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  • 1.
    Abuabaid, Hanan
    et al.
    Örebro University, School of Science and Technology.
    Karlsson, Mattias
    Örebro University, School of Science and Technology.
    Scherbak, Nikolai
    Örebro University, School of Science and Technology.
    Olsson, Per-Erik
    Örebro University, School of Science and Technology.
    Jass, Jana
    Örebro University, School of Science and Technology.
    Probiotic Lactobacillus rhamnosus alters inflammatory responses of bladder epithelial and macrophage-like cells in co-cultureManuscript (preprint) (Other academic)
  • 2.
    Asghar, Naveed
    et al.
    Södertörn University, School of Natural Science, Technology & Environmental Studies, Huddinge, Sweden .
    Lee, Yi-Ping
    Umeå University, Department of Clinical Microbiology, Virology, Umeå, Sweden; Umeå University, The Laboratory for Molecular Medicine Sweden (MIMS), Umeå, Sweden.
    Nilsson, Emma
    Umeå University, Department of Clinical Microbiology, Virology, Umeå, Sweden; Umeå University, The Laboratory for Molecular Medicine Sweden (MIMS), Umeå, Sweden.
    Lindqvist, Richard
    Umeå University, Department of Clinical Microbiology, Virology, Umeå, Sweden; Umeå University, The Laboratory for Molecular Medicine Sweden (MIMS), Umeå, Sweden.
    Melik, Wessam
    Örebro University, School of Medical Sciences.
    Kröger, Andrea
    Helmholtz Centre for Infection Research, Innate Immunity and Infection, Braunschweig, Germany; University of Magdeburg, Institute for Microbiology, Magdeburg, Germany.
    Överby, Anna K.
    Umeå University, Department of Clinical Microbiology, Virology, Umeå, Sweden; Umeå University, The Laboratory for Molecular Medicine Sweden (MIMS), Umeå, Sweden.
    Johansson, Magnus
    Örebro University, School of Medical Sciences.
    The role of the poly(A) tract in the replication and virulence of tick-borne encephalitis virus2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, 39265Article in journal (Refereed)
    Abstract [en]

    The tick-borne encephalitis virus (TBEV) is a flavivirus transmitted to humans, usually via tick bites. The virus causes tick-borne encephalitis (TBE) in humans, and symptoms range from mild flu-like symptoms to severe and long-lasting sequelae, including permanent brain damage. It has been suggested that within the population of viruses transmitted to the mammalian host, quasispecies with neurotropic properties might become dominant in the host resulting in neurological symptoms. We previously demonstrated the existence of TBEV variants with variable poly(A) tracts within a single blood-fed tick. To characterize the role of the poly(A) tract in TBEV replication and virulence, we generated infectious clones of Torö-2003 with the wild-type (A)3C(A)6 sequence (Torö-6A) or with a modified (A)3C(A)38 sequence (Torö-38A). Torö-38A replicated poorly compared to Torö-6A in cell culture, but Torö-38A was more virulent than Torö-6A in a mouse model of TBE. Next-generation sequencing of TBEV genomes after passaging in cell culture and/or mouse brain revealed mutations in specific genomic regions and the presence of quasispecies that might contribute to the observed differences in virulence. These data suggest a role for quasispecies development within the poly(A) tract as a virulence determinant for TBEV in mice.

  • 3.
    Asghar, Naveed
    et al.
    School of Natural Science, Technology & Environmental Studies, Södertörn University, Huddinge, Sweden.
    Lindblom, Pontus
    Division of Medical Microbiology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.
    Melik, Wessam
    School of Natural Science, Technology & Environmental Studies, Södertörn University, Huddinge, Sweden.
    Lindqvist, Richard
    Department of Clinical Microbiology, Virology, Umeå University, Umeå, Sweden.
    Haglund, Mats
    Department of Infectious Diseases, County Hospital, Kalmar, Sweden.
    Forsberg, Pia
    Division of Infectious Diseases, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden; Clinic of Infectious Diseases, Linköping University Hospital, Linköping, Sweden.
    Överby, Anna K.
    Department of Clinical Microbiology, Virology, Umeå University, Umeå, Sweden.
    Andreassen, Åshild
    Division of Infectious Disease Control, Department of Virology, Norwegian Institute of Public Health, Oslo, Norway.
    Lindgren, Per-Eric
    Division of Medical Microbiology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden; Division of Medical Services, Department of Microbiology, County Hospital Ryhov, Jönköping, Sweden.
    Johansson, Magnus
    Örebro University, School of Medicine, Örebro University, Sweden. School of Natural Science, Technology & Environmental Studies, Södertörn University, Huddinge, Sweden; RiSC - Inflammatory Response and Infection Susceptibility Centre, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
    Tick-Borne Encephalitis Virus Sequenced Directly from Questing and Blood-Feeding Ticks Reveals Quasispecies Variance2014In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 7, e103264Article in journal (Refereed)
    Abstract [en]

    The increased distribution of the tick-borne encephalitis virus (TBEV) in Scandinavia highlights the importance of characterizing novel sequences within the natural foci. In this study, two TBEV strains: the Norwegian Mandal 2009 (questing nymphs pool) and the Swedish Saringe 2009 (blood-fed nymph) were sequenced and phylogenetically characterized. Interestingly, the sequence of Mandal 2009 revealed the shorter form of the TBEV genome, similar to the highly virulent Hypr strain, within the 3' non-coding region (3'NCR). A different genomic structure was found in the 3'NCR of Saringe 2009, as in-depth analysis demonstrated TBEV variants with different lengths within the poly(A) tract. This shows that TBEV quasispecies exists in nature and indicates a putative shift in the quasispecies pool when the virus switches between invertebrate and vertebrate environments. This prompted us to further sequence and analyze the 3'NCRs of additional Scandinavian TBEV strains and control strains, Hypr and Neudoerfl. Toro 2003 and Habo 2011 contained mainly a short (A) 3C(A)6 poly(A) tract. A similar pattern was observed for the human TBEV isolates 1993/783 and 1991/4944; however, one clone of 1991/4944 contained an (A) 3C(A)11 poly(A) sequence, demonstrating that quasispecies with longer poly(A) could be present in human isolates. Neudoerfl has previously been reported to contain a poly(A) region, but to our surprise the resequenced genome contained two major quasispecies variants, both lacking the poly(A) tract. We speculate that the observed differences are important factors for the understanding of virulence, spread, and control of the TBEV.

  • 4.
    Asghar, Naveed
    et al.
    Södertörns Högskola, Huddinge, Sweden.
    Wessam, Melik
    Södertörns Högskola, Huddinge, Sweden.
    Lindblom, Pontus
    Linköpings Universitet, Linköping, Sweden.
    Lindgren, Per-Erik
    Linköpings Universitet, Linköping, Sweden.
    Andreassen, Åshild
    Norska folkhälsoinstitutet, Oslo, Norway.
    Johansson, Magnus
    Örebro University, School of Health and Medical Sciences, Örebro University, Sweden. Örebro University, School of Medicine, Örebro University, Sweden.
    Genomic Sequencing of Tick-borne Encephalitis Virus frin Questing and Blood-Feeding Ixodes ricinus2013Conference paper (Other academic)
  • 5.
    Bang, Charlotte Sahlberg
    et al.
    Örebro University, School of Health Sciences.
    Demirel, Isak
    Örebro University, School of Medical Sciences.
    Kruse, Robert
    Örebro University, School of Medical Sciences.
    Persson, Katarina
    Örebro University, School of Medical Sciences.
    Global gene expression profiling and antibiotic susceptibility after repeated exposure to the carbon monoxide-releasing molecule-2 (CORM-2) in multidrug-resistant ESBL-producing uropathogenic Escherichia coli2017In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, no 6, e0178541Article in journal (Refereed)
    Abstract [en]

    Treatment of urinary tract infections is today a challenge due to the increasing prevalence of multidrug-resistant ESBL-producing uropathogenic Escherichia coli (UPEC). There is an urgent need for new treatment strategies for multidrug-resistant UPEC and preferably with targets that have low potential for development of resistance. Carbon monoxide-releasing molecules (CORMs) are novel and potent antibacterial agents. The present study examines the transcriptomic targets of CORM-2 in a multidrug-resistant ESBL-producing UPEC isolate in response to a single exposure to CORM-2 and after repeated exposure to CORM-2. The bacterial viability and minimal inhibitory concentration (MIC) were also examined after repeated exposure to CORM-2. Microarray analysis revealed that a wide range of processes were affected by CORM-2, including a general trend of down-regulation in energy metabolism and biosynthesis pathways and up-regulation of the SOS response and DNA repair. Several genes involved in virulence (ibpB), antibiotic resistance (marAB, mdtABC) and biofilm formation (bhsA, yfgF) were up-regulated, while some genes involved in virulence (kpsC, fepCEG, entABE), antibiotic resistance (evgA) and biofilm formation (artIP) were down-regulated. Repeated exposure to CORM-2 did not alter the gene expression patterns, the growth inhibitory response to CORM-2 or the MIC values for CORM-2, cefotaxime, ciprofloxacin and trimethoprim. This study identifies several enriched gene ontologies, modified pathways and single genes that are targeted by CORM-2 in a multidrug-resistant UPEC isolate. Repeated exposure to CORM-2 did not change the gene expression patterns or fold changes and the susceptibility to CORM-2 remained after repeated exposure.

  • 6.
    Bang, Charlotte Sahlberg
    et al.
    Örebro University, School of Health and Medical Sciences, Örebro University, Sweden.
    Kinnunen, Annica
    Univ Örebro, IRiSC, Fac Med & Hlth, Örebro, Sweden.
    Karlsson, Marie
    Univ Örebro, IRiSC, Fac Med & Hlth, Örebro, Sweden.
    Önnberg, Anna
    Örebro University, School of Health and Medical Sciences, Örebro University, Sweden. Örebro Univ Hosp, Dept Lab Med, Örebro, Sweden.
    Söderquist, Bo
    Örebro University, School of Medicine, Örebro University, Sweden. Örebro University Hospital. Dept Lab Med.
    Persson, Katarina
    Örebro University, School of Medicine, Örebro University, Sweden.
    The antibacterial effect of nitric oxide against ESBL-producing uropathogenic E-coli is improved by combination with miconazole and polymyxin B nonapeptide2014In: BMC Microbiology, ISSN 1471-2180, E-ISSN 1471-2180, Vol. 14, 65Article in journal (Refereed)
    Abstract [en]

    Background: Nitric oxide (NO) is produced as part of the host immune response to bacterial infections, including urinary tract infections. The enzyme flavohemoglobin, coded by the hmp gene, is involved in protecting bacterial cells from the toxic effects of NO and represents a potentially interesting target for development of novel treatment concepts against resistant uropathogenic bacteria. The aim of the present study was to investigate if the in vitro antibacterial effects of NO can be enhanced by pharmacological modulation of the enzyme flavohemoglobin.

    Results: Four clinical isolates of multidrug-resistant extended-spectrum beta-lactamase (ESBL)-producing uropathogenic E. coli were included in the study. It was shown that the NO-donor substance DETA/NO, but not inactivated DETA/NO, caused an initial growth inhibition with regrowth noted after 8 h of exposure. An hmp-deficient strain showed a prolonged growth inhibition in response to DETA/NO compared to the wild type. The imidazole antibiotic miconazole, that has been shown to inhibit bacterial flavohemoglobin activity, prolonged the DETA/NO-evoked growth inhibition. When miconazole was combined with polymyxin B nonapeptide (PMBN), in order to increase the bacterial wall permeability, DETA/NO caused a prolonged bacteriostatic response that lasted for up to 24 h.

    Conclusion: An NO-donor in combination with miconazole and PMBN showed enhanced antimicrobial effects and proved effective against multidrug-resistant ESBL-producing uropathogenic E. coli.

  • 7. Baskar, Sushmitha
    et al.
    Baskar, Ramanathan
    Routh, Joyanto
    Örebro University, School of Science and Technology.
    Biogenic evidences of moonmilk deposition in the Mawmluh cave, Meghalaya, India2011In: Geomicrobiology Journal, ISSN 0149-0451, E-ISSN 1521-0529, Vol. 28, no 3, 252-265 p.Article in journal (Refereed)
    Abstract [en]

    Moonmilk, a microcrystalline secondary cave deposit, actively forms on the floor of Krem Mawmluh - a limestone cave in Meghalaya, Northeastern India. Due to the abundance of micrite and calcified microbial filaments, we hypothesize that these deposits form as a result of ongoing microbial interactions. Consistent with this idea, we report electron microscopic and microbiological evidences for the biological origin of moonmilk in Krem Mawmluh. Scanning electron microscopy indicated abundant calcified microbial filaments, needle calcite, fibre calcites (micro-fibre and nano-fibre calcite crystals), biofilm and microbial filaments in the moonmilk. The total viable culturable microbes showed high population densities for microbes in the moonmilk and moonmilk pool waters. In vitro culture experiments, confirmed the capability of many of the isolated strains to precipitate calcite and some of the identified isolates belonged to the Bacillus sp. and Actinomycetes. These results clearly support the biogenic nature of the deposits.

