91 results on '"Kabisch J"'
Search Results
2. DNA scanner: A web application for comparing DNA synthesis feasibility, price and turnaround time across vendors
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Doçi, G, Fuchs, L, Kharbanda, Y, Schickling, P, Zulkower, V, Hillson, N, Oberortner, E, Swainston, N, and Kabisch, J
- Abstract
DNA synthesis has become a major enabler of modern bioengineering, allowing scientists to simply order online in silico-designed DNA molecules. Rapidly decreasing DNA synthesis service prices and the concomitant increase of research and development scales bolstered by computer-aided DNA design tools and laboratory automation has driven up the demand for synthetic DNA. While vendors provide user-friendly online portals for purchasing synthetic DNA, customers still face the time-consuming task of checking each vendor of choice for their ability and pricing to synthesize the desired sequences. As a result, ordering large batches of DNA sequences can be a laborious manual procedure in an otherwise increasingly automatable workflow. Even when they are available, there is a high degree of technical knowledge and effort required to integrate vendors’ application programming interfaces (APIs) into computer-aided DNA design tools or automated lab processes. Here, we introduce DNA Scanner, a software package comprising (i) a web-based user interface enabling users to compare the feasibility, price and turnaround time of synthetic DNA sequences across selected vendors and (ii) a Python API enabling integration of these functionalities into computer-aided DNA design tools and automated lab processes. We have developed DNA Scanner to uniformly streamline interactions between synthetic DNA vendors, members of the Global Biofoundry Alliance and the scientific community at large.
- Published
- 2020
3. Umfassende Untersuchung unerwünschter Stoffe und mikrobiologischer Kontamination in pflanzlichen Drinks
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Gützkow, K. L., primary, Lencioni, A., additional, Schwake‐Anduschus, C., additional, Müller, A., additional, Kabisch, J., additional, Grundmann, V. L., additional, Stöckl, M., additional, and Maul, R., additional
- Published
- 2024
- Full Text
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4. Reformulierung von Lebensmitteln: Strategien zur sensorischen Optimierung von natriumreduziertem Schnittkäse
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Bartsch, K., primary, Schrader, K., additional, Kabisch, J., additional, and Fritsche, J., additional
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- 2023
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5. Vortragstitel Reformulierung von Lebensmitteln: Erste Ergebnisse der sensorischen Optimierung von natriumreduziertem Schnittkäse (Senopt‐Käse) anhand der Vorstufe Käsegeschmacksmatrix mit Hilfe von Salzsubstituten
- Author
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Bartsch, K., primary, Schrader, K., additional, Kabisch, J., additional, and Fritsche, J., additional
- Published
- 2023
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6. 2099 Aluminum-Lithium with Key-Locked Inserts for Aerospace Applications
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Babel, H., Gibson, J., Tarkanian, M., Parrish, C., Prietto, M., Ordonez-Chu, A., Haberl, H., Kabisch, J., Clark, R., Ogren, J., and Es Said, O.S.
- Published
- 2007
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7. Effects of a high-cultivation temperature on the physiology of three different Yarrowia lipolytica strains
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Hackenschmidt, S, primary, Bracharz, F, additional, Daniel, R, additional, Thürmer, A, additional, Bruder, S, additional, and Kabisch, J, additional
- Published
- 2019
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8. Characterization of threeYarrowia lipolyticastrains in respect to different cultivation temperatures and metabolite secretion
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Hackenschmidt, S, primary, Bracharz, F, additional, Daniel, R, additional, Thürmer, A, additional, Bruder, S, additional, and Kabisch, J, additional
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- 2019
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9. Endometrial biopsies of old mares – What to expect?!
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Kabisch, J, primary, Klose, K, additional, and Schoon, H-A, additional
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- 2019
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10. Aquatic adaptation of a laterally acquired pectin degradation pathway in marine gammaproteobacteria
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Hehemann, J., Le Truong, V., Unfried, F., Welsch, N., Kabisch, J., Heiden, S., Junker, S., Becher, D., Thuermer, A., Daniel, R., Amann, R., and Schweder, T.
- Subjects
food and beverages - Abstract
Mobile genomic islands distribute functional traits between microbes and habitats, yet it remains unclear how their proteins adapt to new environments. Here we used a comparative phylogenomic and proteomic approach to show that the marine bacterium Pseudoalteromonas haloplanktis ANT/505 acquired a genomic island with a functional pathway for pectin catabolism. Bioinformatics and biochemical experiments revealed that this pathway encodes a series of carbohydrate-active enzymes including two multimodular pectate lyases, PelA and PelB. PelA is a large enzyme with a polysaccharide lyase family 1 (PL1) domain and a carbohydrate esterase family 8 domain, and PelB contains a PL1 domain and two carbohydrate-binding domains of family 13. Comparative phylogenomic analyses indicate that the pathway was most likely acquired from terrestrial microbes, yet we observed multi-modular orthologues only in marine bacteria. Proteomic experiments showed that P. haloplanktis ANT/505 secretes both pectate lyases into the environment in the presence of pectin. These multi-modular enzymes may therefore represent a marine innovation that enhances physical interaction with pectins to reduce loss of substrate and enzymes by diffusion. Our results revealed that marine bacteria can catabolize pectin, and highlight enzyme fusion as a potential adaptation that may facilitate microbial consumption of polymeric substrates in aquatic environments.
- Published
- 2017
11. Effects of ad libitum butter consumption on intestinal microbiota composition and markers of metabolic disorders and general health in middle aged female and male C57BL/6 mice
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Ghadimi, D, additional, Frahm, SO, additional, Röcken, C, additional, Ebsen, M, additional, Schwiertz, A, additional, Softic, S, additional, Heller, KJ, additional, Bockelmann, W, additional, and Kabisch, J, additional
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- 2017
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12. In vitro, ex vivo and in vivo effects of egg consumption (and egg microbiota) on the microbial community composition of gut microbiota and on immunological/metabolic/inflammatory biomarkers
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Ghadimi, D, primary, Ebsen, M, additional, Kabisch, J, additional, Röcken, C, additional, Moghadasian, MH, additional, Heller, KJ, additional, Bockelmann, W, additional, and Franz, C, additional
- Published
- 2015
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13. Functional characterization of two antifreeze proteins from a polar diatom (Fragilariopsis cylindrus)
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Uhlig, Christiane, Kabisch, J., Palm, G. J., Valenin, K., Krell, Andreas, Uhlig, Christiane, Kabisch, J., Palm, G. J., Valenin, K., and Krell, Andreas
- Published
- 2011
14. Shaping the neighborhood - Ice-binding-proteins in polar diatoms
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Uhlig, Christiane, Bayer-Giraldi, Maddalena, Eberlein, Tim, Kabisch, J., Besir, H., Dieckmann, Gerhard, Krell, Andreas, Uhlig, Christiane, Bayer-Giraldi, Maddalena, Eberlein, Tim, Kabisch, J., Besir, H., Dieckmann, Gerhard, and Krell, Andreas
- Published
- 2010
15. ICE-BINDING-PROTEINS IN POLAR DIATOMS THEIR DIVERSITY AND FUNCTION IN THE GENUS FRAGILARIOPSIS
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Uhlig, Christiane, Bayer-Giraldi, Maddalena, Kabisch, J., Besir, H., Schweder, T., Dieckmann, Gerhard, Krell, Andreas, Uhlig, Christiane, Bayer-Giraldi, Maddalena, Kabisch, J., Besir, H., Schweder, T., Dieckmann, Gerhard, and Krell, Andreas
- Published
- 2009
16. Report on the Workshop on Wrapper Techniques for Legacy Data Systems
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Risch, Tore, Thiran, Ph, Costilla, C, Henrard, J, Kabisch, J, Petrini, Johan, van den Heuvel, W-J, Hainaut, J-L, Risch, Tore, Thiran, Ph, Costilla, C, Henrard, J, Kabisch, J, Petrini, Johan, van den Heuvel, W-J, and Hainaut, J-L
- Published
- 2005
17. Scale down simulator for studying the impact of industrial scale inhomogeneities on Bacillus subtilis processes
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Junne, S., primary, Klingner, A., additional, Kabisch, J., additional, Schweder, T., additional, and Neubauer, P., additional
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- 2010
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18. ICE-BINDING-PROTEINS IN POLAR DIATOMS -THEIR DIVERSITY AND FUNCTION IN THE GENUS FRAGILARIOPSIS.
