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  • 1.
    Emmerich, Katja
    et al.
    Karlsruhe Institute of Technology.
    Schuhmann, Reiner
    Petrick, Kerstin
    Karlsruhe Institute of Technology.
    Menger-Krug, Eve
    Karlsruhe Institute of Technology.
    Kaden, Rene
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine, Clinical Bacteriology.
    Dieterle, Matthias
    Kuch, Paul
    Diedel, Ralf
    Peuker, Miriam
    Huber, Stefan
    Fischer, Heike
    Beyer, Daniel
    Zehnsdorf, Andreas
    Krolla-Sidenstein, Peter
    Comprehensive material characterisation of clay mineral raw materials for the development of microbiological processing technologies2009In: CFI. Ceramic forum international, ISSN 0173-9913, Vol. 86, no 3, p. 29-34Article in journal (Refereed)
  • 2.
    Kaden, Rene
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine, Clinical Bacteriology.
    Mikrobiologische Charakterisierung von Tonrohstoffen unter Berücksichtigung des Alterationsprozesses Mauken2011Book (Refereed)
  • 3.
    Kaden, Rene
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine, Clinical Bacteriology. National Veterinary Institute of Sweden, Swedish Forum for Biopreparedness Diagnostics.
    Menger-Krug, Eve
    Karlsruhe Institute of Technology.
    Emmerich, Katja
    Karlsruhe Institute of Technology.
    Petrick, Kerstin
    Karlsruhe Institute of Technology.
    Krolla-Sidenstein, Peter
    Karlsruhe Institute of Technology.
    Application of the Dynamic Cultivation System for Microorganisms – a new way to culture the unculturables2014In: Clays and clay minerals, ISSN 0009-8604, E-ISSN 1552-8367, Vol. 62, no 3-4, p. 203-210Article in journal (Refereed)
    Abstract [en]

    To date, ~1% of all bacteria that occur in environmental ecosystems such as soil, sedimentary rocks, and groundwater have been described. Comprehensive explanation of ecological interactions on a microscale level is thus almost impossible. The Dynamic Cultivation System (DCS) was developed in order to detect more microbial taxa than with common cultivation approaches, as well as previously undescribed bacterial species. The DCS is a quick and easy in situ method for the cultivation of numerous bacterial taxa in support of the description of microbial colonized ecosystems. To investigate the bacterial populations within a clay-maturation process after mining the raw material, the DCS was used to increase the microbial biomass for further molecular analysis. Two different methods were applied to extract the bacteria from the DCS and these were compared in terms of efficiency at detection of large numbers of different taxa and in terms of applicability to the detection of previously undescribed species in raw clays. A collection of different undescribed species was detected with sequencing. While direct picking of bacterial colonies leads to the detection of different genera, species mainly of the genus Arthobacter were proved in the phosphate-buffered saline-suspended biomass. Thus, a combination of the approaches mentioned above is recommended to increase the number of detectable species. The DCS will help to describe better the microbial content of ecosystems, especially soils that contain charged particles.

  • 4.
    Kaden, Rene
    et al.
    Karlsruhe Institute of Technology (KIT), Institute of Functional Interfaces (IFG), Eggenstein-Leopoldshafen, Germany.
    Menger-Krug, Eve
    Karlsruhe Institute of Technology.
    Emmerich, Katja
    Karlsruhe Institute of Technology.
    Petrick, Kerstin
    Karlsruhe Institute of Technology.
    Mühling, Martin
    Freiberg University.
    Krolla-Sidenstein, Peter
    Karlsruhe Institute of Technology.
    The Dynamic Cultivation System: A new method for the detection of temporal shifts in microbial community structure in clay2012In: Applied Clay Science, ISSN 0169-1317, E-ISSN 1872-9053, Vol. 65–66, no 1, p. 53-56Article in journal (Refereed)
    Abstract [en]

    A major problem in the analysis of natural bacterial populations is that probably less than 1% of species were so far cultured and described. In order to overcome this disadvantage, culture independent DNA based methods, such as comparison of PCR-amplified 16S rRNA genes, are used for the description of the bacterial diversity and the identification of various species. Unfortunately, each molecule of DNA, including those of dead organisms and allochthonous genomes, can be detected by PCR-based molecular fingerprint techniques within a sample besides the DNA of native organisms. Hence, an adequate image of the actually active population composition cannot be projected with these methods. An additional challenge is the extraction of DNA from charged particles and the presence of inhibitors for downstream molecular analyses. This study reports the results of a new cultivation approach that allows to overcome these problems and to obtain almost total environmental DNA of microorganisms for subsequent genetic DNA fingerprint techniques.

    This new approach, the Dynamic Cultivation System (DCS) is characterized by special nutrient availability to simulate the bacterial natural habitat and the cell–cell interaction for various processes, such as collective degradation of compounds.