  • 8.
    Berndtson, Eva
    et al.
    Department of Food Hygiene, Faculty of Veterinary Medicine, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Danielsson Tham, Marie-Louise
    Department of Food Hygiene, Faculty of Veterinary Medicine, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Engvall, Anders
    Department of Epizootiology, National Veterinary Institute, Uppsala, Sweden.
    Experimental colonization of mice with Campylobacter jejuni1994In: Veterinary Microbiology, ISSN 0378-1135, E-ISSN 1873-2542, Vol. 41, no 1-2, 183-188 p.Article in journal (Refereed)
    Abstract [en]

    The ability of one human and two chicken strains of Campylobacter jejuni to colonise and survive in three different strains of laboratory mice (NMRI, CBA and C57-Black) was studied. Mice were inoculated orally with Campylobacter jejuni and faeces samples were cultured at regular intervals during the following months. The length of colonisation of mice differed between mouse strains but also between Campylobacter strains. The mouse strain C57-Black was not colonised with C. jejuni to the same degree as the other mouse strains. It is concluded that mice can become colonised for prolonged periods and that they may act as reservoirs of Campylobacter for other species.

  • 9.
    Beuchat, L. R.
    et al.
    Center for Food Safety and Department of Food Science and Technology, University of Georgia, Griffin, GA, USA.
    Frändberg, E.
    Biology Division, National Food Administration, Uppsala, Sweden.
    Deak, T.
    Center for Food Safety and Department of Food Science and Technology, University of Georgia, Griffin, GA, USA; Department of Microbiology and Biotechnology, Szent Istvan University, Budapest, Hungary.
    Alzamora, S. M.
    Pabellon de Industrias, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina.
    Chen, J.
    Center for Food Safety and Department of Food Science and Technology, University of Georgia, Griffin, GA, USA.
    Guerrero, S.
    Pabellon de Industrias, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina.
    López-Malo, A.
    Departmento de Ingenieria Quimica y Alimentos, Universidad de la Americas-Puebla, Sta. Catarina Martir, Puebla, Mexico.
    Ohlsson, I.
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Olsen, M.
    Biology Division, National Food Administration, Uppsala, Sweden.
    Peinado, J. M.
    Departmento de Microbiologia, Facultad de Biologia, Universidad Completense de Madrid, Madrid, Spain.
    Schnürer, Johan
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    de Siloniz, M. I.
    Departmento de Microbiologia, Facultad de Biologia, Universidad Completense de Madrid, Madrid, Spain.
    Tornai-Lehoczki, J.
    National Collection of Agricultural and Industrial Microorganisms, Szent Istvan University, Budapest, Hungary.
    Performance of mycological media in enumerating desiccated food spoilage yeasts: an interlaboratory study2001In: International Journal of Food Microbiology, ISSN 0168-1605, E-ISSN 1879-3460, Vol. 70, no 1-2, 89-96 p.Article in journal (Refereed)
    Abstract [en]

    Dichloran 18% glycerol agar (DG18) was originally formulated to enumerate nonfastidious xerophilic moulds in foods containing rapidly growing Eurotium species. Some laboratories are now using DG18 as a general purpose medium for enumerating yeasts and moulds, although its performance in recovering yeasts from dry foods has not been evaluated. An interlaboratory study compared DG18 with dichloran rose bengal chloramphenicol agar (DRBC), plate count agar supplemented with chloramphenicol (PCAC), tryptone glucose yeast extract chloramphenicol agar (TGYC), acidified potato dextrose agar (APDA), and orange serum agar (OSA) for their suitability to enumerate 14 species of lyophilized yeasts. The coefficient of variation for among-laboratories repeatability within yeast was 1.39% and reproducibility of counts among laboratories was 7.1%. The order of performance of media for recovering yeasts was TGYC > PCAC = OSA > APDA > DRBC > DG18. A second study was done to determine the combined effects of storage time and temperature on viability of yeasts and suitability of media for recovery. Higher viability was retained at - 18 degreesC than at 5 degreesC or 25 degreesC for up to 42 weeks, although the difference in mean counts of yeasts stored at - 18 degreesC and 25 degreesC was only 0.78 log(10) cfu/ml of rehydrated suspension. TGYC was equal to PCAC and superior to the other four media in recovering yeasts stored at - 18 degreesC, 5 degreesC, or 25 degreesC for up to 42 weeks. Results from both the interlaboratory study and the storage study support the use of TGYC for enumerating desiccated yeasts. DG18 is not recommended as a general purpose medium for recovering yeasts from a desiccated condition.

  • 10.
    Björk, Robert G.
    et al.
    Örebro University, School of Science and Technology. Univ Gothenburg, Dept Plant & Environm Sci, SE-40530 Gothenburg, Sweden.
    Ernfors, Maria
    Univ Gothenburg, Dept Plant & Environm Sci, SE-40530 Gothenburg, Sweden.
    Sikström, Ulf
    Forestry Res Inst Sweden Skogforsk, Uppsala, Sweden.
    Nilsson, Mats B.
    Swedish Univ Agr Sci SLU, Dept Forest Ecol & Management, Umea, Sweden.
    Andersson, Mats X.
    Univ Gothenburg, Dept Plant & Environm Sci, SE-40530 Gothenburg, Sweden.
    Rutting, Tobias
    Univ Gothenburg, Dept Plant & Environm Sci, SE-40530 Gothenburg, Sweden.
    Klemedtsson, Leif
    Univ Gothenburg, Dept Plant & Environm Sci, SE-40530 Gothenburg, Sweden.
    Contrasting effects of wood ash application on microbial community structure, biomass and processes in drained forested peatlands2010In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 73, no 3, 550-562 p.Article in journal (Refereed)
    Abstract [en]

    The effects of wood ash application on soil microbial processes were investigated in three drained forested peatlands, which differed in nutrient status and time since application. Measured variables included the concentrations of soil elements and phospholipid fatty acids (PLFAs), net nitrogen (N) mineralization, nitrification and denitrification enzyme activity, potential methane (CH(4)) oxidation, CH(4) production and microbial respiration kinetics. Wood ash application had a considerable influence on soil element concentrations. This mirrored a decrease in the majority of the microbial biomarkers by more than one-third in the two oligotrophic peatlands, although the microbial community composition was not altered. The decreases in PLFAs coincided with reduced net ammonification and net N mineralization. Other measured variables did not change systematically as a result of wood ash application. No significant changes in microbial biomass or processes were found in the mesotrophic peatland, possibly because too little time (1 year) had elapsed since the wood ash application. This study suggests that oligotrophic peatlands can be substantially affected by wood ash for a period of at least 4 years after application. However, within 25 years of the wood ash application, the microbial biomass seemed to have recovered or adapted to enhanced element concentrations in the soil.

  • 11.
    Blomqvist, J.
    et al.
    Department of Microbiology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    South, E.
    Department of Microbiology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Tiukova, L.
    Department of Microbiology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Momeni, M. H.
    Department of Molecular Biology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Hansson, H.
    Department of Molecular Biology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Ståhlberg, J.
    Department of Molecular Biology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Horn, S. J.
    NDepartment of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
    Schnürer, Johan
    Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Passoth, V.
    Department of Microbiology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Fermentation of lignocellulosic hydrolysate by the alternative industrial ethanol yeast Dekkera bruxellensis2011In: Letters in Applied Microbiology, ISSN 0266-8254, E-ISSN 1472-765X, Vol. 53, no 1, 73-78 p.Article in journal (Refereed)
    Abstract [en]

    Aim: Testing the ability of the alternative ethanol production yeast Dekkera bruxellensis to produce ethanol from lignocellulose hydrolysate and comparing it to Saccharomyces cerevisiae.

    Methods and Results: Industrial isolates of D. bruxellensis and S. cerevisiae were cultivated in small-scale batch fermentations of enzymatically hydrolysed steam exploded aspen sawdust. Different dilutions of hydrolysate were tested. None of the yeasts grew in undiluted or 1 : 2 diluted hydrolysate [final glucose concentration always adjusted to 40 g l(-1) (0.22 mol l(-1))]. This was most likely due to the presence of inhibitors such as acetate or furfural. In 1 : 5 hydrolysate, S. cerevisiae grew, but not D. bruxellensis, and in 1 : 10 hydrolysate, both yeasts grew. An external vitamin source (e.g. yeast extract) was essential for growth of D. bruxellensis in this lignocellulosic hydrolysate and strongly stimulated S. cerevisiae growth and ethanol production. Ethanol yields of 0 42 +/- 0 01 g ethanol (g glucose)(-1) were observed for both yeasts in 1 : 10 hydrolysate. In small-scale continuous cultures with cell recirculation, with a gradual increase in the hydrolysate concentration, D. bruxellensis was able to grow in 1 : 5 hydrolysate. In bioreactor experiments with cell recirculation, hydrolysate contents were increased up to 1 : 2 hydrolysate, without significant losses in ethanol yields for both yeasts and only slight differences in viable cell counts, indicating an ability of both yeasts to adapt to toxic compounds in the hydrolysate.

    Conclusions: Dekkera bruxellensis and S. cerevisiae have a similar potential to ferment lignocellulose hydrolysate to ethanol and to adapt to fermentation inhibitors in the hydrolysate.

    Significance and Impact of the study: This is the first study investigating the potential of D. bruxellensis to ferment lignocellulosic hydrolysate. Its high competitiveness in industrial fermentations makes D. bruxellensis an interesting alternative for ethanol production from those substrates.

  • 12.
    Boysen, Marianne E.
    et al.
    Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Jacobsson, Karl-Gustav
    Feed Laboratory, National Veterinary Institute, Uppsala, Sweden.
    Schnürer, Johan
    Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Molecular identification of species from the Penicillium roqueforti group associated with spoiled animal feed2000In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 66, no 4, 1523-1526 p.Article in journal (Refereed)
    Abstract [en]

    The Penicillium roqueforti group has recently been split into three species, P, roqueforti, Penicillium carneum, and Penicillium paneum, on the basis of differences in ribosomal DNA sequences and secondary metabolite profiles. We reevaluated the taxonomic identity of 52 livestock feed isolates from Sweden, previously identified by morphology as P. roqueforti, by comparing the sequences of the ribosomal internal transcribed spacer region. Identities were confirmed with random amplified polymorphic DNA analysis and secondary metabolite profiles. Of these isolates, 48 were P. roqueforti, 2 were P. paneum, and 2 were Penicillium expansum. No P. carneum isolates were found, The three species produce different mycotoxins, but no obvious relationship between mold and animal disease was detected, based on medical records, P. roqueforti appears to dominate in silage, but the ecological and toxicological importance of P. carneum and P. paneum as feed spoilage fungi is not clear. This is the first report of P. expansum in silage.

  • 13.
    Broberg, Anders
    et al.
    Department of Chemistry, Swedish University of Agricultural Sciences, Sweden.
    Jacobsson, Karin
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Ström, Katrin
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Schnürer, Johan
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Metabolite profiles of lactic acid bacteria in grass silage2007In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 73, no 17, 5547-5552 p.Article in journal (Refereed)
    Abstract [en]

    The metabolite production of lactic acid bacteria JAB) on silage was investigated. The aim was to compare the production of antifungal metabolites in silage with the production in liquid cultures previously studied in our laboratory. The following metabolites were found to be present at elevated concentrations in silos inoculated with LAB strains: 3-hydroxydecanoic acid, 2-hydroxy-4-methylpentanoic acid, benzoic acid, catechol, hydrocinnamic acid, salicylic acid, 3-phenyllactic acid, 4-hydroxybenzoic acid, (trans, trans)-3,4-dihydroxycyclohexane-1-carboxylic acid, p-hydrocoumaric acid, vanillic acid, azelaic acid, hydroferulic acid, p-coumaric acid, hydrocaffeic acid, ferulic acid, and caffeic acid. Among these metabolites, the antifungal compounds 3-phenyllactic acid and 3-hydroxydecanoic acid were previously isolated in our laboratory from liquid cultures of the same LAB strains by bioassay-guided fractionation. It was concluded that other metabolites, e.g., p-hydrocoumaric acid, hydroferulic acid, and p-coumaric acid, were released from the grass by the added LAB strains. The antifungal activities of the identified metabolites in 100 mM lactic acid were investigated. The MICs against Pichia anomala, Penicillium roqueforti, and Aspergillus fumigatus were determined, and 3-hydroxydecanoic acid showed the lowest MIC (0.1 mg ml(-1) for two of the three test organisms).

