Search

Your search keyword '"Sibel Berger"' showing total 12 results
Start Over Author "Sibel Berger"
12 results on '"Sibel Berger"'

1. Interactions between snow chemistry, mercury inputs and microbial population dynamics in an Arctic snowpack.

Author

Catherine Larose, Emmanuel Prestat, Sébastien Cecillon, Sibel Berger, Cédric Malandain, Delina Lyon, Christophe Ferrari, Dominique Schneider, Aurélien Dommergue, and Timothy M Vogel

Subjects
Medicine, Science
Abstract

We investigated the interactions between snowpack chemistry, mercury (Hg) contamination and microbial community structure and function in Arctic snow. Snowpack chemistry (inorganic and organic ions) including mercury (Hg) speciation was studied in samples collected during a two-month field study in a high Arctic site, Svalbard, Norway (79 °N). Shifts in microbial community structure were determined by using a 16S rRNA gene phylogenetic microarray. We linked snowpack and meltwater chemistry to changes in microbial community structure by using co-inertia analyses (CIA) and explored changes in community function due to Hg contamination by q-PCR quantification of Hg-resistance genes in metagenomic samples. Based on the CIA, chemical and microbial data were linked (p = 0.006) with bioavailable Hg (BioHg) and methylmercury (MeHg) contributing significantly to the ordination of samples. Mercury was shown to influence community function with increases in merA gene copy numbers at low BioHg levels. Our results show that snowpacks can be considered as dynamic habitats with microbial and chemical components responding rapidly to environmental changes.

Published
2013
Full Text
View/download PDF

2. Variability in molecular characteristics of Hepatitis E virus quasispecies could modify viral surface properties and transmission

Author

Alexis Gentilhomme, Christophe Gantzer, Evelyne Schvoerer, Honorine Fenaux, Cédric Hartard, Jean-Pierre Bronowicki, M. Bensenane, Elodie Laugel, Thomas Remen, Sibel Berger, Hélène Jeulin, Alexis de Rougemont, Isabelle Bertrand, Elma H. Akand, Armand Maul, John M. Murray, Service de Virologie [CHRU Nancy], Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Laboratoire de Chimie Physique et Microbiologie pour les Matériaux et l'Environnement (LCPME), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), School of Mathematics and Statistics, University of New South Wales [Sydney] (UNSW), Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Terre et Environnement de Lorraine (OTELo), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Centre National de Référence des virus entériques [CHU de Dijon] (CNR virus entériques), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Délégation à la Recherche Clinique et à l'Innovation [CHRU Nancy] (DRCI), Service d'Hépato-gastro-entérologie [CHRU Nancy], and Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Antigenicity, Surface Properties, Swine, [SDV]Life Sciences [q-bio], viruses, Viral quasispecies, Biology, medicine.disease_cause, 03 medical and health sciences, 0302 clinical medicine, Hepatitis E virus, Virology, Genotype, medicine, Animals, Humans, 030212 general & internal medicine, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, chemistry.chemical_classification, Hepatology, Transmission (medicine), Developed Countries, Pathogenicity, Hepatitis E, 3. Good health, Amino acid, Quasispecies, Infectious Diseases, chemistry, Infected patient, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, 030211 gastroenterology & hepatology, Rabbits
Abstract

Hepatitis E virus (HEV) usually causes self-limited liver diseases but can also result in severe cases. Genotypes 1 (G1) and 2 circulate in developing countries are human-restricted and waterborne, while zoonotic G3 and G4 circulating in industrialized countries preferentially infect human through consumption of contaminated meat. Our aims were to identify amino acid patterns in HEV variants that could be involved in pathogenicity or in transmission modes, related to their impact on antigenicity and viral surface hydrophobicity. HEV sequences from human (n = 37) and environmental origins (wild boar [n = 3], pig slaughterhouse effluent [n = 6] and urban wastewater [n = 2]) were collected for the characterization of quasispecies using ultra-deep sequencing (ORF2/ORF3 overlap). Predictive and functional assays were carried out to investigate viral particle antigenicity and hydrophobicity. Most quasispecies showed a major variant while a mixture was observed in urban wastewater and in one chronically infected patient. Amino acid signatures were identified, as a rabbit-linked HEV pattern in two infected patients, or the S68L (ORF2) / H81C (ORF3) residue mostly identified in wild boars. By comparison with environmental strains, molecular patterns less likely represented in humans were identified. Patterns impacting viral hydrophobicity and/or antigenicity were also observed, and the higher hydrophobicity of HEV naked particles compared with the enveloped forms was demonstrated. HEV variants isolated from human and environment present molecular patterns that could impact their surface properties as well as their transmission. These molecular patterns may concern only one minor variant of a quasispecies and could emerge under selective pressure.

