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  • 1.
    Ahlstrom, Christina A.
    et al.
    US Geol Survey, AK 99508 USA.
    Bonnedahl, Jonas
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology, Infection and Inflammation. Linköping University, Faculty of Medicine and Health Sciences. Kalmar Cty Council, Sweden.
    Woksepp, Hanna
    Kalmar Cty Hosp, Sweden.
    Hernandez, Jorge
    Kalmar Cty Hosp, Sweden.
    Reed, John A.
    US Geol Survey, AK 99508 USA.
    Tibbitts, Lee
    US Geol Survey, AK 99508 USA.
    Olsen, Bjoern
    Uppsala Univ, Sweden.
    Douglas, David C.
    US Geol Survey, AK USA.
    Ramey, Andrew M.
    US Geol Survey, AK 99508 USA.
    Satellite tracking of gulls and genomic characterization of faecal bacteria reveals environmentally mediated acquisition and dispersal of antimicrobial-resistant Escherichia coli on the Kenai Peninsula, Alaska2019In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 10, p. 2531-2545Article in journal (Refereed)
    Abstract [en]

    Gulls (Larus spp.) have frequently been reported to carry Escherichia coli exhibiting antimicrobial resistance (AMR E. coli); however, the pathways governing the acquisition and dispersal of such bacteria are not well described. We equipped 17 landfill-foraging gulls with satellite transmitters and collected gull faecal samples longitudinally from four locations on the Kenai Peninsula, Alaska to assess: (a) gull attendance and transitions between sites, (b) spatiotemporal prevalence of faecally shed AMR E. coli, and (c) genomic relatedness of AMR E. coli isolates among sites. We also sampled Pacific salmon (Oncorhynchus spp.) harvested as part of personal-use dipnet fisheries at two sites to assess potential contamination with AMR E. coli. Among our study sites, marked gulls most commonly occupied the lower Kenai River (61% of site locations) followed by the Soldotna landfill (11%), lower Kasilof River (5%) and upper Kenai River (amp;lt;1%). Gulls primarily moved between the Soldotna landfill and the lower Kenai River (94% of transitions among sites), which were also the two locations with the highest prevalence of AMR E. coli. There was relatively high spatial and temporal variability in AMR E. coli prevalence in gull faeces and there was no evidence of contamination on salmon harvested in personal-use fisheries. We identified E. coli sequence types and AMR genes of clinical importance, with some isolates possessing genes associated with resistance to as many as eight antibiotic classes. Our findings suggest that gulls acquire AMR E. coli at habitats with anthropogenic inputs and subsequent movements may represent pathways through which AMR is dispersed.

  • 2.
    Ahlstrom, Christina A.
    et al.
    US Geol Survey, AK 99508 USA.
    Ramey, Andrew M.
    US Geol Survey, AK 99508 USA.
    Woksepp, Hanna
    Kalmar Council, Sweden.
    Bonnedahl, Jonas
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology, Infection and Inflammation. Linköping University, Faculty of Medicine and Health Sciences. Kalmar Council, Sweden.
    Early emergence of mcr-1-positive Enterobacteriaceae in gulls from Spain and Portugal2019In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229Article in journal (Refereed)
    Abstract [en]

    We tested extended-spectrum beta-lactamase producing bacteria from wild gulls (Larus spp.) sampled in 2009 for the presence of mcr-1. We report the detection of mcr-1 and describe genome characteristics of four Escherichia coli and one Klebsiella pneumoniae isolate from Spain and Portugal that also exhibited colistin resistance. Results represent the earliest evidence for colistin-resistant bacteria in European wildlife.

  • 3.
    Ahlstrom, Christina A.
    et al.
    US Geol Survey, AK 99508 USA.
    Ramey, Andrew M.
    US Geol Survey, AK 99508 USA.
    Woksepp, Hanna
    Dept Dev and Publ and Hlth, Sweden.
    Bonnedahl, Jonas
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology, Infection and Inflammation. Linköping University, Faculty of Medicine and Health Sciences. Dept Infect Dis, Sweden.
    Repeated Detection of Carbapenemase-Producing Escherichia coil in Gulls Inhabiting Alaska2019In: Antimicrobial Agents and Chemotherapy, ISSN 0066-4804, E-ISSN 1098-6596, Vol. 63, no 8, article id e00758-19Article in journal (Refereed)
    Abstract [en]

    Here, we report the first detection of carbapenemase-producing Escherichia coli in Alaska and in wildlife in the United States. Wild bird (gull) feces sampled at three locations in Southcentral Alaska yielded isolates that harbored plasmidencoded bla(kpc-2), or chromosomally encoded bla(OXA-48) and genes associated with antimicrobial resistance to up to eight antibiotic classes.

  • 4.
    Atterby, Clara
    et al.
    Uppsala University, Sweden.
    Borjesson, Stefan
    National Vet Institute SVA, Sweden.
    Ny, Sofia
    Public Health Agency Sweden, Sweden; Karolinska Institute, Sweden.
    Jarhult, Josef D.
    Uppsala University, Sweden.
    Byfors, Sara
    Public Health Agency Sweden, Sweden.
    Bonnedahl, Jonas
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences. Linnaeus University, Sweden; Kalmar County Council, Sweden.
    ESBL-producing Escherichia coli in Swedish gulls: A case of environmental pollution from humans?2017In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, no 12, article id e0190380Article in journal (Refereed)
    Abstract [en]

    ESBL-producing bacteria are present in wildlife and the environment might serve as a resistance reservoir. Wild gulls have been described as frequent carriers of ESBL-producing E. coli strains with genotypic characteristics similar to strains found in humans. Therefore, potential dissemination of antibiotic resistance genes and bacteria between the human population and wildlife need to be further investigated. Occurrence and characterization of ESBL-producing E. coli in Swedish wild gulls were assessed and compared to isolates from humans, livestock and surface water collected in the same country and similar time-period. Occurrence of ESBL-producing E. coli in Swedish gulls is about three times higher in gulls compared to Swedish community carriers (17% versus 5%) and the genetic characteristics of the ESBL-producing E. coli population in Swedish wild gulls and Swedish human are similar. ESBL-plasmids IncF-and IncI1-type carrying ESBL-genes blaCTX-M-15 or blaCTX-M-14 were most common in isolates from both gulls and humans, but there was limited evidence of clonal transmission. Isolates from Swedish surface water harbored similar genetic characteristics, which highlights surface waters as potential dissemination routes between wildlife and the human population. Even in a low-prevalence country such as Sweden, the occurrence of ESBL producing E. coli in wild gulls and the human population appears to be connected and the occurrence of ESBL-producing E. coli in Swedish gulls is likely a case of environmental pollution.

  • 5.
    Backlund, Emma
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Assessment of ventricular morphology using echocardiography in Ornate tinamous (Nothoprocta ornata) and domestic chickens (Gallus domesticus)2014Independent thesis Basic level (degree of Bachelor), 10,5 credits / 16 HE creditsStudent thesis
    Abstract [en]

    The Ornate Tinamou (Nothoprocta ornata), an ancient bird, has adapted to life at high altitude (>2.400 m.a.s.l) for a longer period than the domestic chicken (Gallus domesticus), which came to South America with the Spanish conquerors. Ornate tinamous have a smaller heart in relation to body size than domestic chickens. This study was made to evaluate heart morphometric measurements comparing Ornate Tinamou and domestic chicken using echocardiography measurements to determine wall thickness and chamber size and to evaluate whether it can retrieve measurements consistent with previous results on dissected hearts. I was also interested in evaluating potential adaptations of the Ornate Tinamou to life in hypoxic environments by exposing the heart to positive inotropic stimulation. The results were compared with those previously obtained on dissected hearts. The results showed that the chamber size of the domestic chicken was significantly larger than in Ornate Tinamou, both in conscious and anesthetized birds. Injection of 1µg/kg isoproterenol caused domestic chickens’ systolic chamber size to decrease significantly and fractional shortening to increase significantly. The same changes were seen in the Ornate Tinamou but they were not significant. In conclusion, this study confirms that echocardiography is a valid method for retrieving cardiac measurements without euthanizing animals, opening for the possibility of taking several measurements at different ages.

  • 6.
    Baskar, Sushmitha
    et al.
    1Department of Environmental Science and Engineering, Guru Jambheshwar University of Science and Technology, Hisar, Haryana, India.
    Baskar, Ramanathan
    1Department of Environmental Science and Engineering, Guru Jambheshwar University of Science and Technology, Hisar, Haryana, India.
    Routh, Joyanto
    Department of Earth Sciences, IISER-Kolkata, Mohanpur, India / Department of Natural Sciences and Technology, MTM, Örebro University, Örebro, Sweden.
    Biogenic evidences of moonmilk deposition in the Mawmluh cave, Meghalaya, India2011In: Geomicrobiology Journal, ISSN 0149-0451, E-ISSN 1521-0529, Vol. 28, no 3, p. 252-265Article 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.

  • 7.
    Baskar, Sushmitha
    et al.
    Indira Gandhi National Open University, India; University of Bergen, Norway.
    Routh, Joyanto
    Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences.
    Baskar, Ramanathan
    Guru Jambheshwar University of Science and Technology, India.
    Kumar, Abhinav
    Indian Institute Science Educ and Research Kolkata, India.
    Miettinen, Hanna
    VTT Technical Research Centre Finland Ltd, Finland.
    Itaevaara, Merja
    VTT Technical Research Centre Finland Ltd, Finland.
    Evidences for Microbial Precipitation of Calcite in Speleothems from Krem Syndai in Jaintia Hills, Meghalaya, India2016In: Geomicrobiology Journal, ISSN 0149-0451, E-ISSN 1521-0529, Vol. 33, no 10, p. 906-933Article, review/survey (Refereed)
    Abstract [en]

    Speleothems from Krem Syndai, Meghalaya in Northeast India were studied for their microbial diversity using 16S rDNA-based phylogenetic approach and conventional microbiological techniques along with geochemistry, mineralogy and in vitro experiments to understand participation of microorganisms in CaCO3 precipitation. Speleothems imaged by scanning electron microscopy showed round coccoid-like, sporangia-like and spinose calcified structures, numerous broken cocci shells with spotted interiors inside a calcite crystal, honeycomb long reticulate, smooth, flat, twisted, ribbon-like, tubular, beaded, microbe-mineralized filaments and extracellular polymeric substances (EPS). Fourier spectroscopy indicated the presence of various organic compounds. C-13 and O-18 isotopic ratios of speleothems ranged from -4.65 to -7.34 parts per thousand and -3.06 to -6.80 parts per thousand, respectively. Total number of microbial cells using SYBR Gold was high. Fluorescence in situ hybridization (FISH) indicated approximately 3x 10(5) to 5x 10(5) cells g sed(-1) in the speleothems out of which the number of microbes belonging to Eubacteria ranged from 1.8x 10(5) to 3.6x 10(5) cells, g sed(-1). FISH showed approximate to 45% active microbial cells of the total cell number in samples. DNA-based high-throughput amplicon sequencing revealed 19 bacterial phyla in the speleothem. Approximately 42% of the sequences were similar to Proteobacteria (Alphaproteobacteria: 22.4%, Betaproteobacteria: 8.9%, Gammaproteobacteria: 8.6%). Sequences similar to Nitrospiraceae (22.8%) had the highest proportion of sequences belonging to a single family. Bacterial strains isolated from the speleothems raised alkalinity and precipitated calcite in the laboratory cultures which was confirmed by X-ray diffraction (XRD) analyses. These isolates belonged to Bacillus spp., Actinomycetes spp., Streptomyces spp., Pseudomonas spp., Micrococcus spp., Staphylococcus spp., Xanthobacter spp. and Arthrobacter spp. Overall, the results showed unequivocal evidence of bacterial fingerprints during CaCO3 precipitation in the cave.

  • 8.
    Benselfelt, Tobias
    Linköping University, Department of Physics, Chemistry and Biology, Biotechnology. Linköping University, The Institute of Technology.
    Flow Cytometry Sensor System Targeting Escherichia Coli as an Indicator of Faecal Contamination of Water Sources2014Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Poor water quality is a global health concern affecting one billion people around the world. It is important to monitor water sources in order to maintain the quality of our drinking water and to avoid disease outbreaks. Targeting Escherichia coli as a faecal indicator is a widely used procedure, but the current methods are time consuming and not adequate to prevent spreading of faecal influence.

     

    This Master thesis demonstrates the development of a near infrared fluorescence flow cytometer sensor system targeting Escherichia coli, using fluorescently labeled chicken IgY antibodies. The near infrared light was chosen to avoid fluorescence from blue-green algae that are present in the water source.

     

    The hardware was developed with a 785  nm laser line to detect Alexa Fluor 790 labeled antibodies, using a photomultiplier tube or two different CMOS cameras. The antibodies were labeled using a commercial labeling kit, and evaluated using antibody binding assays and the developed hardware.

     

    The IgY antibodies were successfully labeled with Alexa Fluor 790 and the function was maintained after the labeling process. The result demonstrates the principles of the sensor system and how it solved to the problem with fluorescence from blue-green algae. An aperture was used to overcome the suboptimal laser and filter setup, and to increase the sensitivity of the system. However, only a small fraction of the cells could be detected, due to challenges with the focal depth and loss of sensitivity in the photomultiplier tube at near infrared wavelengths. Further development is required to create a working product.

  • 9.
    Bialowas, Sonja
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Health Sciences.
    Hagbom, Marie
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Health Sciences.
    Karlsson, Thommie
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Health Sciences.
    Nordgren, Johan
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Health Sciences.
    Sharma, Sumit
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Health Sciences.
    Magnusson, Karl-­Eric
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Health Sciences.
    Svensson, Lennart
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Health Sciences.
    Intracellularly expressed rotavirus NSP4 stimulates release of serotonin (5-HT) from human enterochromaffin cellsManuscript (preprint) (Other academic)
    Abstract [en]

    Rotavirus (RV) is associated with diarrhoea and vomiting, but the mechanisms behind these symptoms remain unresolved. While RV have been shown to infect and stimulate secretion of serotonin (5-hydroxytryptamine; 5-HT) from human enterochromaffin (EC) cells and to infect EC cells in the small intestine of mice, it remains to identify which intracellularly expressed viral protein (VP) being responsible for this novel property.

    To address this issue, human EC cells were transfected with small interfering RNA (siRNA) targeting the structural (VP4, VP6 and VP7) and the non-structural protein 4 (NSP4) followed by infection with Rhesus rotavirus (RRV). siRNA specific to NSP4 (siRNANSP4) significantly attenuated secretion of 5-HT compared to siRNAVP4, siRNAVP6 , siRNAVP7 and non-targeting (Nt) siRNAnt. Intracellular calcium clamping with BABTA/AM showed that intracellularly expressed NSP4-stimulated secretion of 5-HT from EC cells was calcium-dependent. Furthermore RV down-regulated the 5-HT transporter (SERT) mRNA in ileum but not tryptophan hydroxylase 1 (TPH1) mRNA the rate-limiting enzyme for 5-HT synthesis. The unaffected expression of TPH1 mRNA in the intestinal segments suggests that release of 5- HT primarily originates from pre-made 5-HT rather than from newly synthesised 5-HT mRNA. Moreover, down-regulation of SERT mRNA in ileum presumably resulted in reduced re- uptake of 5-HT by SERT to EC cells and thus increased extracellular 5-HT in the small intestine. Moreover, 7/7 infant mice responded following intraperitoneal administration of 5-HT with rapid (<30 min) diarrhoea in dose-dependent manner. In the light of these results and the fact that both 5-HT and NSP4 can induce diarrhoea in mice, a disease mechanism to RV diarrhoea is proposed.

  • 10.
    Börjesson, Stefan
    Linköping University, Department of Clinical and Experimental Medicine, Medical Microbiology . Linköping University, Faculty of Health Sciences.
    Antibiotic Resistance in Wastewater: Methicillin-resistant Staphylococcus aureus (MRSA)and antibiotic resistance genes2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    A large part of the antibiotics consumed ends up in wastewater, and in the wastewater the antibiotics may exert selective pressure for or maintain resistance among microorganisms. Antibiotic resistant bacteria and genes encoding antibiotic resistance are commonly detected in wastewater, often at higher rates and concentrations compared to surface water. Wastewater can also provide favourable conditions for the growth of a diverse bacterial community, which constitutes a basis for the selection and spread of antibiotic resistance. Therefore, wastewater treatment plants have been suggested to play a role in the dissemination and development of antibiotic resistant bacteria. Methicillin-resistant Staphylococcus aureus (MRSA) is a large problem worldwide as a nosocomial pathogen, but knowledge is limited about occurrence in non-clinical environments, such as wastewater, and what role wastewater plays in dissemination and development of MRSA.

     

    In this thesis we investigated the occurrence of MRSA in a full-scale wastewater treatment plant (WWTP). We also investigated the concentration of genes encoding resistance to aminoglycosides (aac(6’)-Ie+aph(2’’)), β-lactam antibiotics (mecA) and tetracyclines (tetA and tetB) in three wastewater-associated environments: (1) soil from an overland flow area treating landfill leachates, (2) biofilm from a municipal wastewater treatment plant, and (3) sludge from a hospital wastewater pipeline. In addition, concentrations of mecA, tetA and tetB were investigated over the treatment process in the WWTP. These investigations were performed to determine how the prevalence and concentration of MRSA and the antibiotic resistence genes are affected in wastewater and wastewater treatment processes over time. The occurrence of MRSA was investigated by cultivation and a commercially available real-time PCR assay. In order to determine concentrations of the genes aac(6’)-Ie+aph(2’’), mecA, tetA and tetB in wastewater we developed a LUXTM real-time PCR assay for each gene.

     

    Using cultivation and real-time PCR we could for the first time describe the occurrence of MRSA in wastewater and show that it had a stable occurrence over time in a WWTP. MRSA could mainly be detected in the early treatment steps in the WWTP, and the wastewater treatment process reduced the number and diversity of cultivated MRSA. However, our results also indicate that the treatment process selects for strains with more extensive resistance and possibly higher virulence. The isolated wastewater MRSA strains were shown to have a close genetic relationship to clinical isolates, and no specific wastewater lineages could be detected, indicating that they are a reflection of carriage in the community. Taken together, these data indicate that wastewater may be a potential reservoir for MRSA and that MRSA are more prevalent in wastewater than was previously thought.