  • 14.
    Båth, Klara
    et al.
    Swedish University of Agricultural Sciences, Department of Microbiology, Uppsala Biocenter, Uppsala, Sweden; The Swedish Institute for Food and Biotechnology, Göteborg, Sweden.
    Persson, Karin Neil
    Swedish University of Agricultural Sciences, Department of Microbiology, Uppsala Biocenter, Uppsala, Sweden.
    Schnürer, Johan
    Swedish University of Agricultural Sciences, Department of Microbiology, Uppsala Biocenter, Uppsala, Sweden.
    Leong, Su-lin L.
    Swedish University of Agricultural Sciences, Department of Microbiology, Uppsala Biocenter, Uppsala, Sweden.
    Microbiota of an unpasteurised cellar-stored goat cheese from northern Sweden2012In: Agricultural and Food Science, ISSN 1459-6067, E-ISSN 1795-1895, Vol. 21, no 2, 197-203 p.Article in journal (Refereed)
    Abstract [en]

    This qualitative study reports on lactic acid bacteria (LAB), yeasts and moulds isolated from three artisanal Swedish cellar-stored goat cheeses aged for 1, 3 and 5 months. Starter culture LAB dominated in the younger cheeses, and Leuconostoc pseudomesenteroides, common in raw goats' milk, had persisted from the unpasteurised milk into all the cheeses. Non-starter LAB dominated in the 5 month cheese, in particular, Lactobacillus sakei, a meat-associated LAB not previously isolated from cheese. Debaryomyces hansenii, and Penicillium and Mucor species were dominant among the yeasts and moulds, respectively. The cheese rind was not formed primarily from Penicillium species as in traditional cheeses such as Camembert - rather, mycelium from Mucor mucedo contributed to rind formation. Mould species known to produce sterigmatocystin, aflatoxins or ochratoxin A in cheese were not isolated in this study; growth of mycotoxigenic Aspergilli may have been inhibited by the cool conditions in the earth-cellar (4-6 degrees C).

  • 15.
    Börjesson, Thomas
    et al.
    The Swedish Institute for Food Research, Göteborg, Sweden; Department of Microbiology, The Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Stöllman, Ulla
    The Swedish Institute for Food Research, Göteborg, Sweden.
    Schnürer, Johan
    Department of Microbiology, The Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Volatile Metabolites and Other Indicators of Penicillium aurantiogriseum Growth on Different Substrates1990In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 56, no 12, 3705-3710 p.Article in journal (Refereed)
    Abstract [en]

    Penicillium aurantiogriseum Dierckx was cultivated on six agar substrates (barley meal agar, oat meal agar, wheat meal agar, malt extract agar, Czapek agar, and Norkrans agar) and on oat grain for 5 days in cultivation vessels provided with an inlet and an outlet for air. Volatile metabolites produced by the cultures were collected on a porous polymer adsorbent by passing an airstream through the vessel. Volatile metabolites were collected between days 2 and 5 after inoculation. CO2 production was simultaneously measured, and after the cultivation period ergosterol contents and the numbers of CFU of the cultures were determined. Alcohols of low molecular weight and sesquiterpenes were the dominant compounds found. During growth on oat grain the production of 8-carbon alcohols and 3-methyl-1-butanol was higher and the production of terpenes was lower than during growth on agar substrates. The compositions of the volatile metabolites from oat grain were more similar to those from wheat grain, which was used as a substrate in a previous investigation, than to those produced on any of the agar substrates. Regarding the agar substrates, the production of terpenes was most pronounced on the artificial substrates (Czapek agar and Norkrans agar) whereas alcohol production was highest on substrates based on cereals. The production of volatile metabolites was highly correlated with the production of CO2 and moderately correlated with ergosterol contents, whereas no correlation with the numbers of CFU was found. Thus, the volatile metabolites formed and the ergosterol contents of fungal cultures should be good indicators of present and past fungal activity.

  • 16.
    Börjesson, Thomas
    et al.
    SIK - The Swedish Institute for Food Research, Göteborg, Sweden; Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Stöllman, Ulla
    SIK - The Swedish Institute for Food Research, Göteborg, Sweden.
    Schnürer, Johan
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Volatile Metabolites Produced by Six Fungal Species Compared with Other Indicators of Fungal Growth on Cereal Grains1992In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 58, no 8, 2599-2605 p.Article in journal (Refereed)
    Abstract [en]

    Six fungal species, Penicillium brevicompactum, P. glabrum, P. roqueforti, Aspergillus flavus, A. versicolor, and A. candidus, were inoculated on moistened and autoclaved wheat and oat grains. They were cultivated in glass vessels provided with an inlet and outlet for air. Air was passed through the vessels to collect volatile fungal metabolites on porous polymer adsorbents attached to the outlet. Samples were collected at two fungal growth stages. Adsorbed compounds were thermally desorbed, separated by gas chromatography, and identified by mass spectrometry. Differences in the production of volatile metabolites depended more on the fungal species than on the grain type. The fungal growth stage was not an important factor determining the composition of volatiles produced. 3-Methylfuran was produced in similar amounts regardless of the fungal species and substrate (oat versus wheat). The production of volatile metabolites was compared with the production of ergosterol and CO2 and the number of CFU. The production of volatile metabolites was more strongly correlated with accumulated CO2 production than with actual CO2 production and more strongly correlated with ergosterol contents of the grain than with numbers of CFU.

  • 17.
    Dal Bello, F.
    et al.
    Department of Food Science, Food Technology and Nutrition, National University of Ireland, Cork, Ireland.
    Clarke, C. I.
    Department of Food Science, Food Technology and Nutrition, National University of Ireland, Cork, Ireland.
    Ryan, L. A. M.
    Department of Food Science, Food Technology and Nutrition, National University of Ireland, Cork, Ireland.
    Ulmer, H.
    Department of Food Science, Food Technology and Nutrition, National University of Ireland, Cork, Ireland; National Food Biotechnology Centre, National University of Ireland, Cork, Ireland.
    Schober, T. J.
    Department of Food Science, Food Technology and Nutrition, National University of Ireland, Cork, Ireland; National Food Biotechnology Centre, National University of Ireland, Cork, Ireland.
    Ström, K.
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Sjögren, J.
    Department of Chemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    van Sinderen, D.
    National Food Biotechnology Centre, National University of Ireland, Cork, Ireland.
    Schnürer, Johan
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Arendt, E. K.
    Department of Food Science, Food Technology and Nutrition, National University of Ireland, Cork, Ireland.
    Improvement of the quality and shelf life of wheat bread by fermentation with the antifungal strain Lactobacillus plantarum FST 1.72007In: Journal of Cereal Science, ISSN 0733-5210, E-ISSN 1095-9963, Vol. 45, no 3, 309-318 p.Article in journal (Refereed)
    Abstract [en]

    Lactobacillus plantarum FST 1.7 was screened for in vitro antimicrobial activity and was shown to be active against spoilage moulds and bacteria. Isolation of antimicrobial compounds from cell-free supernatant identified lactic acid, phenyllactic acid and the two cyclic dipeptides cyclo ((L)-Leu-(L)-Pro) and cyclo ((L)-Phe-(L)-Pro) as the major components responsible for this activity. L. plantarum FST 1.7 was tested for the ability to produce the antifungal compounds during sourdough fermentation and to produce bread of good quality and increased shelf-life. A rheofermentometer was used to examine the gaseous release and development characteristics of the dough. A range of parameters was determined including pH, TTA and specific loaf volume. The results were compared with those obtained using Lactobacillus sanfranciscensis, a chemically acidified and a non-acidified dough. The quality of sourdough and bread produced using L. plantarum FST 1.7 was comparable to that obtained using common sourdough starters, e.g. L. sanfranciscensis. Sourdoughs and breads were evaluated for the ability to retard growth of Fusarium culmorum and Fusarium graminearum two fungi found on breads. Sourdough and bread produced with strain FST 1.7 showed consistent ability to retard the growth of both Fusarium species, thus indicating that L. plantarum FST 1.7 has also the potential to improve the shelf-life of wheat bread.

  • 18.
    Demczuk, Walter
    et al.
    Bacteriology and Enteric Diseases Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
    Martin, Irene
    Bacteriology and Enteric Diseases Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
    Peterson, Shelley
    Bacteriology and Enteric Diseases Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
    Bharat, Amrita
    Bacteriology and Enteric Diseases Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
    Van Domselaar, Gary
    Science Technology Cores and Services Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada; Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.
    Graham, Morag
    Science Technology Cores and Services Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada; Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.
    Lefebvre, Brigitte
    Laboratoire de Santé Publique du Québec, Ste-Anne-de-Bellevue, Québec, Canada.
    Allen, Vanessa
    Public Health Ontario Laboratories, Toronto, Ontario, Canada.
    Hoang, Linda
    British Columbia Centres for Disease Control Public Health Microbiology & Reference Laboratory, Vancouver, British Columbia, Canada.
    Tyrrell, Greg
    Provincial Laboratory for Public Health, Edmonton, Alberta, Canada.
    Horsman, Greg
    Saskatchewan Disease Control Laboratory, Regina, Saskatchewan, Canada.
    Wylie, John
    Cadham Provincial Laboratory, Winnipeg, Manitoba, Canada.
    Haldane, David
    iQueen Elizabeth II Health Sciences Centre, Halifax, Nova Scotia, Canada.
    Archibald, Chris
    Centre for Communicable Diseases and Infection Control, Public Health Agency of Canada, Ottawa, Ontario, Canada.
    Wong, Tom
    First Nations and Inuit Health Branch, Health Canada, Ottawa, Ontario, Canada.
    Unemo, Magnus
    Örebro University, School of Health Sciences. Department of Laboratory Medicine, Microbiology, Faculty of Medicine and Health.
    Mulvey, Michael R
    Bacteriology and Enteric Diseases Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
    Genomic epidemiology and molecular resistance mechanisms of azithromycin resistant Neisseria gonorrhoeae in Canada from 1997 to 20142016In: Journal of Clinical Microbiology, ISSN 0095-1137, E-ISSN 1098-660X, Vol. 54, no 5, 1304-1313 p.Article in journal (Refereed)
    Abstract [en]

    The emergence of Neisseria gonorrhoeae with decreased susceptibility to cephalosporins and azithromycin resistance (AZM-R) represent a public health threat of untreatable gonorrhoea infections. Genomic epidemiology through whole genome sequencing was used to describe the emergence, dissemination, and spread of AZM-R strains. The genomes of 213 AZM-R and 23 AZM-susceptible N. gonorrhoeae isolates collected in Canada from 1989 to 2014 were sequenced. Core single nucleotide polymorphism (SNP) phylogenomic analysis resolved 246 isolates into 13 lineages. High-level AZM-R (minimum inhibitory concentration ≥256 μg/ml) was found in 5 phylogenetically diverse isolates, all of which possessed the A2059G mutation (Escherichia coli numbering) in all four 23S rRNA alleles. One high-level AZM-R isolate collected in 2009 concurrently had decreased susceptibility to ceftriaxone (MIC=0.125 μg/ml). An increase in the number of 23S rRNA alleles with the C2611T mutations (E. coli numbering) conferred low to moderate AZM-R (2 to 4 and 8 to 32 μg/mL, respectively). Low level AZM-R was also associated with mtrR promoter mutations including -35A deletion and the presence of N. meningitidis-like sequences. Geographic and temporal phylogenetic clustering indicate emergent AZM-R strains arise independently and can then rapidly expand clonally in a region through local sexual networks.

  • 19.
    Demirel, Isak
    et al.
    Örebro University, School of Health and Medical Sciences, Örebro University, Sweden.
    Kinnunen, Annica
    Örebro University, School of Science and Technology.
    Önnberg, Anna
    Örebro University, School of Health and Medical Sciences, Örebro University, Sweden. Department of Laboratory Medicine, Clinical Microbiology, Örebro University Hospital, Örebro, Sweden.
    Söderquist, Bo
    Örebro University, School of Medicine, Örebro University, Sweden. Örebro University Hospital. Department of Laboratory Medicine, Clinical Microbiology.
    Persson, Katarina
    Örebro University, School of Health and Medical Sciences, Örebro University, Sweden.
    Comparison of host response mechanisms evoked by extended spectrum beta lactamase (ESBL)- and non-ESBL-producing uropathogenic E. coli2013In: BMC Microbiology, ISSN 1471-2180, E-ISSN 1471-2180, Vol. 13, 181Article in journal (Refereed)
    Abstract [en]

    Background: Infections caused by extended spectrum beta-lactamases (ESBL)-producing bacteria have been emerging worldwide and the majority of ESBL-producing E. coli strains are isolated from patients with urinary tracts infections. The purpose of this study was to compare the host-response mechanisms in human polymorphonucleated leukocytes (PMN) and renal epithelial cells when stimulated by ESBL-or non-ESBL-producing uropathogenic E. coli (UPEC) isolates. The host-pathogen interaction of these ESBL-producing strains in the urinary tract is not well studied.

    Results: The ability of ESBL strains to evoke ROS-production from PMN cells was significantly higher than that of the non-ESBL strains. The growth of ESBL strains was slightly suppressed in the presence of PMN compared to non-ESBL strains after 30 min and 2 h, but the opposite was observed after 5 and 6 h. The number of migrating PMN was significantly higher in response to ESBL strains compared to non-ESBL strains. Stimulation of A498 cells with ESBL strains elicited lower production of IL-6 and IL-8 compared to non-ESBL strains.