Published
2021
Full Text
View/download PDF

3. Full‐length genome sequencing of RNA viruses—How the approach can enlighten us on hepatitis C and hepatitis E viruses

Author

Hélène Jeulin, Sibel Berger, Véronique Venard, Jean-Pierre Bronowicki, Elodie Laugel, Evelyne Schvoerer, Cédric Hartard, Laboratoire de Chimie Physique et Microbiologie pour les Matériaux et l'Environnement (LCPME), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Service de Virologie [CHRU Nancy], Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), and Service d'Hépatogastroentérologie [CHRU Nancy]

Subjects
viruses, Hepatitis C virus, Genomics, Genome, Viral, Hepacivirus, Biology, medicine.disease_cause, Genome, 03 medical and health sciences, 0302 clinical medicine, Hepatitis E virus, Virology, medicine, Animals, Humans, RNA Viruses, 030212 general & internal medicine, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Full length genome, 0303 health sciences, Whole Genome Sequencing, fungi, virus diseases, food and beverages, RNA, Hepatitis C, Hepatitis E, medicine.disease, digestive system diseases, 3. Good health, Infectious Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, RNA, Viral
Abstract

Among the five main viruses responsible for human hepatitis, hepatitis C virus (HCV) and hepatitis E virus (HEV) are different while sharing similarities. Both viruses can be transmitted by blood or derivatives whereas HEV can also follow environmental or zoonotic routes. These highly variable RNA viruses can cause chronic hepatitis potentially leading to hepatocarcinoma. HCV and HEV can develop new structures and functions under selective pressure to adapt to host immunity, human tissues, treatments or even various animal reservoirs. Elsewhere, with directly acting antiviral treatments, HCV can be eradicated whereas HEV is an emerging pathogen against which specific treatments have to be improved. As a unique molecular tool able to explore viral genomic plasticity, full-length genome (FLG) sequencing has become easier, faster and cheaper. The present review will show how FLG sequencing can explore these RNA viruses with the aim to investigate key genomics data to improve basic knowledge, patients' healthcare and preventive tools.

Published
2020
Full Text
View/download PDF

4. The variability of hepatitis B envelope is associated with HBs antigen persistence in either chronic or acute HBV genotype A infection

Author

M. Bensenane, Thierry May, Honorine Fenaux, Fabien Zoulim, Evelyne Schvoerer, Brice Malve, Jean-Pierre Bronowicki, François Goehringer, Sibel Berger, Aurélie Velay, Hélène Jeulin, Jean-Pol Frippiat, Marine Eschlimann, Stress, Immunité, Pathogènes (SIMPA), Université de Lorraine (UL), Virology Laboratory, General Hospital Papageorgiou, Virus des hépatites et pathologies associées, Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Nutrition-Génétique et Exposition aux Risques Environnementaux (NGERE), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lorraine (UL), and Service de Virologie [CHRU Nancy]

Subjects
0301 basic medicine, Adult, Male, Antigenicity, HBsAg, Hepatitis B virus, Genotype, HIV Infections, medicine.disease_cause, Persistence (computer science), Cohort Studies, 03 medical and health sciences, 0302 clinical medicine, Viral Envelope Proteins, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virology, medicine, Humans, ComputingMilieux_MISCELLANEOUS, Aged, Sequence Deletion, Mutation, Hepatitis B Surface Antigens, business.industry, Coinfection, Haplotype, virus diseases, Hepatitis B, Middle Aged, Viral Load, medicine.disease, digestive system diseases, 3. Good health, Chronic infection, 030104 developmental biology, Infectious Diseases, Immunology, DNA, Viral, 030211 gastroenterology & hepatology, business
Abstract

