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Alexander Mellmann - One of the best experts on this subject based on the ideXlab platform.
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Carriage of Shiga toxin phage profoundly affects Escherichia coli gene expression and carbon source utilization
BMC Genomics, 2019Co-Authors: Petya Berger, Ivan U. Kouzel, Michael Berger, Nadja Haarmann, Ulrich Dobrindt, Gerald B. Koudelka, Alexander MellmannAbstract:Background Enterohemorrhagic Escherichia coli ( E. coli ) are intestinal pathogenic bacteria that cause life-threatening disease in humans. Their cardinal virulence factor is Shiga toxin (Stx), which is encoded on lambdoid phages integrated in the chromosome. Stx phages can infect and lysogenize susceptible bacteria, thus either increasing the virulence of already pathogenic bacterial hosts or transforming commensal strains into potential pathogens. There is increasing evidence that Stx phage-encoded factors adaptively regulate bacterial host gene expression. Here, we investigated the effects of Stx phage carriage in E. coli K-12 strain MG1655. We compared the transcriptome and phenotype of naive MG1655 and two lysogens carrying closely related Stx2a phages: ϕO104 from the exceptionally pathogenic 2011 E. coli O104:H4 outbreak strain and ϕPA8 from an E. coli O157:H7 isolate. Results Analysis of quantitative RNA sequencing results showed that, in comparison to naive MG1655, genes involved in Mixed Acid Fermentation were upregulated, while genes encoding NADH dehydrogenase I, TCA cycle enzymes and proteins involved in the transport and assimilation of carbon sources were downregulated in MG1655::ϕO104 and MG1655::ϕPA8. The majority of the changes in gene expression were found associated with the corresponding phenotypes. Notably, the Stx2a phage lysogens displayed moderate to severe growth defects in minimal medium supplemented with single carbon sources, e.g. galactose, ribose, L-lactate. In addition, in phenotype microarray assays, the Stx2a phage lysogens were characterized by a significant decrease in the cell respiration with gluconeogenic substrates such as amino Acids, nucleosides, carboxylic and dicarboxylic Acids. In contrast, MG1655::ϕO104 and MG1655::ϕPA8 displayed enhanced respiration with several sugar components of the intestinal mucus, e.g. arabinose, fucose, N-acetyl-D-glucosamine. We also found that prophage-encoded factors distinct from CI and Cro were responsible for the carbon utilization phenotypes of the Stx2a phage lysogens. Conclusions Our study reveals a profound impact of the Stx phage carriage on E. coli carbon source utilization. The Stx2a prophage appears to reprogram the carbon metabolism of its bacterial host by turning down aerobic metabolism in favour of Mixed Acid Fermentation.
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Carriage of Shiga toxin phage profoundly affects Escherichia coli gene expression and carbon source utilization.
BMC genomics, 2019Co-Authors: Petya Berger, Ivan U. Kouzel, Michael Berger, Nadja Haarmann, Ulrich Dobrindt, Gerald B. Koudelka, Alexander MellmannAbstract:Enterohemorrhagic Escherichia coli (E. coli) are intestinal pathogenic bacteria that cause life-threatening disease in humans. Their cardinal virulence factor is Shiga toxin (Stx), which is encoded on lambdoid phages integrated in the chromosome. Stx phages can infect and lysogenize susceptible bacteria, thus either increasing the virulence of already pathogenic bacterial hosts or transforming commensal strains into potential pathogens. There is increasing evidence that Stx phage-encoded factors adaptively regulate bacterial host gene expression. Here, we investigated the effects of Stx phage carriage in E. coli K-12 strain MG1655. We compared the transcriptome and phenotype of naive MG1655 and two lysogens carrying closely related Stx2a phages: ϕO104 from the exceptionally pathogenic 2011 E. coli O104:H4 outbreak strain and ϕPA8 from an E. coli O157:H7 isolate. Analysis of quantitative RNA sequencing results showed that, in comparison to naive MG1655, genes involved in Mixed Acid Fermentation were upregulated, while genes encoding NADH dehydrogenase I, TCA cycle enzymes and proteins involved in the transport and assimilation of carbon sources were downregulated in MG1655::ϕO104 and MG1655::ϕPA8. The majority of the changes in gene expression were found associated with the corresponding phenotypes. Notably, the Stx2a phage lysogens displayed moderate to severe growth defects in minimal medium supplemented with single carbon sources, e.g. galactose, ribose, L-lactate. In addition, in phenotype microarray assays, the Stx2a phage lysogens were characterized by a significant decrease in the cell respiration with gluconeogenic substrates such as amino Acids, nucleosides, carboxylic and dicarboxylic Acids. In contrast, MG1655::ϕO104 and MG1655::ϕPA8 displayed enhanced respiration with several sugar components of the intestinal mucus, e.g. arabinose, fucose, N-acetyl-D-glucosamine. We also found that prophage-encoded factors distinct from CI and Cro were responsible for the carbon utilization phenotypes of the Stx2a phage lysogens. Our study reveals a profound impact of the Stx phage carriage on E. coli carbon source utilization. The Stx2a prophage appears to reprogram the carbon metabolism of its bacterial host by turning down aerobic metabolism in favour of Mixed Acid Fermentation.