    Conclusion: Significant differences in host-response mechanisms were identified when host cells were stimulated by ESBL-or non-ESBL producing strains. The obtained results on the early interactions of ESBL-producing strains with the host immune system may provide valuable information for management of these infections.

  • 20.
    Donà, Valentina
    et al.
    Institute for Infectious Diseases, University of Bern, Bern, Switzerland.
    Kasraian, Sara
    Institute for Infectious Diseases, University of Bern, Bern, Switzerland.
    Lupo, Agnese
    Institute for Infectious Diseases, University of Bern, Bern, Switzerland.
    Guilarte, Yuvia N.
    Institute for Infectious Diseases, University of Bern, Bern, Switzerland.
    Hauser, Christoph
    Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland.
    Furrer, Hansjakob
    Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland.
    Unemo, Magnus
    Örebro University, School of Health Sciences.
    Low, Nicola
    Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland.
    Endimiani, Andrea
    Institute for Infectious Diseases, University of Bern, Bern, Switzerlanda.
    Multiplex real-time PCR assay with high-resolution melting analysis for characterization of antimicrobial resistance in neisseria gonorrhoeae2016In: Journal of Clinical Microbiology, ISSN 0095-1137, E-ISSN 1098-660X, Vol. 54, no 8, 2074-2081 p.Article in journal (Refereed)
    Abstract [en]

    Resistance to antibiotics used against Neisseria gonorrhoeae infections is a major public health concern. Antimicrobial resistance (AMR) testing relies on time-consuming culture-based methods. Development of rapid molecular tests for detecting AMR determinants could provide valuable tools for surveillance, epidemiological studies and to inform individual case management. We developed a fast (<1.5 hrs) SYBR-green based real-time PCR method with high resolution melting (HRM) analysis. One triplex and three duplex reactions included two sequences for N. gonorrhoeae identification and seven determinants of resistance to extended-spectrum cephalosporins (ESCs), azithromycin, ciprofloxacin, and spectinomycin. The method was validated by testing 39 previously fully-characterized N. gonorrhoeae strains, 19 commensal Neisseria spp., and an additional panel of 193 gonococcal isolates. Results were compared with culture-based AMR determination. The assay correctly identified N. gonorrhoeae and the presence or absence of the seven AMR determinants. There was some cross-reactivity with non-gonococcal Neisseria species and the detection limit was 10(3)-10(4) gDNA copies/reaction. Overall, the platform accurately detected resistance to ciprofloxacin (sensitivity and specificity, 100%), ceftriaxone (sensitivity 100%, specificity 90%), cefixime (sensitivity 92%, specificity 94%), azithromycin and spectinomycin (both sensitivity and specificity, 100%). In conclusion, our methodology accurately detects mutations generating resistance to antibiotics used to treat gonorrhea. Low assay sensitivity prevents direct diagnostic testing of clinical specimens but this method can be used to screen collections of gonococcal isolates for AMR more quickly than with current culture-based AMR testing.

  • 21.
    Druvefors, Ulrika
    et al.
    Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Jonsson, Nils
    Swedish Institute of Agricultural and Environmental Engineering (JTI), Uppsala, Sweden.
    Boysen, Marianne E.
    Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Schnürer, Johan
    Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Efficacy of the biocontrol yeast Pichia anomala during long-term storage of moist feed grain under different oxygen and carbon dioxide regimens2002In: FEMS yeast research (Print), ISSN 1567-1356, E-ISSN 1567-1364, Vol. 2, no 3, 389-394 p., PII S1567-1356(02)00091-0Article in journal (Refereed)
    Abstract [en]

    The yeast Pichia anomala inhibits the spoilage mold Penicillium roqueforti in laboratory experiments with high-moisture wheat in malfunctioning airtight storage. The ability of P. anomala to prevent mold growth during 14 months of grain storage was evaluated in outdoor silos with different air permeabilities. Freshly harvested wheat in 160-kg portions was inoculated with 10(2) colony-forming units (cfu) g(-1) P. roqueforti, alone or together with 10(4) cfu, g(-1) P. anomala. During the first month P. anomala increased to about 10(6) cfu g(-1) in the treated silos to reach 10(7) cfu g(-1) after 9 months. Naturally occurring P. anomala in the untreated silos increased from 10(2) to about 10(3) cfu g(-1) during the first month and reached the same level as the treated silos after 9 months. Oxygen levels were reduced below the detection limit within 1 day, while carbon dioxide levels increased to 80-90% during the first month. P. roqueforti did not grow in wheat treated with P. anomala, regardless of silo permeability, but had increased to 10(5) cfu g(-1) in the untreated silos after 14 months of storage.

  • 22.
    Druvefors, Ulrika Ädel
    et al.
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Passoth, Volkmar
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Schnürer, Johan
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Nutrient effects on biocontrol of Penicillium roqueforti by Pichia anomala J121 during airtight storage of wheat2005In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 71, no 4, 1865-1869 p.Article in journal (Refereed)
    Abstract [en]

    The biocontrol yeast Pichia anomala inhibits the growth of a variety of mold species. We examined the mechanism underlying the inhibition of the grain spoilage mold Penicillium roqueforti by the biocontrol yeast P. anomala J121 during airtight storage. The biocontrol effect in a model grain silo with moist wheat (water activity of 0.96) was enhanced when complex medium, maltose, or glucose was added. Supplementation with additional nitrogen or vitamin sources did not affect the biocontrol activity of the yeast. The addition of complex medium or glucose did not significantly influence the yeast cell numbers in the silos, whether in the presence or absence of P. roqueforti. Mold growth was not influenced by the addition of nutrients, if cultivated without yeast. The products of glucose metabolism, mainly ethanol and ethyl acetate, increased after glucose addition to P. anomala-inoculated treatments. Our results suggest that neither competition for nutrients nor production of a glucose-repressible cell wall lytic enzyme is the main mode of action of biocontrol by P. anomala in this grain system. Instead, the mold-inhibiting effect probably is due to the antifungal action of metabolites, most likely a combination of ethyl acetate and ethanol, derived from glycolysis. The discovery that sugar amendments enhance the biocontrol effect of P. anomala suggests novel ways of formulating biocontrol yeasts.

  • 23.
    Druvefors, Ulrika Ädel
    et al.
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Schnürer, Johan
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Mold-inhibitory activity of different yeast species during airtight storage of wheat grain2005In: FEMS yeast research (Print), ISSN 1567-1356, E-ISSN 1567-1364, Vol. 5, no 4-5, 373-378 p.Article in journal (Refereed)
    Abstract [en]

    The yeast Pichia anomala J121 inhibits spoilage by Penicillium roqueforti in laboratory and pilot studies with high-moisture wheat in malfunctioning airtight storage. We tested the biocontrol ability of an additional 57 yeast species in a grain mini silo system. Most yeast species grew to CFU levels comparable to that of P. anomala J121 after 14 days of incubation (> 10(6) CF U g(-1)). Of the 5 8 species, 38 (63 strains) had no mold-inhibitory effects (Pen. roqueforti levels > 10(5) CFU g(-1)). Among these were 11 species (18 strains) that did not grow on the wheat grain. Several of the non-inhibiting yeast species have previously been reported as biocontrol agents in other postharvest environments. Weak inhibitory activity, reducing Pen. roqueforti levels to between 10(4) and 10(5) CFU g(-1), was observed with 11 species (12 strains). Candida silvicola and Pichia guillermondii reduced Pen. roqueforti to <10(4) CFU g(-1). Candida fennica, Candida pelliculosa, Candida silvicultrix, P. anomala (29 strains), Pichia burtonii, Pichia farinosa and Pichia membranifaciens strongly inhibited Pen. roqueforti (< 10(3) CFU g(-1)) in the mini silos, but none had higher biocontrol activity than P. anomala strain J121. This report is the first of biocontrol activity of C fennica and C silvicultrix. The ability of 27 yeast species to grow to high CFU values without inhibiting mold growth suggests that nutrient competition may not be the main mode of action of P. anomala J121.

  • 24.
    Elmarghani, Ebraheem [Ibrahim] Daabag
    et al.
    Örebro University, School of Science and Technology.
    Poonlapthawee, Sirirat
    Örebro University, School of Science and Technology.
    Olsson, Per-Erik
    Örebro University, School of Science and Technology.
    Jass, Jana
    Örebro University, School of Science and Technology.
    Antibiotic resistance in fecal indicator bacteria in Hjälmaren lake systemManuscript (preprint) (Other academic)
    Abstract [en]

    Background: Increasing levels of multi-antibiotic resistant bacteria are ound in the environment, causing serious concerns for treatment of infectious diseases. his increase is believed to be due to release of antibiotic resistant bacteria and election pressure resulting from pharmaceuticals in the environment.

    Objectives: We evaluated the presence of multi-antibiotic resistant fecal ndicator bacteria from the surface waters of a recipient river and lake downstream of he wastewater treatment plant (WWTP) in Sweden.

    Methods: Surface waters from Svartån river and Hjälmaren lake in Sweden were ampled in 2010 and 2011. The waters were analyzed for fecal indicator bacteria Escherichia coli, enterococci) by membrane filtration and selective agar plating. E. coli nd enterococci were evaluated by Etest for resistance to tetracycline, chloramphenicol, alidixic acid, trimethoprim-sulfamethoxazole, ciprofloxacin, cefotaxime, ceftazidime, eropenem, imipenem, ampicillin, vancomycin, gentamycin and streptomycin.

    Results: The highest concentration of E. coli and enterococci were found in vartån river at Naturens Hus closest site downstream of the WWTP. Tetracycline resistance as the most prominent in both fecal indicator bacteria. Over the two years, there was 42% (13/31) and 24% (7/29) multi-antibiotic resistant (≥2 antibiotics) E. coli and nterococci, respectively. Furthermore, we identified one ESBL and one AmpC hyperproducing . coli in 2010 and vancomycin (vanA) resistant E. faecium in 2011.

    Conclusions: The presence, of multi-antibiotic resistant strains of fecal ndicator organisms in regions considered predominantly clean, is of great concern. While t currently may not be a major threat in the region, it is demonstrating the accelerating incidence and spread of antibiotic resistance worldwide.

  • 25.
    Elmarghani, Ebraheem M.
    Örebro University, School of Science and Technology.
    Enterococcal distribution and responses toenvironmental waters2013Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    The release of antibiotics and pharmaceuticals into environmental waters contribute to the increasing risk of antibiotic resistant bacteria. The spread of antibiotic resistant bacteria in the environment increases the health risks to the community. Enterococci are fecal indicator bacteria (FIB) in aquatic environments for determining water quality. In order to study enterococcal distribution and their response to environmental waters, we first screened for fecal indicator bacteria and their antibiotic resistance. Samples were collected from different locations of inland waters near Örebro city, Sweden at 4 time points during 2010 and 2011. Waters were filtered and the bacteria were cultured on selective media. We observed that the distribution of fecal indicator bacteria was higher at Svartån at Naturens Hus (≤705 CFU/100 ml for enterococci and ≤5867 CFU/100 for E. coli) near the effluent of the wastewater treatment plant (WWTP) than other locations tested. The eastern side of Hjälmaren lake, Storhjälmaren, had the lowest number of FIB (0 CFU/100 ml for enterococci and ≤2 CFU/100 ml for E.coli). Isolated E. coli, E. faecalis and E. faecium were evaluated for antibiotic resistance. We observed that ≤18% of E. coli environmental isolates and 12% of E. faecium and E. feacalis isolates were resistant to antibiotics during 2010 and 2011. Fifteen percent of these were multi antibiotic resistant (MAR) enterococci in 2010 and 31% in 2011. Tetracycline resistance was the most widespread antibiotic resistance found in FIB insolates. Extended spectrum β-lactamase expressing E. coli strains were found to also be MAR. Vancomycin and imipenem resistance was found in E. faecium isolate. Our results suggest that WWTP contributes to the distribution of FIB and antibiotic resistance. Secondly we aimed to evaluate the cellular responses of human and bacterial cells in environmental waters. We found that the pro-inflammatory response (IL-1β and TNF-α) of THP-1 cell was significantly higher in Svartån at Naturens Hus downstream of WWTP than the other locations. Based on this we evaluated E. feacalis responses to the same water. There were no statistical significant changes in gene response found in E. feacalis isolates, suggesting that environmental waters contain unidentified substances can effect on human cells responses but not bacteria. In this report we conclude that transferring of MAR strains in the environmental waters were increased annually in enterococci and E. feacalis did not initiate a response to the unknown substances that are present in river. 

    List of papers
    1. Antibiotic resistance in fecal indicator bacteria in Hjälmaren lake system
    Open this publication in new window or tab >>Antibiotic resistance in fecal indicator bacteria in Hjälmaren lake system
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Background: Increasing levels of multi-antibiotic resistant bacteria are ound in the environment, causing serious concerns for treatment of infectious diseases. his increase is believed to be due to release of antibiotic resistant bacteria and election pressure resulting from pharmaceuticals in the environment.