Background More than 240 million people are chronically infected by hepatitis B virus (HBV) worldwide. Envelope proteins play a crucial role in viral cellular entry and immune recognition. The loss of HBs antigen (HBsAg) correlated with a good clinical prognosis is rarely achieved with or without treatment (3–16%). Objectives HBV envelope variability was investigated according to HBsAg persistence. Study design The cohort consisted of 15 HBV genotype A-infected patients divided into “resolvers”, with HBsAg clearance, and “non-resolvers”, with HBsAg persistence and in subgroups: acute (n = 5, AHBV) or chronic infection (n = 4, CHBV) and HBV/HIV coinfection (n = 6, CHBV/HIV). HBV S and preS sequences were studied by direct and ultra-deep sequencing. Amino acid sequences were analyzed with bioinformatics for predicted antigenicity. Results In S gene, the complexity was lower in AHBV than in chronic-infected patients (p = 0.046). Major mutations, detected using direct sequencing, were more frequent in AHBV developing chronicity (p = 0.01) than in AHBV resolvers. In the Major Hydrophilic Region, more frequent mutations were observed in non-resolvers versus resolvers (p = 0.047) and non-resolvers tended to have more haplotypes with a reduced predicted antigenicity (p = 0.07). Most of the mutations in preS/S region were found rather in epitopic than in non-epitopic areas (p = 0.025). Interestingly, the mutation sY161F found in 3/8 non-resolvers was associated with a decrease in predicted antigenicity (28%; AnTheProt). Conclusions HBsAg persistence was correlated with mutations and deletions in areas playing a key role in immune recognition. These data suggest that variability in HBV envelope could favor immune escape in various clinical settings of HBV genotype A-infected patients.

Published
2017
Full Text
View/download PDF

5. nimH, a novel nitroimidazole resistance gene contributing to metronidazole resistance in Bacteroides fragilis

Author

Hélène Marchandin, Hélène Jean-Pierre, Sibel Berger, Estelle Jumas-Bilak, Alain Lozniewski, Luc Dubreuil, Corentine Alauzet, Stress, Immunité, Pathogènes (SIMPA), Université de Lorraine (UL), Laboratoire de Bactériologie [CHU Nancy], Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Hydrosciences Montpellier (HSM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Lille Inflammation Research International Center - U 995 (LIRIC), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Centre Hospitalier Universitaire de Nîmes (CHU Nîmes), Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Institut Pasteur de Lille, and Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)

Subjects
0301 basic medicine, Microbiology (medical), 030106 microbiology, Drug resistance, Microbiology, Bacteroides fragilis, 03 medical and health sciences, chemistry.chemical_compound, Anti-Infective Agents, DNA Transposable Elements, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Metronidazole, Drug Resistance, Bacterial, Gene Order, Humans, Pharmacology (medical), Gene, ComputingMilieux_MISCELLANEOUS, Biotransformation, Metronidazole resistance, Pharmacology, Nitroimidazole, biology, Sequence Analysis, DNA, biology.organism_classification, 3. Good health, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, Genes, Bacterial, Nitroimidazoles, [SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, Oxidoreductases
Abstract

International audience

Published
2017
Full Text
View/download PDF

6. Optimising the diagnostic strategy for onychomycosis from sample collection to FUNGAL identification evaluation of a diagnostic kit for real-time PCR

Author

Anne Debourgogne, Dimitri Petinataud, Nelly Contet-Audonneau, Sibel Berger, Marie Machouart, Cyril Ferdynus, Service de Parasitologie-Mycologie [CHRU Nancy], Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Service de Virologie [CHRU Nancy], Centre Hospitalier Universitaire de La Réunion (CHU La Réunion), Stress, Immunité, Pathogènes (SIMPA), and Université de Lorraine (UL)

Subjects
Male, 0301 basic medicine, medicine.medical_specialty, Pathology, Time Factors, Sample (material), 030106 microbiology, Direct examination, Culture, Medical laboratory, Dermatology, Real-Time Polymerase Chain Reaction, Sensitivity and Specificity, Specimen Handling, 030207 dermatology & venereal diseases, 03 medical and health sciences, 0302 clinical medicine, Onychomycosis, Diagnosis, Humans, Medicine, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, DNA, Fungal, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Aged, Retrospective Studies, biology, business.industry, Arthrodermataceae, Fungi, Kit, General Medicine, Diagnostic strategy, biology.organism_classification, 3. Good health, Infectious Diseases, Real-time polymerase chain reaction, PCR, Female, Identification (biology), Reagent Kits, Diagnostic, Sample collection, business
Abstract