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Uhlig, C., Bayer-Giraldi, M., Kabisch, J., Besir, H., Schweder, T., S.^Dieckmann, G., and Krell, A.
- Subjects
CARRIER proteins - Abstract
An abstract of the article "Ice-Binding-Proteins in Polar Diatoms-Their Diversity and Function in the Genus Fragilariopsis," by C. Uhlig and colleagues is presented.
- Published
- 2009
19. Agricultural cooperative 'Co.r.ag.gio.', an example of urban agriculture in Rome (Italy) as a resilient strategy against urban climate change
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MARICCHIOLO, FRIDANNA, PANNO, ANGELO, CARRUS, GIUSEPPE, Lepri, G., Brizi, A., N. Kabisch, J, Stadler, S. Duffield, H. Korn, A. Bonn, Maricchiolo, Fridanna, Lepri, G., Brizi, A., Panno, Angelo, and Carrus, Giuseppe
- Abstract
In urban contexts, cultivated agricultural land increases permeability, improves positive atmospheric exchanges, protects the complexity of agricultural ecosystem and helps general resilience to urban climate changes. We present the Italian case study of the EU-FP7 funded project called “GLAMURS - Green Lifestyles, alternative models and upscaling regional sustainability” (www.glamurs.eu). GLAMURS investigates transitions to sustainable lifestyles and green economies, through an interdisciplinary approach in seven different regions of Europe. In the Lazio Region of Italy, the young agricultural cooperative "Co.R.Ag.Gio" (“Courage”), COoperativa Romana AGricoltura GIOvani (Roman Agricultural Cooperative of Youth), encourages citizens and institutions to conserve environmental heritages abandoned in the Roman agricultural outskirts. CoRAgGio was founded in 2011, as a free association of young people (farmers, agronomists, chefs, architects, day workers, industrial worker, anthropologists, educators). It promotes an original work perspective in this economic crisis, enhancing passions and experiences in agricultural and horticultural activities, teaching and training (educational farms, courses in sustainable agriculture), food (spreading good practices, 0-km production), crafts. It strives to make public land available to all citizens, and preserve agricultural soils from the expansion of the building sector. It promotes an agricultural urban model that is healthy, organic, multi-functional, replacing the degraded concrete buildings with a proposal of a new way of living, based on ecological concerns, respecting labour dignity, and social meanings of agriculture. The implications of promoting sustainable urban agriculture will be discussed, in terms of economic values, ecological services and food production, improvement of life quality, soil protection, earth resources and biodiversity conservation.
- Published
- 2017
20. Digital holographic microscopy is suitable for lipid accumulation analysis in single cells of Yarrowia lipolytica.
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Briel SC, Feuser N, Moldenhauer EJ, Kabisch J, Neubauer P, and Junne S
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- Lipid Metabolism, Lipids analysis, Fatty Acids metabolism, Fatty Acids analysis, Quantitative Phase Imaging, Yarrowia metabolism, Yarrowia cytology, Holography methods, Single-Cell Analysis methods, Microscopy methods
- Abstract
Digital holographic microscopy (DHM) is a label-free analytical technique for the determination of the cells' volume and their cytosolic refractive index. Here, we demonstrate the suitability of DHM for the quantification of total lipid accumulation in the oleaginous yeast Yarrowia lipolytica. Presently, microbial lipids are gaining increasing attention due to their nutritional value in feed and food applications. Their microbiological synthesis in algae and yeast is subject to optimization studies, which necessitates rapid quantification of total lipids for faster progress and the possibility of process control. So far, quantification of the total intracellular long-chain fatty acid concentration in yeast cells is time-consuming though when common chromatography for a volumetric analysis or staining and flow cytometry for a single-cell based analysis are used. This study, however, demonstrates that 3D-DHM facilitates a quasi-real-time measurement that allows for a rapid quantification of total intracellular lipid accumulation on a single-cell level without cell staining. Data from wild-type and lipid overproducing Y. lipolytica strains with specific yields of long-chain fatty acids in a range between 70 and 360 mg/gCDW show a good correlation with the optical volume determined by DHM, as the total lipid accumulation in the cell is typically well correlated with the long-chain fatty acid concentration. The results further correlate with data obtained from gas chromatography and flow cytometry of Nile Red-stained cells, which proves the reliability of DHM for lipid quantification in Y. lipolytica., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)
- Published
- 2025
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21. Implementation of Spore Display in Paenibacillus polymyxa with Different Hydrolytic Enzymes.
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Zander M, Schmid J, and Kabisch J
- Abstract
Biotechnological processes are essential for producing climate-friendly high-value chemicals or pharmaceutical compounds, which can include steps catalyzed by enzymes. Therefore, establishing new, robust, and cheap enzyme production processes is desirable. One possible way to enhance processes is through the use of the spore display method. Spore display can present heterologous proteins on the surface of bacterial spores, offering numerous advantages in a range of biotechnological applications. This study demonstrates the implementation of the spore display method in Paenibacillus polymyxa, achieved by modifying the spore surface, incorporating an anchoring protein, and attaching green fluorescent protein to it, allowing the visualization of fluorescent spores. Following the initial experiment, a native lipase (Lip3), a heterologous lipase (LipA) from Bacillus subtilis , a native esterase (PnbA) from P. polymyxa, and a lipoyl synthase were expressed during sporulation and displayed on the spore surface. The activity profiles were determined in the temperature range from 4 °C to 70 °C. The PnbA reached its optimum at 4 °C, whereas the LipA from B. subtilis showed 4.4-fold higher activity at 42 °C compared to the control. Furthermore, we explored a possible new technique for the purification of enzymes with the TEV cleavage site between the anchor and the protein of interest. Finally, we showed a not-yet-described side activity of the lipoyl synthase over a wide temperature range.
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- 2024
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22. Corrigendum: Genome reduction in Paenibacillus polymyxa DSM 365 for chassis development.
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Ravagnan G, Lesemann J, Müller MF, Poehlein A, Daniel R, Noack S, Kabisch J, and Schmid J
- Abstract
[This corrects the article DOI: 10.3389/fbioe.2024.1378873.]., (Copyright © 2024 Ravagnan, Lesemann, Müller, Poehlein, Daniel, Noack, Kabisch and Schmid.)
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- 2024
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23. Genome reduction in Paenibacillus polymyxa DSM 365 for chassis development.
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Ravagnan G, Lesemann J, Müller MF, Poehlein A, Daniel R, Noack S, Kabisch J, and Schmid J
- Abstract
The demand for highly robust and metabolically versatile microbes is of utmost importance for replacing fossil-based processes with biotechnological ones. Such an example is the implementation of Paenibacillus polymyxa DSM 365 as a novel platform organism for the production of value-added products such as 2,3-butanediol or exopolysaccharides. For this, a complete genome sequence is the first requirement towards further developing this host towards a microbial chassis. A genome sequencing project has just been reported for P. polymyxa DSM 365 showing a size of 5,788,318 bp with a total of 47 contigs. Herein, we report the first complete genome sequence of P. polymyxa DSM 365, which consists of 5,889,536 bp with 45 RNAs, 106 tRNAs, 5,370 coding sequences and an average GC content of 45.6%, resulting in a closed genome of P. polymyxa 365. The additional nucleotide data revealed a novel NRPS synthetase that may contribute to the production of tridecaptin. Building on these findings, we initiated the top-down construction of a chassis variant of P. polymyxa . In the first stage, single knock-out mutants of non-essential genomic regions were created and evaluated for their biological fitness. As a result, two out of 18 variants showed impaired growth. The remaining deletion mutants were combined in two genome-reduced P. polymyxa variants which either lack the production of endogenous biosynthetic gene clusters (GR1) or non-essential genomic regions including the insertion sequence IS Pap1 (GR2), with a decrease of the native genome of 3.0% and 0.6%, respectively. Both variants, GR1 and GR2, showed identical growth characteristics to the wild-type. Endpoint titers of 2,3-butanediol and EPS production were also unaffected, validating these genome-reduced strains as suitable for further genetic engineering., Competing Interests: Authors M-FM and SN were employed by Forschungszentrum Jülich GmbH. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2024 Ravagnan, Lesemann, Müller, Poehlein, Daniel, Noack, Kabisch and Schmid.)