     

    The real-time PCR assays, for aac(6’)-Ie+aph(2’’), mecA, tetA, and tetB that we developed, were shown to be sensitive, fast, and reproducible methods for detection and quantification of these genes in wastewater environments. The highest concentrations of all genes were observed in the hospital pipeline, and the lowest in the overland flow system, with tetA and aac(6´)-Ie+aph(2´´) detected in all three environments. In the full-scale WWTP, we continuously detected mecA, tetA and tetB over the treatment process and over time. In addition, it was shown that the treatment process reduces concentrations of all three genes. The data presented in this thesis also indicate that the reduction for all three genes may be connected to the removal of biomass, and in the reduction of tetA and tetB, sedimentation and precipitation appear to play an important role.

    List of papers
    1. Quantification of genes encoding resistance to aminoglycosides, β-lactams and tetracyclines in wastewater environments by real-time PCR
    Open this publication in new window or tab >>Quantification of genes encoding resistance to aminoglycosides, β-lactams and tetracyclines in wastewater environments by real-time PCR
    Show others...
    2009 (English)In: International Journal of Environmental Health Research, ISSN 0960-3123, E-ISSN 1369-1619, p. 1-12Article in journal (Refereed) Published
    Abstract [en]

    In this study real-time PCR assays, based on the LUX-technique, were developed for quantification of genes mediating resistance to aminoglycosides [aac(6 ')-Ie + aph(2 ' ')], beta-lactams (mecA), and tetracyclines (tetA and tetB), for use in wastewater environments. The developed assays were applied on DNA extracted from three wastewater-associated environments: soil from an overland flow area treating landfill leachates, biofilm from a municipal wastewater treatment plant, and sludge from a hospital wastewater pipeline. The highest concentration of all genes was observed in the hospital pipeline and the lowest in the overland flow system. TetA and aac(6 ')-Ie + aph(2 ' ') could be detected in all environments. The tetB gene was detected in the overland flow area and the hospital wastewater pipeline and mecA was detected in the wastewater treatment plant and the hospital pipeline. The developed LUX real-time PCR assays were shown to be fast and reproducible tools for detection and quantification of the four genes encoding antibiotic resistance in wastewater.

    Place, publisher, year, edition, pages
    Taylor & Francis, 2009
    Keywords
    Water pollutants; sewage pollution; water quality; aac(6')-Ie + aph(2''); mecA; tetA; tetB; LUX™ real-time PCR
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:liu:diva-18293 (URN)10.1080/09603120802449593 (DOI)19370439 (PubMedID)
    Available from: 2009-05-15 Created: 2009-05-15 Last updated: 2017-12-13Bibliographically approved
    2. A seasonal study of the mecA gene and Staphylococcus aureus including methicillin-resistant S. aureus in a municipal wastewater treatment plant
    Open this publication in new window or tab >>A seasonal study of the mecA gene and Staphylococcus aureus including methicillin-resistant S. aureus in a municipal wastewater treatment plant
    2009 (English)In: Water Research, ISSN 0043-1354, E-ISSN 1879-2448, Vol. 43, no 4, p. 925-932Article in journal (Refereed) Published
    Abstract [en]

    The spread of methicillin-resistant Staphylococcus aureus (MRSA), in which the mecA gene mediates resistance, threatens the treatment of staphylococcal diseases. The aims were to determine the effect of wastewater treatment processes on mecA gene concentrations, and the prevalence of S. aureus and MRSA over time. To achieve this a municipal wastewater treatment plant was investigated for the mecA gene, S. aureus and MRSA, using real-time PCR assays. Water samples were collected monthly for one year, at eight sites in the plant, reflecting different aspects of the treatment process. The mecA gene and S. aureus could be detected throughout the year at all sampling sites. MRSA could also be detected, but mainly in the early treatment steps. The presence of MRSA was verified through cultivation from inlet water. The concentration of the mecA gene varied between months and sampling sites, but no obvious seasonal variation could be determined. The wastewater treatment process reduced the mecA gene concentration in most months. Taken together our results show that the mecA gene, S. aureus and MRSA occur over the year at all sites investigated.

    Keywords
    Methicillin-resistant, Staphylococcus aureus, mecA, LUX (TM) real-time PCR, spa Typing, Wastewater treatment plant, Seasonal study
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:liu:diva-17599 (URN)10.1016/j.watres.2008.11.036 (DOI)19084256 (PubMedID)
    Note
    Original Publication: Stefan Börjesson, Sara Melin, Andreas Matussek and Per-Eric Lindgren, A seasonal study of the mecA gene and Staphylococcus aureus including methicillin-resistant S. aureus in a municipal wastewater treatment plant, 2009, Water Research, (43), 4, 925-932. http://dx.doi.org/10.1016/j.watres.2008.11.036 Copyright: Elsevier Science B.V., Amsterdam. http://www.elsevier.com/ Available from: 2009-07-09 Created: 2009-04-06 Last updated: 2017-12-13Bibliographically approved
    3. Methicillin-resistant Staphylococcus aureus (MRSA) in municipal wastewater: An uncharted threat?
    Open this publication in new window or tab >>Methicillin-resistant Staphylococcus aureus (MRSA) in municipal wastewater: An uncharted threat?
    Show others...
    (English)Manuscript (Other academic)
    Abstract [en]

    Methicillin-resistant S. aureus (MRSA) was recently detected in municipal wastewater, why there is a need for further studies to elucidate if MRSA in wastewater constitutes a health risk, and to determine how wastewater treatment processes affects MRSA. We cultivated MRSA from a full-scale wastewater treatment plant to characterise the indigenous MRSA-flora and to investigate how the wastewater treatment process affects the clonal distribution. MRSA isolates were characterised using spa typing, antibiograms, SSCmec typing and detection of Panton Valentine leukocidin (PVL) genes. We found that the wastewater MRSA-flora has a close genetic relationship to clinical isolates, but we also isolated novel spa types, primarily from the activated sludge treatment step. The number of isolates and the diversity of MRSA are reduced by the treatment process, but the process also selects for more extensive antibiotic resistant strains as well as for PVL positive strains.

    Keywords
    Staphylococcus aureus, MRSA, methicillin, β-lactam, SCCmec, spa typing, Panton Valentine leukocidin, PVL, antibiotic resistance, antibiogram
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:liu:diva-18295 (URN)
    Available from: 2009-05-15 Created: 2009-05-15 Last updated: 2010-01-14Bibliographically approved
    4. Genes encoding tetracycline resistance in a full-scale municipal wastewater treatment plant investigated during one year
    Open this publication in new window or tab >>Genes encoding tetracycline resistance in a full-scale municipal wastewater treatment plant investigated during one year
    (English)Manuscript (Other academic)
    Abstract [en]

    Tetracycline-resistant bacteria and genes encoding tetracycline resistance are common in anthropogenic environments. We studied how wastewater treatment affects the prevalence and concentration of two genes that encode resistance to tetracycline: tetA and tetB. Using real-time PCR we analysed wastewater samples collected monthly for one year at eight key-sites in a full-scale municipal wastewater treatment plant (WWTP). We detected tetA and tetB at each sampling site and the concentration of both genes, expressed per wastewater volume or per total-DNA, decreased over the treatment process. The reduction of tetA and tetB was partly the result of the sedimentation process. The ratio of tetA and tetB, respectively, to total DNA was lower in or after the biological processes. Taken together our data show that tetracycline resistance genes occur throughout the WWTP and that the concentrations are reduced under conventional operational strategies. However, it is not possible to conclude the eventual risk for humans with respect to resistance spreading.

    Keywords
    tetA, tetB, tetracycline, LUXTM real-time PCR, wastewater treatment plant
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:liu:diva-18296 (URN)
    Available from: 2009-05-15 Created: 2009-05-15 Last updated: 2010-01-14Bibliographically approved
  • 11.
    Collins, Matthew D.
    et al.
    School of Food Biosciences, University of Reading, Whiteknights, Reading RG6 6AP, UK.
    Routh, Joyanto
    Department of Geology and Geochemistry, Stockholm University, Stockholm, Sweden .
    Saraswathy, Ambujom
    Department of Geology and Geochemistry, Stockholm University, Stockholm, Sweden .
    Lawson, Paul A.
    School of Food Biosciences, University of Reading, Whiteknights, Reading RG6 6AP, UK.
    Schumann, Peter
    DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany.
    Welinder-Olsson, Christina
    Culture Collection, Department of Clinical Bacteriology, University of Göteborg, Göteborg, Sweden.
    Falsen, Enevold
    Culture Collection, Department of Clinical Bacteriology, University of Göteborg, Göteborg, Sweden.
    Arsenicicoccus bolidensis gen. nov., sp. nov., a novel actinomycete isolated from contaminated lake sediment2004In: International Journal of Systematic and Evolutionary Microbiology, ISSN 1466-5026, E-ISSN 1466-5034, Vol. 54, no 2, p. 605-608Article in journal (Refereed)
    Abstract [en]

    An unknown Gram-positive, catalase-positive, facultatively anaerobic, non-spore-forming, coccus-shaped bacterium originating from sediment was characterized using phenotypic, molecular chemical and molecular phylogenetic methods. Chemical studies revealed the presence of a cell-wall murein based on ll-diaminopimelic acid (type ll-Dpm-glycine1), a complex mixture of saturated, monounsaturated and iso- and anteiso-methyl-branched, non-hydroxylated, long-chain cellular fatty acids and tetrahydrogenated menaquinones with eight isoprene units [MK-8(H4)] as the major respiratory lipoquinone. This combination of characteristics somewhat resembled members of the suborder Micrococcineae, but did not correspond to any currently described species. Comparative 16S rRNA gene sequencing confirmed that the unidentified coccus-shaped organism is a member of the Actinobacteria and represents a hitherto-unknown subline related to, albeit different from, a number of taxa including Intrasporangium, Janibacter, Terrabacter, Terracoccus and Ornithinicoccus. Based on phenotypic and phylogenetic considerations, it is proposed that the unknown bacterium originating from lake sediment be classified as a new genus and species, Arsenicicoccus bolidensis gen. nov., sp. nov. (type strain CCUG 47306T=DSM 15745T).

  • 12.
    Dzidic, Majda
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Neuro and Inflammation Science. Linköping University, Faculty of Medicine and Health Sciences. CSISP FISABIO, Spain; Inst Agrochem and Food Technol IATA CSIC, Spain.
    Collado, Maria C.
    Inst Agrochem and Food Technol IATA CSIC, Spain.
    Abrahamsson, Thomas
    Linköping University, Department of Clinical and Experimental Medicine, Division of Children's and Women's health. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Center of Paediatrics and Gynaecology and Obstetrics, H.K.H. Kronprinsessan Victorias barn- och ungdomssjukhus.
    Artacho, Alejandro
    CSISP FISABIO, Spain.
    Stensson, Malin
    Jonkoping Univ, Sweden.
    Jenmalm, Maria
    Linköping University, Department of Clinical and Experimental Medicine, Division of Neuro and Inflammation Science. Linköping University, Faculty of Medicine and Health Sciences.
    Mira, Alex
    CSISP FISABIO, Spain.
    Oral microbiome development during childhood: an ecological succession influenced by postnatal factors and associated with tooth decay2018In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 12, no 9, p. 2292-2306Article in journal (Refereed)
    Abstract [en]

    Information on how the oral microbiome develops during early childhood and how external factors influence this ecological process is scarce. We used high-throughput sequencing to characterize bacterial composition in saliva samples collected at 3, 6, 12, 24 months and 7 years of age in 90 longitudinally followed children, for whom clinical, dietary and health data were collected. Bacterial composition patterns changed through time, starting with "early colonizers", including Streptococcus and Veillonella; other bacterial genera such as Neisseria settled after 1 or 2 years of age. Dental caries development was associated with diverging microbial composition through time. Streptococcus cristatus appeared to be associated with increased risk of developing tooth decay and its role as potential biomarker of the disease should be studied with species-specific probes. Infants born by C-section had initially skewed bacterial content compared with vaginally delivered infants, but this was recovered with age. Shorter breastfeeding habits and antibiotic treatment during the first 2 years of age were associated with a distinct bacterial composition at later age. The findings presented describe oral microbiota development as an ecological succession where altered colonization pattern during the first year of life may have long-term consequences for childs oral and systemic health.

  • 13.
    Fredriksson (numera: Björn), Annika
    et al.
    Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences.
    Nestor, Gustav
    Linköping University, Department of Thematic Studies, Department of Water and Environmental Studies. Linköping University, Department of Thematic Studies, Tema Environmental Change.
    Svensson, Bo H.
    Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences.
    Effects of an organotin PVC stabiliser on anoxic degradation of organic matter2003In: Vatten, ISSN 0042-2886, Vol. 59, no 4, p. 271-277Article in journal (Refereed)
    Abstract [en]

    Many organotin compounds are toxic, thus their occurrence in the environment is of considerable concern, and several of these substances are regarded as priority pollutants that require further investigation. Organotins are used primarily as heat stabilisers in PVC plastic, and they are therefore found in landfills in which discarded PVC products have been deposited. In an earlier study, it was found that a widely used methyl tin PVC stabiliser inhibited microbial generation of CH4during anoxic degradation, and the objective of the present study was to elucidate possible mechanisms of such inhibition. CH4 and fermentation products were measured continuously for a period of 219 days in waste material amended with a methyl tin stabiliser. The results show that CH4 formation was retarded for 84-198 days during fermentation of the waste material. Furthermore, it seemed that not only the methyl tins, but also their sulphur organic ligands, play an important role in retarding the formation of CH4. The methyl tin stabiliser apparently affected both the fermentative organisms that provided the substrate for the methanogens, as well as the methanogens.

  • 14.
    Generó, Magalí Martí
    et al.
    Linköping University, The Tema Institute, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences.
    Juottonen, Heli
    MEM-group, Department of Biosciences, University of Helsinki, Helsinki, Finland.
    Robroek, Bjorn J.M.
    Ecology and Biodiversity Group, Institute of Environmental Biology, Utrecht University, CH Utrecht, The Netherlands.
    Yrjälä, Kim
    MEM-group, Department of Biosciences, University of Helsinki, Helsinki, Finland.
    Danielsson, Åsa
    Linköping University, The Tema Institute, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences.
    Lindgren, Per-Eric
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Health Sciences.
    Svensson, Bo
    Linköping University, The Tema Institute, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences.
    Nitrogen and methanogen community composition within and among three Sphagnum dominated peatlands in Scandinavia2015In: Soil Biology and Biochemistry, ISSN 0038-0717, E-ISSN 1879-3428, Vol. 81, p. 204-211Article in journal (Refereed)
    Abstract [en]

    Ombrotrophic raised bogs are nutrient poor acidic peatlands accumulating organic matter. They are widely spread on northern latitudes and are substantial sources of methane emissions to the atmosphere being of great concern from a climate change perspective. We investigated the methanogen community composition along microtopographic gradients within three bogs in Scandinavia, receiving different amounts of nitrogen precipitation. Methanogenic community analyses by terminal restriction fragment length polymorphism of the mcrA gene showed different profiles among the three sites, while no in- fluence of the microtopographic gradients was observed. Peat temperature and dissolved organic carbon were the major edaphic variables explaining 38% of the variation of the methanogenic community di- versity among the bogs. The family Methanoregulaceae (hydrogenotrophic methanogens) showed the largest relative proportion and highest activity in all three sites. Quantitative PCR of the mcrA gene and transcripts showed that the most northern site, receiving the lowest atmospheric nitrogen load, had significantly lower abundance and activity of methanogens (4.7 106 and 2.4 104 mcrA copies per gram of soil, respectively), compared to the most southern site (8.2 107 and 4.6 105 mcrA copies per gram of soil, respectively), receiving the highest nitrogen load. No patterns of the mcrA gene and tran- script abundances were observed along the microtopography. The results indicated that the difference in occurrence of methanogens is mainly due to geoclimatological conditions rather than site intrinsic microtopographic variation. The study further suggests that environmental changes on the site intrinsic topography will not affect the methanogenic activity, while increasing average temperatures in Scan- dinavian ombrotrophic raised bogs might contribute to an increase of the methanogenic archaeal activity resulting in an increase of methane production. 

  • 15.
    Gerebring, Linnéa
    Linköping University, Department of Physics, Chemistry and Biology.
    Yeast Saccharomyces cerevisiae strain isolated from lager beer shows tolerance to isobutanol.2016Independent thesis Basic level (degree of Bachelor), 10,5 credits / 16 HE creditsStudent thesis
    Abstract [en]

    The development of biofuels has received much attention due to the global warming and limited resources associated with fossil fuels. Butanol has been identified as a potential option due to its advantages over ethanol, for example higher energy density, compatibility with current infrastructure and its possibility to be blended with gasoline at any ratio. Yeast Saccharomyces cerevisiae can be used as a producer of butanol. However, butanol toxicity to the host limits the yield produced. In this study, four strains of yeast isolated from the habitats of lager beer, ale, wine and baker ́s yeast were grown in YPD media containing isobutanol concentrations of 1.5 %, 2 %, 3 % and 4 %. Growth was measured to determine the most tolerant strain. Gene expression for the genes RPN4, RTG1 and ILV2 was also measured, to determine its involvement in butanol stress. The genes have in previous studies seen to be involved in butanol tolerance or production, and the hypothesis was that they all should be upregulated in response to butanol exposure. It was found that the yeast strain isolated from lager beer was most tolerant to isobutanol concentrations of 2 % and 3 %. It was also found that the gene RPN4 was upregulated in response to isobutanol stress. There was no upregulation of RTG1 or ILV2, which was unexpected. The yeast strain isolated from lager beer and the gene RPN4 is proposed to be investigated further, to be able to engineer a suitable producer of the biofuel butanol. 