Ashok Pandey - One of the best experts on this subject based on the ideXlab platform.
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experimental design to enhance the production of l lactic Acid from steam exploded wood hydrolysate using rhizopus oryzae in a Mixed Acid Fermentation
Process Biochemistry, 1999Co-Authors: Adenise Lorenci Woiciechowski, Carlos Ricardo Soccol, Luis P. Ramos, Ashok PandeyAbstract:Abstract The Fermentation of hemicellulosic hydrolysate from Pinus taeda chips, using the fungal culture Rhizopus oryzae , was carried out to produce l -(+)-lactic Acid and to optimize and enhance the biological conversion of reducing sugar into l -(+)-lactic Acid using the experimental design to evaluate the culture conditions. The first factorial design based on surface response with five factors (agitation level, substrate concentration, CaCO 3 concentration, C/N and C/P ratios) at low levels and one medium point was performed to optimize culture conditions. The second study tested two factors (substrate concentration and C/N ratio) at three levels. The statistical analysis of the data obtained from the factorial study showed that a C/N ratio of 35 and substrate concentration of 90 g/litre were the best conditions to produce l -(+)-lactic Acid with R. oryzae on P. taeda hydrolysate, but in this case the statistical projection was not correct and the real optimized conditions were C/N ratio of 55 and substrate concentration of 75 g/litre of reducing sugar.
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Experimental design to enhance the production of l-(+)-lactic Acid from steam-exploded wood hydrolysate using Rhizopus oryzae in a Mixed-Acid Fermentation
Process Biochemistry, 1999Co-Authors: Adenise Lorenci Woiciechowski, Carlos Ricardo Soccol, Luis P. Ramos, Ashok PandeyAbstract:Abstract The Fermentation of hemicellulosic hydrolysate from Pinus taeda chips, using the fungal culture Rhizopus oryzae , was carried out to produce l -(+)-lactic Acid and to optimize and enhance the biological conversion of reducing sugar into l -(+)-lactic Acid using the experimental design to evaluate the culture conditions. The first factorial design based on surface response with five factors (agitation level, substrate concentration, CaCO 3 concentration, C/N and C/P ratios) at low levels and one medium point was performed to optimize culture conditions. The second study tested two factors (substrate concentration and C/N ratio) at three levels. The statistical analysis of the data obtained from the factorial study showed that a C/N ratio of 35 and substrate concentration of 90 g/litre were the best conditions to produce l -(+)-lactic Acid with R. oryzae on P. taeda hydrolysate, but in this case the statistical projection was not correct and the real optimized conditions were C/N ratio of 55 and substrate concentration of 75 g/litre of reducing sugar.
Mark T Holtzapple - One of the best experts on this subject based on the ideXlab platform.
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propagated fixed bed Mixed Acid Fermentation effect of volatile solid loading rate and agitation at near neutral ph
Bioresource Technology, 2012Co-Authors: Kristina W Golub, Stacey R Golub, D M Meysing, Mark T HoltzappleAbstract:Abstract To increase conversion and product concentration, Mixed-Acid Fermentation can use a countercurrent strategy where solids and liquids pass in opposite directions through a series of fermentors. To limit the requirement for moving solids, this study employed a propagated fixed-bed Fermentation, where solids were stationary and only liquid was transferred. To evaluate the role of agitation, continuous mixing was compared with periodic mixing. The periodically Mixed Fermentation had similar conversion, but lower yield and selectivity. Increasing volatile solid loading rate from 1.5 to 5.1 g non-Acid volatile solids/(L liq ·d) and increasing liquid retention time decreased yield, conversion, selectivity, but increased product concentrations. Compared to a previous study at high pH (∼9), this study achieved higher performance at near neutral pH (∼6.5) and optimal C–N ratios. Compared to countercurrent Fermentation, propagated fixed-bed Fermentations have similar selectivities and produce similar proportions of acetic Acid, but have lower yields, conversion, productivities, and Acid concentrations.
