Publications of Philippe Jacques
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See detailRelationship between lipopeptide biosurfactant and primary metabolite production by Bacillus strains in solid-state and submerged fermentation.
VALDES VELASCO, LUISA MARCELA; FAVELA TORRES, ERNESTO; Théatre, Ariane ULiege et al

in Bioresource Technology (2022), 345

The relationship between lipopeptide and primary metabolite production by Bacillus spp. in solid-state fermentation (SSF) and submerged fermentation (SmF) was evaluated. Four wild-type strains and one ... [more ▼]

The relationship between lipopeptide and primary metabolite production by Bacillus spp. in solid-state fermentation (SSF) and submerged fermentation (SmF) was evaluated. Four wild-type strains and one mutant strain (unable to develop biofilm) were assessed in SSF and SmF, using a defined medium and polyurethane foam as inert support for SSF. Strain ATCC 21,332 in SSF presented the highest lipopeptide production. The wild-type strains revealed higher lipopeptide and biomass production and lower synthesis of primary metabolites in SSF than in SmF. However, the mutant strain showed a slightly higher production of primary metabolites in SSF than in SmF. Carbon balance analysis showed that the carbon flux was mainly directed to lipopeptides in SSF, whereas in SmF, it was directed to the production of primary metabolites and the carbon flux to lipopeptides is inversely related to primary metabolites in both types of cultures. [less ▲]

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See detailValorisation d’un co-produit de la production du bio-éthanol comme substrat de fermentation pour la production de nouvelles formes de biosurfactants plus actives
Lins, Laurence ULiege; Deleu, Magali ULiege; Jacques, Philippe ULiege

Conference (2021, June)

Les surfactants d'origine biologique suscitent un intérêt croissant dans différents domaines applicatifs tels que la détergence, la cosmétique, le traitement des sols pollués ou encore la dispersion des ... [more ▼]

Les surfactants d'origine biologique suscitent un intérêt croissant dans différents domaines applicatifs tels que la détergence, la cosmétique, le traitement des sols pollués ou encore la dispersion des marées noires en raison de leurs propriétés uniques telles que leur spécificité, leur biodégradabilité et leur toxicité potentiellement plus faible. Pour ces applications, l’obstacle majeur reste le coût de production. Dans le cadre du projet européen BestBioSurf, 7 laboratoires et 3 entreprises ont mis ensemble leurs compétences pour développer de nouveaux biosurfactants aux propriétés de détergence accrue ainsi qu’un procédé de production permettant d’en réduire le prix de revient. En se basant sur les propriétés de biosurfactants d’origine microbienne, des outils informatiques de prédiction des relations structure-fonction ont été utilisés pour prédire la(les) structure(s) du biosurfactant la(les) plus optimale(s) en termes de propriétés physico-chimiques. Les souches productrices des biosurfactants les plus efficaces ont été cultivées sur un co-produit de la production du bio-éthanol à partir de céréales. Ce co-produit généré lors de la distillation répond à de nombreux critères essentiels pour être utilisé à cette fin : la présence de tous les substrats nécessaires à la croissance des micro-organismes concernés et à la production des biosurfactants, l’absence d’inhibiteurs, un tonnage important et un coût extrêmement faible. [less ▲]

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See detailNew Continuous Process for the Production of Lipopeptide Biosurfactants in Foam Overflowing Bioreactor
Guez, J.-S.; Vassaux, A.; Larroche, C. et al

in Frontiers in Bioengineering and Biotechnology (2021), 9

In this work, an original culture process in bioreactor named overflowing continuous culture (O-CC) was developed to produce and recover continuously mycosubtilin, a lipopeptide antifungal biosurfactant ... [more ▼]