  • 16.
    Ghosh, Devanita
    Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences.
    Distribution and Biogeochemical Cycling of Arsenic In Grey and Brown Sand Aquifers in the Bengal Delta Plains (India)2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    An elevated level of Arsenic (As) in aquifers from India and Bangladesh affecting the human health has been widely reported since the late 1980s. The thesis aim is to investigate the present status of As contamination and biogeochemical cycling with direct role of diverse indigenous bacterial communities in As cycling in the Bengal Delta Plain (BDP) aquifers in Nadia district, West Bengal (India). The As(III) oxidizing bacterial communities were predominant in grey sand aquifers (GSA), but were characteristically absent in brown sand aquifers (BSA). Rainwater recharge containing inorganic and organic dissolved compounds played an important role in shaping the different groups of bacterial phenotypes. It included thearsenite-oxidizing bacteria as revealed by the aioA and 16S rRNA phylogeny. These bacterial communities in BDP groundwater were assumed to utilize the dissolved and sedimentary organic carbon (DOC and SOC) as the primary carbon source for respiration, and remobilization/immobilization of As involving reductive dissolution of iron oxyhydroxides. Hence, sediment and groundwater of these aquifer waters were characterized for their different inorganic constituents (metals) and organic compound classes. There were notable differences between the groundwater DOC and SOC pools. The only similarity between these carbon pools is presence of petroleum-derived hydrocarbons. The SOC in BSA has good correlation with the clay and silt-rich fraction. Notably, As formed complexes with iron, but not manganese. Biomarker characterization in sediments showed presence of terrigenous inputs along with petroleum-derived hydrocarbons. However, these hydrocarbons were absent in BSA sediments, and so were the arsenite oxidizing bacterial communities. Although DOC in groundwater plays an important role in sustaining the microorganisms, the contrasting character of SOC in BSA and GSA strongly influence the shaping of microbial community structure and biogeochemical cycling of As. This particularly affects the natural ‘safe’ drinking water capacity. Overall, the study gives a new directionfor long-term research on As biogeochemical cycling in the contaminated BDP aquifers.

    List of papers
    1. Arsenic Contamination in Soil and Sediment in India: Sources, Effects, and Remediation
    Open this publication in new window or tab >>Arsenic Contamination in Soil and Sediment in India: Sources, Effects, and Remediation
    2015 (English)In: Current Pollution Reports, ISSN 2198-6592, Vol. 1, no 1, p. 35-46Article in journal (Refereed) Published
    Abstract [en]

    Arsenic contamination is turning out to be a major problem these days with its area coverage and the number of people affected directly or indirectly. Now, the level of the contaminant has spread over the soil and sediments from groundwater and other natural sources. Arsenic poisoning in groundwater events is familiar to the world, but the consequences of soil contamination are still unrevealed to the community, specially the people of contaminated counties. Arsenic is a serious instantaneous concern for the people and other life forms regarding the poisoning through crops and vegetables. Many remediation technologies that mainly include physical, chemical, and a few biological methods have been evolved with time to check its effects. The physical and chemical methods for this purpose are often inefficient and/or very expensive, mainly limited to application in aqueous systems, and produce toxic sludge, which again becomes a matter of concern. But bioremediation relies on the fact that biological organisms have the ability to degrade, detoxify, and even accumulate harmful chemicals and offers attractive perspectives for biomonitoring (via biosensors), treatment of wastewater, and the recycling of polluted soils.

    Place, publisher, year, edition, pages
    Springer, 2015
    National Category
    Environmental Sciences Soil Science Water Engineering Geochemistry Water Treatment Environmental Sciences related to Agriculture and Land-use
    Identifiers
    urn:nbn:se:liu:diva-126596 (URN)10.1007/s40726-015-0004-2 (DOI)
    Available from: 2016-03-31 Created: 2016-03-31 Last updated: 2018-03-23Bibliographically approved
    2. Diversity of arsenite oxidizing bacterial communities in arsenic-rich deltaic aquifers in West Bengal, India
    Open this publication in new window or tab >>Diversity of arsenite oxidizing bacterial communities in arsenic-rich deltaic aquifers in West Bengal, India
    2014 (English)In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 5, no 602, p. 1-14Article in journal (Refereed) Published
    Abstract [en]

    High arsenic (As) concentration in groundwater has affected human health, particularly in South-East Asia putting millions of people at risk. Biogeochemical cycling of As carried out by different bacterial groups are suggested to control the As fluxes in aquifers. A functional diversity approach in link with As precipitation was adopted to study bacterial community structures and their variation within the As contaminated Bengal Delta Plain (BDP) aquifers of India. Groundwater samples collected from two shallow aquifers in Karimpur II (West Bengal, India), during years 2010 and 2011, were investigated to trace the effects immediately after monsoon period (precipitation) on community structure and diversity of bacterial assemblages with a focus on arsenite oxidizing bacterial phyla for two successive years. The study focused on amplification, clone library generation and sequencing of the arsenite oxidase large sub-unit gene aioA and 16S rRNA marker, with respect to changes in elemental concentrations. New set of primers were designed to amplify the aioA gene as a phylogenetic marker to study taxonomically diverse arsenite oxidizing bacterial groups in these aquifers. The overall narrow distribution of bacterial communities based on aioA and 16S rRNA sequences observed was due to poor nutrient status and anoxic conditions in these As contaminated aquifers. Proteobacteria was the dominant phylum detected, within which Acidoyorax, Hydrogenophaga, Albidiferax, Bosea, and Polymorphum were the major arsenite oxidizing bacterial genera based on the number of clones sequenced. The structure of bacterial assemblages including those of arsenite oxidizing bacteria seems to have been affected by increase in major elemental concentrations (e.g., As, Fe, S, and Si) within two sampling sessions, which was supported by statistical analyses. One of the significant findings of this study is detection of novel lineages of 16S rRNA-like bacterial sequences indicating presence of indigenous bacterial communities BDP wells that can play important role in biogeochemical cycling of elements including As.

    Place, publisher, year, edition, pages
    Frontiers, 2014
    Keywords
    Arsenic; aquifer; arsenite oxidation; aioA gene; phylogeny
    National Category
    Earth and Related Environmental Sciences
    Identifiers
    urn:nbn:se:liu:diva-113200 (URN)10.3389/fmicb.2014.00602 (DOI)000345856200001 ()25484877 (PubMedID)
    Note

    Funding Agencies|Swedish Research Link-Asia Program; Department of Science and Technology (DST), Government of India; DST

    Available from: 2015-01-13 Created: 2015-01-12 Last updated: 2017-12-05
    3. Characterization and microbial utilization of dissolved lipid organic fraction in arsenic impacted aquifers (India)
    Open this publication in new window or tab >>Characterization and microbial utilization of dissolved lipid organic fraction in arsenic impacted aquifers (India)
    2015 (English)In: Journal of Hydrology, ISSN 0022-1694, E-ISSN 1879-2707, Vol. 527, p. 221-233Article in journal (Refereed) Published
    Abstract [en]

    The coupled role of organic matter (OM) and microbial activity is widely acknowledged in arsenic (As) biogeochemical cycling in sedimentary environments. However, little is known about OM characteristics particularly the dissolved fraction in the Bengal Delta Plain aquifers – one of the worst As impacted regions in the world. Ongoing investigations in As-rich aquifers in Nadia district (West Bengal, India) indicate presence of arsenite As(III) oxidizing bacterial communities in the Grey Sand Aquifers (GSA), but absent in Brown Sand Aquifers (BSA). In this study, we investigate the key differences in dissolved organic carbon (DOC) characteristics and its relationship with differences in elemental concentrations, distribution of biomarkers, and utilization of DOC by in situ microbial communities in BSA and GSA. We demonstrate a new approach using ENVI™ C-18 DSK discs to pre-concentrate DOC from large volumes of water, and further extract the OM and separate it into different lipid fractions using the solid phase extraction technique. The aquifers show marked heterogeneity in terms of their DOC characteristics and elemental profiles irrespective of their grey or brown color. DOC indicates variable inputs of terrestrial derived OM sources, and OM derived from decomposition and/or microbial cellular components. DOC in the aquifers consist of predominantly n-alkanoic acids (∌80%) followed by n-alkanes and n-alcohols. The GSAs indicate high iron (Fe) and manganese (Mn) concentrations, and presence of mature petroleum derived hydrocarbons in DOC. BSA has comparatively lower concentrations of Fe and Mn, and shows absence of mature hydrocarbons in DOC. Experiments in presence of indigenous bacteria from groundwater with DOC lipid extracts as the sole carbon source indicate higher growth in the GSA samples implying preferential use of DOC. The potential availability of DOC in these aquifers can influence the community composition of indigenous heterotrophic microbial flora, which in turn can affect elemental cycles including that of As.

    Keywords
    Arsenic, Aquifers, DOC, Microbes, Aquatic biomarkers
    National Category
    Geochemistry Water Treatment Analytical Chemistry Microbiology Water Engineering Environmental Sciences
    Identifiers
    urn:nbn:se:liu:diva-126597 (URN)10.1016/j.jhydrol.2015.04.051 (DOI)000358629100021 ()
    Available from: 2016-03-31 Created: 2016-03-31 Last updated: 2018-03-19Bibliographically approved
    4. Elemental and biomarker characteristics in a Pleistocene aquifer vulnerable to arsenic contamination in the Bengal Delta Plain, India
    Open this publication in new window or tab >>Elemental and biomarker characteristics in a Pleistocene aquifer vulnerable to arsenic contamination in the Bengal Delta Plain, India
    2015 (English)In: Applied Geochemistry, ISSN 0883-2927, E-ISSN 1872-9134, Vol. 61, p. 87-98Article in journal (Refereed) Published
    Abstract [en]

    An elevated level of arsenic (As) in the Indo-Gangetic delta plain aquifers has been reported since the 1990s. Organic matter (OM) present in groundwater and aquifer sediments supports the microbial communities in these aquifers. During installation of a drinking water well, 26 sediment intervals of 6 m each were retrieved up till 156 m from a Pleistocene brown sand aquifer (BSA). Grain size distribution, sequential extraction of metals and total extractable lipids were analyzed in each sample. These parameters were statistically correlated in order to establish relationship between the physical vs. inorganic and organic characteristics, and how these properties affected the distribution of As in BSAs. The aquifer sediments consisted of medium to coarse sand except the surface sediments and those at the bottom of the well, which had high clay and slit content. Arsenic (As) concentration in sediments ranged from 2 to 21 mg/kg and indicated a strong correlation with grain size. Arsenic was mostly associated with crystalline oxides and silicate-rich minerals. Arsenic showed significant correlation with Fe in all fractions, and suggests presence of pyrite bound As-bearing minerals in these sediments. The diagnostic sedimentary lipid biomarkers indicated presence of compounds derived from vascular plants and microbial cell wall. This inference was supported by various diagnostic lipid ratios. The biomarkers were abundant in surface and deeper layers, which had high clay and silt content. The BSA sediments indicated preferential preservation of n-alkanes over other functional compounds, which were more reactive and subject to degradation. The thick clay layer at 132-156 m contained visible plant fragments, and OM in this layer indicated preferential preservation of organic carbon most likely due to the absence of specific microbial communities that degraded these compounds and mobilized As. Statistical analyses indicated the influence of selective inorganic and organic components (As, Fe and fatty acids) controlling the co-distribution of various inorganic and organic components in the aquifer.

    Place, publisher, year, edition, pages
    PERGAMON-ELSEVIER SCIENCE LTD, 2015
    National Category
    Earth and Related Environmental Sciences
    Identifiers
    urn:nbn:se:liu:diva-122048 (URN)10.1016/j.apgeochem.2015.05.007 (DOI)000360654200008 ()
    Note

    Funding Agencies|Department of Science and Technology, Government of India; Swedish Research Link-Asia Program [2009-6470]; Linkoping University, Sweden

    Available from: 2015-12-18 Created: 2015-10-19 Last updated: 2017-12-01
  • 17.
    Ghosh, Devanita
    et al.
    Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences. Laboratory of Integrative Taxonomy and Molecular Ecology, Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India.
    Routh, Joyanto
    Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences.
    Bhadury, Punyasloke
    Laboratory of Integrative Taxonomy and Molecular Ecology, Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India.
    Characterization and microbial utilization of dissolved lipid organic fraction in arsenic impacted aquifers (India)2015In: Journal of Hydrology, ISSN 0022-1694, E-ISSN 1879-2707, Vol. 527, p. 221-233Article in journal (Refereed)
    Abstract [en]

    The coupled role of organic matter (OM) and microbial activity is widely acknowledged in arsenic (As) biogeochemical cycling in sedimentary environments. However, little is known about OM characteristics particularly the dissolved fraction in the Bengal Delta Plain aquifers – one of the worst As impacted regions in the world. Ongoing investigations in As-rich aquifers in Nadia district (West Bengal, India) indicate presence of arsenite As(III) oxidizing bacterial communities in the Grey Sand Aquifers (GSA), but absent in Brown Sand Aquifers (BSA). In this study, we investigate the key differences in dissolved organic carbon (DOC) characteristics and its relationship with differences in elemental concentrations, distribution of biomarkers, and utilization of DOC by in situ microbial communities in BSA and GSA. We demonstrate a new approach using ENVI™ C-18 DSK discs to pre-concentrate DOC from large volumes of water, and further extract the OM and separate it into different lipid fractions using the solid phase extraction technique. The aquifers show marked heterogeneity in terms of their DOC characteristics and elemental profiles irrespective of their grey or brown color. DOC indicates variable inputs of terrestrial derived OM sources, and OM derived from decomposition and/or microbial cellular components. DOC in the aquifers consist of predominantly n-alkanoic acids (∌80%) followed by n-alkanes and n-alcohols. The GSAs indicate high iron (Fe) and manganese (Mn) concentrations, and presence of mature petroleum derived hydrocarbons in DOC. BSA has comparatively lower concentrations of Fe and Mn, and shows absence of mature hydrocarbons in DOC. Experiments in presence of indigenous bacteria from groundwater with DOC lipid extracts as the sole carbon source indicate higher growth in the GSA samples implying preferential use of DOC. The potential availability of DOC in these aquifers can influence the community composition of indigenous heterotrophic microbial flora, which in turn can affect elemental cycles including that of As.

  • 18.
    Hagbom, Marie
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Health Sciences.
    Nordgren, Johan
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Health Sciences.
    Ge, Ray
    School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.
    Lundin, Samuel
    Department of Microbiology and Immunology, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden.
    Wigzell, Hans
    Microbiology & Tumor biology Center, Karolinska Institute, Stockholm, Sweden.
    Taylor, John A
    School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.
    Andersson, Ulf
    Department of Women's and Children's Health, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden.
    Svensson, Lennart
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Health Sciences.
    The Cholinergic Anti-Inflammatory Pathway Contributes to the Limited Inflammatory Response following Rotavirus InfectionManuscript (preprint) (Other academic)
    Abstract [en]

    Rotavirus causes acute gastroenteritis in young children and is characterized by severe diarrhoea and vomiting. Surprisingly, although rotavirus infection results in significant intestinal pathology, the inflammatory response is limited. We tested the novel hypothesis that rotavirus infection stimulates the cholinergic anti-inflammatory pathway to suppress gut inflammation. The role of the vagus nerve and the α7 nicotinic acetylcholine receptor (α7 nAChR) in rotavirus infection were explored in α7 nAChR gene-deficient mice, vagotomized mice and wild-type mice treated with the α7 nAChR antagonist mecamylamine. TNF-α, IL-1β and IL-6 were measured in serum, spleen, duodenum, jejunum and ileum at 48 hours post infection. To determine if modulation of the inflammatory response affects virus shedding, α7 nAChRs was blocked and virus quantified in faeces. To investigate if stimulation of α7 nAChRs could attenuate rotavirus toxin NSP4-induced cytokine release, mouse peritoneal- and human blood-macrophages were treated with nicotine before NSP4 stimulation.

    Our results shows that stimulation of the vagus nerve and α7 nAChRs attenuated the pro- inflammatory response during rotavirus infection and blockade of the α7 nAChR reduced virus shedding from infected mice. IL-6 was increased in duodenum (p<0.05) and serum (p<0.05) of vagotomized mice and in jejunum (p<0.05) and spleen (p<0.05) of α7 nAChR gene-deficient mice. Furthermore, IL-6 mRNA (p<0.01) and TNF-α mRNA (p<0.05) were increased in duodenum of vagotomized animals. Similarly, nicotine attenuated the release of TNF-α (p<0.05) and IL-6 (p<0.05) from macrophages stimulated by NSP4 in vitro, all suggesting that the cholinergic anti- inflammatory pathway contributes to attenuate inflammation during rotavirus infection.

  • 19.
    Hammerman, Malin
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Surgery, Orthopedics and Oncology. Linköping University, Faculty of Medicine and Health Sciences.
    Blomgran, Parmis
    Linköping University, Department of Clinical and Experimental Medicine, Division of Surgery, Orthopedics and Oncology. Linköping University, Faculty of Medicine and Health Sciences.
    Dansac, Arie
    Linköping University, Department of Clinical and Experimental Medicine, Division of Surgery, Orthopedics and Oncology. Linköping University, Faculty of Medicine and Health Sciences.
    Eliasson, Pernilla T.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Surgery, Orthopedics and Oncology. Linköping University, Faculty of Medicine and Health Sciences.
    Aspenberg, Per
    Linköping University, Department of Clinical and Experimental Medicine, Division of Surgery, Orthopedics and Oncology. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Center for Surgery, Orthopaedics and Cancer Treatment, Department of Orthopaedics in Linköping.
    Different gene response to mechanical loading during early and late phases of rat Achilles tendon healing2017In: Journal of applied physiology, ISSN 8750-7587, E-ISSN 1522-1601, Vol. 123, no 4, p. 800-815Article in journal (Refereed)
    Abstract [en]

    Mechanical loading stimulates tendon healing both when applied in the inflammatory phase and in the early remodeling phase of the process, although not necessarily via the same mechanisms. We investigated the gene response to mechanical loading in these two phases of tendon healing. The right Achilles tendon in rats was transected, and the hindlimbs were unloaded by tail suspension. The rats were exposed to 5 min of treadmill running 3 or 14 days after tendon transection. Thereafter, they were resuspended for 15 min or 3 h until euthanasia. The controls were suspended continuously. Gene analysis was first performed by microarray analysis followed by quantitative RTPCR on selected genes, focusing on inflammation. Fifteen minutes after loading, the most important genes seemed to be the transcription factors EGR1 and C-FOS, regardless of healing phase. These transcription factors might promote tendon cell proliferation and differentiation, stimulate collagen production, and regulate inflammation. Three hours after loading on day 3, inflammation was strongly affected. Seven inflammation-related genes were upregulated according to PCR: CCL20, CCL7, IL-6, NFIL3, PTX3, SOCS1, and TLR2. These genes can be connected to macrophages, T cells, and recruitment of leukocytes. According to Ingenuity Pathway Analysis, the recruitment of leukocytes was increased by loading on day 3, which also was confirmed by histology. This inflammation-related gene response was not seen on day 14. Our results suggest that the immediate gene response after mechanical loading is similar in the early and late phases of healing but the late gene response is different. NEW amp; NOTEWORTHY This study investigates the direct effect of mechanical loading on gene expression during different healing phases in tendon healing. One isolated episode of mechanical loading was studied in otherwise unloaded healing tendons. This enabled us to study a time sequence, i.e., which genes were the first ones to be regulated after the loading episode.