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influence of carbon to nitrogen ratio on the Mixed Acid Fermentation of wastewater sludge and pretreated bagasse
Bioresource Technology, 2012Co-Authors: Hema Rughoonundun, Romeela Mohee, Mark T HoltzappleAbstract:Abstract In Mixed-Acid Fermentation, carbon and nitrogen are critical nutrients for cell synthesis, growth, and metabolism. To study the effect of C/N ratio on the yield of carboxylic Acids, wastewater sludge was co-digested with pretreated bagasse; the amount of sludge was varied from 0% to 100% (dry weight basis). Fermentation was performed at 55 °C at a solids concentration of 50 g dry solids/L, and Iodoform was used to inhibit methane formation. It was observed that C/N ratio significantly affects yield, especially at extreme ratios. The highest carboxylic Acid yield (0.36 g Acids/g VS fed) was obtained for C/N ratios ranging from 13 to 25 g C/g N. C/N ratio also affected the composition profile of carboxylic Acids. In all mixtures, acetic Acid was the major fraction, followed by butyric Acid. However, i -butyric, valeric Acid, and i -valeric Acid increased with increasing sludge content, which likely resulted from protein degradation.
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propagated fixed bed Mixed Acid Fermentation part i effect of volatile solid loading rate and agitation at high ph
Bioresource Technology, 2011Co-Authors: Kristina W Golub, Andrea K Forrest, Kevin L Mercy, Mark T HoltzappleAbstract:Countercurrent Fermentation is a high performing process design for Mixed-Acid Fermentation. However, there are high operating costs associated with moving solids, which is an integral component of this configuration. This study investigated the effect of volatile solid loading rate (VSLR) and agitation in propagated fixed-bed Fermentation, a configuration which may be more commercially viable. To evaluate the role of agitation on fixed-bed configuration performance, continuous mixing was compared with periodic mixing. VSLR was also varied and not found to affect Acid yields. However, increased VSLR and liquid retention time did result in higher conversions, productivity, Acid concentrations, but lower selectivities. Agitation was demonstrated to be important for this fermentor configuration, the periodically-Mixed Fermentation had the lowest conversion and yields. Operating at a high pH (∼9) contributed to the high selectivity to acetic Acid, which might be industrially desirable but at the cost of lower yield compared to a neutral pH.
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effects of temperature and pretreatment conditions on Mixed Acid Fermentation of water hyacinths using a Mixed culture of thermophilic microorganisms
Bioresource Technology, 2010Co-Authors: Andrea K Forrest, Joan Hernandez, Mark T HoltzappleAbstract:Abstract The MixAlco™ process biologically converts biomass to carboxylate salts that may be chemically converted to a wide variety of chemicals and fuels. This study investigated the use of water hyacinths as a feedstock, comparing digestibility after each of four different pretreatments at two Fermentation temperatures (40 and 55 °C). Water hyacinths were treated with excess lime (0.3 g Ca(OH) 2 /g dry biomass). Short-term treatment occurred for 1 and 2 h at 100 °C. Long-term treatment occurred for 4 and 6 weeks at 50 °C. Treated water hyacinths were fermented with marine microorganisms for 28 days and Acid concentration (g/L), conversion (g volatile solids (VS) digested/g VS fed), and selectivity (g Acid/g VS digested) were measured. All pretreatments out performed fresh feedstock Fermentations. The 40 °C Fermentations exhibited greater Acid yields and selectivity than the 55 °C. The 1-h hot-lime pretreatment exhibited the best overall outcomes at approximately 250%, 200%, and 125% increases relative to the fresh water hyacinths in total Acid, conversion, and selectivity, respectively. The results show that with a gentle 1-h hot-lime pretreatment, water hyacinths can be fermented to produce liquid fuels, thus creating an economic value to water hyacinths that are cleared from choked waterways.