    The DCS was applied in combination with the genetic fingerprint technique Denaturing Gradient Gel Electrophoresis (DGGE) to study changes in the population composition during an alteration process of clay. The results indicate a changing bacterial diversity over time which seems to correlate to the changing pH in the clay samples in situ. This effect was most evident after cultivation on the DCS.

  • 5.
    Kaden, Rene
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine, Clinical Bacteriology.
    Petrick, Kerstin
    Karlsruhe Institute of Technology.
    Emmerich, Katja
    Karlsruhe Institute of Technology.
    Menger-Krug, Eve
    Karlsruhe Institute of Technology.
    Dieterle, Matthias
    Kuch, Paul
    Peuker, Miriam
    Diedel, Ralf
    Huber, Stefan
    Fischer, Heike
    Beyer, Daniel
    Zehnsdorf, Andreas
    Krolla-Sidenstein, Peter
    Karlsruhe Institute of Technology.
    Methoden zur Charakterisierung mikrobieller Populationen in Tonrohstoffen unterschiedlichen Alters2010In: Innovative Feuchtemessung in Forschung und Praxis - Materialeigenschaften und Prozesse, Karlsruhe: KIT , 2010Chapter in book (Refereed)
  • 6.
    Kaden, Rene
    et al.
    National Veterinary Institute SVA, Ulls väg 2b, 75189 Uppsala, Sweden .
    Sproer, Cathrin
    Leibnitz Institute DSMZ.
    Beyer, Daniel
    UFZ Centre for Environmental Research, Leipzig.
    Krolla-Sidenstein, Peter
    Karlsruhe Institute of Technology.
    Rhodoferax saidenbachensis sp. nov., a psychrotolerant, very slowly growing bacterium within the family Comamonadaceae, proposal of appropriate taxonomic position of Albidiferax ferrireducens strain T118T in the genus Rhodoferax and emended description of the genus Rhodoferax2014In: International Journal of Systematic and Evolutionary Microbiology, ISSN 1466-5026, E-ISSN 1466-5034, Vol. 64, no Pt 4, p. 1186-1193Article in journal (Refereed)
    Abstract [en]

    A Gram-stain-negative, oxidase and phosphatase-positive and catalase-negative, short rod-shaped bacterium was isolated from sediment of a drinking water reservoir in Germany. Based on 16S rRNA gene sequence and phenotypic properties, the bacterium belongs to the genus Rhodoferax within the family Comamonadaceae. The new taxon differed from related species mainly with respect to its fatty acid composition, low growth temperature, lack of pigments in young cultures and ability to utilize glycerol and d-mannose but not urea. The major fatty acids were C16 : 1omega7c and/or iso-C15 : 0 2-OH, C16 : 0, and C18 : 1omega7c. The only ubiquinone detected was ubiquinone Q-8. The DNA G+C content was 60.3-61 mol%. Because of the phenotypic and genotypic differences from the most closely related taxa, the new strain represents a novel species for which the name Rhodoferax saidenbachensis sp. nov. is proposed. The type strain is ED16(T) ( = CCUG 57711(T) = ATCC BAA-1852(T) = DSM 22694(T)). An emended description of the genus Rhodoferax is proposed. Based on the results of this study, strain T118(T) (Albidiferax ferrireducens) is properly placed in the genus Rhodoferax as Rhodoferax ferrireducens.

  • 7.
    Kaden, Rene
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine, Clinical Bacteriology. Swedish Forum for Biopreparedness Diagnostics, National Veterinary Institute of Sweden.
    Ågren, Joakim
    National Veterinary Institute of Sweden.
    Båverud, Viveca
    National Veterinary Institute of Sweden, Swedish Forum for Biopreparedness Diagnostics.
    Hallgren, Gunilla
    National Veterinary Institute of Sweden.
    Ferrari, Sevinc
    National Veterinary Institute of Sweden, Swedish Forum for Biopreparedness Diagnostics.
    Börjesson, Joann
    National Veterinary Institute of Sweden.
    Lindberg, Martina
    National Veterinary Institute of Sweden, National Food Agency, Swedish Forum for Biopreparedness Diagnostics.
    Bäckman, Stina
    Swedish Defence Research Institute, Swedish Forum for Biopreparedness Diagnostics.
    Wahab, Tara
    Public Health Agency of Sweden, Swedish Forum for Biopreparedness Diagnostics.
    Brucellosis outbreak in a Swedish kennel in 2013: Determination of genetic markers for source tracing2014In: Veterinary Microbiology, ISSN 0378-1135, E-ISSN 1873-2542, Vol. 174, no 3–4, p. 523-530Article in journal (Refereed)
    Abstract [en]

