| 1. |
- Franzén, Carl Johan, 1966, et al.
(författare)
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The lignocellulosic biorefinery concept is sound: a commentary on Zhao et al.
- 2024
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Ingår i: Trends in Biotechnology. - 0167-7799 .- 1879-3096. ; 42:4, s. 395-396
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- In the opinion paper by Zhao et al. ‘Making the biochemical conversion of lignocellulose more robust’, the authors claim that ‘…lignocellulose biorefinery is conceptually wrong’. In response, we argue that this claim itself has already been proved wrong by several companies.
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| 2. |
- Johanson, Anna, 1985, et al.
(författare)
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Respiratory Physiology of Lactococcus lactis in Chemostat Cultures and Its Effect on Cellular Robustness in Frozen and Freeze-Dried Starter Cultures
- 2020
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Ingår i: Applied and Environmental Microbiology. - 1098-5336 .- 0099-2240. ; 86:6
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Tidskriftsartikel (refereegranskat)abstract
- In this study, we used chemostat cultures to analyze the quantitative effects of the specific growth rate and respiration on the metabolism in Lactococcus lactis CHCC2862 and on the downstream robustness of cells after freezing or freeze-drying. Under anaerobic conditions, metabolism remained homofermentative, although biomass yields varied with the dilution rate (D). In contrast, metabolism shifted with the dilution rate under respiration-permissive conditions. At D = 0.1 h-1, no lactate was produced, while lactate formation increased with higher dilution rates. Thus, a clear metabolic shift was observed, from flavor-forming respiratory metabolism at low specific growth rates to mixed-acid respiro-fermentative metabolism at higher specific growth rates. Quantitative analysis of the respiratory activity, lactose uptake rate, and metabolite production rates showed that aerobic acetoin formation provided most of the NADH consumed in respiration. Moreover, the maintenance-associated lactose consumption under respiration-permissive conditions was only 10% of the anaerobic value, either due to higher respiratory yield of ATP on consumed lactose or due to lower maintenance-related ATP demand. The cultivation conditions also affected the quality of the starter cultures produced. Cells harvested under respiration-permissive conditions at D = 0.1 h-1 were less robust after freeze-drying and had lower acidification activity for subsequent milk acidification, whereas respiration-permissive conditions at the higher dilution rates led to robust cells that performed equally well or better than anaerobic cells.IMPORTANCELactococcus lactis is used in large quantities by the food and biotechnology industries. L. lactis can use oxygen for respiration if heme is supplied in the growth medium. This has been extensively studied in batch cultures using various mutants, but quantitative studies of how the cell growth affects respiratory metabolism, energetics, and cell quality are surprisingly scarce. Our results demonstrate that the respiratory metabolism of L. lactis is remarkably flexible and can be modulated by controlling the specific growth rate. We also link the physiological state of cells during cultivation to the quality of frozen or freeze-dried cells, which is relevant to the industry that may lack understanding of such relationships. This study extends our knowledge of respiratory metabolism in L. lactis and its impact on frozen and freeze-dried starter culture products, and it illustrates the influence of cultivation conditions and microbial physiology on the quality of starter cultures.
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| 3. |
- Nickel, David, 1990, et al.