International audience; Onychomycosis is a common nail disorder mainly due to dermatophytes for which the conventional diagnosis requires direct microscopic observation and culture of a biological sample. Nevertheless, antifungal treatments are commonly prescribed without a mycological examination having been performed, partly because of the slow growth of dermatophytes. Therefore, molecular biology has been applied to this pathology, to support a quick and accurate distinction between onychomycosis and other nail damage. Commercial kits are now available from several companies for improving traditional microbiological diagnosis. In this paper, we present the first evaluation of the real-time PCR kit marketed by Bio Evolution for the diagnosis of dermatophytosis. Secondly, we compare the efficacy of the kit on optimal and non-optimal samples. This study was conducted on 180 nails samples, processed by conventional methods and retrospectively analysed using this kit. According to our results, this molecular kit has shown high specificity and sensitivity in detecting dermatophytes, regardless of sample quality. On the other hand, and as expected, optimal samples allowed the identification of a higher number of dermatophytes by conventional mycological diagnosis, compared to non-optimal samples. Finally, we have suggested several strategies for the practical use of such a kit in a medical laboratory for quick pathogen detection.

Published
2016
Full Text
View/download PDF

7. Discrimination between Native and Tn 6010 -Associated oqxAB in Klebsiella spp., Raoultella spp., and other Enterobacteriaceae by Using a Two-Step Strategy

Author

Sibel Berger, Aymric Kisserli, Alain Lozniewski, Thomas Guillard, Christophe de Champs, Corentine Alauzet, Lars Hestbjerg Hansen, Anne-Laure Lebreil, Entérobactéries Résistance Acquise - EA 4687 (ERA), Université de Reims Champagne-Ardenne (URCA)-SFR CAP Santé (Champagne-Ardenne Picardie Santé), Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV), Laboratoire de Bactériologie–Virologie-Hygiène Hospitalière, Université de Reims Champagne-Ardenne (URCA)-Centre Hospitalier Universitaire de Reims (CHU Reims), Hôpital Robert Debré, Hôpital Robert Debré-Centre Hospitalier Universitaire de Reims (CHU Reims), Laboratoire de Recherche en Nanosciences - EA 4682 (LRN), Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-SFR Condorcet, Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Department of Environmental Science [Roskilde] (ENVS), Aarhus University [Aarhus], Laboratoire de Bactériologie [CHU Nancy], Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Stress, Immunité, Pathogènes (SIMPA), and Université de Lorraine (UL)

Subjects
Klebsiella, Two step, prevalence, Microbial Sensitivity Tests, Escherichia-coli, medicine.disease_cause, Genome, Polymerase Chain Reaction, Plasmid, law.invention, Microbiology, Extended-spectrum, Raoultella, Enterobacteriaceae, law, Mechanisms of Resistance, medicine, Multidrug efflux pump, Pharmacology (medical), Escherichia coli, Polymerase chain reaction, Pharmacology, biology, biology.organism_classification, Pneumoniae, Anti-Bacterial Agents, Olaquindox, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Guinolone resistance, [SDV.IMM]Life Sciences [q-bio]/Immunology
Abstract

We developed a two-step PCR-based strategy to detect genes encoding OqxAB, allowing a specific assignment of Tn 6010 -associated oqxAB in Enterobacteriaceae . Chromosomal location in this setup was confirmed by hybridization with I- Ceu I-restricted genomes. This approach led us to find that Klebsiella sp. and Raoultella sp. reference strains chromosomally carried oqxAB .

