrospective molecular genetic analysis of 166 Mycobacterium intracellulare isolates showed that 143 (86%) strains could be assigned to Mycobacterium chimaera sp. nov. Of 97 patients from whom M. chimaera sp. nov. was isolated, only 3.3% exhibited mycobacterial lung disease, whereas all M. intracellulare isolates caused severe pulmonary infections.
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Affiliation(s)
- Birgitta Schweickert
- Institut für Mikrobiologie und Hygiene, Charité-Universitätsmedizin, Berlin, Germany.
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19
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Troedsson C, Lee RF, Stokes V, Walters TL, Simonelli P, Frischer ME. Development of a denaturing high-performance liquid chromatography method for detection of protist parasites of metazoans. Appl Environ Microbiol 2008; 74:4336-45. [PMID: 18502933 PMCID: PMC2493188 DOI: 10.1128/aem.02131-07] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2007] [Accepted: 05/12/2008] [Indexed: 01/15/2023] Open
Abstract
Increasingly, diseases of marine organisms are recognized as significant biotic factors affecting ecosystem health. However, the responsible disease agents are often unknown and the discovery and description of novel parasites most often rely on morphological descriptions made by highly trained specialists. Here, we describe a new approach for parasite discovery, utilizing denaturing high-performance liquid chromatography (DHPLC) reverse-phase ion-pairing technology. Systematic investigations of major DHPLC variables, including temperature, gradient conditions, and target amplicon characteristics were conducted to develop a mechanistic understanding of DNA fragment separation by DHPLC. As a model system, 18S rRNA genes from the blue crab (Callinectes sapidus) and a parasitic dinoflagellate Hematodinium sp. were used. Binding of 18S rRNA gene PCR amplicons to the DNA separation column in the presence of triethylammonium acetate (TEAA) was inversely correlated with temperature and could be predicted based on the estimated DNA helicity of the PCR amplicon. Amplicons of up to 498 bp were resolved as single chromatographic peaks if they had high (>95%) DNA helicity. Amplicons that differed by as few as 2 bp could be resolved. Separation of 18S rRNA gene PCR amplicons was optimized by simultaneous manipulation of both temperature and solvent gradients. The optimal conditions included targeting regions of high DNA helicity (>95%), temperatures in the range of 57 to 63 degrees C, and a linear acetonitrile gradient from 13.75 to 17.5% acetonitrile in 0.1 M TEAA (55 to 70% buffer B) over a 9-min period. Under these conditions, amplicons from a variety of parasites and their hosts can be separated and detected by DHPLC.
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Affiliation(s)
- Christofer Troedsson
- Skidaway Institute of Oceanography, 10 Ocean Science Circle, Savannah, GA 31411, USA
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Jany JL, Barbier G. Culture-independent methods for identifying microbial communities in cheese. Food Microbiol 2008; 25:839-48. [PMID: 18721671 DOI: 10.1016/j.fm.2008.06.003] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2008] [Revised: 05/30/2008] [Accepted: 06/04/2008] [Indexed: 10/22/2022]
Abstract
This review focuses on the culture-independent methods available for the description of both bacterial and fungal communities in cheese. Important steps of the culture-independent strategy, which relies on bulk DNA extraction from cheese and polymerase chain reaction (PCR) amplification of selected sequences, are discussed. We critically evaluate the identification techniques already used for monitoring microbial communities in cheese, including PCR-denaturing gradient gel electrophoresis (PCR-DGGE), PCR-temporal temperature gradient gel electrophoresis (PCR-TTGE) or single-strand conformation polymorphism-PCR (SSCP-PCR) as well as some other techniques that remain to be adapted to the study of cheese communities. Further, our analysis draws attention to the lack of data available on suitable DNA sequences for identifying fungal communities in cheese and proposes some potential DNA targets.
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Affiliation(s)
- Jean-Luc Jany
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Université Européenne de Bretagne-ESMISAB, Parvis Blaise Pascal, Technopôle de Brest Iroise, Plouzané, France.