(författare)
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Multi-Scale Variability Analysis of Wheat Straw-Based Ethanol Biorefineries Identifies Bioprocess Designs Robust Against Process Input Variations
- 2020
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Ingår i: Frontiers in Energy Research. - : Frontiers Media SA. - 2296-598X. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Bioprocesses based on (ligno-)cellulosic biomass are highly prone to batch-to-batch variations. Varying raw material compositions and enzyme activities hamper the prediction of process yields, economic feasibility and environmental impacts. Commonly, these performance indicators are averaged over several experiments to select suitable process designs. The variabilities in performance indicators resulting from variable process inputs are often neglected, causing a risk for faulty performance predictions and poor process design choices during scale-up. In this paper, a multi-scale variability analysis framework is presented that quantifies the effects of process input variations on performance indicators. Using the framework, a kinetic model describing simultaneous saccharification and ethanol fermentation was integrated with a flowsheet process model, techno-economic analysis and life cycle assessment in order to evaluate a wheat straw-based ethanol biorefinery. Hydrolytic activities reported in the literature for the enzyme cocktail Cellic® CTec2, ranging from 62 to 266 FPU·mL−1, were used as inputs to the multi-scale model to compare the variability in performance indicators under batch and multi-feed operation for simultaneous saccharification and fermentation. Bioprocess simulations were stopped at ethanol productivities ≤0.1 g·L−1·h−1. The resulting spreads in process times, hydrolysis yields, and fermentation yields were incorporated into flowsheet, techno-economic and life cycle scales. At median enzymatic activities the payback time was 7%, equal to 0.6 years, shorter under multi-feed conditions. All other performance indicators showed insignificant differences. However, batch operation is simpler to control and well-established in industry. Thus, an analysis at median conditions might favor batch conditions despite the disadvantage in payback time. Contrary to median conditions, analyzing the input variability favored multi-feed operation due to a lower variability in all performance indicators. Variabilities in performance indicators were at least 50% lower under multi-feed operation. Counteracting the variability in enzymatic activities by adjusting the amount of added enzyme instead resulted in higher uncertainties in environmental impacts. The results show that the robustness of performance indicators against input variations must be considered during process development. Based on the multi-scale variability analysis process designs can be selected which deliver more precise performance indicators at multiple system levels.
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| 4. |
- Schöpping, Marie, 1991, et al.
(författare)
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Genome-Wide Assessment of Stress-Associated Genes in Bifidobacteria
- 2022
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Ingår i: Applied and Environmental Microbiology. - : American Society for Microbiology. - 1098-5336 .- 0099-2240. ; 88:7, s. e0225121-
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Tidskriftsartikel (refereegranskat)abstract
- Over the last decade, the genomes of several Bifidobacterium strains have been sequenced, delivering valuable insights into their genetic makeup. However, bifidobacterial genomes have not yet been systematically mined for genes associated with stress response functions and their regulation. In this work, a list of 76 genes related to stress response in bifidobacteria was compiled from previous studies. The prevalence of the genes was evaluated among the genome sequences of 171 Bifidobacterium strains. Although genes of the protein quality control and DNA repair systems appeared to be highly conserved, genome-wide in silico screening for consensus sequences of putative regulators suggested that the regulation of these systems differs among phylogenetic groups. Homologs of multiple oxidative stress-associated genes are shared across species, albeit at low sequence similarity. Bee isolates were confirmed to harbor unique genetic features linked to oxygen tolerance. Moreover, most studied Bifidobacterium adolescentis and all Bifidobacterium angulatum strains lacked a set of reactive oxygen species-detoxifying enzymes, which might explain their high sensitivity to oxygen. Furthermore, the presence of some putative transcriptional regulators of stress responses was found to vary across species and strains, indicating that different regulation strategies of stress-associated gene transcription contribute to the diverse stress tolerance. The presented stress response gene profiles of Bifidobacterium strains provide a valuable knowledge base for guiding future studies by enabling hypothesis generation and the identification of key genes for further analyses. IMPORTANCE Bifidobacteria are Gram-positive bacteria that naturally inhabit diverse ecological niches, including the gastrointestinal tract of humans and animals. Strains of the genus Bifidobacterium are widely used as probiotics, since they have been associated with health benefits. In the course of their production and administration, probiotic bifidobacteria are exposed to several stressors that can challenge their survival. The stress tolerance of probiotic bifidobacteria is, therefore, an important selection criterion for their commercial application, since strains must maintain their viability to exert their beneficial health effects. As the ability to cope with stressors varies among Bifidobacterium strains, comprehensive understanding of the underlying stress physiology is required for enabling knowledge-driven strain selection and optimization of industrial-scale production processes.
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| 5. |
- Schöpping, Marie, 1991, et al.