    Objectives: We evaluated the presence of multi-antibiotic resistant fecal ndicator bacteria from the surface waters of a recipient river and lake downstream of he wastewater treatment plant (WWTP) in Sweden.

    Methods: Surface waters from Svartån river and Hjälmaren lake in Sweden were ampled in 2010 and 2011. The waters were analyzed for fecal indicator bacteria Escherichia coli, enterococci) by membrane filtration and selective agar plating. E. coli nd enterococci were evaluated by Etest for resistance to tetracycline, chloramphenicol, alidixic acid, trimethoprim-sulfamethoxazole, ciprofloxacin, cefotaxime, ceftazidime, eropenem, imipenem, ampicillin, vancomycin, gentamycin and streptomycin.

    Results: The highest concentration of E. coli and enterococci were found in vartån river at Naturens Hus closest site downstream of the WWTP. Tetracycline resistance as the most prominent in both fecal indicator bacteria. Over the two years, there was 42% (13/31) and 24% (7/29) multi-antibiotic resistant (≥2 antibiotics) E. coli and nterococci, respectively. Furthermore, we identified one ESBL and one AmpC hyperproducing . coli in 2010 and vancomycin (vanA) resistant E. faecium in 2011.

    Conclusions: The presence, of multi-antibiotic resistant strains of fecal ndicator organisms in regions considered predominantly clean, is of great concern. While t currently may not be a major threat in the region, it is demonstrating the accelerating incidence and spread of antibiotic resistance worldwide.

    National Category
    Ecology Microbiology
    Research subject
    Microbiology; Enviromental Science
    Identifiers
    urn:nbn:se:oru:diva-28742 (URN)
    Available from: 2013-04-22 Created: 2013-04-22 Last updated: 2017-10-17Bibliographically approved
    2. The impact of environmental waters on cellular response in human and bacterial cells
    Open this publication in new window or tab >>The impact of environmental waters on cellular response in human and bacterial cells
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    The escalating frequency of pharmaceutical and antibiotic use contributes to the increasing amounts of these substances being released into the environment. While wastewater treatment plants (WWTP) effectively remove substantial amounts of contaminating substances, some are persistent and are released into the environment. It is not possible to identify all of the potentially bioactive substances released into the environment, therefore it is more rational to explore the biological effects of the waters to determine prospective health hazards. The present study evaluates the cellular response of human and bacterial cells (Enterococcus faecalis) to environmental waters upstream anddownstream of the WWTP near the  city of Örebro, Sweden. Water samples werecollected from 4 sites during May 2011. These included a site upstream in Svartån at Tekniska Kvarn, downstream at Naturens Hus near the WWTP, in the recipient Hjälmaren lake and in Ånnaboda lake (control site). THP-1 monocytes exhibited a significant increase in secretion of pro-inflammatory cytokines TNF-α and IL-β when treated with waters from Svartån at Naturens Hus, justdownstream of the WWTP outlet. Water from this site was thereafter tested using an environmental E. faecalis isolate and the stress response, virulence and antibiotic gene expression was evaluated by qPCR. There was no statistically significant effect observed on the selected genes in E. faecalis when treated with the environmental waters compared to MQ water. Thus the waters contained substances that influence inflammatory response in human cells in vitro but did not affect fecal indicator enterococci.

    National Category
    Ecology Microbiology
    Research subject
    Enviromental Science; Microbiology
    Identifiers
    urn:nbn:se:oru:diva-28789 (URN)
    Available from: 2013-04-24 Created: 2013-04-24 Last updated: 2017-10-17Bibliographically approved
  • 26.
    Elmarghani, Ibrahim [Ebraheem]
    et al.
    Örebro University, School of Science and Technology.
    Elmarghani, Ahmed
    Biotechnology research center Tripoli, Libya PO Box 3310.
    Olsson, Per-Erik
    Örebro University, School of Science and Technology.
    Jass, Jana
    Örebro University, School of Science and Technology.
    The impact of environmental waters on cellular response in human and bacterial cellsManuscript (preprint) (Other academic)
    Abstract [en]

    The escalating frequency of pharmaceutical and antibiotic use contributes to the increasing amounts of these substances being released into the environment. While wastewater treatment plants (WWTP) effectively remove substantial amounts of contaminating substances, some are persistent and are released into the environment. It is not possible to identify all of the potentially bioactive substances released into the environment, therefore it is more rational to explore the biological effects of the waters to determine prospective health hazards. The present study evaluates the cellular response of human and bacterial cells (Enterococcus faecalis) to environmental waters upstream anddownstream of the WWTP near the  city of Örebro, Sweden. Water samples werecollected from 4 sites during May 2011. These included a site upstream in Svartån at Tekniska Kvarn, downstream at Naturens Hus near the WWTP, in the recipient Hjälmaren lake and in Ånnaboda lake (control site). THP-1 monocytes exhibited a significant increase in secretion of pro-inflammatory cytokines TNF-α and IL-β when treated with waters from Svartån at Naturens Hus, justdownstream of the WWTP outlet. Water from this site was thereafter tested using an environmental E. faecalis isolate and the stress response, virulence and antibiotic gene expression was evaluated by qPCR. There was no statistically significant effect observed on the selected genes in E. faecalis when treated with the environmental waters compared to MQ water. Thus the waters contained substances that influence inflammatory response in human cells in vitro but did not affect fecal indicator enterococci.

  • 27.
    Ericsson, Henrik
    et al.
    Department of Food Hygiene, Faculty of Veterinary Medicine, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Eklöw, Annelie
    Department of Food Hygiene, Faculty of Veterinary Medicine, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Danielsson-Tham, Marie-Louise
    Department of Food Hygiene, Faculty of Veterinary Medicine, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Loncarevic, Semir
    Department of Food Hygiene, Faculty of Veterinary Medicine, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Mentzing, L.-O.
    Communicable Disease Center for Värmland County, Karlstad Central Hospital, Karlstad, Sweden.
    Persson, I.
    Communicable Disease Center for Värmland County, Karlstad Central Hospital, Karlstad, Sweden.
    Unnerstad, Helle
    Department of Food Hygiene, Faculty of Veterinary Medicine, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Tham, Wilhelm
    Department of Food Hygiene, Faculty of Veterinary Medicine, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    An outbreak of listeriosis suspected to have been caused by rainbow trout1997In: Journal of Clinical Microbiology, ISSN 0095-1137, E-ISSN 1098-660X, Vol. 35, no 11, 2904-2907 p.Article in journal (Refereed)
    Abstract [en]

    An outbreak of listeriosis in Sweden, consisting of nine cases, was investigated by means of molecular typing of strains from patients and strains isolated from suspected foodstuffs, together with interviews of the patients. Listeria monocytogenes was isolated from six of the patients, and all isolates were of the same clonal type. This clonal type was also isolated from a 'gravad' rainbow trout, made by producer Y, found in the refrigerator of one of the patients. Unopened packages obtained from producer y were also found to contain the same clonal type of L. monocytogenes. Based on the interview results and the bacteriological typing, we suspect that at least six of the nine cases were caused by gravad or cold-smoked rainbow trout made by producer Y. To our knowledge, this is the first rainbow trout-borne outbreak of listeriosis ever reported.

  • 28.
    Ericsson, Henrik
    et al.
    Department of Food Hygiene, Faculty of Veterinary Medicine, Swedish University of Agricultural Sciences, Uppsala.
    Stålhandske, Per
    Department of Food Hygiene, Faculty of Veterinary Medicine, Swedish University of Agricultural Sciences, Uppsala.
    Danielsson-Tham, Marie-Louise
    Department of Food Hygiene, Faculty of Veterinary Medicine, Swedish University of Agricultural Sciences, Uppsala.
    Bannerman, Elisabeth
    Medical Bacteriology Laboratory, University Hospital, Lausanne, Switzerland.
    Bille, Jacques
    Medical Bacteriology Laboratory, University Hospital, Lausanne, Switzerland.
    Jacquet, Christine
    Centre National de Référence des Listeria, World Health Organization Collaborating Center for Foodborne Listeriosis, Institut Pasteur, Paris, France.
    Rocourt, Jocelyne
    Centre National de Référence des Listeria, World Health Organization Collaborating Center for Foodborne Listeriosis, Institut Pasteur, Paris, France.
    Tham, Wilhelm
    Department of Food Hygiene, Faculty of Veterinary Medicine, Swedish University of Agricultural Sciences, Uppsala.
    Division of Listeria monocytogenes serovar 4b strains into two groups by PCR and restriction enzyme analysis1995In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 61, no 11, 3872-3874 p.Article in journal (Refereed)
    Abstract [en]

    Altogether, 133 strains of Listeria monocytogenes serovar 4b were investigated, A segment of 2,916 bp containing parts of the two genes inlA and inlB in L. monocytogenes was amplified by the PCR technique. The PCR product obtained was cleaved with the restriction enzyme AluI, and the fragments generated were separated by gel electrophoresis, leading to two distinct groups: PCR-restriction enzyme analysis groups I and II, containing 37 and 96 strains, respectively, The PCR-restriction enzyme analysis method described in this paper could be a useful tool for the subtyping of L. monocytogenes serovar 4b strains.

  • 29.
    Ericsson, Henrik
    et al.
    Department of Food Hygiene, Faculty of Veterinary Medicine, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Unnerstad, Helle
    Department of Food Hygiene, Faculty of Veterinary Medicine, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Mattsson, Jens G.
    Department of Parasitology, National Veterinary Institute, Uppsala, Sweden.
    Danielsson-Tham, Marie-Louise
    Department of Food Hygiene, Faculty of Veterinary Medicine, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Tham, Wilhelm
    Department of Food Hygiene, Faculty of Veterinary Medicine, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Molecular grouping of Listeria monocytogenes based on the sequence of the inlB gene2000In: Journal of Medical Microbiology, ISSN 0022-2615, E-ISSN 1473-5644, ISSN 0022-2615, Vol. 49, no 1, 73-80 p.Article in journal (Refereed)
    Abstract [en]

    The major part of the gene inlB was sequenced in 24 strains of Listeria monocytogenes belonging to serovars 1/2a, 1/2b, 1/2c, 3b and 4b. A phylogenetic analysis based on the inlB nucleotide sequences showed that strains of serovars 1/2a and 1/2c were closely related, as well as those of serovars 1/2b and 3b. Strains sharing serovar 4b could be divided into two distinct groups. There were differences in amino-acid sequence between all serovars except between serovars 1/2b and 3b. Differences in amino-acid sequence were also seen within each of the serovars 1/2a and 4b. The data presented indicate that the inlB gene may be useful for typing purposes as an alternative or complement to serotyping.

  • 30.
    Ezewudo, Matthew N.
    et al.
    Emory Univ, Sch Med, Dept Med, Div Infect Dis, Atlanta, GA 30322 USA..
    Joseph, Sandeep J.
    Emory Univ, Sch Med, Dept Med, Div Infect Dis, Atlanta, GA 30322 USA..
    Castillo-Ramirez, Santiago
    Univ Nacl Autonoma Mexico, Ctr Ciencias Genom, Programa Genom Evolut, Cuernavaca 62191, Morelos, Mexico..
    Dean, Deborah
    Childrens Hosp, Oakland Res Inst, Oakland, CA 94609 USA.;Univ Calif San Francisco, Div Infect Dis, San Francisco, CA 94143 USA..
    del Rio, Carlos
    Emory Univ, Sch Med, Dept Med, Div Infect Dis, Atlanta, GA 30322 USA.;Emory Univ, Hubert Dept Global Hlth, Rollins Sch Publ Hlth, Atlanta, GA 30322 USA..
    Didelot, Xavier
    Univ London Imperial Coll Sci Technol & Med, Dept Infect Dis Epidemiol, London, England..
    Dillon, Jo-Anne
    Univ Saskatchewan, Coll Med, Dept Microbiol & Immunol, Vaccine & Infect Dis Org Int Vaccine Ctr, Saskatoon, SK S7N 0W0, Canada..
    Selden, Richard F.
    NetBio, Waltham, MA USA..
    Shafer, William M.
    Emory Univ, Sch Med, Dept Microbiol & Immunol, Atlanta, GA 30322 USA.;Vet Affairs Med Ctr, Labs Bacterial Pathogenesis, Decatur, GA 30033 USA..
    Turingan, Rosemary S.
    NetBio, Waltham, MA USA..
    Unemo, Magnus
    Örebro University Hospital. WHO Collaborating Ctr Gonorrhoea & Other STIs, Orebro, Sweden..
    Read, Timothy D.
    Emory Univ, Sch Med, Dept Med, Div Infect Dis, Atlanta, GA 30322 USA..
    Population structure of Neisseria gonorrhoeae based on whole genome data and its relationship with antibiotic resistance2015In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 3, e806Article in journal (Refereed)
    Abstract [en]

    Neisseria gonorrhoeae is the causative agent of gonorrhea, a sexually transmitted infection (STI) of major importance. As a result of antibiotic resistance, there are now limited options for treating patients. We collected draft genome sequence data and associated metadata data on 76 N. gonorrhoeae strains from around the globe and searched for known determinants of antibiotics resistance within the strains. The population structure and evolutionary forces within the pathogen population were analyzed. Our results indicated a cosmopolitan gonoccocal population mainly made up of five subgroups. The estimated ratio of recombination to mutation (r/m = 2.2) from our data set indicates an appreciable level of recombination occurring in the population. Strains with resistance phenotypes to more recent antibiotics (azithromycin and cefixime) were mostly found in two of the five population subgroups.