  • 20.
    Hedbrant, Johan
    Linköping University, Department of Management and Engineering, Applied Thermodynamics and Fluid Mechanics. Linköping University, Faculty of Science & Engineering.
    [Meagre knowledge about obesity].: Mager kunskap om fetma.2003In: Läkartidningen, ISSN 0023-7205, E-ISSN 1652-7518, Vol. 100, no 21, p. 1922-Article in journal (Refereed)
  • 21.
    Jakobsen, Carolin
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University.
    Relation of silver release and antimicrobial effect in-vitro of silver containing wound dressings2010Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Silver was used for its antimicrobial effect by the ancient Greeks, long before the existence of microorganisms were first suspected. Nowadays a wide range of antimicrobial dressings containing silver, either incorporated within or applied on the dressings, are available for clinical use. This type of dressings is designed to provide the antimicrobial activity of silver in a more convenient application.

    The aim with this master thesis was to evaluate if silver release and antimicrobial effect of nine silver containing dressings are dependent on the test medium and if there is any relation between silver release and antimicrobial effect.

    Release of silver and antimicrobial effect was evaluated by using a 6-well co-culture system, with inoculated test medium in the wells and dressing pieces in the culture well inserts. Three different test media with increased complexity and nutrient value were inoculated with either

    Results show that release of silver depends on the test fluid used; for phosphate buffered saline (PBS), the silver concentration was as most 1.2 ppm, but for a complex media containing calf serum (SWF), it varied from 9 ppm to 134 ppm. The viable counts in PBS were reduced by at least 3 log units for all dressings and bacteria, whereas in SWF there were no reduction and instead growth was observed. In general, a high release resulted in less bacterial growth. Results also indicated that kinetics of silver release affect the antimicrobial effect. It is likely to assume that it is important for a dressing to release silver quickly.

    It has previously not been possible to correlate silver release of wound care dressings and antimicrobial effect, since the two factors have been measured in different test systems and in different media. Since both factors depend on test medium and method used, it is shown in the present study that it is important to use relevant test medium for in-vitro evaluation. When measuring silver release and antimicrobial effect in the same test system, a relation is found.

  • 22.
    Ji, Yang
    et al.
    Max Planck Institute Terr Microbiol, Germany; University of Vienna, Austria.
    Angel, Roey
    University of Federal Rio de Janeiro, Brazil.
    Klose, Melanie
    University of Vienna, Austria.
    Claus, Peter
    University of Vienna, Austria.
    Marotta, Humberto
    University of Federal Fluminense, Brazil.
    Pinho, Luana
    University of Estado Rio De Janeiro, Brazil.
    Enrich Prast, Alex
    Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences.
    Conrad, Ralf
    University of Vienna, Austria.
    Structure and function of methanogenic microbial communities in sediments of Amazonian lakes with different water types2016In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 18, no 12, p. 5082-5100Article in journal (Refereed)
    Abstract [en]

    Tropical lake sediments are a significant source for the greenhouse gas methane. We studied function (pathway, rate) and structure (abundance, taxonomic composition) of the microbial communities (Bacteria, Archaea) leading to methane formation together with the main physicochemical characteristics in the sediments of four clear water, six white water and three black water lakes of the Amazon River system. Concentrations of sulfate and ferric iron, pH and delta C-13 of organic carbon were usually higher, while concentrations of carbon, nitrogen and rates of CH4 production were generally lower in white water versus clear water or black water sediments. Copy numbers of bacterial and especially archaeal ribosomal RNA genes also tended to be relatively lower in white water sediments. Hydrogenotrophic methanogenesis contributed 58+/-16% to total CH4 production in all systems. Network analysis identified six communities, of which four were comprised mostly of bacteria found in all sediment types, while two were mostly in clear water sediment. Terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing showed that the compositions of the communities differed between the different sediment systems, statistically related to the particular physicochemical conditions and to CH4 production rates. Among the archaea, clear water, white water, and black water sediments contained relatively more Methanomicrobiales, Methanosarcinaceae and Methanocellales, respectively, while Methanosaetaceae were common in all systems. Proteobacteria, Deltaproteobacteria (Myxococcales, Syntrophobacterales, sulfate reducers) in particular, Acidobacteria and Firmicutes were the most abundant bacterial phyla in all sediment systems. Among the other important bacterial phyla, clear water sediments contained relatively more Alphaproteobacteria and Planctomycetes, whereas white water sediments contained relatively more Betaproteobacteria, Firmicutes, Actinobacteria, and Chloroflexi than the respective other sediment systems. The data showed communities of bacteria common to all sediment types, but also revealed microbial groups that were significantly different between the sediment types, which also differed in physicochemical conditions. Our study showed that function of the microbial communities may be understood on the basis of their structures, which in turn are determined by environmental heterogeneity.

  • 23.
    Johansson, Mikaela
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Metaproteogenomics-guided enzyme discovery: Targeted identification of novel proteases in microbial communities2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Industrial biotechnology is a large and growing industry as it is part of establishing a “greener” and more sustainable bioeconomy-based society. Using enzymes as biocatalysts is a viable alternative to chemicals and energy intense industrial processes and is en route to a more sustainable industry. Enzymes have been used in different areas for ages and are today used in many industrial processes such as biofuels production, food industry, tanning, chemical synthesis, pharmaceuticals etc. Enzymes are today a billion-dollar industry in itself and the demand for novel catalysts for various present and future processes of renewable resources are high and perfectly in line with converting to a more sustainable society.

    Most enzymes used in industry today have been identified from isolated and pure cultured microorganisms with identified desirable traits and enzymatic capacities. However, it is known that less than 1% of all microorganisms can be can be obtained in pure cultures. Thus, if we were to rely solely on pure culturing, this would leave the 99% of the microorganisms that constitutes the “microbial dark matter” uninvestigated for their potential in coding for and producing valuable novel enzymes. Therefore, to investigate these “unculturable” microorganisms for novel and valuable enzymes, pure-culture independent methods are needed.

    During the last two decades there has been a fast and extensive development in techniques and methods applicable for this purpose. Especially important has been the advancements made in mass spectrometry for protein identification and next generation sequencing of DNA. With these technical developments new research fields of proteomics and genomics have been developed, by which the complete protein complement of cells (the proteome) and all genes (the genome) of organisms can be investigated. When these techniques are applied to microbial communities these fields of research are known as meta-proteomics and meta-genomics.

    However, when applied to complex microbial communities, difficulties different from those encountered in their original usage for analysis of single multicellular organisms or cell linages arises, and when used independently both methods have their own limitations and bottlenecks. In addition, both metaproteomics and metagenomics are largely non-targeting techniques. Thus, if the purpose is still to - somewhat contradictory – use these non-targeting methods for targeted identification of novel enzymes with certain desired activities and properties from within microbial communities, special measures need to be taken.

    The work presented in this thesis describes the development of a method that combines

    metaproteomics and metagenomics (i.e. metaproteogenomics) for the targeted discovery of novel enzymes with desired activities, and their correct coding genes, from within microbial communities. Thus, what is described is a method that can be used to circumvent the pure-culturing problem so that a much larger fraction of the microbial dark matter can be specifically investigated for the identification of novel valuable enzymes.

    List of papers
    1. Applying theories of microbial metabolism for induction of targeted enzyme activity in a methanogenic microbial community at a metabolic steady state
    Open this publication in new window or tab >>Applying theories of microbial metabolism for induction of targeted enzyme activity in a methanogenic microbial community at a metabolic steady state
    2016 (English)In: Applied Microbiology and Biotechnology, ISSN 0175-7598, E-ISSN 1432-0614, Vol. 100, no 18, p. 7989-8002Article in journal (Refereed) Published
    Abstract [en]

    Novel enzymes that are stable in diverse conditions are intensively sought because they offer major potential advantages in industrial biotechnology, and microorganisms in extreme environments are key sources of such enzymes. However, most potentially valuable enzymes are currently inaccessible due to the pure culturing problem of microorganisms. Novel metagenomic and metaproteomic techniques that circumvent the need for pure cultures have theoretically provided possibilities to identify all genes and all proteins in microbial communities, but these techniques have not been widely used to directly identify specific enzymes because they generate vast amounts of extraneous data. In a first step towards developing a metaproteomic approach to pinpoint targeted extracellular hydrolytic enzymes of choice in microbial communities, we have generated and analyzed the necessary conditions for such an approach by the use of a methanogenic microbial community maintained on a chemically defined medium. The results show that a metabolic steady state of the microbial community could be reached, at which the expression of the targeted hydrolytic enzymes were suppressed, and that upon enzyme induction a distinct increase in the targeted enzyme expression was obtained. Furthermore, no cross talk in expression was detected between the two focal types of enzyme activities under their respective inductive conditions. Thus, the described approach should be useful to generate ideal samples, collected before and after selective induction, in controlled microbial communities to clearly discriminate between constituently expressed proteins and extracellular hydrolytic enzymes that are specifically induced, thereby reducing the analysis to only those proteins that are distinctively up-regulated.

    Place, publisher, year, edition, pages
    Springer, 2016
    Keywords
    Microbial community; Enzyme discovery; Metaproteomics; Biogas; Cellulase; Protease
    National Category
    Microbiology
    Identifiers
    urn:nbn:se:liu:diva-131888 (URN)10.1007/s00253-016-7547-z (DOI)000382008000017 ()27115757 (PubMedID)
    Note

    Funding Agencies|Swedish Research Council [621-2009-4150]; InZymes Biotech AB

    Available from: 2016-10-13 Created: 2016-10-11 Last updated: 2018-05-15
    2. Assessment of sample preparation methods for metaproteomics of extracellular proteins
    Open this publication in new window or tab >>Assessment of sample preparation methods for metaproteomics of extracellular proteins
    2017 (English)In: Analytical Biochemistry, ISSN 0003-2697, E-ISSN 1096-0309, Vol. 516, p. 23-36Article in journal (Refereed) Published
    Abstract [en]

    Enzyme discovery in individual strains of microorganisms is compromised by the limitations of pure culturing. In principle, metaproteomics allows for fractionation and study of different parts of the protein complement but has hitherto mainly been used to identify intracellular proteins. However, the extracellular environment is also expected to comprise a wealth of information regarding important proteins. An absolute requirement for metaproteomic studies of protein expression, and irrespective of downstream methods for analysis, is that sample preparation methods provide clean, concentrated and representative samples of the protein complement. A battery of methods for concentration, extraction, precipitation and resolubilization of proteins in the extracellular environment of a constructed microbial community was assessed by means of 2D gel electrophoresis and image analysis to elucidate whether it is possible to make the extracellular protein complement available for metaproteomic analysis. Most methods failed to provide pure samples and therefore negatively influenced protein gel migration and gel background clarity. However, one direct precipitation method (TCA-DOC/acetone) and one extraction/precipitation method (phenol/methanol) provided complementary high quality 2D gels that allowed for high spot detection ability and thereby also spot detection of less abundant extracellular proteins.

    Place, publisher, year, edition, pages
    Elsevier, 2017
    Keywords
    Enzyme discovery, Microbial community, Metaproteome, Extracellular, Sample preparation, 2D gel electrophoresis
    National Category
    Analytical Chemistry Biocatalysis and Enzyme Technology
    Identifiers
    urn:nbn:se:liu:diva-132902 (URN)10.1016/j.ab.2016.10.008 (DOI)000388056800005 ()27742212 (PubMedID)
    Funder
    Swedish Research Council, 621-2009-4150
    Note

    Funding agencies: Swedish Research Council [621-2009-4150]; Tekniska Verken i Linkoping AB; InZymes Biotech AB

    Available from: 2016-12-01 Created: 2016-12-01 Last updated: 2018-05-15Bibliographically approved
  • 24.
    Khalaf, Hazem
    et al.
    University of Örebro, Sweden.
    Sowdamini Nakka, Sravya
    University of Örebro, Sweden; PEAS Institute AB, Soderleden 1, Linkoping, Sweden.
    Sandén, Camilla
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering.
    Svärd, Anna
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering.
    Hultenby, Kjell
    Karolinska Institute, Sweden.
    Scherbak, Nikolai
    University of Örebro, Sweden.
    Aili, Daniel
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering.
    Bengtsson, Torbjorn
    University of Örebro, Sweden.
    Antibacterial effects of Lactobacillus and bacteriocin PLNC8 alpha beta on the periodontal pathogen Porphyromonas gingivalis2016In: BMC Microbiology, ISSN 1471-2180, E-ISSN 1471-2180, Vol. 16, no 188Article in journal (Refereed)
    Abstract [en]

    Background: The complications in healthcare systems associated with antibiotic-resistant microorganisms have resulted in an intense search for new effective antimicrobials. Attractive substances from which novel antibiotics may be developed are the bacteriocins. These naturally occurring peptides are generally considered to be safe and efficient at eliminating pathogenic bacteria. Among specific keystone pathogens in periodontitis, Porphyromonas gingivalis is considered to be the most important pathogen in the development and progression of chronic inflammatory disease. The aim of the present study was to investigate the antimicrobial effects of different Lactobacillus species and the two-peptide bacteriocin PLNC8 alpha beta on P. gingivalis. Results: Growth inhibition of P. gingivalis was obtained by viable Lactobacillus and culture media from L. plantarum NC8 and 44048, but not L. brevis 30670. The two-peptide bacteriocin from L. plantarum NC8 (PLNC8 alpha beta) was found to be efficient against P. gingivalis through binding followed by permeabilization of the membranes, using Surface plasmon resonance analysis and DNA staining with Sytox Green. Liposomal systems were acquired to verify membrane permeabilization by PLNC8 alpha beta. The antimicrobial activity of PLNC8 alpha beta was found to be rapid (1 min) and visualized by TEM to cause cellular distortion through detachment of the outer membrane and bacterial lysis. Conclusion: Soluble or immobilized PLNC8 alpha beta bacteriocins may be used to prevent P. gingivalis colonization and subsequent pathogenicity, and thus supplement the host immune system against invading pathogens associated with periodontitis.

  • 25.
    Kylin, Henrik
    Linköping University, The Tema Institute, Department of Water and Environmental Studies. Linköping University, Faculty of Arts and Sciences.
    Finns det slemsvampar i havet?2013In: Fauna och flora : populär tidskrift för biologi, ISSN 0014-8903, Vol. 108, no 1, p. 9-9Article in journal (Other (popular science, discussion, etc.))
  • 26.
    Li, Junwei
    et al.
    Univ Murcia, Spain.
    Parrilla, Inmaculada
    Univ Murcia, Spain.
    Ortega, Maria D.
    Univ Murcia, Spain.
    Martinez, Emilio A.
    Univ Murcia, Spain.
    Rodriguez-Martinez, Heriberto
    Linköping University, Department of Clinical and Experimental Medicine, Division of Children's and Women's health. Linköping University, Faculty of Medicine and Health Sciences.
    Roca, Jordi
    Univ Murcia, Spain.
    Post-thaw boar sperm motility is affected by prolonged storage of sperm in liquid nitrogen. A retrospective study2018In: Cryobiology, ISSN 0011-2240, E-ISSN 1090-2392, Vol. 80, p. 119-125Article in journal (Refereed)
    Abstract [en]

    Owing to the quick genetic turnover of the pig industry, most AT-boar sires live 2-3 yr, a period during which for 1-2 yr their semen is extended and used in liquid form for AI. Despite showing low cryosurvival, affecting fertility after AI, boar semen is frozen for easiness of transport overseas and reposition of valuable genetics. For the latter, semen is stored in liquid nitrogen (LN2, cryostorage) for many years, a controversial practice. Here we studied how length of cryostorage could affect sperm quality. Straws (0.5 mL) frozen using the same cryopreservation protocol at one specific location from AI-sires of proven fertility were stored in LN2 for up to 8 yr. Post thaw sperm quality was evaluated after 2, 4 or 8 yr of cryostorage, always compared to early thawing (15 d after freezing). Sperm motility and kinematics were evaluated post-thaw using CASA and sperm viability was cytometrically evaluated using specific fluorophores. Sperm viability was not affected by length of cryostorage, but total and progressive sperm motility were lower (p amp;lt; 0.01) in sperm samples cryostored for 4 or 8 yr compared to those thawed 15 d after freezing. Cryostorage time affected sperm kinetics, but with greater intensity in the samples cryostored for 4 yr (p amp;lt; 0.001) than in those for 2 yr (p amp;lt; 0.01). The fact that the major phenotypic characteristic of boar spermatozoa, motility, is constrained by time of cryostorage should be considered when building cryobanks of pig semen. Attention should be placed on the finding that amp;gt; 2 yr of cryostorage time can be particularly detrimental for the post-thaw motility of some sires, which might require increasing sperm numbers for AI.