    Brucellosis is a highly infectious zoonotic disease but rare in Sweden. Nonetheless, an outbreak of canine brucellosis caused by an infected dog imported to Sweden was verified in 2013. In total 25 dogs were tested at least duplicated by the following approaches: real-time PCR for the detection of Brucella canis, a Brucella genus-specific real-time PCR, selective cultivation, and microscopic examination. The whole genome of B. canis strain SVA13 was analysed regarding genetic markers for epidemiological examination. The genome of an intact prophage of Roseobacter was detected in B. canis strain SVA13 with whole genome sequence prophage analysis (WGS-PA). It was shown that the prophage gene content in the American, African and European isolates differs remarkably from the Asian strains. The prophage sequences in Brucella may therefore serve of use as genetic markers in epidemiological investigations. Phage DNA fragments were also detected in clustered, regularly interspaced short palindromic repeats (CRISPR) in the genome of strain SVA13. In addition to the recommendations for genetic markers in Brucella outbreak tracing, our paper reports a validated two-step stand-alone real-time PCR for the detection of B. canis and its first successful use in an outbreak investigation.

  • 8.
    Kaden, Rene
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine, Clinical Bacteriology. National Veterinary Institute of Sweden, Swedish Forum for Biopreparedness Diagnostics.
    Ågren, Joakim
    National Veterinary Institute of Sweden.
    Ferrari, Sevinc
    National Veterinary Institute, Swedish Forum for Biopreparedness Diagnostics.
    Lindberg, Martina
    National Food Agency, Swedish Forum for Biopreparedness Diagnostics.
    Bäckman, Stina
    Swedish Defence Research Institute, Swedish Forum for Biopreparedness Diagnostics.
    Wahab, Tara
    Public Health Agency of Sweden, Swedish Forum for Biopreparedness Diagnostics.
    Whole-Genome Sequence of Brucella canis Strain SVA13, Isolated from an Infected Dog2014In: Genome Announcements, ISSN 2169-8287, E-ISSN 2169-8287, Vol. 2, no 4, p. e00700-14-Article in journal (Refereed)
    Abstract [en]

    An outbreak of canine brucellosis in Sweden was confirmed by the National Veterinary Institute (SVA) in August 2013. The whole genome of the causative agent was sequenced, assembled, and analyzed.

  • 9.
    Kaden, René
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine, Clinical Bacteriology.
    Mikrobiologische Gewässeranalytik2009Book (Refereed)
  • 10.
    Orthová, Ivana
    et al.
    University of Veterinary Medicine, Vienna.
    Kämpfer, Peter
    University Giessen.
    Glaeser, Stefanie P.
    University Giessen.
    Kaden, René
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine, Clinical Bacteriology.
    Busse, Hans-Jürgen
    University of Veterinary Medicine, Vienna.
    Massilia norwichensis sp. nov., isolated from an air sample2015In: International Journal of Systematic and Evolutionary Microbiology, ISSN 1466-5026, E-ISSN 1466-5034, Vol. 65, no 1, p. 56-64Article in journal (Refereed)
    Abstract [en]

    A Gram-negative, rod-shaped and motile bacterial isolate, designated strain NS9T, isolated from air of the Sainsbury Centre for Visual Arts in Norwich, UK, was subjected to a polyphasic taxonomic study including phylogenetic analyses based on partial 16S rRNA, gyrB and lepA gene sequences and phenotypic characterization. The 16S rRNA gene sequence of NS9T identified Massilia haematophila CCUG 38318T, M. niastensis 5516S-1T (both 97.7 % similarity), M. aerilata 5516S-11T (97.4 %) and M. tieshanensis TS3T (97.4 %) as the next closest relatives. In partial gyrB and lepA sequences, NS9T shared the highest similarities with M. haematophila CCUG 38318T (94.5 %) and M. aerilata 5516-11T (94.3 %), respectively. These sequence data demonstrate the affiliation of NS9T to the genus Massilia. The detection of the predominant ubiquinone Q-8, a polar lipid profile consisting of the major compounds diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol and a polyamine pattern containing 2-hydroxyputrescine and putrescine were in agreement with the assignment of strain NS9T to the genus Massilia. Major fatty acids were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0, C18 : 1ω7c and C10 : 0 3-OH. Dissimilarities in partial lepA and gyrB gene sequences as well as results from DNA–DNA hybridizations demonstrate that strain NS9T is a representative of an as-yet undescribed species of the genus Massilia that is also distinguished from its close relatives based on physiological and biochemical traits. Hence, we describe a novel species, for which we propose the name Massilia norwichensis sp. nov., with the type strain NS9T ( = CCUG 65457T = LMG 28164T).