  • 31.
    Feng, X. M.
    et al.
    Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Olsson, J.
    Centre for Human Studies of Foodstuffs, Uppsala University, Uppsala, Sweden.
    Swanberg, M.
    Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Schnürer, Johan
    Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Rönnow, D.
    Department of Electronics, University of Gävle, Gävle, Sweden.
    Image analysis for monitoring the barley tempeh fermentation process2007In: Journal of Applied Microbiology, ISSN 1364-5072, E-ISSN 1365-2672, Vol. 103, no 4, 1113-1121 p.Article in journal (Refereed)
    Abstract [en]

    Aims: To develop a fast, accurate, objective and nondestructive method for monitoring barley tempeh fermentation.

    Methods and Results: Barley tempeh is a food made from pearled barley grains fermented with Rhizopus oligosporus. Rhizopus oligosporus growth is important for tempeh quality, but quantifying its growth is difficult and laborious. A system was developed for analysing digital images of fermentation stages using two image processing methods. The first employed statistical measures sensitive to image colour and surface structure, and these statistical measures were highly correlated (r = 0.92, n = 75, P < 0.001) with ergosterol content of tempeh fermented with R. oligosporus and lactic acid bacteria (LAB). In the second method, an image-processing algorithm optimized to changes in images of final tempeh products was developed to measure number of visible barley grains. A threshold of 5 visible grains per Petri dish indicated complete tempeh fermentation. When images of tempeh cakes fermented with different inoculation levels of R. oligosporus were analysed the results from the two image processing methods were in good agreement.

    Conclusion: Image processing proved suitable for monitoring barley tempeh fermentation. The method avoids sampling, is nonintrusive, and only requires a digital camera with good resolution and image analysis software.

    Significance and Impact of the Study: The system provides a rapid visualization of tempeh product maturation and qualities during fermentation. Automated online monitoring of tempeh fermentation by coupling automated image acquisition with image processing software could be further developed for process control.

  • 32.
    Feng, Xin Mei
    et al.
    Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Larsen, Thomas Ostenfeld
    Center for Microbial Biotechnology, BioCentrum-DTU, Building 221, Technical University of Denmark, Lyngby, Denmark.
    Schnürer, Johan
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Production of volatile compounds by Rhizopus oligosporus during soybean and barley tempeh fermentation2007In: International Journal of Food Microbiology, ISSN 0168-1605, E-ISSN 1879-3460, Vol. 113, no 2, 133-141 p.Article in journal (Refereed)
    Abstract [en]

    Rhizopus oligosporus Saito can ferment soybeans or cereal grains to tempeh, a sliceable cake with improved nutritional properties. Volatiles produced by different R. oligosporus strains grown on malt extract agar (MEA), barley and soybean were investigated. The effect of co-cultivation with Lactobacillus plantarum on the production of volatiles was also studied. Volatile compounds were collected in situ by headspace diffusion and identified by GC-MS. The ten R. oligosporus strains that had different colony morphologies on MEA produced very similar volatile profiles, except for slight variations among the minor volatile compounds (e.g. sesquiterpenes). Likewise, practically no differences in volatile profiles were observed between three of the strains grown on soybeans. In contrast, the R. oligosporus volatile profile on soybean was different from that on barley from the same strain. Co-cultivation with L. plantarum did not influence volatile production by R. oligosporus. The dominant compounds produced on all three Substrates were ethanol, acetone, ethyl acetate, 2-butanone, 2-methyl-1-propanol, 3-methyl-1-butanol and 2-methyl-1-butanol. Acetaldehyde and 2-methyl-propanal were also produced on MEA and barley, while 2-pentanone, methyl acetate, 2-butanol and 3-methyl-3-buten-1-ol were observed on soybeans. Ethanol, 2-methyl-1-butanol and 3-methyl-1-butanol were the most abundant volatile compounds produced on MEA and barley, while 2-butanone was the dominant volatile metabolite on soybean. The mushroom odour compounds, 3-octanone and 1-octen-3-ol, were only detected from soybean and soybean tempeh.

  • 33.
    Feng, Xin Mei
    et al.
    Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Passoth, Volkmar
    Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Eklund-Jonsson, Charlotte
    Department of Chemical and Biological Engineering, Food Science, Chalmers University of Technology, Göteborg, Sweden.
    Alminger, Marie Larsson
    Department of Chemical and Biological Engineering, Food Science, Chalmers University of Technology, Göteborg, Sweden.
    Schnürer, Johan
    Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Rhizopus oligosporus and yeast co-cultivation during barley tempeh fermentation: Nutritional impact and real-time PCR quantification of fungal growth dynamics2007In: Food microbiology (Print), ISSN 0740-0020, E-ISSN 1095-9998, Vol. 24, no 4, 393-402 p.Article in journal (Refereed)
    Abstract [en]

    Barley tempeh was produced by fermenting barley kernels with Rhizopus oligosporus. The potential of the yeasts Saccharomyces cerevisiae (three strains), S. boulardii (one strain), Pichia anomala (one strain) and Kluyveromyces lactis (one strain) to grow together with R. oligosporus during barley tempeh fermentation was evaluated. All yeast strains grew during the fermentation and even during cold storage of tempeh (P < 0.01). The growth of yeasts slightly increased the ergosterol contents, but did not influence amino acid contents and compositions, and did not reduce phytate contents. Slight increases of vitamins B-6 and niacinamide, and slight decreases of B, and biotin were observed. Quantification of fungal growth is difficult during mixed species fermentations because ergosterol is found in all fungal species, and colony-forming-unit (cfu) estimations are not reliable for R. oligosporus and other sporulating fungi. Therefore, we developed a quantitative real-time PCR method for individually quantifying S. cerevisiae and R. oligosporus growth in barley tempeh. The PCR results were highly correlated with the ergosterol content of R. oligosporus and with the number of cfu of S. cerevisiae. Thus, real-time PCR is a rapid and selective method to quantify yeasts and R. oligosporus during mixed species fermentation of inhomogenous substrate such as barley tempeh.

  • 34.
    Fifer, Helen
    et al.
    Public Health England, London, United Kingdom.
    Natarajan, Usha
    Virgin Care, London, United Kingdom.
    Jones, Lucy
    Virgin Care, London, United Kingdom.
    Alexander, Sarah
    Public Health England, London, United Kingdom.
    Hughes, Gwenda
    Public Health England, London, United Kingdom.
    Golparian, Daniel
    Örebro University, School of Medical Sciences.
    Unemo, Magnus
    Örebro University, School of Health Sciences.
    Failure of Dual Antimicrobial Therapy in Treatment of Gonorrhea2016In: New England Journal of Medicine, ISSN 0028-4793, E-ISSN 1533-4406, Vol. 374, no 25, 2504-2506 p.Article in journal (Refereed)
  • 35.
    Foerster, Sunniva
    et al.
    Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland; Institute for Infectious Diseases, University of Bern, Bern, Switzerland; WHO Collaborating Centre for Gonorrhoea and other STIs, National Reference Laboratory for Pathogenic Neisseria, Faculty of Medicine and Health, Örebro University, Örebro, Sweden; Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland.
    Unemo, Magnus
    Örebro University, School of Health Sciences. WHO Collaborating Centre for Gonorrhoea and other STIs, National Reference Laboratory for Pathogenic Neisseria.
    Hathaway, Lucy J.
    Institute for Infectious Diseases, University of Bern, Bern, Switzerland.
    Low, Nicola
    Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland.
    Althaus, Christian L.
    Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland.
    Time-kill curve analysis and pharmacodynamic modelling for in vitro evaluation of antimicrobials against Neisseria gonorrhoeae2016In: BMC Microbiology, ISSN 1471-2180, E-ISSN 1471-2180, Vol. 16, 216Article in journal (Refereed)
    Abstract [en]

    Background: Gonorrhoea is a sexually transmitted infection caused by the Gram-negative bacterium Neisseria gonorrhoeae. Resistance to first-line empirical monotherapy has emerged, so robust methods are needed to evaluate the activity of existing and novel antimicrobials against the bacterium. Pharmacodynamic models describing the relationship between the concentration of antimicrobials and the minimum growth rate of the bacteria provide more detailed information than the MIC only.

    Results: In this study, a novel standardised in vitro time-kill curve assay was developed. The assay was validated using five World Health Organization N. gonorrhoeae reference strains and a range of ciprofloxacin concentrations below and above the MIC. Then the activity of nine antimicrobials with different target mechanisms was examined against a highly antimicrobial susceptible clinical strain isolated in 1964. The experimental time-kill curves were analysed and quantified with a previously established pharmacodynamic model. First, the bacterial growth rates at each antimicrobial concentration were estimated with linear regression. Second, we fitted the model to the growth rates, resulting in four parameters that describe the pharmacodynamic properties of each antimicrobial. A gradual decrease of bactericidal effects from ciprofloxacin to spectinomycin and gentamicin was found. The beta-lactams ceftriaxone, cefixime and benzylpenicillin showed bactericidal and time-dependent properties. Chloramphenicol and tetracycline were purely bacteriostatic as they fully inhibited the growth but did not kill the bacteria. We also tested ciprofloxacin resistant strains and found higher pharmacodynamic MICs (zMIC) in the resistant strains and attenuated bactericidal effects at concentrations above the zMIC.

    Conclusions: N. gonorrhoeae time-kill curve experiments analysed with a pharmacodynamic model have potential for in vitro evaluation of new and existing antimicrobials. The pharmacodynamic parameters based on a wide range of concentrations below and above the MIC provide information that could support improving future dosing strategies to treat gonorrhoea.

  • 36.
    Fouhy, Fiona
    et al.
    Teagasc Food Research Centre, Fermoy, Cork, Ireland; Microbiology Department, University College Cork, Cork, Ireland .
    Guinane, Caitriona M.
    Teagasc Food Research Centre, Fermoy, Cork, Ireland; Alimentary Pharmabiotic Centre, Cork, Ireland.
    Hussey, Seamus
    Department of Paediatrics and Child Health, University College Cork, Cork, Ireland; Division of Gastroenterology, Hepatology and Nutrition, Hospital for Sick Children, Toronto, ON, Canada.
    Wall, Rebecca
    Teagasc Food Research Centre, Fermoy, Cork, Ireland; Alimentary Pharmabiotic Centre, Cork, Ireland.
    Ryan, C. Anthony
    Department of Paediatrics and Child Health, University College Cork, Cork, Ireland .
    Dempsey, Eugene M.
    Department of Paediatrics and Child Health, University College Cork, Cork, Ireland; Department of Neonatology, Cork University Maternity Hospital, Cork, Ireland.
    Murphy, Brendan
    Department of Paediatrics and Child Health, University College Cork, Cork, Ireland .
    Ross, R. Paul
    Teagasc Food Research Centre, Fermoy, Cork, Ireland; Alimentary Pharmabiotic Centre, Cork, Ireland.
    Fitzgerald, Gerald F
    Microbiology Department, University College Cork, Cork, Ireland; Alimentary Pharmabiotic Centre, Cork, Ireland.
    Stanton, Catherine
    Teagasc Food Research Centre, Fermoy, Cork, Ireland; Alimentary Pharmabiotic Centre, Cork, Ireland.
    Cotter, Paul D.
    Teagasc Food Research Centre, Fermoy, Cork, Ireland; Alimentary Pharmabiotic Centre, Cork, Ireland.
    High-throughput sequencing reveals the incomplete, short-term recovery of infant gut microbiota following parenteral antibiotic treatment with ampicillin and gentamicin2012In: Antimicrobial Agents and Chemotherapy, ISSN 0066-4804, E-ISSN 1098-6596, Vol. 56, no 11, 5811-5820 p.Article in journal (Refereed)
    Abstract [en]

    The infant gut microbiota undergoes dramatic changes during the first 2 years of life. The acquisition and development of this population can be influenced by numerous factors, and antibiotic treatment has been suggested as one of the most significant. Despite this, however, there have been relatively few studies which have investigated the short-term recovery of the infant gut microbiota following antibiotic treatment. The aim of this study was to use high-throughput sequencing (employing both 16S rRNA and rpoB-specific primers) and quantitative PCR to compare the gut microbiota of nine infants who underwent parenteral antibiotic treatment with ampicillin and gentamicin (within 48 h of birth), 4 and 8 weeks after the conclusion of treatment, relative to that of nine matched healthy controls. The investigation revealed that the gut microbiota of the antibiotic-treated infants had significantly higher proportions of Proteobacteria (P = 0.0049) and significantly lower proportions of Actinobacteria (P = 0.00001) (and the associated genus Bifidobacterium [P = 0.0132]) as well as the genus Lactobacillus (P = 0.0182) than the untreated controls 4 weeks after the cessation of treatment. By week 8, the Proteobacteria levels remained significantly higher in the treated infants (P = 0.0049), but the Actinobacteria, Bifidobacterium, and Lactobacillus levels had recovered and were similar to those in the control samples. Despite this recovery of total Bifidobacterium numbers, rpoB-targeted pyrosequencing revealed that the number of different Bifidobacterium species present in the antibiotic-treated infants was reduced. It is thus apparent that the combined use of ampicillin and gentamicin in early life can have significant effects on the evolution of the infant gut microbiota, the long-term health implications of which remain unknown.