In this work, an original culture process in bioreactor named overflowing continuous culture (O-CC) was developed to produce and recover continuously mycosubtilin, a lipopeptide antifungal biosurfactant of major interest. The lipopeptide production was first investigated in shake conical flasks in different culture media [ammonium citrate sucrose (ACS), Difco sporulation medium (DSM), and Landy], followed by a pH condition optimization using 3-(N-morpholino)propanesulfonic acid (MOPS) and 2-(N-morpholino)ethanesulfonic acid (MES) buffered media. A simple theoretical modeling of the biomass evolution combined with an experimental setup was then proposed for O-CC processed in stirred tank reactor at laboratory scale. Seven O-CC experiments were done in modified Landy medium at the optimized pH 6.5 by applying dilution rates comprised between 0.05 and 0.1 h–1. The O-CC allowed the continuous recovery of the mycosubtilin contained in the foam overflowing out of the reactor, achieving a remarkable in situ product removal superior to 99%. The biomass concentration in the overflowing foam was found to be twofold lower than the biomass concentration in the reactor, relating advantageously this process to a continuous one with biomass feedback. To evaluate its performances regarding the type of lipopeptide produced, the O-CC process was tested with strain BBG116, a mycosubtilin constitutive overproducing strain that also produces surfactin, and strain BBG125, its derivative strain obtained by deleting surfactin synthetase operon. At a dilution rate of 0.1 h–1, specific productivity of 1.18 mg of mycosubtilin⋅g–1(DW)⋅h–1 was reached. Compared with other previously described bioprocesses using almost similar culture conditions and strains, the O-CC one allowed an increase of the mycosubtilin production rate by 2.06-fold. © Copyright © 2021 Guez, Vassaux, Larroche, Jacques and Coutte. [less ▲]

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See detailUV-screening pigment enabling ancient photosynthesis
Lara, Yannick ULiege; Mc Cann, Andréa ULiege; Malherbe, Cédric ULiege et al

Conference (2021)

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See detailThe Surfactin-Like Lipopeptides From Bacillus spp.: Natural Biodiversity and Synthetic Biology for a Broader Application Range
Théatre, Ariane ULiege; Cano-Prieto, Carolina; Bartolini, Marco et al

in Frontiers in Bioengineering and Biotechnology (2021), 9

Surfactin is a lipoheptapeptide produced by several Bacillus species and identified for the first time in 1969. At first, the biosynthesis of this remarkable biosurfactant was described in this review ... [more ▼]

Surfactin is a lipoheptapeptide produced by several Bacillus species and identified for the first time in 1969. At first, the biosynthesis of this remarkable biosurfactant was described in this review. The peptide moiety of the surfactin is synthesized using huge multienzymatic proteins called NonRibosomal Peptide Synthetases. This mechanism is responsible for the peptide biodiversity of the members of the surfactin family. In addition, on the fatty acid side, fifteen different isoforms (from C12 to C17) can be incorporated so increasing the number of the surfactin-like biomolecules. The review also highlights the last development in metabolic modeling and engineering and in synthetic biology to direct surfactin biosynthesis but also to generate novel derivatives. This large set of different biomolecules leads to a broad spectrum of physico-chemical properties and biological activities. The last parts of the review summarized the numerous studies related to the production processes optimization as well as the approaches developed to increase the surfactin productivity of Bacillus cells taking into account the different steps of its biosynthesis from gene transcription to surfactin degradation in the culture medium. [less ▲]

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See detailSurfactin Stimulated by Pectin Molecular Patterns and Root Exudates Acts as a Key Driver of the Bacillus-Plant Mutualistic Interaction
Hoff, G.; Arias, A. A.; Boubsi, Farah ULiege et al

in MBio (2021), 12(6),

Bacillus velezensis is considered as a model species belonging to the so-called Bacillus subtilis complex that evolved typically to dwell in the soil rhizosphere niche and establish an intimate ... [more ▼]