Published
2015
Full Text
View/download PDF

8. Characterization of a New blaOXA-48-Carrying Plasmid in Enterobacteriaceae

Author

Alain Lozniewski, Corentine Alauzet, Richard Bonnet, Christian Rabaud, Nejla Aissa, Sibel Berger, Sandrine Henard, Laboratoire de Bactériologie [CHU Nancy], Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Service des Maladies Infectieuses et Tropicales [CHRU Nancy], Service de Bactériologie [CHU Clermont-Ferrand], CHU Gabriel Montpied [Clermont-Ferrand], CHU Clermont-Ferrand-CHU Clermont-Ferrand, and CHU Clermont-Ferrand

Subjects
Male, Imipenem, Turkey, Klebsiella pneumoniae, Spread, Resistance, Molecular Sequence Data, Drug resistance, Microbial Sensitivity Tests, Biology, beta-Lactamases, Strain, Microbiology, 03 medical and health sciences, Feces, Plasmid, Enterobacteriaceae, Mechanisms of Resistance, Drug Resistance, Bacterial, medicine, Humans, Pharmacology (medical), Base sequence, 030304 developmental biology, Pharmacology, 0303 health sciences, Strain (chemistry), Base Sequence, 030306 microbiology, Middle Aged, OXA-48-producing klebsiella-pneumoniae, biology.organism_classification, Virology, 3. Good health, Anti-Bacterial Agents, Klebsiella Infections, Transformation (genetics), Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Genes, Bacterial, [SDV.IMM]Life Sciences [q-bio]/Immunology, France, Transformation, Bacterial, OXA-48-like carbapenemases, medicine.drug, Plasmids
Abstract

In this work, we characterized a new, 160-kb, bla OXA-48 -harboring IncL/M-type plasmid isolated from a Klebsiella pneumoniae strain from France. Moreover, we report the transfer of a 60-kb OXA-48-encoding plasmid from Klebsiella pneumoniae to other Enterobacteriaceae in two patients.

Published
2013
Full Text
View/download PDF

9. Human Pathogens Abundant in the Bacterial Metagenome of Cigarettes

Author

Timothy M. Vogel, Amy R. Sapkota, Sibel Berger, Ampère (AMPERE), École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Maryland Institute for Applied Environmental Health, University of Maryland [College Park], and University of Maryland System-University of Maryland System

Subjects
TOBACCO-SMOKE, Time Factors, NASOPHARYNX, Health, Toxicology and Mutagenesis, Human pathogen, Risk Assessment, tobacco, Tobacco smoke, smoking, Microbiology, 03 medical and health sciences, BACILLUS-THURINGIENSIS, RNA, Ribosomal, 16S, bacterial metagenome, Humans, bacteria, Respiratory Tract Infections, RNA RIBOSOMAL 16S, 030304 developmental biology, Oligonucleotide Array Sequence Analysis, Genetics, Abiotic component, 0303 health sciences, biology, 030306 microbiology, Research, Public Health, Environmental and Occupational Health, pathogens, Environmental exposure, Biodiversity, Environmental Exposure, RECOVERY, biology.organism_classification, POTENTIAL PATHOGENS, CANCER, 3. Good health, PREVALENCE, 13. Climate action, Metagenomics, TAXONOMIC MICROARRAY, Metagenome, ENDOTOXIN, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, cigarettes, Bacteria, PARKINSONISM
Abstract

International audience; BACKGROUND: Many studies have evaluated chemical, heavy metal, and other abiotic substances present in cigarettes and their roles in the development of lung cancer and other diseases, yet no studies have comprehensively evaluated bacterial diversity of cigarettes and the possible impacts of these microbes on respiratory illnesses in smokers and exposed nonsmokers. OBJECTIVES: The goal of this study was to explore the bacterial metagenomes of commercially available cigarettes. METHODS: A 16S rRNA-based taxonomic microarray and cloning and sequencing were used to evaluate total bacterial diversity of four brands of cigarettes. Normalized microarray data were compared using principal component analysis and hierarchical cluster analysis to evaluate potential differences in microbial diversity across cigarette brands. RESULTS: Fifteen different classes of bacteria and a broad range of potentially pathogenic organisms were detected in all cigarette samples. Most notably, we detected Acinetobacter, Bacillus, Burkholderia, Clostridium, Klebsiella, Pseudomonas aeruginosa, and Serratia in >= 90% of all cigarette samples. Other pathogenic bacteria detected included Campylobacter, Enterococcus, Proteus, and Staphylococcus. No significant variability in bacterial diversity was observed across the four different cigarette brands. CONCLUSIONS: Previous studies have shown that smoking is associated with colonization by pathogenic bacteria and an increased risk of lung infections. However, this is the first study to show that cigarettes themselves could be the direct source of exposure to a wide array of potentially pathogenic microbes among smokers and other people exposed to secondhand smoke. The overall public health implications of these findings are unclear at this time, and future studies arc necessary to determine whether bacteria in cigarettes could play important roles in the development of both infectious and chronic respiratory diseases.