  • 37.
    Fredlund, E.
    et al.
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Broberg, A.
    Department of Chemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Boysen, M. E.
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Kenne, L.
    Department of Chemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Schnürer, Johan
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Metabolite profiles of the biocontrol yeast Pichia anomala J121 grown under oxygen limitation2004In: Applied Microbiology and Biotechnology, ISSN 0175-7598, E-ISSN 1432-0614, Vol. 64, no 3, 403-409 p.Article in journal (Refereed)
    Abstract [en]

    The biocontrol yeast Pichia anomala J121 prevents mould growth during the storage of moist grain under low oxygen/high carbon dioxide conditions. Growth and metabolite formation of P. anomala was analyzed under two conditions of oxygen limitation: (a) initial aerobic conditions with restricted oxygen access during the growth period and (b) initial microaerobic conditions followed by anaerobiosis. Major intra- and extracellular metabolites were analyzed by high-resolution magic-angle spinning (HR-MAS) NMR and HPLC, respectively. HR-MAS NMR allows the analysis of major soluble compounds inside intact cells, without the need for an extraction step. Biomass production was higher in treatment (a), whereas the specific ethanol production rate during growth on glucose was similar in both treatments. This implies that oxygen availability affected the respiration and not the fermentation of the yeast. Following glucose depletion, ethanol was oxidized to acetate in treatment (a), but continued to be produced in (b). Arabitol accumulated in the culture substrate of both treatments, whereas glycerol only accumulated in treatment (b). Trehalose, arabitol, and glycerol accumulated inside the cells in both treatments. The levels of these metabolites were generally significantly higher in treatment (b) than in (a), indicating their importance for P. anomala during severe oxygen limitation/anaerobic conditions.

  • 38.
    Fredlund, Elisabeth
    et al.
    Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Beerlage, Christiane
    Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Melin, Petter
    Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Schnürer, Johan
    Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Passoth, Volkmar
    Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Oxygen and carbon source-regulated expression of PDC and ADH genes in the respiratory yeast Pichia anomala2006In: Yeast, ISSN 0749-503X, E-ISSN 1097-0061, Vol. 23, no 16, 1137-1149 p.Article in journal (Refereed)
    Abstract [en]

    We amplified, sequenced and studied the transcriptional regulation of genes of the alcoholic fermentation pathway in the biocontrol and non-Saccharomyces wine yeast, Pichia anomala. Two ADH isogenes, PaADH1 and PaADH2, and one PDC gene, PaPDC1, were amplified from genomic P. anomala DNA by a two-step PCR approach, using degenerated primers against conserved regions of the respective genes for cloning core regions, and PCR-based gene walking for cloning the respective 5' and 3'-ends. According to sequence analysis, ADHI and PDC1 are most likely cytoplasmatic proteins, while ADH2 is most probably localized in the mitochondria. PaADH1 was expressed during aerobic growth on glucose, ethanol and succinate, but was ninefold upregulated in response to oxygen limitation when grown on glucose. The gene seems to be involved in both production and consumption of ethanol. Only low expression of PaADH2 was detected during growth on glucose and ethanol, but it was highly expressed during growth on the non-fermentable carbon source succinate and repressed by the addition of glucose. PaPDC1 was expressed during aerobic growth on glucose and was upregulated four-fold in response to oxygen limitation. PaPDC1 expression was lower in cells grown on ethanol and succinate than on glucose and was up- regulated two- and four-fold, respectively, after glucose addition. Our results demonstrate that transcription of genes of the fermentative pathway is regulated by hypoxia and carbon source but posttranscriptional regulation may play a major role in regulating the metabolic flux.

  • 39.
    Fredlund, Elisabeth
    et al.
    Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Blank, Lars M.
    Institute of Biotechnology, ETH Zürich, Zürich, Switzerland.
    Schnürer, Johan
    Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Sauer, Uwe
    Institute of Biotechnology, ETH Zürich, Zürich, Switzerland.
    Passoth, Volkmar
    Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Oxygen- and glucose-dependent regulation of central carbon metabolism in Pichia anomala2004In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 70, no 10, 5905-5911 p.Article in journal (Refereed)
    Abstract [en]

    We investigated the regulation of the central aerobic and hypoxic metabolism of the biocontrol and non-Saccharomyces wine yeast Pichia anomala. In aerobic batch culture, P. anomala grows in the respiratory mode with a high biomass yield (0.59 g [dry weight] of cells g of glucose(-1)) and marginal ethanol, glycerol, acetate, and ethyl acetate production. Oxygen limitation, but not glucose pulse, induced fermentation with substantial ethanol production and 10-fold-increased ethyl acetate production. Despite low or absent ethanol formation, the activities of pyruvate decarboxylase and alcohol dehydrogenase were high during aerobic growth on glucose or succinate. No activation of these enzyme activities was observed after a glucose pulse. However, after the shift to oxygen limitation, both enzymes were activated threefold. Metabolic flux analysis revealed that the tricarboxylic acid pathway operates as a cycle during aerobic batch culture and as a two-branched pathway under oxygen limitation. Glucose catabolism through the pentose phosphate pathway was lower during oxygen limitation than under aerobic growth. Overall, our results demonstrate that P. anomala exhibits a Pasteur effect and not a Crabtree effect, i.e., oxygen availability, but not glucose concentration, is the main stimulus for the regulation of the central carbon metabolism.

  • 40.
    Fredlund, Elisabeth
    et al.
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Boysen, Marianne
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Schnürer, Johan
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Broberg, Anders
    Department of Chemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Exploring the mode of action of Pichia anomala - a postharvest biocontrol yeast2001In: Yeast, ISSN 0749-503X, E-ISSN 1097-0061, Vol. 18, S212-S212 p.Article in journal (Other academic)
    Abstract [en]

    The ascomycetous yeast Pichia anomala J121, inhibits mould growth in malfunctioning airtight storage systems for moist animal feed grain. Extensive studies of P. anomala J121 have given detailed knowledge of growth physiology and limiting environmental factors, which is necessary to understand the inhibitory activity. Our main objective is to identify the mechanisms behind the inhibitory activity. We have two non-exclusive working hypothesis: I)P. anomala produces antifungal substances and II)P. anomala out-competes the mould for space, nutrients, and oxygen. We have found that volatile metabolites restrict radial growth and sporulation of moulds in mouth-to-mouth assays where agar plates are placed facing each other with the yeast inoculated on the upper plate and the mould on the lower. Previous studies of P. anomala have shown that it produces high quantities of ethyl acetate - a mould-inhibitory substance. We are working to identify homologous genes in P. anomala J121 to the acetyltransferase encoding genes ATF1 and ATF2 in Saccharomyces cerevisiae. Another approach has been to identify intra- and extracellular metabolites during aerobic and oxygen limited growth. Intracellular metabolites were identified by Magic Angle Spinning-High Resolution-Nuclear Magnetic Resonance (MAS-HR- NMR) that allows analysis of living cells. Extracellular metabolites were analysed with HPLC. Glycerol, well known for its role during osmotic stress, is accumulated in response to oxygen stress.

  • 41.
    Fredlund, Elisabeth
    et al.
    Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Druvefors, Ulrika
    Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Boysen, Marianne E.
    Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Lingsten, Karl-Johan
    Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Schnürer, Johan
    Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Physiological characteristics of the biocontrol yeast Pichia anomala J1212002In: FEMS yeast research (Print), ISSN 1567-1356, E-ISSN 1567-1364, Vol. 2, no 3, 395-402 p., PII S1567-1356(02)00098-3Article in journal (Refereed)
    Abstract [en]

    The yeast Pichia anomala J121 prevents mold spoilage and enhances preservation of moist grain in malfunctioning storage systems. Development of P. anomala J121 as a biocontrol agent requires in-depth knowledge about its physiology. P. anomala J121 grew under strictly anaerobic conditions, at temperatures between 3degreesC and 37degreesC, at pH values between 2.0 and 12.4, and at a water activity of 0.92 (NaCl) and 0.85 (glycerol). It could assimilate a wide range of C- and N-sources and produce killer toxin. A selective medium containing starch, nitrate, acetic acid, and chloramphenicol was developed for P. anomala. P. anomala was equally sensitive as Candida albicans to common antifungal compounds. Growth ability at a range of environmental conditions contributes to the competitive ability of the biocontrol yeast P. anomala J121.

  • 42.
    Fredlund, Elisabeth
    et al.
    Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Druvefors, Ulrika Ädel
    Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Olstorpe, Matilda Nilsson
    Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Passoth, Volkmar
    Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Schnürer, Johan
    Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Influence of ethyl acetate production and ploidy on the anti-mould activity of Pichia anomala2004In: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 238, no 1, 133-137 p.Article in journal (Refereed)
    Abstract [en]

    A diploid and a haploid strain of Pichia anomala were tested for their biocontrol ability against the spoilage mould Penicillium roqueforti in glass tubes filled with grain at two water activities (a(w)). At a(w) 0.98, the two yeast strains grew and inhibited mould growth equally well and showed similar patterns of ethyl acetate production, reaching maximum values of 10-14 mug ml(-1) headspace. At a(w) 0.95, both growth and biocontrol performance of the haploid strain were reduced. Ethyl acetate formation was also substantially reduced, with maximum headspace concentrations of 4 mug ml(-1). We conclude that ethyl acetate is a major component of the anti-mould activity. The inhibitory effect of ethyl acetate was confirmed in a bioassay where the pure compound reduced biomass production of P. roqueforti.

  • 43.
    Fredlund, Elisabeth
    et al.
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Druvefors, Ulrika Ädel
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Passoth, Volkmar
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Schnürer, Johan
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    The correlation of oxygen and sugar dependent regulation of glycolysis to the biocontrol activity of the yeast Pichia anomala2003In: Yeast, ISSN 0749-503X, E-ISSN 1097-0061, Vol. 20, S352-S352 p.Article in journal (Other academic)
    Abstract [en]

    Pichia anomala inhibits growth of mould during airtight storage of moist cereal grain for animal feed. The cereal grain is stored in large airtight containers where the anaerobic environment prevents growth of mould. Air can leak into the system due to the removal of grain or technical difficulties in keeping completely anaerobic conditions. This subsequently enables growth of spoilage moulds. Addition of P. anomala cells inhibits the growth of mould making the system more robust [1]. We analysed the physiological basis of the biocontrol activity. P. anomala is a Crabtree negative yeast but in contrast to other Crabtree negative organisms it can grow under anaerobic conditions [2]. The ability to switch between respiratory and fermentative growth in response to O2-availability is essential for its survival in the airtight system and for its biocontrol activity. End products of the sugar metabolism had inhibitory effects on mould growth. Addition of glucose to a model biocontrol system enhanced biocontrol activity without increasing yeast biomass, suggesting the involvement of a product of glycolysis in biocontrol. Sugar consumption, production of ethanol and other metabolites and the activity of key enzymes were investigated in cells grown under defined conditions of oxygen and nutrient supply. The impact of the different parameters on biocontrol activity is discussed. [1] Druvefors et al. (2002) FEMS Yeast Res. 2: 389-394 [2] Fredlund et al. (2002) FEMS Yeast Res. 2: 395-402

  • 44.
    Frändberg, Emma
    et al.
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Petersson, Carl
    Department of Chemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Lundgren, Lennart N.
    Department of Chemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Schnürer, Johan
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Streptomyces halstedii K122 produces the antifungal compounds bafilomycin B1 and C12000In: Canadian journal of microbiology (Print), ISSN 0008-4166, E-ISSN 1480-3275, Vol. 46, no 8, 753-758 p.Article in journal (Refereed)
    Abstract [en]

    Streptomyces halstedii K122 was previously found to produce antifungal compounds on solid substrates that inhibit radial growth of fungi among Ascomycetes, Basidiomycetes, Deuteromycetes, Oomycetes, and Zygomycetes, and strongly affected hyphal branching and morphology. During growth of S. halstedii K122 in submerged culture, no antifungal activity could be detected. However, cultivation of S. halstedii in thin (1 mm) liquid substrate layers in large surface-area tissue culture flasks caused intense growth and sporulation of S. halstedii K122, and the biologically active compounds could be extracted from the mycelium with methanol. Antifungal compounds were purified using C18 solid phase extraction and silica gel column chromatography, and identified as bafilomycins B1 and C1, using 2D NMR and FAB MS. Production of bafilomycins, which are specific inhibitors of vacuolar ATPases, has not been reported from S. halstedii previously. Minimum inhibitory concentrations (MIC) of bafilomycins BI and C1, amphotericin B, and nikkomycin Z were determined at pH 5.5 and 7.0 for the target fungi Aspergillus fumigatus, Mucor hiemalis, Penicillium roqueforti, and Paecilomyces variotii. Penicillium roqueforti was the most sensitive species to all the compounds investigated. The MIC values for amphotericin B were 0.5-4 mu g.mL(-1) for the fungi tested, and pH did not affect the toxicity. The MIC values for nikkomycin Z ranged from <0.5 mu g.mL(-1) for Mucor hiemalis to >500 mu g.mL(-1) for Aspergillus fumigatus, and pH had no influence on toxicity. Bafilomycins B1 and C1 were equally active against the fungal species tested, with MIC values in the range of <0.5-64 mu g.mL(-1). All fungi were more sensitive to both bafilomycin B1 and C1 at pH 7.0 than at pH 5.5.