- Published
- 2024
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24. [Health risks from crop irrigation with treated wastewater containing antibiotic residues, resistance genes, and resistant microorganisms].
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Smalla K, Kabisch J, Fiedler G, Hammerl JA, and Tenhagen BA
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- Anti-Bacterial Agents, Agricultural Irrigation methods, Germany, Water, Wastewater, Waste Disposal, Fluid methods
- Abstract
This review describes the effects and potential health risks of resistant microorganisms, resistance genes, and residues of drugs and biocides that occur when re-using wastewater for crop irrigation. It focusses on specific aspects of these contaminants and their interactions, but does not provide a general risk assessment of the microbial load when using reclaimed water.Antimicrobial residues, antimicrobial resistant microorganisms, and resistance genes are frequently detected in treated wastewater. They have effects on the soil and plant-associated microbiota (total associated microorganisms) and can be taken up by plants. An interaction of residues with microorganisms is mainly expected before using the water for irrigation. However, it may also occur as a combined effect on the plant microbiome and all the abundant resistance genes (resistome). Special concerns are raised as plants are frequently consumed raw, that is, without processing that might reduce the bacterial load. Washing fruits and vegetables only has minor effects on the plant microbiome. On the other hand, cutting and other processes may support growth of microorganisms. Therefore, after such process steps, cooling of the foods is required.Further progress has to be made in the treatment of wastewater that will be used for crop irrigation with respect to removing micropollutants and microorganisms to minimize the risk of an increased exposure of consumers to transferable resistance genes and resistant bacteria., (© 2023. The Author(s).)
- Published
- 2023
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25. Pseudomonas rustica sp. nov., isolated from bulk tank raw milk at a German dairy farm.
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Fiedler G, Gieschler S, Kabisch J, Grimmler C, Brinks E, Wagner N, Hetzer B, Franz CMAP, and Böhnlein C
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- Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Farms, Genes, Bacterial, Nucleic Acid Hybridization, Phylogeny, Pseudomonas, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Fatty Acids chemistry, Milk
- Abstract
Here we present the description of a novel Pseudomonas species, designated Pseudomonas rustica sp. nov., which was isolated from raw milk samples obtained from Germany. Results of initial 16S rRNA gene sequence analysis assigned the strain into the genus Pseudomonas and showed Pseudomonas helmanticensis , Pseudomonas neuropathica and Pseudomonas atagonensis to be its closest relatives. Further studies including sequence analysis of the rpoB gene, multi-gene phylogenetic tree reconstruction, whole-genome sequence comparisons, cellular fatty acid analysis and chemotaxonomic characterization showed a clear separation from the known Pseudomonas species. Isolate MBT-4
T was closely related to Pseudomonas helmanticensis , 'Pseudomonas crudilactis ' and Pseudomonas neuropathica with average nucleotide identities based on blast values of 88.8, 88.8 and 88.6%, respectively. Therefore, the strain can be classified into the Pseudomonas koreensis subgroup of the Pseudomonas fluorescens group. The G+C content of strain MBT-4T was 58.9 mol%. The strain was catalase- and oxidase-positive, while the β-galactosidase reaction was negative. Growth occurred between 4 and 30 °C and at pH values from pH 6.0 to 8.0. In conclusion, strain MBT-4T belongs to a novel species, for which the name Pseudomonas rustica sp. nov. is proposed. The type strain is MBT-4T (=DSM 112348T =LMG 32241T ) and strain MBT-17 is also a representative of this species.- Published
- 2022
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26. HyperXpress: Rapid Single Vessel DNA Assembly and Protein Production in Microliterscale.
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Zibulski DL, Schlichting N, and Kabisch J
- Abstract
Rapid prototyping of biological functions has the common aim of generating, screening, and selecting variant libraries as quickly as possible. This approach is now to be extended by the HyperXpress workflow, which connects ligase cycling reaction for DNA assembly, multiply-primed rolling circle amplification for signal amplification, and cell-free protein synthesis to a single vessel reaction in the lower µl scale. After substantial optimization of the method a proof-of-principle demonstrating the high flexibility of HyperXpress for semi-rational protein engineering by expanding, reducing, and replacing β -strands of three different green fluorescent proteins is described. These single-day experiments resulted in six functional, new-to-nature GFP prototypes., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. TU Darmstadt has applied for a patent in the name of the authors of this publication (EP 21155857.2, pending) covering aspects of the method described in the supplemental protocol., (Copyright © 2022 Zibulski, Schlichting and Kabisch.)
- Published
- 2022
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27. Pipette Show: An Open Source Web Application to Support Pipetting into Microplates.
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Falk J, Mendler M, and Kabisch J
- Subjects
- Automation, Workflow, Software
- Abstract
Despite increasing automation, manual pipetting remains a daily important task in life science laboratories. However, the creation of an efficient work plan is often time-consuming, and its completion is error-prone. Here, we present Pipette Show, a free Vue.js based application that optimizes the generation of an efficient work plan for pipetting into microplates and supports its reliable execution by visual guidance. The basis forms a graphical web interface with a module for building workflows as well as a module displaying the information for each pipetting step by illuminating wells of microplates placed on a tablet.
- Published
- 2022
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28. Functionalizing Cell-Free Systems with CRISPR-Associated Proteins: Application to RNA-Based Circuit Engineering.
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Lehr FX, Kuzembayeva A, Bailey ME, Kleindienst W, Kabisch J, and Koeppl H
- Subjects
- 5' Untranslated Regions, Cell-Free System, Escherichia coli genetics, Green Fluorescent Proteins genetics, Green Fluorescent Proteins metabolism, Logic, Protein Biosynthesis genetics, RNA genetics, RNA, Guide, CRISPR-Cas Systems metabolism, RNA, Messenger metabolism, CRISPR-Associated Proteins genetics, Genetic Engineering methods, RNA metabolism
- Abstract
Cell-free systems have become a compelling choice for the prototyping of synthetic circuits. Many robust protocols for preparing cell-free systems are now available along with toolboxes designed for a variety of applications. Thus far, the production of cell-free extracts has often been decoupled from the production of functionalized proteins. Here, we leveraged a recent protocol for producing an E. coli -based cell-free expression system with two CRISPR-associated proteins, Csy4 and dCas9, expressed prior to harvest. We found that pre-expression did not affect the resulting extract performance, and the final concentrations of the endonucleases matched the level required for synthetic circuit prototyping. We demonstrated the benefits and versatility of dCas9 and Csy4 through the use of RNA circuitry based on a combination of single guide RNAs, small transcriptional activator RNAs, and toehold switches. For instance, we show that Csy4 processing increased 4-fold the dynamic range of a previously published AND-logic gate. Additionally, blending the CRISPR-enhanced extracts enabled us to reduce leakage in a multiple inputs gate, and to extend the type of Boolean functions available for RNA-based circuits, such as NAND-logic. Finally, we reported the use of simultaneous transcriptional and translational reporters in our RNA-based circuits. In particular, the AND-gate mRNA and protein levels were able to be independently monitored in response to transcriptional and translational activators. We hope this work will facilitate the adoption of advanced processing tools for RNA-based circuit prototyping in a cell-free environment.