  • 27.
    Linninge, C.
    et al.
    Lund Univ, Sweden; BioGaia AB, Sweden.
    Xu, Jie
    Linköping University, Department of Clinical and Experimental Medicine, Division of Neuro and Inflammation Science. Linköping University, Faculty of Medicine and Health Sciences.
    Bahl, M. I
    Tech Univ Denmark, Denmark.
    Ahrne, S.
    Lund Univ, Sweden.
    Molin, G.
    Lund Univ, Sweden.
    Lactobacillus fermentum and Lactobacillus plantarum increased gut microbiota diversity and functionality, and mitigated Enterobacteriaceae, in a mouse model2019In: Beneficial Microbes, ISSN 1876-2883, E-ISSN 1876-2891, Vol. 10, no 4, p. 413-424Article in journal (Refereed)
    Abstract [en]

    Probiotics should bring balance to the intestinal microbiota by stimulating beneficial bacteria, whilst mitigating adverse ones. Balance can also be interpreted as high alpha-diversity. Contrary, Escherichia coli is often regarded as an adverse component of the resident intestinal microbiota. The aim of the present study was to implement a mouse model for in vivo screening of Lactobacillus-strains for ability to increase gut-microbiota diversity and to mitigate E. coli. Mice were divided into six groups, two dietary control-groups and four groups administered strains of Lactobacillus fermentum and/or Lactobacillus plantarum. All animals were pre-treated with antibiotics, and E. coli in order to equalise the microbiota from the start. After 7 weeks of Lactobacillus administration, the animals were sacrificed: DNA was extracted from caecum tissue, and the microbiota composition was analysed with terminal restriction fragment length polymorphism (T-RFLP) and 16S rRNA gene sequencing. The diversity of the caecal microbiota decreased when the dietary carbohydrate source was limited to corn starch. Conversely, the diversity was restored by Lactobacillus-supplements. The tested combinations of two Lactobacillus strains exerted different influences, not only on the taxonomic level, but also on the inferred microbiome functions. The mixture of L. fermentum GOS47 and L. fermentum GOS1 showed potential for anti-inflammatory activity and short chain fatty acid production. On the other hand, co-administration of L. fermentum GOS57 and L. plantarum GOS42 significantly decreased the viable count of Enterobacteriaceae. These results warrant further investigation of the tested strains as candidates for probiotics. Furthermore, the findings demonstrated that the current experimental animal model is suitable for in vivo studies of the effect of bacterial supplements on the gut-microbiota.

  • 28.
    Ma, Shizhen
    et al.
    China Agr Univ, Peoples R China.
    Sun, Chengtao
    China Agr Univ, Peoples R China.
    Hulth, Anette
    Publ Hlth Agcy Sweden, Sweden; Karolinska Inst, Sweden.
    Li, Jiyun
    China Agr Univ, Peoples R China.
    Nilsson, Lennart E
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences.
    Zhou, Yuqing
    China Agr Univ, Peoples R China.
    Borjesson, Stefan
    Natl Vet Inst SVA, Sweden.
    Bi, Zhenwang
    Shandong Ctr Dis Control and Prevent, Peoples R China.
    Bi, Zhenqiang
    Shandong Ctr Dis Control and Prevent, Peoples R China.
    Sun, Qiang
    Shandong Univ, Peoples R China; Shandong Univ, Peoples R China.
    Wang, Yang
    China Agr Univ, Peoples R China.
    Mobile colistin resistance gene mcr-5 in porcine Aeromonas hydrophila2018In: Journal of Antimicrobial Chemotherapy, ISSN 0305-7453, E-ISSN 1460-2091, Vol. 73, no 7, p. 1777-1780Article in journal (Refereed)
    Abstract [en]

    Objectives: To characterize the mobile colistin resistance gene mcr-5 in Aeromonas hydrophila from backyard pigs in rural areas of China. Methods: Pig faecal samples from 194 households were directly tested for the presence of mcr-5 by PCR assay and the phenotypic antimicrobial susceptibility profiles of the mcr-5-positive isolates were determined using the broth dilution method. The genomic location and transferability of mcr-5 were analysed by S1-PFGE with Southern blotting and DNA hybridization, and natural transformation, respectively. One strain isolated from an mcr-5-positive sample was subjected to WGS and the stability of the mcr-5-harbouring plasmid over successive generations was examined by subculturing. Results: One mcr-5-positive A. hydrophila isolate showing resistance, with a colistin MIC of 4 mg/L, was isolated from a backyard pig faecal sample. mcr-5 was located on a 7915 bp plasmid designated pI064-2, which could naturally transform into a colistin-susceptible A. hydrophila strain of porcine origin and mediated colistin resistance in both the original isolate and its transformants. The plasmid backbone (3790 bp) of pI064-2 showed 81% nucleotide sequence identity to the corresponding region of the ColE2-type plasmid pAsa1 from Aeromonas salmonicida, while similar replication primases are widely distributed among aeromonads, Enterobacteriaceae and Pseudomonas species. Conclusions: To the best of our knowledge, this is the first identification of the novel colistin resistance gene mcr-5 in an A. hydrophila isolate from the faeces of a backyard pig. mcr-5 is expected to be able to disseminate among different bacterial species and genera.

  • 29.
    Magnusson, Karl-Eric
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Physical studies on the freeze-pressing of biological material1975Doctoral thesis, monograph (Other academic)
  • 30.
    Marcotte, Harold
    et al.
    Karolinska University Hospital Huddinge, Sweden.
    Krogh Andersen, Kasper
    Karolinska University Hospital Huddinge, Sweden.
    Lin, Yin
    Karolinska University Hospital Huddinge, Sweden.
    Zuo, Fanglei
    Karolinska University Hospital Huddinge, Sweden.
    Zeng, Zhu
    Karolinska University Hospital Huddinge, Sweden.
    Larsson, Per-Göran
    Linköping University, Department of Clinical and Experimental Medicine, Division of Children's and Women's health. Linköping University, Faculty of Medicine and Health Sciences. Skaraborg Hospital, Sweden.
    Brandsborg, Erik
    Bifodan AS, Denmark.
    Bronstad, Gunnar
    Neurozym Biotech AS, Norway.
    Hammarstrom, Lennart
    Karolinska University Hospital Huddinge, Sweden.
    Characterization and complete genome sequences of L. rhamnosus DSM 14870 and L-gasseri DSM 14869 contained in the EcoVag (R) probiotic vaginal capsules2017In: Microbiology Research, ISSN 0944-5013, E-ISSN 1618-0623, Vol. 205, p. 88-98Article in journal (Refereed)
    Abstract [en]

    Lactobacillus rhamnosus DSM 14870 and Lactobacillus gasseri DSM 14869 were previously isolated from the vaginal epithelial cells (VEC) of healthy women and selected for the development of the vaginal EcoVag (R) probiotic capsules. EcoVag (R) was subsequently shown to provide long-term cure and reduce relapse of bacterial vaginosis (BV) as an adjunct to antibiotic therapy. To identify genes potentially involved in probiotic activity, we performed genome sequencing and characterization of the two strains. The complete genome analysis of both strains revealed the presence of genes encoding functions related to adhesion, exopolysaccharide (EPS) biosynthesis, antimicrobial activity, and CRISPR adaptive immunity but absence of antibiotic resistance genes. Interesting features of L. rhamnosus DSM 14870 genome include the presence of the spaCBA-srtC gene encoding spaCBA pill and interruption of the gene cluster encoding long galactose-rich EPS by integrases. Unique to L. gasseri DSM 14869 genome was the presence of a gene encoding a putative (1456 amino acid) new adhesin containing two rib/alpha-like repeats. L. rhamnosus DSM 14870 and L. gasseri DSM 14869 showed acidification of the culture medium (to pH 3.8) and a strong adhesion capability to the Caco-2 cell line and VEC. L gasseri DSM 14869 could produce a thick (40 nor) EPS layer and hydrogen peroxide. L. rhamnosus DSM 14870 was shown to produce SpaCBA pili and a 20 nor EPS layer, and could inhibit the growth of Gardnerella vaginalis, a bacterium commonly associated with BV. The genome sequences provide a basis for further elucidation of the molecular basis for their probiotic functions.

  • 31.
    Mernelius, Sara
    Linköping University, Department of Clinical and Experimental Medicine. Linköping University, Faculty of Health Sciences.
    Infection control of Staphylococcus aureus: spa typing to elucidate transmission2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Staphylococcus aureus is a commensal of the human flora, primarily colonizing the anterior nares and throat, but it may also cause infections ranging from mild skin and soft tissue infections to severe diseases such as endocarditis and septicemia. S. aureus is also a major nosocomial problem increasing with the worldwide dissemination of methicillin-resistant S. aureus (MRSA). The main vector for bacterial cross-transmission in healthcare settings is the hands of healthcare workers (HCWs). No S. aureus was detected in the air in this thesis demonstrating that transmission through air is not important. Despite the fact that good compliance with hand hygiene is essential to prevent cross-transmission the compliance is generally less than 50 %. Gold standard to track bacterial transmission in healthcare settings has for long been pulsed-field gel electrophoresis (PFGE), a method that is labor- intensive, lacks consensus protocol and relies on semi-subjective analysis. Molecular typing by sequencing of the hypervariable part of the S. aureus protein A gene (spa typing) has overcome these problems and has shown promising results in epidemiological investigations.

    The aims of this thesis were to study bacterial transmission with S. aureus colonization of newborn infants as a model and to evaluate spa typing as a molecular tool. Additionally, the influence of compliance with hygiene guidelines on S. aureus transmission was assessed.

    Analysis of 280 MRSA isolates by spa typing revealed excellent typeability and epidemiological concordance and satisfactory discriminatory power. Additionally, spa typing was considered superior to PFGE thanks to its accessibility, ease of use and rapidity. Also, spa typing results are registered in a global database, facilitating inter-laboratory comparison.

    The prevalence of S. aureus ranged from 41 % to 66 % in the populations studied and males had the highest colonization rate. Throat was the premier colonization site for adults and transmission from individuals colonized in the throat only was documented, suggesting that throat cultures should be included in S. aureus screening programs. The umbilicus was the premier colonization site for newborn infants. Incubating the swabs in enrichment broth prior to plating increased the prevalence of S. aureus positive samples by 46 %, resulting in prevalence ranging from 51 % to 70 % in the populations studied. Thus enrichment prior to plating is necessary to determine more truthful S. aureus colonization rates. There were no indications of an institutional flora, as the colonization rates, spa type distribution and antibiotic resistance prevalence were similar among parents and HCWs.

    Direct observations and self-reporting by HCWs were both validated as tools for monitoring compliance with hygiene guidelines. The compliance with hygiene guidelines was significantly higher following a 10-point hygiene intervention as compared to baseline. The compliance was also higher three years after the intervention in three of four participating departments. These data show that it is possible to markedly improve the compliance with hygiene guidelines, but to achieve a long-term effect, continuous and varied reminders seems necessary.

    Both at baseline and following the intervention almost 60 % of the colonized infants were colonized with an S. aureus of the same spa type as isolated from their own family. At baseline approximately 25 % of the colonized infants received their S. aureus from non-family individuals, indicating transmission directly or indirectly from HCWs. Despite the improvement in compliance with barrier precautions from 41 % at baseline to 86 % following the hygiene intervention, the transmission from non-family did not decrease. This indicates that other factors may have a prominent impact on bacterial transmission. One factor might be the quality of hand hygiene technique which therefore needs to be studied further. However, to ensure patient safety it is still recommended that all HCWs comply with hygiene guidelines at all time.

    List of papers
    1. Epidemiological typing of methicillin-resistant Staphylococcus aureus (MRSA): spa typing versus pulsed-field gel electrophoresis
    Open this publication in new window or tab >>Epidemiological typing of methicillin-resistant Staphylococcus aureus (MRSA): spa typing versus pulsed-field gel electrophoresis
    Show others...
    2009 (English)In: SCANDINAVIAN JOURNAL OF INFECTIOUS DISEASES, ISSN 0036-5548, Vol. 41, no 6-7, p. 433-439Article in journal (Refereed) Published
    Abstract [en]

    Molecular methods based on sequencing, such as spa typing, have facilitated epidemiological typing of bacterial isolates compared to the gold standard pulsed-field gel electrophoresis (PFGE), a technically more demanding method. We studied methicillin-resistant Staphylococcus aureus (MRSA) in 4 Swedish counties from 2003 through 2005, and compared spa typing and PFGE results to epidemiological data. Of 280 MRSA isolates, 91 were from sporadic cases and 189 were associated with 35 outbreaks. A total of 50 spa types and 74 PFGE patterns were detected. 60 (21%) of the MRSA isolates carried the Panton-Valentine leukocidin (PVL) genes. 12 of the PVL-positive MRSA were healthcare associated. 25 of the spa types and 31 of the PFGE patterns were associated with outbreaks. In 1 of the outbreaks we found isolates with different but closely related spa types, and in 6 of the outbreaks we observed isolates with different but related PFGE patterns. In this low-endemic setting, with outbreaks limited in time and place, we found spa typing to be a useful tool for epidemiological typing of MRSA, due to its rapidity, accessibility, ease of use, and standardized nomenclature.

    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:liu:diva-19886 (URN)10.1080/00365540902962749 (DOI)
    Available from: 2009-08-14 Created: 2009-08-14 Last updated: 2015-04-01
    2. Compliance with hygiene guidelines: The effect of a multimodal hygiene intervention and validation of direct observations
    Open this publication in new window or tab >>Compliance with hygiene guidelines: The effect of a multimodal hygiene intervention and validation of direct observations
    Show others...
    2013 (English)In: American Journal of Infection Control, ISSN 0196-6553, E-ISSN 1527-3296, Vol. 41, no 5, p. E45-E48Article in journal (Refereed) Published
    Abstract [en]

    Background

    Good compliance with hygiene guidelines is essential to prevent bacterial transmission and health care-associated infections. However, the compliance is usually <50%.

    Methods

    A multimodal and multidisciplinary hygiene intervention was launched once the baseline compliance was determined through direct observations in 4 departments of obstetrics and gynecology. Detailed evaluations of the compliance rates were performed at point of stability (at 80%) and follow-up (3 years after hygiene intervention). Validation of direct observations was performed using blinded double appraisal and multiappraisal.

    Results

    At baseline, the compliance with barrier precautions and the dress code at the 4 departments were 39% to 47% and 79% to 98%, respectively. Point of stability was reached approximately 1 year after the hygiene intervention was launched. The compliance with barrier precautions was significantly higher at follow-up compared with baseline in 3 departments. In the validation by double appraisal, 471 of 483 components were judged identical between observers. In the multiappraisal, 95% to 100% of the observers correctly judged the 7 components.

    Conclusion

    It is possible to improve compliance with hygiene guidelines, but, to ensure a long-lasting effect, a continuous focus on barrier precautions is required. Observation is a valid method to monitor compliance.

    Place, publisher, year, edition, pages
    Elsevier, 2013
    Keywords
    Multidisciplinary, Adherence, Double appraisal, Multiappraisal, Self-reporting, Hand hygiene, Barrier precautions, Dress code
    National Category
    Clinical Medicine
    Identifiers
    urn:nbn:se:liu:diva-93971 (URN)10.1016/j.ajic.2012.09.008 (DOI)000318611200002 ()
    Note

    Funding Agencies|Futurum-the Academy for Healthcare, County Council, Jonkoping||Medical Research Council of Southeast Sweden||

    Available from: 2013-06-13 Created: 2013-06-13 Last updated: 2017-12-06Bibliographically approved
    3. The effect of improved compliance with hygiene guidelines on transmission of Staphylococcus aureus to newborn infants: The Swedish Hygiene Intervention and Transmission of S aureus study
    Open this publication in new window or tab >>The effect of improved compliance with hygiene guidelines on transmission of Staphylococcus aureus to newborn infants: The Swedish Hygiene Intervention and Transmission of S aureus study
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    2013 (English)In: American Journal of Infection Control, ISSN 0196-6553, E-ISSN 1527-3296, Vol. 41, no 7, p. 585-590Article in journal (Refereed) Published
    Abstract [en]

    Background: Newborn infants are often colonized with Staphylococcus aureus originating from health care workers (HCWs). We therefore use colonization with S aureus of newborn infants to determine the effect of an improved compliance with hygiene guidelines on bacterial transmission. Methods: Compliance with hygiene guidelines was monitored prior to (baseline) and after (follow-up) a multimodal hygiene intervention in 4 departments of obstetrics and gynecology. spa typing was used to elucidate transmission routes of S aureus collected from newborn infants, mothers, fathers, staff members, and environment. Results: The compliance with hygiene guidelines increased significantly from baseline to follow-up. The transmission of S aureus from HCWs to infants was however not affected. Fathers had the highest colonization rates. Persistent carriage was indicated in 18% of the HCWs. The most commonly isolated spa type was t084, which was not detected in a previous study from the same geographic area. Conclusion: It is possible to substantially improve the compliance with hygiene guidelines, by using multimodal hygiene intervention. The improved compliance did not decrease the transmission of S aureus from sources outside the own family to newborn infants. Furthermore, we show the establishment of a new spa type (t084), which now is very common in our region. Copyright (C) 2013 by the Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

    Place, publisher, year, edition, pages
    Elsevier, 2013
    Keywords
    Compliance rates; The Swedish HITS-study; spa typing; Persistent carriage; Colonization; Carriage; Multimodal hygiene intervention
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:liu:diva-96178 (URN)10.1016/j.ajic.2012.09.014 (DOI)000321046300004 ()
    Available from: 2013-08-14 Created: 2013-08-14 Last updated: 2017-12-06
    4. The role of broth enrichment in Staphylococcus aureus cultivation and transmission from the throat to newborn infants: results from the Swedish hygiene intervention and transmission of S-aureus study
    Open this publication in new window or tab >>The role of broth enrichment in Staphylococcus aureus cultivation and transmission from the throat to newborn infants: results from the Swedish hygiene intervention and transmission of S-aureus study
    2013 (English)In: European Journal of Clinical Microbiology and Infectious Diseases, ISSN 0934-9723, E-ISSN 1435-4373, Vol. 32, no 12, p. 1593-1598Article in journal (Refereed) Published
    Abstract [en]

    Staphylococcus aureus is detected by direct plating, whereas incubation in enrichment broth prior to plating to increase the proportion of positive samples has not been fully evaluated. S. aureus throat colonization has been suggested to be more common than colonization of the anterior nares, but no data are available on the transmission of S. aureus from the throat. Swab samples were collected from the anterior nares and umbilicus from newborn infants (n = 168), anterior nares, throat, skin lesions, and vagina from parents (n = 332), and anterior nares, throat, and skin lesions from healthcare workers (n = 231) at three maternity wards. spa typing was used to elucidate the transmission routes of S. aureus. The use of enrichment broth prior to plating increased the proportion of positive samples by 46 %. The prevalence of S. aureus colonization in adults was 58 %. Throat colonization (47 %) was significantly more common than colonization in any of the other screened sites (p andlt; 0.001). In total, 103 out of 168 (61 %) newborn infants were colonized during their hospital stay. Overall, 124 S. aureus transmissions to newborn infants were detected. Although we detected an increased risk of transmission from the nares as compared to the throat, with an odds ratio of 4.8 [95 % confidence interval (CI) 1.8-12.7], we detected a transmission rate of 7 % from the throat. We show that S. aureus throat colonization is more common than colonization in any of the other sites among the parents and staff. We also show evidence of transmission from the throat.