Published
2010
Full Text
View/download PDF

10. Microbial sequences retrieved from environmental samples from seasonal Arctic snow and meltwater from Svalbard, Norway

Author

Christophe Ferrari, Elisabeth Navarro, Sibel Berger, Catherine Larose, Timothy M. Vogel, Aurélien Dommergue, Dominique Schneider, Laboratoire de glaciologie et géophysique de l'environnement (LGGE), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Grenoble (OSUG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble] (LAPM), Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), Ampère (AMPERE), École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), CHANG (CHANG), Laboratoire d'étude des transferts en hydrologie et environnement (LTHE), Institut National Polytechnique de Grenoble (INPG)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Grenoble (OSUG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique de Grenoble (INPG)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Grenoble (OSUG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), grants from EC2CO/CYTRIX (Programme National INSU), LEFE, IPEV CHIMERPOL program (399), Observatoire des Sciences de l'Univers de Grenoble (OSUG), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Ampère, Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), CHANG, and Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Grenoble (OSUG)

Subjects
VARIATION SAISONNIERE, Meltwater, ADN, DIVERSITY, FONCTIONNEMENT DE L'ECOSYSTEME, BACTERIE, DIVERSITE SPECIFIQUE, COUVERTURE NEIGEUSE, STRUCTURE DE POPULATION, Diversity index, Arctic, Sphingobacteria, Environmental samples, RNA, Ribosomal, 16S, Snow, MICROORGANISMS, Phylogeny, 0303 health sciences, geography.geographical_feature_category, biology, Norway, Ecology, CLOSTRIDIA, Betaproteobacteria, General Medicine, Biodiversity, Cold Climate, COMMUNITY, Geography, BACTERIA, GLACIER, Molecular Medicine, Seasons, FONTE DES GLACIERS, Water Microbiology, DNA, Bacterial, CRYOSPHERE, ECOLOGY, Microbiology, 03 medical and health sciences, MILIEU GLACIAIRE, medicine, Ecosystem, Alphaproteobacteria, DNA Primers, Gene Library, 030304 developmental biology, Base Sequence, ACTIVITE BIOLOGIQUE, Bacteroidetes, 030306 microbiology, BIODIVERSITE, ICE, MICROORGANISME, Glacier, Seasonality, medicine.disease, biology.organism_classification, LIBRARIES, ANTARCTICA, Snow bacteria, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Acidobacteria
Abstract

International audience; 16S rRNA gene (rrs) clone libraries were constructed from two snow samples (May 11, 2007 and June 7, 2007) and two meltwater samples collected during the spring of 2007 in Svalbard, Norway (79 degrees N). The libraries covered 19 different microbial classes, including Betaproteobacteria (21.3%), Sphingobacteria (16.4%), Flavobacteria (9.0%), Acidobacteria (7.7%) and Alphaproteobacteria (6.5%). Significant differences were detected between the two sets of sample libraries. First, the meltwater libraries had the highest community richness (Chao1: 103.2 and 152.2) and Shannon biodiversity indices (between 3.38 and 3.59), when compared with the snow libraries (Chao1: 14.8 and 59.7; Shannon index: 1.93 and 3.01). Second, integral-LIBSHUFF analyses determined that the bacterial communities in the snow libraries were significantly different from those of the meltwater libraries. Despite these differences, our data also support the theory that a common core group of microbial populations exist within a variety of cryohabitats. Electronic supplementary material The online version of this article (doi:10.1007/s00792-009-0299-2) contains supplementary material, which is available to authorized users.