- Published
- 2021
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29. High-Throughput Screening of an Octanoic Acid Producer Strain Library Enables Detection of New Targets for Increasing Titers in Saccharomyces cerevisiae .
- Author
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Baumann L, Bruder S, Kabisch J, Boles E, and Oreb M
- Subjects
- Biosensing Techniques methods, Fatty Acids biosynthesis, Flow Cytometry methods, Gene Expression, Gene Library, Green Fluorescent Proteins genetics, Microorganisms, Genetically-Modified, Promoter Regions, Genetic, Saccharomyces cerevisiae genetics, Caprylates metabolism, High-Throughput Screening Assays methods, Metabolic Engineering methods, Phosphotransferases (Phosphate Group Acceptor) genetics, Saccharomyces cerevisiae metabolism, Saccharomyces cerevisiae Proteins genetics, Serine Proteases genetics
- Abstract
Octanoic acid is an industrially relevant compound with applications in antimicrobials or as a precursor for biofuels. Microbial biosynthesis through yeast is a promising alternative to current unsustainable production methods. To increase octanoic acid titers in Saccharomyces cerevisiae , we use a previously developed biosensor that is based on the octanoic acid responsive pPDR12 promotor coupled to GFP. We establish a biosensor strain amenable for high-throughput screening of an octanoic acid producer strain library. Through development, optimization, and execution of a high-throughput screening approach, we were able to detect two new genetic targets, KCS1 and FSH2 , which increased octanoic acid titers through combined overexpression by about 55% compared to the parental strain. Neither target has yet been reported to be involved in fatty acid biosynthesis. The presented methodology can be employed to screen any genetic library and thereby more genes involved in improving octanoic acid production can be detected in the future.
- Published
- 2021
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30. Taxonomic Evaluation of the Heyndrickxia (Basonym Bacillus ) sporothermodurans Group ( H. sporothermodurans , H. vini , H. oleronia ) Based on Whole Genome Sequences.
- Author
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Fiedler G, Herbstmann AD, Doll E, Wenning M, Brinks E, Kabisch J, Breitenwieser F, Lappann M, Böhnlein C, and Franz CMAP
- Abstract
The genetic heterogeneity of Heyndrickxia sporothermodurans (formerly Bacillus sporothermodurans) was evaluated using whole genome sequencing. The genomes of 29 previously identified Heyndrickxia sporothermodurans and two Heyndrickxia vini strains isolated from ultra-high-temperature (UHT)-treated milk were sequenced by short-read (Illumina) sequencing. After sequence analysis, the two H. vini strains could be reclassified as H. sporothermodurans . In addition, the genomes of the H. sporothermodurans type strain (DSM 10599
T ) and the closest phylogenetic neighbors Heyndrickxia oleronia (DSM 9356T ) and Heyndrickxia vini (JCM 19841T ) were also sequenced using both long (MinION) and short-read (Illumina) sequencing. By hybrid sequence assembly, the genome of the H. sporothermodurans type strain was enlarged by 15% relative to the short-read assembly. This noticeable increase was probably due to numerous mobile elements in the genome that are presumptively related to spore heat tolerance. Phylogenetic studies based on 16S rDNA gene sequence, core genome, single-nucleotide polymorphisms and ANI/dDDH, showed that H. vini is highly related to H. sporothermodurans . When examining the genome sequences of all H. sporothermodurans strains from this study, together with 4 H. sporothermodurans genomes available in the GenBank database, the majority of the 36 strains examined occurred in a clonal lineage with less than 100 SNPs. These data substantiate previous reports on the existence and spread of a genetically highly homogenous and heat resistant spore clone, i.e., the HRS-clone.- Published
- 2021
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31. Fast and Easy Phage-Tagging and Live/Dead Analysis for the Rapid Monitoring of Bacteriophage Infection.
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Low HZ, Böhnlein C, Sprotte S, Wagner N, Fiedler G, Kabisch J, and Franz CMAP
- Abstract
Use of bacteriophages, which are viruses that kill bacteria, for biocontrol of pathogens and antimicrobial resistant bacteria has become increasingly important in recent years. As traditional culture-based methods are laborious and time-consuming, practicable use of bacteriophages will hinge on development of rapid and high throughput methods to analyze, characterize and screen large bacteriophage libraries. We thus established a novel method to fluorescently tag bacteriophages for virus screening and interaction studies, without the need for complicated and laborious purification procedures or genetic engineering of viruses to express fluorescent proteins. Bacteriophage PMBT14 was tagged using DNA dye Syto 13. Simply by using a membrane filter, tagged bacteriophages can be separated from non-sequestered excess dye rapidly, effortlessly, and cheaply. The procedure takes less than 30 min and makes use of simple laboratory consumables that are already commonly used for bacteriophage preparations. As proof of concept, we present here flow cytometric methods to analyze bacteriophage binding, infection and killing that are very accessible for high throughput analysis. We show that the resulting fluorescently tagged bacteriophage can be used to specifically stain its host bacterium Pseudomonas fluorescens DSM 50090. Individual fluorescent bacteriophages, their binding to and initial infection of bacteria could also be observed using confocal microscopy. The infection process was halted by the metabolic inhibitor sodium azide, suggesting a requirement of host metabolic processes for penetration by PMBT14. Flow cytometric live/dead assays was used as a complementary method to determine bacteriophage infection of its host. We made preliminary efforts to adapt the tagging method to two other bacteriophages and discuss potential pitfalls and solutions in the use of tagged phages. Fluorescent phage tagging has previously been demonstrated to facilitate analysis of bacteriophage-host interactions. The method adopted in this study makes it fast, easy as well as cost effective., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2020 Low, Böhnlein, Sprotte, Wagner, Fiedler, Kabisch and Franz.)
- Published
- 2020
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32. Complete Genome Sequence of a Shiga Toxin-Producing Escherichia coli O26:H11 Strain (Sequence Type 21) and Two Draft Genome Sequences of Listeria monocytogenes Strains (Clonal Complex 1 [CC1] and CC59) Isolated from Fresh Produce in Germany.
- Author
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Fiedler G, Kabisch J, Brinks E, Sprotte S, Boehnlein C, and Franz CMAP
- Abstract
The complete genome sequence of a Shiga toxin-producing Escherichia coli (STEC) O26:H11 strain, MBT-5 (sequence type 21 [ST21], stx
1a , stx2a , eae , ehxA ), and two draft genome sequences of Listeria monocytogenes strains MBT-6 and MBT-7 belonging to the virulent sequence types 1 (ST1, clonal complex 1 [CC1]) and 59 (ST59, CC59), respectively, were determined. The strains were isolated in 2015 from ready-to-eat mixed greens in Germany., (Copyright © 2020 Fiedler et al.)- Published
- 2020
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33. Microbial quality and safety of milk and milk products in the 21st century.
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Fusco V, Chieffi D, Fanelli F, Logrieco AF, Cho GS, Kabisch J, Böhnlein C, and Franz CMAP
- Subjects
- Animals, Bacteria growth & development, Dairy Products standards, Food Quality, Food Safety, Milk standards, Dairy Products microbiology, Food Microbiology, Milk microbiology
- Abstract
Milk and milk products have been utilized by humans for many thousands of years. With the advent of metagenomic studies, our knowledge on the microbiota of milk and milk products, especially as affected by the environment, production, and storage parameters, has increased. Milk quality depends on chemical parameters (fat and protein content and absence of inhibitory substances), as well as microbial and somatic cells counts, and affects the price of milk. The effects of hygiene and effective cooling on the spoilage microbiota have shown that proteolytic and lipolytic bacteria such as Pseudomonas or Acinetobacter spp. predominate the spoilage bacterial populations. These bacteria can produce heat-stable proteases and lipases, which remain active after pasteurization and thus can spoil the milk during prolonged storage. Additionally, milk can become contaminated after pasteurization and therefore there is still a high demand on developing better cleaning and sanitation regimes and equipment, as well as test systems to (quantitatively) detect relevant pathogenic or spoilage microorganisms. Raw milk and raw milk cheese consumption is also increasing worldwide with the growing demand of minimally processed, sustainable, healthy, and local foods. In this context, emerging and re-emerging pathogens once again represent a major food safety challenge. As a result of global warming, it is conceivable that not only microbiological risks but also chemical risks relating to presence of mycotoxins or plant toxins in milk will increase. Herein, we provide an overview of the major microbial hazards occurring in the 21st century., (© 2020 Institute of Food Technologists®.)