Bacillus velezensis is considered as a model species belonging to the so-called Bacillus subtilis complex that evolved typically to dwell in the soil rhizosphere niche and establish an intimate association with plant roots. This bacterium provides protection to its natural host against diseases and represents one of the most promising biocontrol agents. However, the molecular basis of the cross talk that this bacterium establishes with its natural host has been poorly investigated. We show here that these plant-associated bacteria have evolved a polymer-sensing system to perceive their host and that, in response, they increase the production of the surfactin-type lipopeptide. Furthermore, we demonstrate that surfactin synthesis is favored upon growth on root exudates and that this lipopeptide is a key component used by the bacterium to optimize biofilm formation, motility, and early root colonization. In this specific nutritional context, the bacterium also modulates qualitatively the pattern of surfactin homologues coproduced in planta and forms mainly variants that are the most active at triggering plant immunity. Surfactin represents a shared good as it reinforces the defensive capacity of the host. © 2021 Hoff et al. [less ▲]

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See detailLimiting factors of mycopesticide development
Zaki, Omran ULiege; Weekers, F; Thonart, Philippe ULiege et al

in Biological Control (2020)

Phytosanitary crop protection products have shown their impact on the environment. They may not be very selective and their excessive use in agriculture causes pollution of soil and groundwater ... [more ▼]

Phytosanitary crop protection products have shown their impact on the environment. They may not be very selective and their excessive use in agriculture causes pollution of soil and groundwater, destruction of many beneficial insects and the emergence of resistant pests. Hence there is strong public and political pressure driven by consumers to implement phytosanitary alternatives that are less aggressive to the environment, such of biopesticides. Biopesticides and, in particular, mycopesticides are frequently used as an environmentally friendly tools to reduce plant diseases by inhibiting the growth of pathogens and inducing resistance in plants. <br /> <br />In this review, we will first analyze the current evolution of the global market of biopesticides. Boosted by different political initiatives all over the world, this market has increased 6-fold between 2005 and 2016. In 2016, it represented 6% of the global pesticide market with a compound annual growth rate (CGAR) of 14.1%. The mycopesticides accounted for only 10% of the global biopesticide market of 2016. <br /> <br />We then focused on two main factors which should contribute to the future development of mycopesticides: the large panel of their modes of action and the physiological state of the active product. Indeed, several modes of action could, in some instances, increase the efficacy of a biopesticide and postpone the emergence of resistance mechanism. The broad set of mechanisms use by Trichoderma harzianum and T. atroviride to reduce plant diseases: nutrient competition, direct antagonism, mycoparasitism and induction of resistance mechanism in plants were developed as an example. Stability of the active substance is another essential factor for creating competitive mycopesticides. For this, the choice of propagule types could be a major factor in enhancing their stability. This choice was discussed highlighting the advantages of conidia or sporidia from solid-state fermentation. <br /> <br />To end with, the registration process in European Union was described revealing another limiting factor that delays the development of mycopesticides in this zone. [less ▲]

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See detailOverall strategy to implement NRPS production in fungal host
Vassau, A; Fickers, Patrick ULiege; Leclere, V et al

Conference (2020)

Detailed reference viewed: 21 (1 ULiège)
See detailOptimization of biosurfactant production in a trickle-bed biofilm reactor with genetically improved bacteria
Brück, Hannah ULiege; Coutte, François; Delvigne, Frank ULiege et al

Poster (2020)

The Gram-positive soil bacterium Bacillus subtilis is a potential producer of the very powerful biosurfactant surfactin [1]. In the phytosanitary field, surfactin gains increasing attention for the use as ... [more ▼]

The Gram-positive soil bacterium Bacillus subtilis is a potential producer of the very powerful biosurfactant surfactin [1]. In the phytosanitary field, surfactin gains increasing attention for the use as biocontrol agent since it is able to induce systemic resistance in plants [1]. Furthermore, surfactin has many applications in different industrial sectors due to the exceptional foaming and emulsifying properties [1]. Biofilm bioreactors are efficient alternative production systems for bacterial biosurfactants since excessive foam formation can be avoided while a high air/liquid mass transfer can be obtained [2-5]. The widely used B. subtilis 168 strain has very low cell adhesion capacities and thus a reduced growth in biofilm-based systems. In this work, genetically modified B. subtilis 168 mutants have been designed to improve the natural cell immobilization via biofilm formation. The mutants were first cultivated in a drip-flow biofilm reactor to assess their biofilm formation capacities [6]. Then, the strains with the best performances were selected for the cultivation in a trickle-bed biofilm reactor. The mutants with functional biofilm matrix production showed a significantly improved adhesion capacity compared to the control strain as well as an improved surfactin productivity. The introduced cell filamentation seemed to improve cell cohesion and to decrease cell detachment. [less ▲]