Published
2010
Full Text
View/download PDF

11. ASSESSING INTERACTIONS BETWEEN MERCURY AND MICROBIAL POPULATIONS IN THE SNOWPACK: A METAGENOMIC APPROACH

Author

Catherine Larose, Sibel Berger, Christophe Ferrari, Elisabeth Navarro, Aurélien Dommergue, Nicolas Marusczak, Sébastien Cecillon, Dominique Schneider, Timothy Vogel, Ampère (AMPERE), École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de glaciologie et géophysique de l'environnement (LGGE), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Grenoble (OSUG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble] (LAPM), Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Ampère, Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Observatoire des Sciences de l'Univers de Grenoble (OSUG), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), and Ampère, Publications

Subjects
[SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SPI.NRJ]Engineering Sciences [physics]/Electric power, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SPI.NRJ] Engineering Sciences [physics]/Electric power
Abstract

International audience; Mercury (Hg), a persistent and toxic element, is found both naturally and as an anthropogenically-produced compound in the environment. Industrial use of Hg, and its subsequent release to the environment, has contributed to increasing Hg levels in soil, sediments and aquatic ecosystems worldwide. The Arctic is at risk for Hg toxicity. This is particularly the case for coastal sites, which appear to be involved in Hg cycling. The role of micro-organisms in the biogeochemical Hg cycle has recently become the focus of a large number of studies. The inorganic form of Hg, HgII, can be reduced to the relatively inert gaseous elemental mercury (GEM) form by bacteria possessing the mer operon. Bacteria, such as sulphate or iron reducers, are also reported to mediate the transformation of HgII to the more toxic and bioaccumulative organic form, methyl mercury (MeHg). However, the extent to which bacterial populations interact with mercury remains to be elucidated, especially in polar ecosystems. In order to understand how microbial populations respond to mercury, we used a metagenomic approach to describe both community structure and gene function variations in the Arctic snow pack over a two-month period during the spring of 2008 in Ny-Alesund, Svalbard, Norway. Using taxonomic DNA microarrays, a high throughput molecular biology technique, we monitored the evolution of bacterial communities within the snowpack. Community structure was then correlated to environmental factors and mercury concentrations. Gene function was analyzed by pyrosequencing as well as Q-PCR. The potential interdependence of the microbial community controlled mercury transformations and the community structure could provide insights into mercury cycling in the Arctic. In addition, the role of mercury resistant bacteria in the survival of the entire microbial community can be induced by the correlation between community members and mercury functional genes.

Published
2009

12. GENOME FLEXIBILITY ACROSS DIFFERENT STRAINS OF THE HEXACHLOROCYCLANE-DEGRADING BACTERIUM SPHINGOBIUM FRANCENSE SP+ IDENTIFIED BY A GLOBAL APPROACH OF GENOME SEQUENCING AND MICROARRAY COMPARATIVE GENOMIC HYBRIDIZATION

Author

Sibel Berger, Sébastien Cecillon, Cécile Thion, Maude David, Timothy Vogel, Ampère (AMPERE), École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Ampère, Publications

Subjects
[SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SPI.NRJ]Engineering Sciences [physics]/Electric power, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SPI.NRJ] Engineering Sciences [physics]/Electric power
Abstract

International audience; Phenotypic and genomic dynamics enable bacteria to adapt quickly to various ecological niches and environmental fluctuations such as the presence of xenobiotic compounds. We explored the different adaptive mechanisms in the bacterium Sphingobium francense, which is able to degrade lindane, a chlorinated xenobiotic compound historically used in agricultural and medicine. Previous studies demonstrated the association of mobile genetic elements with lin genes implicated in lindane catabolic pathways. We also observed that the wildtype, sp+, a lindane degrading strain, produces mutants (at a rate of 4 percent per replating) unable to degrade lindane. In order to study the role of mobile genetic elements in the adaptability of this bacterium, we developed an original strategy based on the pyrosequencing data obtained for the genome of Sphingobium francense sp+ and microarray comparative genomic hybridizations. This approach uses a two-color process to estimate the different types of genomic rearrangements that occurred in a mutant genome in comparison to the reference strain sp+ genome. For this study, five non-lindane degrading mutants and one revertant, which recovered the capacity to degrade lindane, were characterized. Analyzes of each microarray showed that the nonlindane degrading mutants underwent large genomic rearrangements and the selected mutants were genetically different. Moreover, we established the proximity between some environmental genes and mobile genetic elements. Some of these regions were deleted in the mutants reinforcing the observation that mobile genetic elements play an important role in bacterial adaptation to environmental perturbation. Thus, all the data obtained confirms the extraordinary plasticity of the Sphingobium genome linked to the presence of multiple mobile genetic elements, which are involved in the instability of lindane degradation capability and other environmental functional genes.

Catalog

Books, media, physical & digital resources
See catalog results