    Place, publisher, year, edition, pages
    Springer Verlag (Germany), 2013
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:liu:diva-102493 (URN)10.1007/s10096-013-1917-6 (DOI)000326896700014 ()
    Note

    Funding Agencies|Futurum-the Academy for Healthcare||Jonkoping County Council||Medical Research Council of Southeast Sweden||

    Available from: 2013-12-13 Created: 2013-12-12 Last updated: 2019-02-11
  • 32.
    Najafi, Davood
    et al.
    Baqiyatallah Univ Med Sci, Iran; Univ Tabriz, Iran.
    Taheri, Ramezan Ali
    Baqiyatallah Univ Med Sci, Iran.
    Najafi, Abouzar
    Baqiyatallah Univ Med Sci, Iran; Univ Tabriz, Iran.
    Rouhollahi, Abbas Abbas
    Univ Tehran, Iran.
    Alvarez-Rodriguez, Manuel
    Linköping University, Department of Clinical and Experimental Medicine, Division of Children's and Women's health. Linköping University, Faculty of Medicine and Health Sciences. Univ Autonoma Barcelona, Spain.
    Effect of Achillea millefolium-loaded nanophytosome in the post-thawing sperm quality and oxidative status of rooster semen2018In: Cryobiology, ISSN 0011-2240, E-ISSN 1090-2392, Vol. 82, p. 37-42Article in journal (Refereed)
    Abstract [en]

    The aim of this study was to compare the effectiveness of antioxidants including Achillea millefolium extract (AmE) (n0t1.5: 1.5, n0t3: 3 and n0t4.5: 4.5 mg/L) and AmE loaded in nano phytosome (n1t1.5: 1.5, n1t3: 3 and n1t4.5: 4.5 mg/L) in the freezing of Ross 308 rooster semen. Sperm motility (CASA), membrane integrity (HOS test), viability, total abnormality and enzymatic parameters (SOD, CAT and GPx) were assessed after thawing. AmE-loaded nano phytosome at a concentration of 3 mg/l resulted in significantly (P amp;lt; 0.05) higher total motility (MOT) (73.78 +/- 2.92) and at concentrations of 1.5 mg/L and 3 mg/L in progressive motility (PROG) (14.12 +/- 0.38, 16.78 +/- 0.38) in comparison with the control group (MOT: 58.48 +/- 2.92; PROG: 9.08 +/- 0.38). Sperm viability (Vi) was higher (P amp;lt; 0.05) in n1t3 (74.62 +/- 1.55) and membrane integrity (Mi) in n0t3 and n1t3 groups (65.91 +/- 1.91, 63.73 +/- 1.91, respectively) compared to the control groups (Vi: 66.85 +/- 1.55; Mi: 53.18 +/- 1.91). Moreover, the lowest percentage of MDA was measured in n1t3 group (1.31 +/- 0.31). There was no significant difference for SOD and CAT values with the use of various extenders. In conclusion, we suggest that AmE loaded in nano phytosome at 3 mg/l dose can be added to basic extender for improving rooster sperm motility, viability and oxidative stress values during the freezing procedure.

  • 33.
    Raffetseder, Johanna
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences.
    Interplay of human macrophages and Mycobacterium tuberculosis phenotypes2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Mycobacterium tuberculosis (Mtb) is the pathogen causing tuberculosis (TB), a disease most often affecting the lung. 1.5 million people die annually due to TB, mainly in low-income countries. Usually considered a disease of the poor, also developed nations recently put TB back on their agenda, fueled by the HIV epidemic and the global emergence of drug-resistant Mtb strains. HIV-coinfection is a predisposing factor for TB, and infection with multi-drug resistant and extremely drug resistant strains significantly impedes and lengthens antibiotic treatment, and increases fatality. Mtb is transmitted from a sick individual via coughing, and resident macrophages are the first cells to encounter the bacterium upon inhalation. These cells phagocytose intruders and subject them to a range of destructive mechanisms, aiming at killing pathogens and protecting the host. Mtb, however, has evolved to cope with host pressures, and has developed mechanisms to submerge macrophage defenses. Among these, inhibition of phagosomal maturation and adaptation to the intracellular environment are important features. Mtb profoundly alters its phenotype inside host cells, characterized by altered metabolism and slower growth. These adaptations contribute to the ability of Mtb to remain dormant inside a host during latent TB infection, a state that can last for decades. According to recent estimates, one third of the world’s population is latently infected with Mtb, which represents a huge reservoir for active TB disease. Mtb is also intrinsically tolerant to many antibiotics, and adaptation to host pressures enhances tolerance to first-line TB drugs. Therefore, TB antibiotic therapy takes 6 to 9 months, and current treatment regimens involve a combination of several antibiotics. Patient noncompliance due to therapeutic side effects as well as insufficient penetration of drugs into TB lesions are reasons for treatment failure and can lead to the rise of drug-resistant populations. In view of the global spread of drug-resistant strains, new antibiotics and treatment strategies are urgently needed.

    In this thesis, we studied the interplay of the primary host cell of Mtb, human macrophages, and different Mtb phenotypes. A low-burden infection resulted in restriction of Mtb replication via phagolysosomal effectors and the maintenance of an inactive Mtb phenotype reminiscent of dormant bacteria. Macrophages remained viable for up to 14 days, and profiling of secreted cytokines mirrored a silent infection. On the contrary, higher bacterial numbers inside macrophages could not be controlled by phagolysosomal functions, and intracellular Mtb shifted their phenotype towards active replication. Although slowed mycobacterial replication is believed to render Mtb tolerant to antibiotics, we did not observe such an effect. Mtb-induced macrophage cell death is dependent on ESAT6, a small mycobacterial virulence factor involved in host cell necrosis and the spread of the pathogen. Although well-studied, the fate of ESAT6 inside infected macrophages has been enigmatic. Cultivation of Mtb is commonly carried out in broth containing detergent to avoid aggregation of bacilli due to their waxy cell wall. Altering cultivation conditions revealed the presence of a mycobacterial capsule, and ESAT6 situated on the mycobacterial surface. Infection of macrophages with this encapsulated Mtb phenotype resulted in rapid ESAT6-dependent host cell death, and ESAT6 staining was lost as bacilli were ingested by macrophages. These observations could reflect the earlier reported integration of ESAT6 into membranes followed by membrane rupture and host cell death.

    In conclusion, the work presented in this thesis shows that the phenotype of Mtb has a significant impact on the struggle between the pathogen and human macrophages. Taking the bacterial phenotype into account can lead to the development of drugs active against altered bacterial populations that are not targeted by conventional antibiotics. Furthermore, deeper knowledge on Mtb virulence factors can inform the development of virulence blockers, a new class of antibiotics with great therapeutic potential.

    List of papers
    1. Importance of phagosomal functionality for growth restriction of Mycobacterium tuberculosis in primary human macrophages
    Open this publication in new window or tab >>Importance of phagosomal functionality for growth restriction of Mycobacterium tuberculosis in primary human macrophages
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    2011 (English)In: Journal of Innate Immunity, ISSN 1662-811X, E-ISSN 1662-8128, Vol. 3, no 5, p. 508-518Article in journal (Refereed) Published
    Abstract [en]

    The best characterized survival mechanism of Mycobacterium tuberculosis inside the macrophage is the inhibition of phagosomal maturation. Phagosomal maturation involves several steps including fusion with lysosomes and acidification. However, it has not been elucidated which components of phagosomal maturation correlate with growth restriction of virulent mycobacteria in human macrophages, and we aimed to study this. We infected human monocyte-derived macrophages with M. tuberculosis and assessed bacterial replication, translocation of CD63 to the phagosome, and phagosomal acidification. We found that unstimulated macrophages were able to control infection with M. tuberculosis upon inoculation at a low, but not high, multiplicity of infection (MOI). H37Rv and H37Ra infection, at both high and low MOI, led to equally ineffective translocation of CD63 to the phagosome. This was true despite the impaired growth ability of H37Rv at the low MOI and of H37Ra even at the high MOI, indicating that inhibition of CD63 translocation was not sufficient for growth to occur. On the other hand, acidification of mycobacterial phagosomes was more efficient at a low MOI with both mycobacterial strains, consistent with a role for phagosomal acidification in restricting M. tuberculosis growth. Inhibition of the vacuolar H+-ATPase as well as of cathepsin D led to enhanced mycobacterial replication inside the macrophage. We conclude that acidification and related functional aspects of the mature phagosome are important factors for restriction of M. tuberculosis replication in human macrophages.

    Place, publisher, year, edition, pages
    S. Karger, 2011
    National Category
    Basic Medicine
    Identifiers
    urn:nbn:se:liu:diva-65447 (URN)10.1159/000325297 (DOI)000294572500008 ()21576918 (PubMedID)
    Note

    Funding Agencies|Swedish Research Council|529-2003-5994,2005-7046,2006-5968,2007-2673,2009-3821|Bill and Melinda Gates Foundation||SIDA/SAREC||Ekhaga Foundation||Carl Trygger Foundation||King Gustaf V 80-Year Memorial Foundation||County Council of Ostergotland||Swedish Heart Lung Foundation||Oskar II Jubilee Foundation||Clas Groschinsky Foundation||Soderbergs Foundation||Colorado State University, Fort Collins (NIH, NIAID)|HHSN26620040 0091C|

    Available from: 2011-02-08 Created: 2011-02-08 Last updated: 2018-01-12Bibliographically approved
    2. Replication Rates of Mycobacterium tuberculosis in Human Macrophages Do Not Correlate with Mycobacterial Antibiotic Susceptibility
    Open this publication in new window or tab >>Replication Rates of Mycobacterium tuberculosis in Human Macrophages Do Not Correlate with Mycobacterial Antibiotic Susceptibility
    Show others...
    2014 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 11, p. e112426-Article in journal (Refereed) Published
    Abstract [en]

    The standard treatment of tuberculosis (TB) takes six to nine months to complete and this lengthy therapy contributes to the emergence of drug-resistant TB. TB is caused by Mycobacterium tuberculosis (Mtb) and the ability of this bacterium to switch to a dormant phenotype has been suggested to be responsible for the slow clearance during treatment. A recent study showed that the replication rate of a non-virulent mycobacterium, Mycobacterium smegmatis, did not correlate with antibiotic susceptibility. However, the question whether this observation also holds true for Mtb remains unanswered. Here, in order to mimic physiological conditions of TB infection, we established a protocol based on long-term infection of primary human macrophages, featuring Mtb replicating at different rates inside the cells. During conditions that restricted Mtb replication, the bacterial phenotype was associated with reduced acid-fastness. However, these phenotypically altered bacteria were as sensitive to isoniazid, pyrazinamide and ethambutol as intracellularly replicating Mtb. In support of the recent findings with M. smegmatis, we conclude that replication rates of Mtb do not correlate with antibiotic tolerance.

    Place, publisher, year, edition, pages
    Public Library of Science, 2014
    National Category
    Clinical Medicine Basic Medicine
    Identifiers
    urn:nbn:se:liu:diva-113014 (URN)10.1371/journal.pone.0112426 (DOI)000345250400061 ()25386849 (PubMedID)
    Note

    Funding Agencies|Bill and Melinda Gates Foundation; Swedish Research Council [2009-3821, 2012-3349]; Swedish International Development Cooperation Agency; Swedish Heart-Lung Foundation; King Oscar II Foundation; Carl Trygger Foundation; Clas Groschinsky Foundation

    Available from: 2015-01-12 Created: 2015-01-08 Last updated: 2018-01-11
  • 34.
    Ranjan, Rajesh Kumar
    et al.
    Biogeochemistry Laboratory, School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.
    Routh, Joyanto
    Department of Earth Sciences, IISER-Kolkata, Mohanpur, India.
    Ramanathan, A. L.
    Biogeochemistry Laboratory, School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.
    Bulk organic matter characteristics in the Pichavaram mangrove: estuarine complex, south-eastern India2010In: Applied Geochemistry, ISSN 0883-2927, E-ISSN 1872-9134, Vol. 25, no 8, p. 1176-1186Article in journal (Refereed)
    Abstract [en]

    The Pichavaram mangrove ecosystem is located between the Vellar and Coleroon Estuaries in south-eastern India. To document the spatial-depth-based variabilities in organic matter (OM) input and cycling, five sediment cores were collected. A comparative study was carried out of grain-size composition, pore water salinity, dissolved organic C (DOC), loss-on-ignition (LOI), elemental ratios (C/N and H/C), pigments (Chl a, Chl b, and total carotenoids), and humification indices. Sand is the major fraction in these cores ranging from 60% to 99% followed by silt and clay; cores from the estuarine margin have high sand content. In mangrove forests, pore-water DOC concentrations are high (32 +/- 14 mg L(-1)), whereas salinity levels are low (50 +/- 5.5 parts per thousand). Likewise, LOI, organic C and N, and pigment concentrations are high in mangroves. OM is mainly derived from upstream terrestrial matter and/or mangrove litter, and marine OM. The humification indices do not vary significantly with depth because of rapid OM turnover. The bulk parameters indicate that the Vellar and Coleroon Estuaries are more affected by anthropogenic processes than mangrove forests. Finally, greater variability and sometimes lack of specific trends in bulk parameters implies that the 2004 tsunami caused extensive mixing in sediments. (C) 2010 Elsevier Ltd. All rights reserved.

  • 35.
    Routh, Joyanto
    et al.
    Department of Geology and Geophysics, Texas A&M University, College Station, TX, 77843, USA.
    Grossman, Ethan L.
    Department of Geology and Geophysics, Texas A&M University, College Station, TX, 77843, USA.
    Ulrich, Glenn A.
    Institute for Energy and the Environment, Department of Botany and Microbiology, 770 Van Vleet Oval, University of Oklahoma, Norman, OK, 73019-0245, USA.
    Suflita, Joseph M.
    Institute for Energy and the Environment, Department of Botany and Microbiology, 770 Van Vleet Oval, University of Oklahoma, Norman, OK, 73019-0245, USA.
    Volatile organic acids and microbial processes in the Yegua formation, east-central Texas2001In: Applied Geochemistry, ISSN 0883-2927, E-ISSN 1872-9134, Vol. 16, no 2, p. 183-195Article in journal (Refereed)
    Abstract [en]

    Geochemical and microbiological evidence indicates that viable microorganisms produce and consume volatile organic acids (VOA) in the Yegua formation. Acetic and propionic acid concentrations in mudstones range from 200 to 1270 and 20 to 38 nmol·gdw−1 respectively, whereas concentrations in sands are 50–200 and less than 20 nmol·gdw−1. VOA concentrations in sediments and in laboratory incubations suggest net production of VOAs by microorganisms in mudstones, and net consumption of VOAs by SO4 reducing bacteria (SRB) in sands. Notably, SRB activity is mostly confined to aquifer sands. Vertical diffusion and advection were modeled to estimate acetic acid transport from aquitard to aquifer. Assuming that SRB completely respire the acetic acid transported into the aquifer (3.2 μmol·l−1·m·a−1), the CO2 production rate in the aquifer sands is 5.3 μmol·l−1·a−1. This slow mineralization rate of in situ organic matter is within the range for deep aquifers, and probably accounts for the long-term survival of microorganisms in oligotrophic environments. Finally, the microbial communities in Yegua sediments appear to exhibit a loose commensalism, with microorganisms in aquitards providing VOAs for respiratory processes (i.e., SO4 reduction) in aquifers.

  • 36.
    Safaric, Luka
    et al.
    Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences.
    Shakeri Yekta, Sepehr
    Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences.
    Liu, Tong
    Swedish Univ Agr Sci, Sweden.
    Svensson, Bo
    Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences.
    Schnürer, Anna
    Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences. Swedish Univ Agr Sci, Sweden.
    Bastviken, David
    Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences.
    Björn, Annika
    Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences.
    Dynamics of a Perturbed Microbial Community during Thermophilic Anaerobic Digestion of Chemically Defined Soluble Organic Compounds2018In: MICROORGANISMS, ISSN 2076-2607, Vol. 6, no 4, article id 105Article in journal (Refereed)
    Abstract [en]

    Knowledge of microbial community dynamics in relation to process perturbations is fundamental to understand and deal with the instability of anaerobic digestion (AD) processes. This study aims to investigate the microbial community structure and function of a thermophilic AD process, fed with a chemically defined substrate, and its association with process performance stability. Next generation amplicon sequencing of 16S ribosomal RNA (rRNA) genes revealed that variations in relative abundances of the predominant bacterial species, Defluviitoga tunisiensis and Anaerobaculum hydrogeniformans, were not linked to the process performance stability, while dynamics of bacterial genera of low abundance, Coprothermobacter and Defluviitoga (other than D. tunisiensis), were associated with microbial community function and process stability. A decrease in the diversity of the archaeal community was observed in conjunction with process recovery and stable performance, implying that the high abundance of specific archaeal group(s) contributed to the stable AD. Dominance of hydrogenotrophic Methanoculleus particularly corresponded to an enhanced microbial acetate and propionate turnover capacity, whereas the prevalence of hydrogenotrophic Methanothermobacter and acetoclastic Methanosaeta was associated with instable AD. Acetate oxidation via syntrophic interactions between Coprothermobacter and Methanoculleus was potentially the main methane-formation pathway during the stable process. We observed that supplementation of Se and W to the medium improved the propionate turnover by the thermophilic consortium. The outcomes of our study provided insights into the community dynamics and trace element requirements in relation to the process performance stability of thermophilic AD.