  • 11.
    Petrick, Kerstin
    et al.
    Karlsruhe Institute of Technology.
    Diedel, Ralf
    Peuker, Miriam
    Dieterle, Matthias
    Kuch, Paul
    Kaden, Rene
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine, Clinical Bacteriology.
    Krolla-Sidenstein, Peter
    Karlsruhe Institute of Technology.
    Schuhmann, Reiner
    Emmerich, Katja
    Karlsruhe Institute of Technology.
    Character and amount of I–S mixed-layer minerals and physical–chemical parameters of two ceramic clays from Westerwald, Germany: Implications for processing properties2011In: Clays and clay minerals, ISSN 0009-8604, E-ISSN 1552-8367, Vol. 59, no 1, p. 58-74Article in journal (Refereed)
    Abstract [en]

    The industrial assessment of ceramic clays commonly consists of the determination of just two parameters, the particle-size distribution and the chemical composition; other parameters may also be important, however. The aim of the present study was to show that a careful determination of the mineralogical phase content provides valuable additional information on the processing behavior of ceramic clays. Two ceramic clays (W1 and W2) from the Westerwald area, Germany, were evaluated as being the same with respect to industrial screening criteria, but showed different processing properties. In order to elucidate the different behaviors, both clays were investigated comprehensively using a multi-method approach combining physical-chemical and mineralogical methods. Different aggregation characteristics for the two clays were revealed by determining the grain-size distribution with and without Na-pyrophosphate as a dispersant. In addition, W1 showed a greater electrical conductivity and soluble-salt concentration which promoted dispersion behavior. The phase content was identified both for bulk materials and for several grain-size fractions by X-ray diffraction (XRD) and Rietveld analysis. The quantitative phase content was crosschecked with the chemical composition by X-ray fluorescence (XRF) analysis. Additional information was gathered by thermal analysis, cation exchange capacity (CEC) measurements, Mossbauer spectroscopy, and optical microscopy. While bulk samples of W1 and W2 showed nearly the same mineralogical and chemical compositions, investigation of the clay-size fractions (0.6-2 gm, <0.6 gm) revealed differences in the composition of the 2:1 layer silicates.

    The percentages of smectite in the mixed-layer I-S, as well as the amount of kaolinite, discrete illite, and smectite were determined by one-dimensional XRD profile fitting (ODPF). Best-fitting results for W1 were achieved for a physical mixture of an illite-rich I-S mixed-layer mineral (R3 I(0.9)-S) with discrete smectite, whereas W2 was characterized by a greater proportion of smectite in the mixed-layer (R1 I(0.8)-S), without discrete smectite. Based on the different structural features of the swellable clays, a qualitative delamination model for the 2:1 layer silicates during processing of the clays was derived.

    The model provides a further approach, aside from aggregation characteristics, to help understand the clay-processing behavior, which was found to be different for the two ceramic clays investigated.

  • 12.
    Petrick, Kerstin
    et al.
    Karlsruhe Institute of Technology.
    Emmerich, Katja
    Karlsruhe Institute of Technology.
    Menger-Krug, Eve
    Karlsruhe Institute of Technology.
    Kaden, Rene
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine, Clinical Bacteriology.
    Dieterle, Matthias
    Kuch, Paul
    Diedel, Ralf
    Peuker, Miriam
    Krolla-Sidenstein, Peter
    Karlsruhe Institute of Technology.
    Why do two apparently similar German ceramic clays display different rheological properties during maturation?2008Conference paper (Refereed)
  • 13.
    Wahab, Tara
    et al.
    Public Health Agency of Sweden, Swedish Forum for Biopreparedness Diagnostics.
    Ferrari, Sevinc
    National Veterinary Institute, Swedish Forum for Biopreparedness Diagnostics.
    Lindberg, Martina
    National Food Agency, Swedish Forum for Biopreparedness Diagnostics.
    Bäckman, Stina
    Swedish Defence Research Institute, Swedish Forum for Biopreparedness Diagnostics.
    Kaden, Rene
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine, Clinical Bacteriology. National Veterinary Institute of Sweden, Swedish Forum for Biopreparedness Diagnostics.
    Draft Genome Sequences of Brucella suis Biovar 4 Strain NCTC 10385, Brucella ceti Strain NCTC 12891T, Brucella inopinata Strain CAMP 6436T, and Brucella neotomae Strain ATCC 23459T2014In: Genome Announcements, ISSN 2169-8287, E-ISSN 2169-8287, Vol. 2, no 5, p. e00783-14-Article in journal (Refereed)
    Abstract [en]

    With the aim of developing quantitative PCR methods for the detection and differentiation of Brucella species, the genomes of Brucella ceti, Brucella inopinata, Brucella netotomae, and Brucella suis biovar 4 were sequenced and analyzed.

1 - 13 of 13
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