- Published
- 2020
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34. The life and times of yeasts in traditional food fermentations.
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Tofalo R, Fusco V, Böhnlein C, Kabisch J, Logrieco AF, Habermann D, Cho GS, Benomar N, Abriouel H, Schmidt-Heydt M, Neve H, Bockelmann W, and Franz CMAP
- Subjects
- Animals, Beer, Bread, Fermentation, Food Microbiology, Yeasts
- Abstract
Yeasts are eukaryotic microorganisms which have a long history in the biotechnology of food production, as they have been used since centuries in bread-making or in the production of alcoholic beverages such as wines or beers. Relative to this importance, a lot of research has been devoted to the study of yeasts involved in making these important products. The role of yeasts in other fermentations in association with other microorganisms - mainly lactic acid bacteria - has been relatively less studied, and often it is not clear if yeasts occurring in such fermentations are contaminants with no role in the fermentation, spoilage microorganisms or whether they actually serve a technological or functional purpose. Some knowledge is available for yeasts used as starter cultures in fermented raw sausages or in the production of acid curd cheeses. This review aimed to summarize the current knowledge on the taxonomy, the presence and potential functional or technological roles of yeasts in traditional fermented plant, dairy, fish and meat fermentations.
- Published
- 2020
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35. Antibiotics resistance and toxin profiles of Bacillus cereus-group isolates from fresh vegetables from German retail markets.
- Author
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Fiedler G, Schneider C, Igbinosa EO, Kabisch J, Brinks E, Becker B, Stoll DA, Cho GS, Huch M, and Franz CMAP
- Subjects
- Bacillus cereus drug effects, Bacillus cereus isolation & purification, Food Contamination analysis, Food Microbiology, Gene Expression Regulation, Bacterial, Genome, Bacterial, Germany, Phylogeny, Whole Genome Sequencing, Anti-Bacterial Agents pharmacology, Bacillus cereus physiology, Bacterial Toxins genetics, Drug Resistance, Microbial, Vegetables microbiology
- Abstract
Background: This study aimed to evaluate the safety of raw vegetable products present on the German market regarding toxin-producing Bacillus cereus sensu lato (s.l.) group bacteria., Results: A total of 147 B. cereus s.l. group strains isolated from cucumbers, carrots, herbs, salad leaves and ready-to-eat mixed salad leaves were analyzed. Their toxinogenic potential was assessed by multiplex PCR targeting the hemolysin BL (hbl) component D (hblD), non-hemolytic enterotoxin (nhe) component A (nheA), cytotoxin K-2 (cytK-2) and the cereulide (ces) toxin genes. In addition, a serological test was used to detect Hbl and Nhe toxins. On the basis of PCR and serological results, none of the strains were positive for the cereulide protein/genes, while 91.2, 83.0 and 37.4% were positive for the Hbl, Nhe and CytK toxins or their genes, respectively. Numerous strains produced multiple toxins. Generally, strains showed resistance against the β-lactam antibiotics such as penicillin G and cefotaxim (100%), as well as amoxicillin/clavulanic acid combination and ampicillin (99.3%). Most strains were susceptible to ciprofloxacin (99.3%), chloramphenicol (98.6%), amikacin (98.0%), imipenem (93.9%), erythromycin (91.8%), gentamicin (88.4%), tetracycline (76.2%) and trimethoprim/sulfamethoxazole combination (52.4%). The genomes of eight selected strains were sequenced. The toxin gene profiles detected by PCR and serological test mostly agreed with those from whole-genome sequence data., Conclusions: Our study showed that B. cereus s.l. strains encoding toxin genes occur in products sold on the German market and that these may pose a health risk to the consumer if present at elevated levels. Furthermore, a small percentage of these strains harbor antibiotic resistance genes. The presence of these bacteria in fresh produce should, therefore, be monitored to guarantee their safety.
- Published
- 2019
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36. Drop-in biofuel production using fatty acid photodecarboxylase from Chlorella variabilis in the oleaginous yeast Yarrowia lipolytica .
- Author
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Bruder S, Moldenhauer EJ, Lemke RD, Ledesma-Amaro R, and Kabisch J
- Abstract
Background: Oleaginous yeasts are potent hosts for the renewable production of lipids and harbor great potential for derived products, such as biofuels. Several promising processes have been described that produce hydrocarbon drop-in biofuels based on fatty acid decarboxylation and fatty aldehyde decarbonylation. Unfortunately, besides fatty aldehyde toxicity and high reactivity, the most investigated enzyme, aldehyde-deformylating oxygenase, shows unfavorable catalytic properties which hindered high yields in previous metabolic engineering approaches., Results: To demonstrate an alternative alkane production pathway for oleaginous yeasts, we describe the production of diesel-like, odd-chain alkanes and alkenes, by heterologously expressing a recently discovered light-driven oxidase from Chlorella variabilis (CvFAP) in Yarrowia lipolytica. Initial experiments showed that only strains engineered to have an increased pool of free fatty acids were susceptible to sufficient decarboxylation. Providing these strains with glucose and light in a synthetic medium resulted in titers of 10.9 mg/L of hydrocarbons. Using custom 3D printed labware for lighting bioreactors, and an automated pulsed glycerol fed-batch strategy, intracellular titers of 58.7 mg/L were achieved. The production of odd-numbered alkanes and alkenes with a length of 17 and 15 carbons shown in previous studies could be confirmed., Conclusions: Oleaginous yeasts such as Yarrowia lipolytica can transform renewable resources such as glycerol into fatty acids and lipids. By heterologously expressing a fatty acid photodecarboxylase from the algae Chlorella variabilis hydrocarbons were produced in several scales from microwell plate to 400 mL bioreactors. The lighting turned out to be a crucial factor in terms of growth and hydrocarbon production, therefore, the evaluation of different conditions was an important step towards a tailor-made process. In general, the developed bioprocess shows a route to the renewable production of hydrocarbons for a variety of applications ranging from being substrates for further enzymatic or chemical modification or as a drop-in biofuel blend., Competing Interests: Competing interestsThe authors declare that they have no competing interests.
- Published
- 2019
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37. Optimization of the experimental parameters of the ligase cycling reaction.
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Schlichting N, Reinhardt F, Jager S, Schmidt M, and Kabisch J
- Abstract
The ligase cycling reaction (LCR) is a scarless and efficient method to assemble plasmids from fragments of DNA. This assembly method is based on the hybridization of DNA fragments with complementary oligonucleotides, so-called bridging oligos (BOs), and an experimental procedure of thermal denaturation, annealing and ligation. In this study, we explore the effect of molecular crosstalk of BOs and various experimental parameters on the LCR by utilizing a fluorescence-based screening system. The results indicate an impact of the melting temperatures of BOs on the overall success of the LCR assembly. Secondary structure inhibitors, such as dimethyl sulfoxide and betaine, are shown to negatively impact the number of correctly assembled plasmids. Adjustments of the annealing, ligation and BO-melting temperature further improved the LCR. The optimized LCR was confirmed by validation experiments. Based on these findings, a step-by-step protocol is offered within this study to ensure a routine for high efficient LCR assemblies., (© The Author(s) 2019. Published by Oxford University Press.)
- Published
- 2019
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38. Quantification and isolation of Bacillus subtilis spores using cell sorting and automated gating.