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See detailGrowth Dynamics of Bacterial Populations in a Two-Compartment Biofilm Bioreactor Designed for Continuous Surfactin Biosynthesis
Brück, Hannah ULiege; Coutte, François; Dhulster, Pascal et al

in Microorganisms (2020)

Biofilm bioreactors are promising systems for continuous biosurfactant production since they provide process stability through cell immobilization and avoid foam formation. In this work, a two-compartment ... [more ▼]

Biofilm bioreactors are promising systems for continuous biosurfactant production since they provide process stability through cell immobilization and avoid foam formation. In this work, a two-compartment biofilm bioreactor was designed consisting of a stirred tank reactor and a trickle-bed reactor containing a structured metal packing for biofilm formation. A strong and poor biofilm forming B. subtilis 168 strain due to restored exopolysaccharides (EPS) production or not were cultivated in the system to study the growth behavior of the planktonic and biofilm population for the establishment of a growth model. A high dilution rate was used in order to promote biofilm formation on the packing and wash out unwanted planktonic cells. Biofilm development kinetics on the packing were assessed through a total organic carbon mass balance. The EPS+ strain showed a significantly improved performance in terms of adhesion capacity and surfactin production. The mean surfactin productivity of the EPS+ strain was about 37% higher during the continuous cultivation compared to the EPS- strain. The substrate consumption together with the planktonic cell and biofilm development were properly predicted by the model (α = 0.05). The results show the efficiency of the biofilm bioreactor for continuous surfactin production using an EPS producing strain. [less ▲]

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See detailPalantir: a springboard for the analysis of secondary metabolite gene clusters in large-scale genome mining projects.
Meunier, Loïc ULiege; Tocquin, Pierre ULiege; Cornet, Luc ULiege et al

in Bioinformatics (Oxford, England) (2020), 36(15), 4345-4347

SUMMARY: To support small and large-scale genome mining projects, we present Palantir (Post-processing Analysis tooLbox for ANTIsmash Reports), a dedicated software suite for handling and refining ... [more ▼]

SUMMARY: To support small and large-scale genome mining projects, we present Palantir (Post-processing Analysis tooLbox for ANTIsmash Reports), a dedicated software suite for handling and refining secondary metabolite biosynthetic gene cluster (BGC) data annotated with the popular antiSMASH pipeline. Palantir provides new functionalities building on NRPS/PKS predictions from antiSMASH, such as improved BGC annotation, module delineation and easy access to sub-sequences at different levels (cluster, gene, module, domain). Moreover, it can parse user-provided antiSMASH reports and reformat them for direct use or storage in a relational database. AVAILABILITY: Palantir is released both as a Perl API available on CPAN (https://metacpan.org/release/Bio-Palantir) and as a web application (http://palantir.uliege.be). As a practical use case, the web interface also features a database built from the mining of 1616 cyanobacterial genomes, of which 1488 were predicted to encode at least one BGC. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. [less ▲]

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See detailAgrobacterium tumefaciens C58 presence affects Bacillus velezensis 32a ecological fitness in the tomato rhizosphere
Abdallah, D. B.; Krier, F.; Jacques, Philippe ULiege et al

in Environmental Science and Pollution Research (2020), 27(22), 28429-28437

The persistence of pathogenic Agrobacterium strains as soil-associated saprophytes may cause an inconsistency in the efficacy of the biocontrol inoculants under field condition. The study of the ... [more ▼]