(författare)
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Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modeling
- 2021
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Ingår i: npj Systems Biology and Applications. - : Springer Science and Business Media LLC. - 2056-7189. ; 7:1
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Tidskriftsartikel (refereegranskat)abstract
- Although bifidobacteria are widely used as probiotics, their metabolism and physiology remain to be explored in depth. In this work, strain-specific genome-scale metabolic models were developed for two industrially and clinically relevant bifidobacteria, Bifidobacterium animalis subsp. lactis BB-12® and B. longum subsp. longum BB-46, and subjected to iterative cycles of manual curation and experimental validation. A constraint-based modeling framework was used to probe the metabolic landscape of the strains and identify their essential nutritional requirements. Both strains showed an absolute requirement for pantethine as a precursor for coenzyme A biosynthesis. Menaquinone-4 was found to be essential only for BB-46 growth, whereas nicotinic acid was only required by BB-12®. The model-generated insights were used to formulate a chemically defined medium that supports the growth of both strains to the same extent as a complex culture medium. Carbohydrate utilization profiles predicted by the models were experimentally validated. Furthermore, model predictions were quantitatively validated in the newly formulated medium in lab-scale batch fermentations. The models and the formulated medium represent valuable tools to further explore the metabolism and physiology of the two species, investigate the mechanisms underlying their health-promoting effects and guide the optimization of their industrial production processes.
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| 6. |
- Schöpping, Marie, 1991, et al.
(författare)
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Novel Insights into the Molecular Mechanisms Underlying Robustness and Stability in Probiotic Bifidobacteria
- 2023
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Ingår i: Applied and Environmental Microbiology. - : American Society for Microbiology. - 1098-5336 .- 0099-2240. ; 89:3
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Tidskriftsartikel (refereegranskat)abstract
- Probiotics are industrially and clinically important microorganisms. To exert their health-promoting effects, probiotic microorganisms must be administered at high counts, while maintaining their viability at the time of consumption. Some probiotic bifidobacteria are highly robust and shelf-stable, whereas others are difficult to produce, due to their sensitivity to stressors. This limits their potential use as probiotics. Here, we investigate the molecular mechanisms underlying the variability in stress physiologies of Bifidobacterium animalis subsp. lactis BB-12 and Bifidobacterium longum subsp. longum BB-46, by applying a combination of classical physiological characterization and transcriptome profiling. The growth behavior, metabolite production, and global gene expression profiles differed considerably between the strains. BB-12 consistently showed higher expression levels of multiple stress-associated genes, compared to BB-46. This difference, besides higher cell surface hydrophobicity and a lower ratio of unsaturated to saturated fatty acids in the cell membrane of BB-12, should contribute to its higher robustness and stability. In BB-46, the expression of genes related to DNA repair and fatty acid biosynthesis was higher in the stationary than in the exponential phase, which was associated with enhanced stability of BB-46 cells harvested in the stationary phase. The results presented herein highlight important genomic and physiological features contributing to the stability and robustness of the studied Bifidobacterium strains.IMPORTANCE Probiotics are industrially and clinically important microorganisms. To exert their health-promoting effects, probiotic microorganisms must be administered at high counts, while maintaining their viability at the time of consumption. In addition, intestinal survival and bioactivity are important criteria for probiotics. Although bifidobacteria are among the most well-documented probiotics, the industrial-scale production and commercialization of some Bifidobacterium strains is challenged by their high sensitivity to environmental stressors encountered during manufacturing and storage. Through a comprehensive comparison of the metabolic and physiological characteristics of 2 Bifidobacterium strains, we identify key biological markers that can serve as indicators for robustness and stability in bifidobacteria.
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| 7. |
- Schöpping, Marie, 1991, et al.