- Author
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Karava M, Bracharz F, and Kabisch J
- Subjects
- Bacillus subtilis genetics, Bacterial Proteins chemistry, Bacteriological Techniques, Flow Cytometry, Fluorescent Dyes chemistry, Gene Expression Regulation, Bacterial, Gene Knockout Techniques, Normal Distribution, Spores, Bacterial genetics, Bacillus subtilis physiology, Bacterial Proteins genetics, Spores, Bacterial isolation & purification
- Abstract
The Gram-positive bacterium Bacillus subtilis is able to form endospores which have a variety of biotechnological applications. Due to this ability, B. subtilis is as well a model organism for cellular differentiation processes. Sporulating cultures of B. subtilis form sub-populations which include vegetative cells, sporulating cells and spores. In order to readily and rapidly quantify spore formation we employed flow cytometric and fluorescence activated cell sorting techniques in combination with nucleic acid fluorescent staining in order to investigate the distribution of sporulating cultures on a single cell level. Automated gating procedures using Gaussian mixture modeling (GMM) were employed to avoid subjective gating and allow for the simultaneous measurement of controls. We utilized the presented method for monitoring sporulation over time in germination deficient strains harboring different genome modifications. A decrease in the sporulation efficiency of strain Bs02018, utilized for the display of sfGFP on the spores surface was observed. On the contrary, a double knock-out mutant of the phosphatase gene encoding Spo0E and of the spore killing factor SkfA (Bs02025) exhibited the highest sporulation efficiency, as within 24 h of cultivation in sporulation medium, cultures of BS02025 already consisted of 80% spores as opposed to 18% for the control strain. We confirmed the identity of the different subpopulations formed during sporulation by employing sorting and microscopy., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2019
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39. Pseudomonas kielensis sp. nov. and Pseudomonas baltica sp. nov., isolated from raw milk in Germany.
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Gieschler S, Fiedler G, Böhnlein C, Grimmler C, Franz CMAP, and Kabisch J
- Abstract
In this study, nine Gram-negative, motile and rod-shaped bacteria were isolated during a Germany-wide investigation of raw milk microbiota. The strains could be differentiated from their closest relatives by phenotypic and chemotaxonomic characterization and average nucleotide identity (ANIb) values calculated from draft genome assemblies. Strains MBT-1
T , MBT-8, MBT-9, MBT-10, MBT-11 and MBT-12 were related to the Pseudomonas chlororaphis subgroup. Isolates MBT-2T , MBT-13 and MBT-14 were closely related to Pseudomonas rhizosphaerae DSM 16299T with an ANIb of 88.2 % and a genome-to-genome distance result of 36.0 %. The G+C content of the DNA of strains MBT-1T and MBT-2T was 60.84 and 62.48 mol%, respectively. The major fatty acids were C16 : 1 ω7 c (summed feature 3), C16 : 0 and C18 : 1 ω7 c (summed feature 8). The strains were catalase-positive, while production of urease, β-galactosidase and indole were negative. Growth occurred at 4-30 °C and at pH values of pH 6.0-8.0. Based on these results, we conclude that the strains belong to two novel species, for which the names Pseudomonas kielensis sp. nov. and Pseudomonas baltica sp. nov. are proposed. The type strains are MBT-1T (=DSM 111668T = LMG 31954T ) and MBT-2T (=DSM 111761T =LMG 31955T ).- Published
- 2019
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40. Fungal biotransformation of short-chain n-alkylcycloalkanes.
- Author
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Schlüter R, Dallinger A, Kabisch J, Duldhardt I, and Schauer F
- Subjects
- Biotransformation, Chromatography, High Pressure Liquid, Environmental Pollutants metabolism, Gas Chromatography-Mass Spectrometry, Candida metabolism, Cyclohexanes metabolism, Metabolic Networks and Pathways, Trichosporon metabolism
- Abstract
The cycloalkanes, comprising up to 45% of the hydrocarbon fraction, occur in crude oil or refined oil products (e.g., gasoline) mainly as alkylated cyclohexane derivatives and have been increasingly found in environmental samples of soil and water. Furthermore, short-chain alkylated cycloalkanes are components of the so-called volatile organic compounds (VOCs). This study highlights the biotransformation of methyl- and ethylcyclohexane by the alkane-assimilating yeast Candida maltosa and the phenol- and benzoate-utilizing yeast Trichosporon mucoides under laboratory conditions. In the course of this biotransformation, we detected 25 different metabolites, which were analyzed by HPLC and GC-MS. The biotransformation process of methylcyclohexane in both yeasts involve (A) ring hydroxylation at different positions (C2, C3, and C4) and subsequent oxidation to ketones as well as (B) oxidation of the alkyl side chain to hydroxylated and acid products. The yeast T. mucoides additionally performs ring hydroxylation at the C1-position and (C) oxidative decarboxylation and (D) aromatization of cyclohexanecarboxylic acid. Both yeasts also oxidized the saturated ring system and the side chain of ethylcyclohexane. However, the cyclohexylacetic acid, which was formed, seemed not to be substrate for aromatization. This is the first report of several new transformation reactions of alkylated cycloalkanes for eukaryotic microorganisms.
- Published
- 2019
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41. CopySwitch- in vivo Optimization of Gene Copy Numbers for Heterologous Gene Expression in Bacillus subtilis .
- Author
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Nadler F, Bracharz F, and Kabisch J
- Abstract
The Gram-positive bacterium Bacillus subtilis has long been used as a host for production and secretion of industrially relevant enzymes like amylases and proteases. It is imperative for optimal efficiency, to balance protein yield and correct folding. While there are numerous ways of doing so on protein or mRNA level, our approach aims for the underlying number of coding sequences. Gene copy numbers are an important tuning valve for the optimization of heterologous gene expression. While some genes are best expressed from many gene copies, for other genes, medium or even single copy numbers are the only way to avoid formation of inclusion bodies, toxic gene dosage effects or achieve desired levels for metabolic engineering. In order to provide a simple and robust method to address above-mentioned issues in the Gram-positive bacterium Bacillus subtilis , we have developed an automatable system for the tuning of heterologous gene expression based on the host's intrinsic natural competence and homologous recombination capabilities. Strains are transformed with a linearized, low copy number plasmid containing an antibiotic resistance marker and homology regions up- and downstream of the gene of interest. Said gene is copied onto the vector, rendering it circular and replicative and thus selectable. We could show an up to 3.6-fold higher gfp (green fluorescent protein) expression and up to 1.3-fold higher mPLC (mature phospholipase C) expression after successful transformation. Furthermore, the plasmid-borne gfp expression seems to be more stable, since over the whole cultivation period the share of fluorescent cells compared to all measured cells is consistently higher. A major benefit of this method is the ability to work with very large regions of interest, since all relevant steps are carried out in vivo and are thus far less prone to mechanical DNA damage.
- Published
- 2019
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42. Influence of iodized table salt on fermentation characteristics and bacterial diversity during sauerkraut fermentation.