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21
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Kjellerup BV, Sun X, Ghosh U, May HD, Sowers KR. Site-specific microbial communities in three PCB-impacted sediments are associated with different in situ dechlorinating activities. Environ Microbiol 2008; 10:1296-309. [DOI: 10.1111/j.1462-2920.2007.01543.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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Kuramitsu HK, He X, Lux R, Anderson MH, Shi W. Interspecies interactions within oral microbial communities. Microbiol Mol Biol Rev 2007; 71:653-70. [PMID: 18063722 PMCID: PMC2168648 DOI: 10.1128/mmbr.00024-07] [Citation(s) in RCA: 404] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
While reductionism has greatly advanced microbiology in the past 400 years, assembly of smaller pieces just could not explain the whole! Modern microbiologists are learning "system thinking" and "holism." Such an approach is changing our understanding of microbial physiology and our ability to diagnose/treat microbial infections. This review uses oral microbial communities as a focal point to describe this new trend. With the common name "dental plaque," oral microbial communities are some of the most complex microbial floras in the human body, consisting of more than 700 different bacterial species. For a very long time, oral microbiologists endeavored to use reductionism to identify the key genes or key pathogens responsible for oral microbial pathogenesis. The limitations of reductionism forced scientists to begin adopting new strategies using emerging concepts such as interspecies interaction, microbial community, biofilms, polymicrobial disease, etc. These new research directions indicate that the whole is much more than the simple sum of its parts, since the interactions between different parts resulted in many new physiological functions which cannot be observed with individual components. This review describes some of these interesting interspecies-interaction scenarios.
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Affiliation(s)
- Howard K Kuramitsu
- Department of Oral Boiology, School of Dental Medicine, State University of New York, Buffalo, New York, USA
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Abstract
The focus of this review is the evolution of biochemical phenotypic yeast identification methods with emphasis on conventional approaches, rapid screening tests, chromogenic agars, comprehensive commercial methods, and the eventual migration to genotypic methods. As systemic yeast infections can be devastating and resistance is common in certain species, accurate identification to the species level is paramount for successful therapy and appropriate patient care.
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Affiliation(s)
- D H Pincus
- bioMérieux, Inc., Hazelwood, Missouri 63042, USA.
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Goldenberg O, Herrmann S, Marjoram G, Noyer-Weidner M, Hong G, Bereswill S, Göbel UB. Molecular monitoring of the intestinal flora by denaturing high performance liquid chromatography. J Microbiol Methods 2007; 68:94-105. [PMID: 16904779 DOI: 10.1016/j.mimet.2006.06.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2006] [Revised: 06/14/2006] [Accepted: 06/23/2006] [Indexed: 11/16/2022]
Abstract
Gut flora analysis is hampered by the complexity of the intestinal microbiota and by inherent limitations of culture-based approaches. Therefore, culture-independent molecular methods based upon 16S rRNA gene analysis were applied successfully for the analysis of complex microbial communities. However, generally accepted and validated profiling methods such as denaturing and temperature gradient gel electrophoresis (DGGE/TGGE) are still laborious and time consuming. Thus, we adapted the separation of amplified bacterial 16S rRNA gene fragments by denaturing high performance liquid chromatography (DHPLC) using the WAVE Microbial Analysis System as a rapid and convenient means to display complex intestinal bacterial communities and to monitor changes in the gut flora. The separation of 16S rRNA gene fragments amplified from reference strains representing main gut bacterial populations and from human stool samples revealed that DHPLC analysis effectively detects bacterial groups predominant in the human gut flora. The investigation of faecal samples from hospitalized patients before, during and after antibiotic therapy showed that PCR-based DHPLC can be used to monitor gut flora changes. Results from DHPLC analysis were comparable with DGGE profiles generated from the same samples, demonstrating that the adapted DHPLC protocol is well suited for the analysis of complex microbial communities.
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Affiliation(s)
- Oliver Goldenberg
- Institut für Mikrobiologie und Hygiene, Charité-Universitätsmedizin Berlin, Campus Charité Mitte, Dorotheenstrasse 96, D-10117 Berlin, Germany
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Lista S, Emanuele E. Analysis of mitochondrial DNA by PCR/DHPLC as a diagnostic tool to differentiate schistosomes species and strains. Med Hypotheses 2006; 68:707-8. [PMID: 17055179 DOI: 10.1016/j.mehy.2006.09.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Accepted: 09/06/2006] [Indexed: 11/25/2022]
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Current awareness on yeast. Yeast 2006. [DOI: 10.1002/yea.1316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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