  • 37.
    Schaufler, Katharina
    et al.
    Ernst Moritz Arndt Univ Greifswald, Germany; Free Univ Berlin, Germany.
    Semmler, Torsten
    Robert Koch Inst, Germany.
    Wieler, Lothar H.
    Robert Koch Inst, Germany.
    Trott, Darren J.
    Univ Adelaide, Australia.
    Pitout, Johann
    Calgary Lab Serv, Canada; Univ Calgary, Canada.
    Peirano, Gisele
    Calgary Lab Serv, Canada; Univ Calgary, Canada.
    Bonnedahl, Jonas
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology, Infection and Inflammation. Linköping University, Faculty of Medicine and Health Sciences. Kalmar Cty Council, Sweden.
    Dolejska, Monika
    Univ Vet and Pharmaceut Sci Brno, Czech Republic; Univ Vet and Pharmaceut Sci Brno, Czech Republic.
    Literak, Ivan
    Univ Vet and Pharmaceut Sci Brno, Czech Republic; Univ Vet and Pharmaceut Sci Brno, Czech Republic.
    Fuchs, Stephan
    Robert Koch Inst, Germany.
    Ahmed, Niyaz
    Int Ctr Diarrheal Dis Res Bangladesh, Bangladesh.
    Grobbel, Mirjam
    German Fed Inst Risk Assessment, Germany.
    Torres, Carmen
    Univ La Rioja, Spain.
    McNally, Alan
    Univ Birmingham, England.
    Pickard, Derek
    Wellcome Trust Sanger Inst, England.
    Ewers, Christa
    Justus Liebig Univ Giessen, Germany.
    Croucher, Nicholas J.
    Imperial Coll, England.
    Corander, Jukka
    Wellcome Trust Sanger Inst, England; Univ Helsinki, Finland; Univ Oslo, Norway.
    Guenther, Sebastian
    Free Univ Berlin, Germany; Ernst Moritz Arndt Univ Greifswald, Germany.
    Genomic and Functional Analysis of Emerging Virulent and Multidrug-Resistant Escherichia coli Lineage Sequence Type 6482019In: Antimicrobial Agents and Chemotherapy, ISSN 0066-4804, E-ISSN 1098-6596, Vol. 63, no 6, article id e00243-19Article in journal (Refereed)
    Abstract [en]

    The pathogenic extended-spectrum-beta-lactamase (ESBL)-producing Escherichia coli lineage ST648 is increasingly reported from multiple origins. Our study of a large and global ST648 collection from various hosts (87 whole-genome sequences) combining core and accessory genomics with functional analyses and in vivo experiments suggests that ST648 is a nascent and generalist lineage, lacking clear phylogeographic and host association signals. By including large numbers of ST131 (n = 107) and ST10 (n = 96) strains for comparative genomics and phenotypic analysis, we demonstrate that the combination of multidrug resistance and high-level virulence are the hallmarks of ST648, similar to international high-risk clonal lineage ST131. Specifically, our in silico, in vitro, and in vivo results demonstrate that ST648 is well equipped with biofilm-associated features, while ST131 shows sophisticated signatures indicative of adaption to urinary tract infection, potentially conveying individual ecological niche adaptation. In addition, we used a recently developed NFDS (negative frequency-dependent selection) population model suggesting that ST648 will increase significantly in frequency as a cause of bacteremia within the next few years. Also, ESBL plasmids impacting biofilm formation aided in shaping and maintaining ST648 strains to successfully emerge worldwide across different ecologies. Our study contributes to understanding what factors drive the evolution and spread of emerging international high-risk clonal lineages.

  • 38.
    Speda, Jutta
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Methods development for metaproteomics-guided bioprospecting of novel enzymes2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Industrial biotechnology has been announced by several organizations and governments as a key enabling technology for the enhanced economic growth in a low-carbon and knowledge-based bioeconomy. An important goal to promote an environment friendly and sustainable industrial biotechnology is the discovery of new enzymes.

    To date, almost all enzymes used in industry have been discovered by pure culturing of microorganisms, however, it is known that less than 1% of all microorganisms can be obtained in pure cultures. The remaining majority of microorganisms is only viable by close biological interactions provided in microbial communities and is not available for enzyme discovery using the classical pure culture approaches. The investigation of microbial communities, which can be viewed as metaorganisms, has been enabled during the last two decades by refining established methods for the analysis of genes, mRNA or proteins and are called metagenomics, metatranscriptomics and metaproteomics, respectively. To date, these techniques have mostly been used in the field of microbial ecology for the understanding of the composition, function and metabolism of microbial communities but not for the purpose of bioprospecting for novel enzymes. Identification of genes that code for possible enzyme candidates is hindered, due to the fact that 30-40% of the sequenced metagenomes contain genes coding for unidentified proteins. Additionally, the -omics techniques generate large amounts of data that need to be analyzed and the outcome of the analysis does not necessarily lead to the discovery of novel applicable enzymes.

    The work presented in this thesis describes the establishment of the necessary conditions for a metaproteomics-based method that allows for a straightforward and targeted identification of novel enzymes with desired activity from microbial communities. The approach provides a valuable alternative to the incomplete and inefficient analysis of non-targeting data and laborious workflow, which is typically generated by the established meta-omics techniques. In developing the methods presented in this thesis, microbial communities in constructed environments were established, which allowed for the controlled expression of extracellular hydrolytic enzymes under defined conditions. By combination and modulation of advanced metaproteomics and metagenomics techniques, we were able to directly identify the enzymes and the corresponding gene sequences of several cellulolytic enzymes as a first example for the feasibility of this approach.

    List of papers
    1. Applying theories of microbial metabolism for induction of targeted enzyme activity in a methanogenic microbial community at a metabolic steady state
    Open this publication in new window or tab >>Applying theories of microbial metabolism for induction of targeted enzyme activity in a methanogenic microbial community at a metabolic steady state
    2016 (English)In: Applied Microbiology and Biotechnology, ISSN 0175-7598, E-ISSN 1432-0614, Vol. 100, no 18, p. 7989-8002Article in journal (Refereed) Published
    Abstract [en]

    Novel enzymes that are stable in diverse conditions are intensively sought because they offer major potential advantages in industrial biotechnology, and microorganisms in extreme environments are key sources of such enzymes. However, most potentially valuable enzymes are currently inaccessible due to the pure culturing problem of microorganisms. Novel metagenomic and metaproteomic techniques that circumvent the need for pure cultures have theoretically provided possibilities to identify all genes and all proteins in microbial communities, but these techniques have not been widely used to directly identify specific enzymes because they generate vast amounts of extraneous data. In a first step towards developing a metaproteomic approach to pinpoint targeted extracellular hydrolytic enzymes of choice in microbial communities, we have generated and analyzed the necessary conditions for such an approach by the use of a methanogenic microbial community maintained on a chemically defined medium. The results show that a metabolic steady state of the microbial community could be reached, at which the expression of the targeted hydrolytic enzymes were suppressed, and that upon enzyme induction a distinct increase in the targeted enzyme expression was obtained. Furthermore, no cross talk in expression was detected between the two focal types of enzyme activities under their respective inductive conditions. Thus, the described approach should be useful to generate ideal samples, collected before and after selective induction, in controlled microbial communities to clearly discriminate between constituently expressed proteins and extracellular hydrolytic enzymes that are specifically induced, thereby reducing the analysis to only those proteins that are distinctively up-regulated.

    Place, publisher, year, edition, pages
    Springer, 2016
    Keywords
    Microbial community; Enzyme discovery; Metaproteomics; Biogas; Cellulase; Protease
    National Category
    Microbiology
    Identifiers
    urn:nbn:se:liu:diva-131888 (URN)10.1007/s00253-016-7547-z (DOI)000382008000017 ()27115757 (PubMedID)
    Note

    Funding Agencies|Swedish Research Council [621-2009-4150]; InZymes Biotech AB

    Available from: 2016-10-13 Created: 2016-10-11 Last updated: 2018-05-15
    2. Assessment of sample preparation methods for metaproteomics of extracellular proteins
    Open this publication in new window or tab >>Assessment of sample preparation methods for metaproteomics of extracellular proteins
    2017 (English)In: Analytical Biochemistry, ISSN 0003-2697, E-ISSN 1096-0309, Vol. 516, p. 23-36Article in journal (Refereed) Published
    Abstract [en]

    Enzyme discovery in individual strains of microorganisms is compromised by the limitations of pure culturing. In principle, metaproteomics allows for fractionation and study of different parts of the protein complement but has hitherto mainly been used to identify intracellular proteins. However, the extracellular environment is also expected to comprise a wealth of information regarding important proteins. An absolute requirement for metaproteomic studies of protein expression, and irrespective of downstream methods for analysis, is that sample preparation methods provide clean, concentrated and representative samples of the protein complement. A battery of methods for concentration, extraction, precipitation and resolubilization of proteins in the extracellular environment of a constructed microbial community was assessed by means of 2D gel electrophoresis and image analysis to elucidate whether it is possible to make the extracellular protein complement available for metaproteomic analysis. Most methods failed to provide pure samples and therefore negatively influenced protein gel migration and gel background clarity. However, one direct precipitation method (TCA-DOC/acetone) and one extraction/precipitation method (phenol/methanol) provided complementary high quality 2D gels that allowed for high spot detection ability and thereby also spot detection of less abundant extracellular proteins.

    Place, publisher, year, edition, pages
    Elsevier, 2017
    Keywords
    Enzyme discovery, Microbial community, Metaproteome, Extracellular, Sample preparation, 2D gel electrophoresis
    National Category
    Analytical Chemistry Biocatalysis and Enzyme Technology
    Identifiers
    urn:nbn:se:liu:diva-132902 (URN)10.1016/j.ab.2016.10.008 (DOI)000388056800005 ()27742212 (PubMedID)
    Funder
    Swedish Research Council, 621-2009-4150
    Note

    Funding agencies: Swedish Research Council [621-2009-4150]; Tekniska Verken i Linkoping AB; InZymes Biotech AB

    Available from: 2016-12-01 Created: 2016-12-01 Last updated: 2018-05-15Bibliographically approved
  • 39.
    Speda, Jutta
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Johansson, Mikaela
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Jonsson, Bengt-Harald
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Karlsson, Martin
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering. InZymes Biotech AB, Gjuterigatan 1B, S-58273 Linkoping, Sweden.
    Applying theories of microbial metabolism for induction of targeted enzyme activity in a methanogenic microbial community at a metabolic steady state2016In: Applied Microbiology and Biotechnology, ISSN 0175-7598, E-ISSN 1432-0614, Vol. 100, no 18, p. 7989-8002Article in journal (Refereed)
    Abstract [en]

    Novel enzymes that are stable in diverse conditions are intensively sought because they offer major potential advantages in industrial biotechnology, and microorganisms in extreme environments are key sources of such enzymes. However, most potentially valuable enzymes are currently inaccessible due to the pure culturing problem of microorganisms. Novel metagenomic and metaproteomic techniques that circumvent the need for pure cultures have theoretically provided possibilities to identify all genes and all proteins in microbial communities, but these techniques have not been widely used to directly identify specific enzymes because they generate vast amounts of extraneous data. In a first step towards developing a metaproteomic approach to pinpoint targeted extracellular hydrolytic enzymes of choice in microbial communities, we have generated and analyzed the necessary conditions for such an approach by the use of a methanogenic microbial community maintained on a chemically defined medium. The results show that a metabolic steady state of the microbial community could be reached, at which the expression of the targeted hydrolytic enzymes were suppressed, and that upon enzyme induction a distinct increase in the targeted enzyme expression was obtained. Furthermore, no cross talk in expression was detected between the two focal types of enzyme activities under their respective inductive conditions. Thus, the described approach should be useful to generate ideal samples, collected before and after selective induction, in controlled microbial communities to clearly discriminate between constituently expressed proteins and extracellular hydrolytic enzymes that are specifically induced, thereby reducing the analysis to only those proteins that are distinctively up-regulated.

  • 40.
    Speda, Jutta
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Jonsson, Bengt-Harald
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Carlsson, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Karlsson, Martin
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering. InZymes Biotech AB, Gjuterigatan 1B, S-58273 Linkoping, Sweden.
    Metaproteomics-guided selection of targeted enzymes for bioprospecting of mixed microbial communities2017In: Biotechnology for Biofuels, ISSN 1754-6834, E-ISSN 1754-6834, Vol. 10, article id 128Article in journal (Refereed)
    Abstract [en]

    Background: Hitherto, the main goal of metaproteomic analyses has been to characterize the functional role of particular microorganisms in the microbial ecology of various microbial communities. Recently, it has been suggested that metaproteomics could be used for bioprospecting microbial communities to query for the most active enzymes to improve the selection process of industrially relevant enzymes. In the present study, to reduce the complexity of metaproteomic samples for targeted bioprospecting of novel enzymes, a microbial community capable of producing cellulases was maintained on a chemically defined medium in an enzyme suppressed metabolic steady state. From this state, it was possible to specifically and distinctively induce the desired cellulolytic activity. The extracellular fraction of the protein complement of the induced sample could thereby be purified and compared to a non-induced sample of the same community by differential gel electrophoresis to discriminate between constitutively expressed proteins and proteins upregulated in response to the inducing substance. Results: Using the applied approach, downstream analysis by mass spectrometry could be limited to only proteins recognized as upregulated in the cellulase-induced sample. Of 39 selected proteins, the majority were found to be linked to the need to degrade, take up, and metabolize cellulose. In addition, 28 (72%) of the proteins were non-cytosolic and 17 (44%) were annotated as carbohydrate-active enzymes. The results demonstrated both the applicability of the proposed approach for identifying extracellular proteins and guiding the selection of proteins toward those specifically upregulated and targeted by the enzyme inducing substance. Further, because identification of interesting proteins was based on the regulation of enzyme expression in response to a need to hydrolyze and utilize a specific substance, other unexpected enzyme activities were able to be identified. Conclusions: The described approach created the conditions necessary to be able to select relevant extracellular enzymes that were extracted from the enzyme-induced microbial community. However, for the purpose of bioprospecting for enzymes to clone, produce, and characterize for practical applications, it was concluded that identification against public databases was not sufficient to identify the correct gene or protein sequence for cloning of the identified novel enzymes.

  • 41.
    Sun, Pan
    et al.
    Shandong University, Peoples R China.
    Bi, Zhenwang
    Shandong Centre Disease Control and Prevent, Peoples R China.
    Nilsson, Maud
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences.
    Zheng, Beiwen
    Zhejiang University, Peoples R China.
    Berglund, Björn
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences.
    Stalsby Lundborg, Cecilia
    Karolinska Institute, Sweden.
    Borjesson, Stefan
    National Vet Institute, Sweden.
    Li, Xuewen
    Shandong University, Peoples R China.
    Chen, Baoli
    Shandong Centre Disease Control and Prevent, Peoples R China.
    Yin, Hong
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences.
    Nilsson, Lennart E
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences.
    Occurrence of bla(KPC-2), bla(CTX-M), and mcr-1 in Enterobacteriaceae from Well Water in Rural China2017In: Antimicrobial Agents and Chemotherapy, ISSN 0066-4804, E-ISSN 1098-6596, Vol. 61, no 4, article id e02569Article in journal (Refereed)
    Abstract [en]

    We report on the coexistence of mcr-1 and blaCTX-M in multidrugresistant, extended-spectrum beta-lactamase-producing Escherichia coli belonging to the sequence type 10 complex isolated from well water in rural China. Raoultella ornithinolytica with bla(KPC-2) was also detected in well water from the same area. This study shows that genes coding for resistance to last-resort antibiotics are present in wells in rural China, indicating a potential source of antibiotic resistance.

  • 42.
    Sundh, Ingvar
    et al.
    Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Bastviken, David
    Linköping University, Department of Thematic Studies, Department of Water and Environmental Studies. Linköping University, Faculty of Arts and Sciences.
    Tranvik, Lars J.
    Limnology, Department of Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
    Abundance, activity, and community structure of pelagic methane-oxidizing bacteria in temperate lakes2005In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 71, no 11, p. 6746-6752Article in journal (Refereed)
    Abstract [en]

    The abundance and activity of methane-oxidizing bacteria (MOB) in the water column were investigated in three lakes with different contents of nutrients and humic substances. The abundance of MOB was determined by analysis of group-specific phospholipid fatty acids from type I and type 11 MOB, and in situ activity was measured with a 14 CH, transformation method. The fatty acid analyses indicated that type I MOB most similar to species of Methylomonas, Methylomicrobium, and Methylosarcina made a substantial contribution (up to 41%) to the total bacterial biomass, whereas fatty acids from type 11 MOB generally had very low concentrations. The MOB biomass and oxidation activity were positively correlated and were highest in the hypo- and metalimnion during summer stratification, whereas under ice during winter, maxima occurred close to the sediments. The methanotroph biomass-specific oxidation rate (V) ranged from 0.001 to 2.77 mg CH4-C mg(-1) C day(-1) and was positively correlated with methane concentration, suggesting that methane supply largely determined the activity and biomass distribution of MOB. Our results demonstrate that type I MOB often are a large component of pelagic bacterial communities in temperate lakes. They represent a potentially important pathway for reentry of carbon and energy into pelagic food webs that would otherwise be lost as evasion of CH,.