  • 45.
    Frändberg, Emma
    et al.
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Schnürer, Johan
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Antifungal activity of chitinolytic bacteria isolated from airtight stored cereal grain1998In: Canadian journal of microbiology (Print), ISSN 0008-4166, E-ISSN 1480-3275, Vol. 44, no 2, 121-127 p.Article in journal (Refereed)
    Abstract [en]

    Chitinolytic bacteria are used as biocontrol agents of plant pathogenic fungi. They might also potentially inhibit growth of molds, e.g., Aspergillus spp. and Penicillium spp., in stored plant material. We isolated chitinolytic bacteria from airtight stored cereal grain and evaluated their antifungal capacity. Between 0.01 and 0.5% of the total aerobic counts were chitinolytic bacteria. Gram-negative bacteria, mainly Pseudomonadaceae, constituted approximately 80% of the chitinolytic population. Gram-positive isolates belonged predominantly to the Corynebacterium-Arthrobacter group, Streptomyces, and Bacillus. Chitinolytic activity was evaluated using culture filtrates from chitin-grown isolates as the release of p-nitrophenol from p-nitrophenyl N,N'-diacetylchitobiose and as the formation of clearing zones on chitin agar. No correlation between chitinolytic activity and antifungal effects was found when challenging Penicillium roqueforti Dierckx with bacterial isolates on chitin agar in a dual culture bioassay. Fungal hyphae frequently grew seemingly unaffected through the bacterial colony of a high chitinase producer on colloidal chitin. Only 4% of the chitinolytic isolates had strong effects on fungal growth. Among these, Streptomyces halstedii (K122) and Streptomyces coelicolor (K139) inhibited growth of a broad range of fungi. Streptomyces halstedii affected hyphal morphology and decreased the radial growth rate of all fungi investigated. These effects were not caused by volatile metabolites, polyenes, or N-carbamoyl-D-glucosamine.

  • 46.
    Frändberg, Emma
    et al.
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Schnürer, Johan
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Chitinolytic properties of Bacillus pabuli K11994In: Journal of Applied Bacteriology, ISSN 0021-8847, Vol. 76, no 4, 361-367 p.Article in journal (Refereed)
    Abstract [en]

    The chitinolytic properties of Bacillus pabuli KI isolated from mouldy grain was studied. Chitinase activity was measured as the release of p-nitrophenol from p-nitrophenyl-N,N'-diacetylchitobiose. Influences of substrate concentration and different environmental variables on growth and chitinase activity were determined. The optimum environmental conditions for chitinase production were: 30 degrees C, initial pH 8, initial oxygen 10% and a(w) > 0.99. Chitinase production was induced when B. pabuli KI was grown on colloidal chitin. The smallest chito-oligosaccharide able to induce chitinase production was N,N'-diacetylchitobiose, (GlcNAc)(2). Production was also induced by (GlcNAc)(3) and (GlcNAc)(4). When the bacterium was grown on glucose or N-acetylglucosamine, no chitinases were formed. The highest chitinase production observed was obtained with colloidal chitin as substrate. The production of chitinases by B. pabuli K1 growing on chitin was repressed by high levels (0.6%) of glucose. The production was also repressed by 0.6% starch, laminarin and beta-glucan from barley and by glycerol. The addition of pectin and carboxymethyl cellulose increased chitinase production.

  • 47.
    Frändberg, Emma
    et al.
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Schnürer, Johan
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Evaluation of a chromogenic chito-oligosaccharide analogue, p-nitrophenyl-β-D-N,N'-diacetylchitobiose, for the measurement of the chitinolytic activity of bacteria1994In: Journal of Applied Bacteriology, ISSN 0021-8847, Vol. 76, no 3, 259-263 p.Article in journal (Refereed)
    Abstract [en]

    Three methods of quantifying chitinase activity were compared. The activities of crude chitinases of 10 bacterial isolates from different environments were estimated in terms of(l) the release of p-nitrophenol from the chromogenic chito-oligosaccharide analogues, p-nitrophenyl-beta-D-N,N'-diacetylchitobiose, p-nitrophenyl-N-acetyl-beta-D-glucosamine and p-nitrophenyl-beta-D-N,N',N''-triacetylchitotriose, (2) the release of reducing sugars from chitin and (3) the formation of clearing zones on chitin agar. When crude chitinase from Bacillus pabuli was used the hydrolysis of p-nitrophenyl-beta-D-N,N'-diacetylchitobiose correlated well with the release of reducing sugars from chitin and the formation of clearing zones on chitin agar. However, when the activity of crude chitinases from the different bacterial isolates were compared no agreement was found between the hydrolysis of p-nitrophenyl-beta-D-N,N'-diacetylchitobiose and the release of reducing sugars from chitin or the formation of clearing zones on chitin agar. It was concluded that the assay with chromogenic p-nitrophenyl chito-oligosaccharide analogues is not well suited for studies that compare the chitinase activity of different bacteria.

  • 48.
    Gkarmiri, Konstantia
    et al.
    Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Mahmood, Shahid
    Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Ekblad, Alf
    Örebro University, School of Science and Technology.
    Alström, Sadhna
    Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Högberg, Nils
    Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Finlay, Roger
    Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Identifying the Active Microbiome Associated with Roots and Rhizosphere Soil of Oilseed Rape2017In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 83, no 22, e01938-17Article in journal (Refereed)
    Abstract [en]

    RNA stable isotope probing and high-throughput sequencing were used to characterize the active microbiomes of bacteria and fungi colonizing the roots and rhizosphere soil of oilseed rape to identify taxa assimilating plant-derived carbon following (13)CO2 labeling. Root- and rhizosphere soil-associated communities of both bacteria and fungi differed from each other, and there were highly significant differences between their DNA- and RNA-based community profiles. Verrucomicrobia, Proteobacteria, Planctomycetes, Acidobacteria, Gemmatimonadetes, Actinobacteria, and Chloroflexi were the most active bacterial phyla in the rhizosphere soil. Bacteroidetes were more active in roots. The most abundant bacterial genera were well represented in both the (13)C- and (12)C-RNA fractions, while the fungal taxa were more differentiated. Streptomyces, Rhizobium, and Flavobacterium were dominant in roots, whereas Rhodoplanes and Sphingomonas (Kaistobacter) were dominant in rhizosphere soil. "Candidatus Nitrososphaera" was enriched in (13)C in rhizosphere soil. Olpidium and Dendryphion were abundant in the (12)C-RNA fraction of roots; Clonostachys was abundant in both roots and rhizosphere soil and heavily (13)C enriched. Cryptococcus was dominant in rhizosphere soil and less abundant, but was (13)C enriched in roots. The patterns of colonization and C acquisition revealed in this study assist in identifying microbial taxa that may be superior competitors for plant-derived carbon in the rhizosphere of Brassica napusIMPORTANCE This microbiome study characterizes the active bacteria and fungi colonizing the roots and rhizosphere soil of Brassica napus using high-throughput sequencing and RNA-stable isotope probing. It identifies taxa assimilating plant-derived carbon following (13)CO2 labeling and compares these with other less active groups not incorporating a plant assimilate. Brassica napus is an economically and globally important oilseed crop, cultivated for edible oil, biofuel production, and phytoextraction of heavy metals; however, it is susceptible to several diseases. The identification of the fungal and bacterial species successfully competing for plant-derived carbon, enabling them to colonize the roots and rhizosphere soil of this plant, should enable the identification of microorganisms that can be evaluated in more detailed functional studies and ultimately be used to improve plant health and productivity in sustainable agriculture.

  • 49.
    Gkarmiri, Konstantia
    et al.
    Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden .
    Mahmood, Shahid
    Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden .
    Ekblad, Alf
    Örebro University, School of Science and Technology.
    Alström, Sadhna
    Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden .
    Högberg, Nils
    Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden .
    Finlay, Roger
    Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden .
    Identifying the Active Microbiome Associated with Roots and Rhizosphere Soil of Oilseed Rape2017In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 83, no 22, UNSP e01938-17Article in journal (Refereed)
    Abstract [en]

    RNA stable isotope probing and high-throughput sequencing were used to characterize the active microbiomes of bacteria and fungi colonizing the roots and rhizosphere soil of oilseed rape to identify taxa assimilating plant-derived carbon following (CO2)-C-13 labeling. Root-and rhizosphere soil-associated communities of both bacteria and fungi differed from each other, and there were highly significant differences between their DNA-and RNA-based community profiles. Verrucomicrobia, Proteobacteria, Planctomycetes, Acidobacteria, Gemmatimonadetes, Actinobacteria, and Chloroflexi were the most active bacterial phyla in the rhizosphere soil. Bacteroidetes were more active in roots. The most abundant bacterial genera were well represented in both the C-13- and C-12-RNA fractions, while the fungal taxa were more differentiated. Streptomyces, Rhizobium, and Flavobacterium were dominant in roots, whereas Rhodoplanes and Sphingomonas (Kaistobacter) were dominant in rhizosphere soil. "Candidatus Nitrososphaera" was enriched in C-13 in rhizosphere soil. Olpidium and Dendryphion were abundant in the C-12-RNA fraction of roots; Clonostachys was abundant in both roots and rhizosphere soil and heavily C-13 enriched. Cryptococcus was dominant in rhizosphere soil and less abundant, but was C-13 enriched in roots. The patterns of colonization and C acquisition revealed in this study assist in identifying microbial taxa that may be superior competitors for plant-derived carbon in the rhizosphere of Brassica napus.

    IMPORTANCE This microbiome study characterizes the active bacteria and fungi colonizing the roots and rhizosphere soil of Brassica napus using high-throughput sequencing and RNA-stable isotope probing. It identifies taxa assimilating plant-derived carbon following (CO2)-C-13 labeling and compares these with other less active groups not incorporating a plant assimilate. Brassica napus is an economically and globally important oilseed crop, cultivated for edible oil, biofuel production, and phytoextraction of heavy metals; however, it is susceptible to several diseases. The identification of the fungal and bacterial species successfully competing for plant-derived carbon, enabling them to colonize the roots and rhizosphere soil of this plant, should enable the identification of microorganisms that can be evaluated in more detailed functional studies and ultimately be used to improve plant health and productivity in sustainable agriculture.

  • 50.
    Golparian, Daniel
    et al.
    WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, Swedish Reference Laboratory for Pathogenic Neisseria, Department of Laboratory Medicine, Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden .
    Boräng, Stina
    Department of Clinical Microbiology, Karolinska University Hospital, Huddinge, Sweden .
    Sundqvist, Martin
    Örebro University, School of Health and Medical Sciences, Örebro University, Sweden. WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, Swedish Reference Laboratory for Pathogenic Neisseria, Department of Laboratory Medicine, Microbiology.
    Unemo, Magnus
    Örebro University, School of Health and Medical Sciences, Örebro University, Sweden. WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, Swedish Reference Laboratory for Pathogenic Neisseria, Department of Laboratory Medicine, Microbiology.
    Evaluation of the New BD Max GC Real-Time PCR Assay, Analytically and Clinically as a Supplementary Test for the BD ProbeTec GC Qx Amplified DNA Assay, for Molecular Detection of Neisseria gonorrhoeae2015In: Journal of Clinical Microbiology, ISSN 0095-1137, E-ISSN 1098-660X, Vol. 53, no 12, 3935-3937 p.Article in journal (Refereed)
    Abstract [en]

    The new BD Max GC real-time PCR assay showed high clinical and analytical sensitivity and specificity. It can be an effective and accurate supplementary test for the BD ProbeTec GC Qx amplified DNA assay, which had suboptimal specificity, and might also be used for initial detection of Neisseria gonorrhoeae.

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