(författare)
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Stress Response in Bifidobacteria
- 2022
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Ingår i: Microbiology and Molecular Biology Reviews. - : American Society for Microbiology. - 1092-2172 .- 1098-5557. ; 86:4
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Forskningsöversikt (refereegranskat)abstract
- Bifidobacteria naturally inhabit diverse environments, including the gastrointestinal tracts of humans and animals. Members of the genus are of considerable scientific interest due to their beneficial effects on health and, hence, their potential to be used as probiotics. By definition, probiotic cells need to be viable despite being exposed to several stressors in the course of their production, storage, and administration. Examples of common stressors encountered by probiotic bifidobacteria include oxygen, acid, and bile salts. As bifidobacteria are highly heterogenous in terms of their tolerance to these stressors, poor stability and/or robustness can hamper the industrial-scale production and commercialization of many strains. Therefore, interest in the stress physiology of bifidobacteria has intensified in recent decades, and many studies have been established to obtain insights into the molecular mechanisms underlying their stability and robustness. By complementing traditional methodologies, omics technologies have opened new avenues for enhancing the understanding of the defense mechanisms of bifidobacteria against stress. In this review, we summarize and evaluate the current knowledge on the multilayered responses of bifidobacteria to stressors, including the most recent insights and hypotheses. We address the prevailing stressors that may affect the cell viability during production and use as probiotics. Besides phenotypic effects, molecular mechanisms that have been found to underlie the stress response are described. We further discuss strategies that can be applied to improve the stability of probiotic bifidobacteria and highlight knowledge gaps that should be addressed in future studies. Bifidobacteria naturally inhabit diverse environments, including the gastrointestinal tracts of humans and animals. Members of the genus are of considerable scientific interest due to their beneficial effects on health and, hence, their potential to be used as probiotics.
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| 8. |
- Schöpping, Marie, 1991, et al.
(författare)
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Why are you stressed? A systems-level comparison of two Bifidobacterium strains with different stability characteristics
- 2021
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Bifidobacteria are widely used as probiotics, owing to their well-documented health-promoting properties. Throughout production, downstream processing and administration, probiotic bifidobacteria are exposed to various stressors that may affect the physiological state of the cells. The stability of bifidobacteria varies between strains and the sensitivity of some strains hampers their industrial production. Therefore, it is crucial to gain a more comprehensive, systems-level understanding of their metabolism and physiology, which may result in the identification of potential factors and metabolic bottlenecks influencing both growth and long-term viability. In this work, we compare the metabolic characteristics of two industrially relevant bifidobacterial strains that vary in their stability. Our approach relies on the integration of different phenotypic measurements using a constraint-based metabolic modelling framework. In order to identify the correlation between cellular characteristics and stability, the strains were studied in lab-scale pH-controlled fermentations in chemically-defined medium and their final stability was assessed. The cultivations were monitored by assessing growth and metabolite production. In addition, global transcriptome profiling and differential gene expression analysis were used to gain better insights into the metabolic differences between the strains. The genome-scale metabolic models of the strains were used as platforms for the integration of experimental data.
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| 9. |
- Wang, Ruifei, 1985, et al.
(författare)
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Analysis of methods for quantifying yeast cell concentration in complex lignocellulosic fermentation processes
- 2021
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322 .- 2045-2322. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Cell mass and viability are tightly linked to the productivity of fermentation processes. In 2 generation lignocellulose-based media quantitative measurement of cell concentration is challenging because of particles, auto-fluorescence, and intrinsic colour and turbidity of the media. We systematically evaluated several methods for quantifying total and viable yeast cell concentrations to validate their use in lignocellulosic media. Several automated cell counting systems and stain-based viability tests had very limited applicability in such samples. In contrast, manual cell enumeration in a hemocytometer, plating and enumeration of colony forming units, qPCR, and in situ dielectric spectroscopy were further investigated. Parameter optimization to measurements in synthetic lignocellulosic media, which mimicked typical lignocellulosic fermentation conditions, resulted in statistically significant calibration models with good predictive capacity for these four methods. Manual enumeration of cells in a hemocytometer and of CFU were further validated for quantitative assessment of cell numbers in simultaneous saccharification and fermentation experiments on steam-exploded wheat straw. Furthermore, quantitative correlations could be established between these variables and in situ permittivity. In contrast, qPCR quantification suffered from inconsistent DNA extraction from the lignocellulosic slurries. Development of reliable and validated cell quantification methods and understanding their strengths and limitations in lignocellulosic contexts, will enable further development, optimization, and control of lignocellulose-based fermentation processes.
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