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Mixed Acid Fermentation of paper fines and industrial biosludge
Bioresource Technology, 2004Co-Authors: Susan B Domke, Cateryna Aiellomazzarri, Mark T HoltzappleAbstract:Abstract This paper uses countercurrent Fermentation to anaerobically convert paper fines and industrial biosludge to carboxylate salts using a Mixed culture of Acid-forming microorganisms. Using the MixAlco process, the carboxylate salts can be thermally converted to ketones and hydrogenated into Mixed alcohol fuels. Continuum particle distribution modeling (CPDM) correlated batch Fermentation data to countercurrent Fermentation data, allowing the prediction of product concentrations and conversions over a wide range of solid loading rates and liquid residence times. For 80% paper/20% biosludge, the predicted product concentrations agreed with the data within 7.7%. The predicted conversion agreed with the actual conversion within 27.8%. By correcting for varying selectivity, the predicted conversion agreed with the actual conversions within 15.2%. For 40% paper/60% biosludge, the predicted product concentrations agreed with the data within 9.6%. The predicted conversion agreed with the actual conversion within 28.3%. By correcting for varying selectivity, the predicted conversion agreed with the actual conversions within 15.4%. For both the 80/20 and 40/60 cases, CPDM predicts that 90% conversion is possible with a 20 g/l product concentration, 300 g/l substrate concentration, 16 day liquid residence time, and 2.5 g/(l d) solids loading rate. Before proceeding to an industrial plant, these predictions must be verified in a pilot plant.
Petya Berger - One of the best experts on this subject based on the ideXlab platform.
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Carriage of Shiga toxin phage profoundly affects Escherichia coli gene expression and carbon source utilization
BMC Genomics, 2019Co-Authors: Petya Berger, Ivan U. Kouzel, Michael Berger, Nadja Haarmann, Ulrich Dobrindt, Gerald B. Koudelka, Alexander MellmannAbstract:Background Enterohemorrhagic Escherichia coli ( E. coli ) are intestinal pathogenic bacteria that cause life-threatening disease in humans. Their cardinal virulence factor is Shiga toxin (Stx), which is encoded on lambdoid phages integrated in the chromosome. Stx phages can infect and lysogenize susceptible bacteria, thus either increasing the virulence of already pathogenic bacterial hosts or transforming commensal strains into potential pathogens. There is increasing evidence that Stx phage-encoded factors adaptively regulate bacterial host gene expression. Here, we investigated the effects of Stx phage carriage in E. coli K-12 strain MG1655. We compared the transcriptome and phenotype of naive MG1655 and two lysogens carrying closely related Stx2a phages: ϕO104 from the exceptionally pathogenic 2011 E. coli O104:H4 outbreak strain and ϕPA8 from an E. coli O157:H7 isolate. Results Analysis of quantitative RNA sequencing results showed that, in comparison to naive MG1655, genes involved in Mixed Acid Fermentation were upregulated, while genes encoding NADH dehydrogenase I, TCA cycle enzymes and proteins involved in the transport and assimilation of carbon sources were downregulated in MG1655::ϕO104 and MG1655::ϕPA8. The majority of the changes in gene expression were found associated with the corresponding phenotypes. Notably, the Stx2a phage lysogens displayed moderate to severe growth defects in minimal medium supplemented with single carbon sources, e.g. galactose, ribose, L-lactate. In addition, in phenotype microarray assays, the Stx2a phage lysogens were characterized by a significant decrease in the cell respiration with gluconeogenic substrates such as amino Acids, nucleosides, carboxylic and dicarboxylic Acids. In contrast, MG1655::ϕO104 and MG1655::ϕPA8 displayed enhanced respiration with several sugar components of the intestinal mucus, e.g. arabinose, fucose, N-acetyl-D-glucosamine. We also found that prophage-encoded factors distinct from CI and Cro were responsible for the carbon utilization phenotypes of the Stx2a phage lysogens. Conclusions Our study reveals a profound impact of the Stx phage carriage on E. coli carbon source utilization. The Stx2a prophage appears to reprogram the carbon metabolism of its bacterial host by turning down aerobic metabolism in favour of Mixed Acid Fermentation.
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Carriage of Shiga toxin phage profoundly affects Escherichia coli gene expression and carbon source utilization.