- Author
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Müller A, Rösch N, Cho GS, Meinhardt AK, Kabisch J, Habermann D, Böhnlein C, Brinks E, Greiner R, and Franz CMAP
- Subjects
- Bacteria classification, Bacteria genetics, Brassica chemistry, Fermentation, Fermented Foods analysis, Food Microbiology, Hydrogen-Ion Concentration, Lactobacillus plantarum genetics, Lactobacillus plantarum isolation & purification, Lactobacillus plantarum metabolism, Leuconostoc genetics, Leuconostoc isolation & purification, Leuconostoc metabolism, Bacteria isolation & purification, Bacteria metabolism, Biodiversity, Brassica microbiology, Fermented Foods microbiology, Iodine metabolism, Sodium Chloride, Dietary metabolism
- Abstract
The effect of iodine present in 1.0% table salt in combination with the use of starter cultures in sauerkraut fermentations were investigated in order to determine whether iodine interferes with lactic acid bacteria responsible for the fermentation. The effect of iodine was tested in fermentations performed using selected starter cultures or without starters (spontaneous fermentation). Lactobacillus plantarum and Leuconostoc mesenteroides used as starters at levels of ca. 1 × 10
7 cfu ml-1 led to a quick establishment of lactic acid bacteria (LAB) as predominant microorganisms, reaching 1 × 109 cfu ml-1 after 24 h decreasing the pH to below 4.0. In contrast, LAB counts in control fermentations without starters increased slower from 1 × 105 cfu ml-1 to 1 × 109 cfu ml-1 and a pH reduction below 4.0 was achieved only after 3 days fermentation. A metagenomic investigation showed a more diverse bacterial community in fermentations without starters, consisting of enterobacteria and pseudomonads in the first days of fermentation, and of LAB such as lactococci in the later stages. In fermentations with starters, lactobacilli predominated. Leuconostocs also occurred, but at much lower sequence abundance than lactobacilli, and thus were not able to predominate. Determination of iodine in the fermentation with starter bacteria and with iodized salt showed that the fermentation did not affect iodine concentration. The use of iodized salt did not statistically significantly influence microbial populations in the fermentation. Thus, there is no basis for the popular held belief that the use of iodized salt inhibits the growth of the bacteria important for the sauerkraut fermentation. A statistically near significant effect (p = 0.06), however, was noted for the effect of iodine on yeasts and mould populations in the fermentations performed without starter cultures. As sauerkraut is usually produced without starters, this should be further investigated., (Copyright © 2018 Elsevier Ltd. All rights reserved.)- Published
- 2018
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43. Isolation and Characterization of Lactic Acid Bacteria from Fermented Goat Milk in Tajikistan.
- Author
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Cho GS, Cappello C, Schrader K, Fagbemigum O, Oguntoyinbo FA, Csovcsics C, Rösch N, Kabisch J, Neve H, Bockelmann W, Briviba K, Modesto M, Cilli E, Mattarelli P, and Franz CMAP
- Subjects
- Animals, Anti-Bacterial Agents pharmacology, Coculture Techniques, Fermentation, Genome, Bacterial genetics, Goats, Hydrogen-Ion Concentration, Lactobacillales classification, Microbial Sensitivity Tests, Microbial Viability drug effects, Milk microbiology, RNA, Ribosomal, 16S genetics, Tajikistan, Viscosity, Cultured Milk Products microbiology, Food Microbiology, Lactobacillales isolation & purification, Lactobacillales physiology
- Abstract
The lactobacilli associated with a fermented goat milk product from Tajikistan were isolated to characterize their technological properties and antibiotic resistances in order to assess their suitability for development as starter cultures. In this study, twenty three strains were identified by 16S rRNA sequencing as typical dairy-associated lactic acid bacterial strains, i.e. L. plantarum , L. pentosus , L. delbrueckii , L. helveticus and L. paracasei . These strains were generally susceptible to most antibiotics tested in this study and this allowed a selection of strains as safe starters. The draft genomes of four representative strains were sequenced and the number of contigs of the four assembled genomes ranged from 51 to 245 and the genome sizes ranged from 1.75 to 3.24 Mbp. These representative strains showed differences in their growth behavior and pH-reducing abilities in in vitro studies. The co-inoculation of these Lactobacillus spp. strains together with a yeast Kluyveromyces marxianus MBT-5698, or together with the yeast and an additional Streptococcus thermophilus MBT-2, led to a pH reduction to 3.4 after 48 h. Only in the case of fermentation inoculated with the co-culture, the viscosity of the milk increased noticeably. In contrast, fermentations with single strains did not lead to gelation of the milk or to a decrease in the pH after 24h. The results of this study provide a comprehensive understanding of the predominant lactobacilli related to Tajikistani fermented milk products.
- Published
- 2018
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44. Draft Genome Sequence of the Intimin-Positive Enteropathogenic Escherichia albertii Strain MBT-EA1, Isolated from Lettuce.
- Author
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Fiedler G, Brinks E, Böhnlein C, Cho GS, Koberg S, Kabisch J, and Franz CMAP
- Abstract
The genome of the intimin ( eae )-harboring Escherichia albertii strain MBT-EA1, isolated from lettuce in Germany, was sequenced. Sequence analysis showed the assembled draft genome size to be 4,560,948 bp, containing a predicted total of 4,414 protein-encoding genes, 11 rRNAs, and 82 tRNAs. Furthermore, three plasmid sequences were found., (Copyright © 2018 Fiedler et al.)
- Published
- 2018
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45. Diversity and Antibiotic Susceptibility of Acinetobacter Strains From Milk Powder Produced in Germany.
- Author
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Cho GS, Li B, Rostalsky A, Fiedler G, Rösch N, Igbinosa E, Kabisch J, Bockelmann W, Hammer P, Huys G, and Franz CMAP
- Abstract
Forty-seven Acinetobacter spp. isolates from milk powder obtained from a powdered milk producer in Germany were investigated for their antibiotic resistance susceptibilities, in order to assess whether strains from food harbor multiple antibiotic resistances and whether the food route is important for dissemination of resistance genes. The strains were identified by 16S rRNA and rpo B gene sequencing, as well as by whole genome sequencing of selected isolates and their in silico DNA-DNA hybridization (DDH). Furthermore, they were genotyped by rep-PCR together with reference strains of pan-European groups I, II, and III strains of Acinetobacter baumannii . Of the 47 strains, 42 were identified as A. baumannii , 4 as Acinetobacter Pittii , and 1 as Acinetobacter calcoaceticus based on 16S rRNA gene sequencing. In silico DDH with the genome sequence data of selected strains and rpo B gene sequencing data suggested that the five non- A. baumannii strains all belonged to A. pittii , suggesting that the rpo B gene is more reliable than the 16S rRNA gene for species level identification in this genus. Rep-PCR genotyping of the A. baumannii strains showed that these could be grouped into four groups, and that some strains clustered together with reference strains of pan-European clinical group II and III strains. All strains in this study were intrinsically resistant toward chloramphenicol and oxacillin, but susceptible toward tetracycline, tobramycin, erythromycin, and ciprofloxacin. For cefotaxime, 43 strains (91.5%) were intermediate and 3 strains (6.4%) resistant, while 3 (6.4%) and 21 (44.7%) strains exhibited resistance to cefepime and streptomycin, respectively. Forty-six (97.9%) strains were susceptible to amikacin and ampicillin-sulbactam. Therefore, the strains in this study were generally not resistant to the clinically relevant antibiotics, especially tobramycin, ciprofloxacin, cefepime, and meropenem, suggesting that the food route probably poses only a low risk for multidrug resistant Acinetobacter strains or resistance genes.
- Published
- 2018
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46. Co-expression of an alcohol dehydrogenase and a cyclohexanone monooxygenase for cascade reactions facilitates the regeneration of the NADPH cofactor.
- Author
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Kohl A, Srinivasamurthy V, Böttcher D, Kabisch J, and Bornscheuer UT
- Subjects
- Acinetobacter calcoaceticus enzymology, Acinetobacter calcoaceticus genetics, Alcohol Dehydrogenase genetics, Bacterial Proteins genetics, Bacterial Proteins metabolism, Biocatalysis, Candida enzymology, Candida genetics, Cyclohexanols metabolism, Escherichia coli genetics, Escherichia coli metabolism, Fungal Proteins genetics, Fungal Proteins metabolism, Genetic Vectors, Lactobacillus enzymology, Lactobacillus genetics, Lipase genetics, Lipase metabolism, Mutagenesis, Site-Directed, Oxygenases genetics, Protein Engineering methods, Recombinant Proteins genetics, Recombinant Proteins metabolism, Alcohol Dehydrogenase metabolism, NADP metabolism, Oxygenases metabolism
- Abstract
The introduction of a three-enzyme cascade (comprising a cyclohexanone monooxygenase (CHMO), an alcohol dehydrogenase (ADH) and a lipase (CAL-A)) for the production of oligo-ε-caprolactone provided self-sufficiency with respect to NADPH-cofactor regeneration and reduced inhibiting effects on the central CHMO enzyme. For further optimization of cofactor regeneration, now a co-expression of CHMO and ADH in E. coli using a Duet™ vector was performed. This led to higher conversion values of the substrate cyclohexanol in whole-cell biocatalysis compared to an expression of both enzymes from two separate plasmids. Furthermore, a more advantageous balance of expression levels between the partial cascade enzymes was achieved via engineering of the ribosome binding site. This contributed to an even faster cofactor regeneration rate., (Copyright © 2017 Elsevier Inc. All rights reserved.)