  • 43.
    Turner, Anthony
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biosensors and Bioelectronics. Linköping University, The Institute of Technology.
    Sebastian-Avila, J. L.
    Beni, Valerio
    Linköping University, Department of Physics, Chemistry and Biology, Biosensors and Bioelectronics. Linköping University, The Institute of Technology.
    Samitier, J.
    Prieto-Simon, B.
    Aptamer-based electrochemical assay fordetection of Salmonella typhimurium2013In: BioSensing Technologies, 2013 / [ed] Richard Luxton, Amsterdam: Elsevier, 2013, p. P 214-Conference paper (Other academic)
  • 44.
    Ulrich, G. A.
    et al.
    Department of Botany and Microbiology, 770 Van Vleet Oval, University of Oklahoma, Norman, OK 73019-0245, USA.
    Martino, D.
    Department of Oceanography, Texas A&M University, College Station, TX 77843, USA.
    Burger, K.
    Department of Geology and Geophysics, Texas A&M University, College Station, TX 77843, USA.
    Routh, Joyanto
    Department of Geology and Geophysics, Texas A&M University, College Station, TX 77843, USA.
    Grossman, E. L.
    Department of Geology and Geophysics, Texas A&M University, College Station, TX 77843, USA.
    Ammerman, J. W.
    Department of Oceanography, Texas A&M University, College Station, TX 77843, USA.
    Suflita, J. M.
    Department of Botany and Microbiology, 770 Van Vleet Oval, University of Oklahoma, Norman, OK 73019-0245, USA.
    Sulfur Cycling in the Terrestrial Subsurface: Commensal Interactions, Spatial Scales, and Microbial Heterogeneity1998In: Microbial Ecology, ISSN 0095-3628, E-ISSN 1432-184X, Vol. 36, no 2, p. 141-151Article in journal (Refereed)
    Abstract [en]

    Microbiological, geochemical, and isotopic analyses of sediment and water samples from the unconsolidated Yegua formation in east-central Texas were used to assess microbial processes in the terrestrial subsurface. Previous geochemical studies suggested that sulfide oxidation at shallow depths may provide sulfate for sulfate-reducing bacteria (SRB) in deeper aquifer formations. The present study further examines this possibility, and provides a more detailed evaluation of the relationship between microbial activity, lithology, and the geochemical environment on meter-to-millimeter scales. Sediment of varied lithology (sands, silts, clays, lignite) was collected from two boreholes, to depths of 30 m. Our findings suggest that pyrite oxidation strongly influences the geochemical environment in shallow sediments ( 5 m), and produces acidic waters (pH 3.8) that are rich in sulfate (28 mM) and ferrous iron (0.3 mM). Sulfur and iron-oxidizing bacteria are readily detected in shallow sediments; they likely play an indirect role in pyrite oxidation. In consistent fashion, there is a relative paucity of pyrite in shallow sediments and a low 34S/32S-sulfate ratio (0.2ᅵ) (reflecting contributions from 34S-depleted sulfides) in shallow regions. Pyrite oxidation likely provides a sulfate source for both oxic and anoxic aquifers in the region. A variety of assays and direct-imaging techniques of 35S-sulfide production in sediment cores indicates that sulfate reduction occurs in both the oxidizing and reducing portions of the sediment profile, with a high degree of spatial variability. Narrow zones of activity were detected in sands that were juxtaposed to clay or lignite-rich sediments. The fermentation of organic matter in the lignite-rich laminae provides small molecular weight organic acids to support sulfate reduction in neighboring sands. Consequently, sulfur cycling in shallow sediments, and sulfate transport represent important mechanisms for commensal interaction among subsurface microorganisms by providing electron donors for chemoautotrophic bacteria and electron acceptors for SRB. The activity of SRB is linked to the availability of suitable electron donors from spatially distinct zones.

  • 45.
    Vadovic, P.
    et al.
    Laboratory for Diagnosis and Prevention of Rickettsial and Chlamydial Infections, Institute of Virology, SAS, Bratislava, Slovakia, Czech Republic.
    Fuleova, A.
    Laboratory for Diagnosis and Prevention of Rickettsial and Chlamydial Infections, Institute of Virology, SAS, Bratislava, Slovakia, Czech Republic.
    Ihnatko, Robert
    Laboratory for Diagnosis and Prevention of Rickettsial and Chlamydial Infections, Institute of Virology, SAS, Bratislava, Slovakia, Czech Republic.
    Skultety, L.
    Laboratory for Diagnosis and Prevention of Rickettsial and Chlamydial Infections, Institute of Virology, SAS, Bratislava, Slovakia, Czech Republic.
    Halada, P.
    Institute of Microbiology, v.v.i, CAS, Prague, Czech Republic.
    Toman, R.
    Laboratory for Diagnosis and Prevention of Rickettsial and Chlamydial Infections, Institute of Virology, SAS, Bratislava, Slovakia, Czech Republic.
    Structural studies of lipid A from a lipopolysaccharide of the Coxiella burnetii isolate RSA 514 (Crazy)2009In: Clinical Microbiology and Infection, ISSN 1198-743X, E-ISSN 1469-0691, Vol. 15, p. 198-199Article in journal (Refereed)
    Abstract [en]

    Coxiella burnetii is the aetiological agent of Q fever. LPS is a major factor of virulence of the bacterium, and therefore studies of its structure/function relationship studies are of potential interest. In virulent phase I, C. burnetii biosynthesises smooth LPS I with an O-specific chain, whereas in avirulent phase II, it synthesises rough LPS II [1]. Both LPSs were isolated [1] from the C. burnetii isolates RSA 493, clone 7, and RSA 439, clone 4, respectively. We investigated an LPS from the C. burnetii clonal derivative RSA 514 named ‘Crazy’ (Cr), which was isolated from the placental tissue of a guinea pig infected with the RSA 493 isolate for 343 days [2]. The major emphasis was put on the lipid A as no data on its structure have been available thus far. It has been recognised recently that variation of the lipid A domain of LPS serves as one strategy utilised [3] by Gram-negative bacteria to promote survival by providing resistance to components of the innate immune system and helping to evade recognition by Toll-like receptor 4. Thus, it was of interest to see if the long-term survival of the microorganism in the host led to modifications in its lipid A in comparison with the known structures for lipid A from the C. burnetii isolate Priscilla [4] and also those established most recently in the LPS I and LPS II (P.V. Vadovic and R.T. Toman, unpublished results).

  • 46.
    Wiberg, Heli
    Linköping University, The Department of Physics, Chemistry and Biology.
    Termofil rötning av drankvatten2007Independent thesis Advanced level (degree of Magister), 20 points / 30 hpStudent thesis
    Abstract [sv]

    Biogasprocessen är en komplex anaerob nedbrytningskedja där olika mikroorganismer är inblandade. Vanligast är att biogas produceras i mesofil rötning (cirka 38 oC), men även termofil rötning används (> 50 oC).

    Svensk Biogas i Norrköping använder återstoden av etanoldestillationen hos en närliggande etanolproducent (drankvatten) som substrat. Substratets höga temperatur vid leverans motiverar termofilt rötningsförsök av drankvatten.

    Försöket genomfördes i 55 oC med två kontinuerligt omrörda tankreaktorer (CSTR) och en termofil ymp. Biogasproduktion av drankvatten undersöktes. Sätt att hantera och motverka höga ammoniumhalter, samt effekter av näringslösningstillsats undersöktes. Det tog cirka 30 dagar för ympen att acceptera det nya substratet och då hade tillsats av processhjälpmedel KMB1 samt järnklorid använts. Reaktorerna kunde belastas med 3 g VS / (L • dygn) (VS, volatile solids, glödförlust). Den specifika gasproduktionen var 0,6 – 0,7 L / g VS och metanhalten ungefär 45 %. Höga ammoniumhalter motverkades genom förkortning av uppehållstiden. Under en period tillsattes nickelklorid i en av reaktorerna och under denna period hade reaktorn med nickelkloridtillsats något bättre specifik gasproduktion jämfört med reaktorn där ingen nickelklorid tillsattes.

    Drankvatten kan rötas under termofila förhållanden. För att temperaturförändring vid biogasanläggningen i Norrköping ska var ekonomiskt försvarbart måste processen klara högre belastning.

  • 47.
    Ziels, Ryan
    et al.
    Linköping University, Biogas Research Center. Civil and Environmental Engineering, University of Washington, WA, USA.
    Karlsson, Anna
    Linköping University, Biogas Research Center. Scandinavian Biogas Fuels AB, Sweden.
    Beck, David A.C.
    Science Institute, University of Washington, WA, USA.
    Ejlertsson, Jörgen
    Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Biogas Research Center. Linköping University, Faculty of Arts and Sciences. Scandinavian Biogas Fuels AB, Sweden.
    Shakeri Yekta, Sepehr
    Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Biogas Research Center. Linköping University, Faculty of Arts and Sciences.
    Björn, Annika
    Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Biogas Research Center. Linköping University, Faculty of Arts and Sciences.
    Stensel, H. David
    Civil and Environmental Engineering, University of Washington, WA, USA.
    Svensson, Bo H.
    Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Biogas Research Center. Linköping University, Faculty of Arts and Sciences.
    Microbial community adaptation influences long-chain fatty acidconversion during anaerobic codigestion of fats, oils, and grease withmunicipal sludge2016In: Water Research, ISSN 0043-1354, E-ISSN 1879-2448, Vol. 103, p. 372-382Article in journal (Refereed)
    Abstract [en]

    Codigesting fats, oils, and greases with municipal wastewater sludge can greatly improve biomethanerecovery at wastewater treatment facilities. Process loading rates of fats, oils, and greases have beenpreviously tested with little knowledge of the digester microbial community structure, and high transientfat loadings have led to long chain fatty acid (LCFA) accumulation and digester upsets. This studyutilized recently-developed quantitative PCR assays for syntrophic LCFA-degrading bacteria along with16S amplicon sequencing to relate changes in microbial community structure to LCFA accumulationduring transient loading increases to an anaerobic codigester receiving waste restaurant oil andmunicipal wastewater sludge. The 16S rRNA gene concentration of the syntrophic b-oxidizing genusSyntrophomonas increased to ~15% of the Bacteria community in the codigester, but stayed below 3% inthe control digester that was fed only wastewater sludge. Methanosaeta and Methanospirillum were thedominant methanogenic genera enriched in the codigester, and together comprised over 80% of theArchaea community by the end of the experimental period. Constrained ordination showed that changesin the codigester Bacteria and Archaea community structures were related to measures of digester performance.Notably, the effluent LCFA concentration in the codigester was positively correlated to thespecific loading rate of waste oil normalized to the Syntrophomonas 16S rRNA concentration. Specificloading rates of 0e1.5 1012 g VS oil/16S gene copies-day resulted in LCFA concentrations below 30 mg/g TS, whereas LCFA accumulated up to 104 mg/g TS at higher transient loading rates. Based on thecommunity-dependent loading limitations found, enhanced biomethane production from high loadingsof fats, oils and greases can be achieved by promoting a higher biomass of slow-growing syntrophicconsortia, such as with longer digester solids retention times. This work also demonstrates the potentialfor controlling the loading rate of fats, oils, and greases based on the analysis of the codigester communitystructure, such as with quantitative PCR measurements of syntrophic LCFA-degrading bacteriaabundance.

  • 48.
    Ziels, Ryan M.
    et al.
    University of Washington, WA 98195 USA.
    Beck, David A. C.
    University of Washington, WA 98195 USA; University of Washington, WA 98195 USA.
    Genero, Magalí Martí
    Linköping University, The Tema Institute, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences.
    Gough, Heidi L.
    University of Washington, WA 98195 USA.
    Stensel, H. David
    University of Washington, WA 98195 USA.
    Svensson, Bo
    Linköping University, The Tema Institute, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences.
    Monitoring the dynamics of syntrophic beta-oxidizing bacteria during anaerobic degradation of oleic acid by quantitative PCR2015In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 91, no 4Article in journal (Refereed)
    Abstract [en]

    The ecophysiology of long-chain fatty acid-degrading syntrophic beta-oxidizing bacteria has been poorly understood due to a lack of quantitative abundance data. Here, TaqMan quantitative PCR (qPCR) assays targeting the 16S rRNA gene of the known mesophilic syntrophic beta-oxidizing bacterial genera Syntrophomonas and Syntrophus were developed and validated. Microbial community dynamics were followed using qPCR and Illumina-based high-throughput amplicon sequencing in triplicate methanogenic bioreactors subjected to five consecutive batch feedings of oleic acid. With repeated oleic acid feeding, the initial specific methane production rate significantly increased along with the relative abundances of Syntrophomonas and methanogenic archaea in the bioreactor communities. The novel qPCR assays showed that Syntrophomonas increased from 7 to 31% of the bacterial community 16S rRNA gene concentration, whereas that of Syntrophus decreased from 0.02 to less than 0.005%. High-throughput amplicon sequencing also revealed that Syntrophomonas became the dominant genus within the bioreactor microbiomes. These results suggest that increased specific mineralization rates of oleic acid were attributed to quantitative shifts within the microbial communities toward higher abundances of syntrophic beta-oxidizing bacteria and methanogenic archaea. The novel qPCR assays targeting syntrophic beta-oxidizing bacteria may thus serve as monitoring tools to indicate the fatty acid beta-oxidization potential of anaerobic digester communities.

  • 49.
    Ziels, Ryan M.
    et al.
    Department of Civil Engineering, The University of British Columbia, Vancouver, BC, Canada.
    Svensson, Bo H
    Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences. Linköping University, Biogas Research Center.
    Sundberg, Carina
    Linköping University, Department of Management and Engineering, Environmental Technology and Management. Linköping University, Faculty of Arts and Sciences.
    Larsson, Madeleine
    Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences. Linköping University, Biogas Research Center.
    Karlsson, Anna
    Scandinavian Biogas Fuels AB, Stockholm, Sweden.
    Shakeri Yekta, Sepehr
    Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences. Linköping University, Biogas Research Center.
    Microbial rRNA gene expression and co-occurrence profiles associate with biokinetics and elemental composition in full-scale anaerobic digesters2018In: Microbial Biotechnology, ISSN 1751-7907, E-ISSN 1751-7915, Vol. 11, no 4, p. 694-709Article in journal (Refereed)
    Abstract [en]

    This study examined whether the abundance and expression of microbial 16S rRNA genes were associated with elemental concentrations and substrate conversion biokinetics in 20 full-scale anaerobic digesters, including seven municipal sewage sludge (SS) digesters and 13 industrial codigesters. SS digester contents had higher methane production rates from acetate, propionate and phenyl acetate compared to industrial codigesters. SS digesters and industrial codigesters were distinctly clustered based on their elemental concentrations, with higher concentrations of NH3-N, Cl, K and Na observed in codigesters. Amplicon sequencing of 16S rRNA genes and reverse-transcribed 16S rRNA revealed divergent grouping of microbial communities between mesophilic SS digesters, mesophilic codigesters and thermophilic digesters. Higher intradigester distances between Archaea 16S rRNA and rRNA gene profiles were observed in mesophilic codigesters, which also had the lowest acetate utilization biokinetics. Constrained ordination showed that microbial rRNA and rRNA gene profiles were significantly associated with maximum methane production rates from acetate, propionate, oleate and phenyl acetate, as well as concentrations of NH3-N, Fe, S, Mo and Ni. A co-occurrence network of rRNA gene expression confirmed the three main clusters of anaerobic digester communities based on active populations. Syntrophic and methanogenic taxa were highly represented within the subnetworks, indicating that obligate energy-sharing partnerships play critical roles in stabilizing the digester microbiome. Overall, these results provide new evidence showing that different feed substrates associate with different micronutrient compositions in anaerobic digesters, which in turn may influence microbial abundance, activity and function.

  • 50.
    Zou, Huiyun
    et al.
    Shandong Univ, Peoples R China.
    Zheng, Beiwen
    Zhejiang Univ, Peoples R China.
    Sun, Mingli
    Ctr Dis Prevent and Control, Peoples R China.
    Ottoson, Jakob
    Natl Food Agcy, Sweden.
    Li, Yubo
    Ctr Dis Prevent and Control, Peoples R China.
    Berglund, Björn
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology, Infection and Inflammation. Linköping University, Faculty of Medicine and Health Sciences. Zhejiang Univ, Peoples R China.
    Chi, Xiaohui
    Shandong Univ, Peoples R China.
    Ji, Xiang
    Shandong Univ, Peoples R China.
    Li, Xuewen
    Shandong Univ, Peoples R China.
    Lundborg, Cecilia Stalsby
    Karolinska Inst, Sweden.
    Nilsson, Lennart
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology, Infection and Inflammation. Linköping University, Faculty of Medicine and Health Sciences.
    Evaluating Dissemination Mechanisms of Antibiotic-Resistant Bacteria in Rural Environments in China by Using CTX-M-Producing Escherichia coli as an Indicator2019In: Microbial Drug Resistance, ISSN 1076-6294, E-ISSN 1931-8448Article in journal (Refereed)
    Abstract [en]

    It is becoming increasingly recognized that the environment plays an important role both in the emergence and in dissemination of antibiotic-resistant bacteria (ARB), Mechanisms and factors facilitating this development are, however, not yet well understood. The high detection rate of CTX-M genes in environmental sources provides an opportunity to explore this issue. In this study, 88 CTX-M-producing Escherichia coli were isolated from 30 pig feces samples from 30 pig farms and 201 environmental samples. CTX-M-producing E. coli was detected with the following frequencies in the different types of samples: pig feces, 73%; river water, 64%; river sediment, 52%; wastewater, 31%; drinking water, 23%; outlet sediment, 21%; soil, 17%; and vegetables, 4.4%. Dissemination of CTX-M-producing E. coli to different environmental matrices was evaluated by analyzing the genetic relatedness of isolates from different environmental sources, and putative transmission routes through bird feces, pig feces, drinking water, river sediment, river water, and wastewater were hypothesized. Dissemination through these routes is likely facilitated by anthropogenic activities and environmental factors. Wild birds as potential vectors for dissemination of CTX-M-producing E. coli have the capacity to spread ARB across long distances. Regional dissemination between different environmental matrices of CTX-M-producing E. coli increases the exposure risk of humans and animals in the area.

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