BMC genomics, 2019Co-Authors: Petya Berger, Ivan U. Kouzel, Michael Berger, Nadja Haarmann, Ulrich Dobrindt, Gerald B. Koudelka, Alexander MellmannAbstract:Enterohemorrhagic Escherichia coli (E. coli) are intestinal pathogenic bacteria that cause life-threatening disease in humans. Their cardinal virulence factor is Shiga toxin (Stx), which is encoded on lambdoid phages integrated in the chromosome. Stx phages can infect and lysogenize susceptible bacteria, thus either increasing the virulence of already pathogenic bacterial hosts or transforming commensal strains into potential pathogens. There is increasing evidence that Stx phage-encoded factors adaptively regulate bacterial host gene expression. Here, we investigated the effects of Stx phage carriage in E. coli K-12 strain MG1655. We compared the transcriptome and phenotype of naive MG1655 and two lysogens carrying closely related Stx2a phages: ϕO104 from the exceptionally pathogenic 2011 E. coli O104:H4 outbreak strain and ϕPA8 from an E. coli O157:H7 isolate. Analysis of quantitative RNA sequencing results showed that, in comparison to naive MG1655, genes involved in Mixed Acid Fermentation were upregulated, while genes encoding NADH dehydrogenase I, TCA cycle enzymes and proteins involved in the transport and assimilation of carbon sources were downregulated in MG1655::ϕO104 and MG1655::ϕPA8. The majority of the changes in gene expression were found associated with the corresponding phenotypes. Notably, the Stx2a phage lysogens displayed moderate to severe growth defects in minimal medium supplemented with single carbon sources, e.g. galactose, ribose, L-lactate. In addition, in phenotype microarray assays, the Stx2a phage lysogens were characterized by a significant decrease in the cell respiration with gluconeogenic substrates such as amino Acids, nucleosides, carboxylic and dicarboxylic Acids. In contrast, MG1655::ϕO104 and MG1655::ϕPA8 displayed enhanced respiration with several sugar components of the intestinal mucus, e.g. arabinose, fucose, N-acetyl-D-glucosamine. We also found that prophage-encoded factors distinct from CI and Cro were responsible for the carbon utilization phenotypes of the Stx2a phage lysogens. Our study reveals a profound impact of the Stx phage carriage on E. coli carbon source utilization. The Stx2a prophage appears to reprogram the carbon metabolism of its bacterial host by turning down aerobic metabolism in favour of Mixed Acid Fermentation.
Wolfgang Nitschke - One of the best experts on this subject based on the ideXlab platform.
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Carbon Fixation: “Let Things Flow Naturally Forward in Whatever Way They Like”
Current biology : CB, 2018Co-Authors: Wolfgang NitschkeAbstract:Mixed-Acid Fermentation generates H2 and CO2 from formate. As shown in a recent study, the formate oxidation reaction can be driven backwards when sufficiently high partial pressures of the gases are applied, suggesting potentially interesting biotechnological applications.
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Carbon Fixation: “Let Things Flow Naturally Forward in Whatever Way They Like”
Current Biology - CB, 2018Co-Authors: Wolfgang NitschkeAbstract:Mixed-Acid Fermentation generates H2 and CO2 from formate. As shown in a recent study, the formate oxidation reaction can be driven backwards when sufficiently high partial pressures of the gases are applied, suggesting potentially interesting biotechnological applications. Escherichia coli grown in the presence of glucose — but in the absence of electron acceptors — ferments the sugar to a mix of organic Acids; specifically, lactic, succinic and formic Acids. The formic Acid produced in this 'Mixed-Acid Fermentation' is further reacted with protons to yield two gases, CO2 and H2. In this redox process, the electrons derived from the oxidation of formate to CO2 are used for the reduction of two protons to yield molecular hydrogen. Oxidising formate to CO2 (which escapes into the gas phase) by using ubiquitously available protons as electron acceptors is a clever way to prevent the main Fermentation reaction from stalling due to product inhibition. All this was elucidated almost a century ago [1,2], and the process has since become a standard entry in textbooks on microbial physiology. As a sorted-out mechanism, it was further studied only by a fringe community of microbiologists in more recent years. That changed dramatically when molecular details of the enzyme carrying out the final step (oxidation of formate to CO2) started to emerge [3,4]. The so-called 'formate hydrogenlyase' (FHL) turned out to be a textbook example for the construction-kit strategy that life almost exclusively applies during evolutionary innovation and diversification [5]. FHL revealed itself to be composed of protein subunits belonging to the vast superfamily of