- Published
- 2018
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47. Halomonas nigrificans sp. nov., isolated from cheese.
- Author
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Oguntoyinbo FA, Cnockaert M, Cho GS, Kabisch J, Neve H, Bockelmann W, Wenning M, Franz CMAP, and Vandamme P
- Subjects
- Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Europe, Genes, Bacterial, Halomonas genetics, Halomonas isolation & purification, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Cheese microbiology, Food Microbiology, Halomonas classification, Phylogeny
- Abstract
A Gram-stain-negative, rod-shaped Proteobacteria isolate, MBT G8648
T , was obtained from an acid curd cheese called Quargel. The isolate was moderately salt tolerant and motile, with numerous peritrichous flagella. The 16S rRNA gene sequence analysis indicated that the strain belongs to the genus Halomonas, with 98.42 % 16S rRNA gene sequence similarity with Halomonas titanicae BH1T as nearest related neighbour. Further comparative sequence analysis of secA and gyrB genes, as well as physiological and biochemical tests, revealed that this bacterium formed a taxon well-separated from its nearest neighbours and other established Halomonas species. Thus, the strain represents a new species, for which the name Halomonas nigrificans sp. nov. is proposed, with strain MBT G8648T (=LMG 29097T =DSM 105749T ) as type strain.- Published
- 2018
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48. Persistence and reduction of Shiga toxin-producing Escherichia coli serotype O26:H11 in different types of raw fermented sausages.
- Author
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Böhnlein C, Kabisch J, Müller-Herbst S, Fiedler G, Franz CMAP, and Pichner R
- Subjects
- Animals, Disease Outbreaks, Escherichia coli Infections epidemiology, Europe epidemiology, Fermentation, Humans, Meat Products analysis, Serogroup, Shiga Toxin genetics, Shiga-Toxigenic Escherichia coli genetics, Shiga-Toxigenic Escherichia coli metabolism, Escherichia coli Infections microbiology, Food Contamination analysis, Meat Products microbiology, Shiga-Toxigenic Escherichia coli isolation & purification
- Abstract
Fermented sausages have been identified as source of several outbreaks of Shiga toxin-producing Escherichia coli (STEC). Illnesses linked to non-O157 STEC serotypes appear to be on the rise worldwide, and serogroup O26 is the second most reported in Europe after O157. However, data on the behavior of serogroup O26 in food are rare, so that the aim of this study was to investigate the survival of STEC O26:H11 in different types of fermented sausages ("Teewurst", fast-ripened and long-fermented salami). Challenge studies were performed with an inoculation cocktail which consisted of three STEC O26:H11 strains isolated from human, cattle and food sources. In the short-ripened spreadable sausage type "Teewurst" STEC counts decreased by only 0.5 log
10 within 28days. In contrast, STEC reductions from 2.2 to 2.6 log10 units were observed in the different salami products, while the most pronounced decrease of 1.0 log10 unit within one day was detected in fast-ripened sausages with glucono delta-lactone (GdL). Moreover, numbers of the food-associated E. coli O26:H11 strain were significantly higher (p<0.001) than those of the human and cattle STEC O26:H11 strains in all types of fermented sausages. Approximately 60% of all STEC isolates from GdL salami shared the genotypic virulence profile of the food-associated E. coli O26:H11 strain. In summary, hurdles of acidification and drying during salami ripening resulted in reductions of STEC O26:H11 counts. However, our results also indicate that STEC O26:H11 can persist in the environment of "Teewurst" and might therefore pose a risk to public health., (Copyright © 2017 Elsevier B.V. All rights reserved.)- Published
- 2017
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49. Presence of Human Pathogens in Produce from Retail Markets in Northern Germany.
- Author
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Fiedler G, Kabisch J, Böhnlein C, Huch M, Becker B, Cho GS, and Franz CMAP
- Subjects
- Germany, Humans, Listeria monocytogenes genetics, Salmonella genetics, Shiga-Toxigenic Escherichia coli genetics, Food Microbiology, Listeria monocytogenes isolation & purification, Salmonella isolation & purification, Shiga-Toxigenic Escherichia coli isolation & purification, Vegetables microbiology
- Abstract
Two hundred fresh produce samples (cucumber, carrots, herbs, leaf lettuce, and ready-to-eat mixed salad leaves) were obtained from retail in northern Germany in 2015. These were investigated for microbial contamination and the presence of foodborne pathogens, including Listeria monocytogenes, Salmonella serovars, presumptive Bacillus (B.) cereus, and Shiga toxin-producing Escherichia coli using culture-dependent (enrichment, plating on selective media) and -independent (real-time polymerase chain reaction [PCR]) techniques. Overall, our results showed that the fresh produce samples generally showed high mean aerobic mesophilic bacterial counts of between 7 and 8 log
10 cfu/g. However, there was also a considerable variation in total aerobic bacterial counts between different product samples. Although real-time PCR signals for pathogenic E. coli were detected in 14.0% of total samples analyzed, only one (0.5%) Shiga toxin-producing E. coli isolate of serotype O26:H11 was recovered from mixed salad leaves and contained stx1, stx2, and eae genes. Two L. monocytogenes isolates (1% of total samples) were recovered from packaged mixed salad leaves and belonged to PCR serogroups IIb and IVb, respectively. One Salmonella isolate (0.5%) was recovered after selective enrichment also from mixed salad leaves and it was identified as Salmonella Szentes serotype 16:k:1,2. Overall the incidence of foodborne pathogens on the northern German retail market in 2015 was very low.- Published
- 2017
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50. Aquatic adaptation of a laterally acquired pectin degradation pathway in marine gammaproteobacteria.
- Author
-
Hehemann JH, Truong LV, Unfried F, Welsch N, Kabisch J, Heiden SE, Junker S, Becher D, Thürmer A, Daniel R, Amann R, and Schweder T
- Subjects
- Amino Acid Sequence, Gammaproteobacteria genetics, Gene Transfer, Horizontal genetics, Interspersed Repetitive Sequences genetics, Proteomics, Adaptation, Physiological genetics, Gammaproteobacteria metabolism, Pectins metabolism, Polysaccharide-Lyases genetics
- Abstract
Mobile genomic islands distribute functional traits between microbes and habitats, yet it remains unclear how their proteins adapt to new environments. Here we used a comparative phylogenomic and proteomic approach to show that the marine bacterium Pseudoalteromonas haloplanktis ANT/505 acquired a genomic island with a functional pathway for pectin catabolism. Bioinformatics and biochemical experiments revealed that this pathway encodes a series of carbohydrate-active enzymes including two multi-modular pectate lyases, PelA and PelB. PelA is a large enzyme with a polysaccharide lyase family 1 (PL1) domain and a carbohydrate esterase family 8 domain, and PelB contains a PL1 domain and two carbohydrate-binding domains of family 13. Comparative phylogenomic analyses indicate that the pathway was most likely acquired from terrestrial microbes, yet we observed multi-modular orthologues only in marine bacteria. Proteomic experiments showed that P. haloplanktis ANT/505 secretes both pectate lyases into the environment in the presence of pectin. These multi-modular enzymes may therefore represent a marine innovation that enhances physical interaction with pectins to reduce loss of substrate and enzymes by diffusion. Our results revealed that marine bacteria can catabolize pectin, and highlight enzyme fusion as a potential adaptation that may facilitate microbial consumption of polymeric substrates in aquatic environments., (© 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.)
- Published
- 2017
- Full Text
- View/download PDF
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