The persistence of pathogenic Agrobacterium strains as soil-associated saprophytes may cause an inconsistency in the efficacy of the biocontrol inoculants under field condition. The study of the interaction occurring in the rhizosphere between the beneficial and the pathogenic microbes is thus interesting for the development of effective biopesticides for the management of crown gall disease. However, very little is still known about the influence of these complex interactions on the biocontrol determinants of beneficial bacteria, especially Bacillus strains. This study aimed to evaluate the effect of the soil borne pathogen Agrobacterium tumefaciens C58 on root colonization and lipopeptide production by Bacillus velezensis strain 32a during interaction with tomato plants. Results show that the presence of A. tumefaciens C58 positively impacted the root colonization level of the Bacillus strain. However, negative impact on surfactin production was observed in Agrobacterium-treated seedling, compared with control. Further investigation suggests that these modulations are due to a modified tomato root exudate composition during the tripartite interaction. Thus, this work contributes to enhance the knowledge on the impact of interspecies interaction on the ecological fitness of Bacillus cells living in the rhizosphere. © 2020, Springer-Verlag GmbH Germany, part of Springer Nature. [less ▲]

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See detailNorine: update of the nonribosomal peptide resource
Flissi, A.; Ricart, E.; Campart, C. et al

in Nucleic Acids Research (2020), 48(D1), 465-469

Norine, the unique resource dedicated to nonribosomal peptides (NRPs), is now updated with a new pipeline to automate massive sourcing and enhance annotation. External databases are mined to extract NRPs ... [more ▼]

Norine, the unique resource dedicated to nonribosomal peptides (NRPs), is now updated with a new pipeline to automate massive sourcing and enhance annotation. External databases are mined to extract NRPs that are not yet in Norine. To maintain a high data quality, successive filters are applied to automatically validate the NRP annotations and only validated data is inserted in the database. External databases were also used to complete annotations of NRPs already in Norine. Besides, annotation consistency inside Norine and between Norine and external sources have reported annotation errors. Some can be corrected automatically, while others need manual curation. This new approach led to the insertion of 539 new NRPs and the addition or correction of annotations of nearly all Norine entries. Two new tools to analyse the chemical structures of NRPs (rBAN) and to infer a molecular formula from the mass-to-charge ratio of an NRP (Kendrick Formula Predictor) were also integrated. Norine is freely accessible from the following URL: https://bioinfo.cristal.univ-lille.fr/norine/. © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. [less ▲]

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See detailAntarctic cyanobacteria sources of biosignatures
Lara, Yannick ULiege; Demoulin, Catherine ULiege; Lambion, Alexandre ULiege et al

Conference (2019, September 05)

The high UV intensities and extreme seasonality make some of Antarctic habitats interesting to the study life adaptive strategies in extreme conditions, and the biosignatures that can be preserved. In ... [more ▼]

The high UV intensities and extreme seasonality make some of Antarctic habitats interesting to the study life adaptive strategies in extreme conditions, and the biosignatures that can be preserved. In Antarctica, most of the surface, lacustrine and endolithic photosynthetic niches are occupied by cyanobacteria, which are well equipped to survive cold, desiccation or UV exposure. To provide a better understanding of the cyanobacteria survival strategies to extreme conditions, we used transmitted light and TEM microscopy as well as high-throughput sequencing technologies on the Antarctic lineage Phormidesmis priestleyi. We observed and characterized the production of a gloeocapsin-like UV-screening pigment and compared it to the pigment produced by Gloeocapsa alpina. Cyanobacteria are considered to be the inventors of oxygenic photosynthesis and therefore played a pivotal role in early Life and Earth evolution during the Precambrian. However, to perform photosynthesis in the UV exposure of the Early Earth unprotected by an ozone layer, their ancestors must have developed multiple molecular strategies. The presence of a gloeocapsin-like pigment in different cyanobacterial lineages may suggest its early production by their common ancestor, potentially present before the oxidation of the atmosphere. In Polar regions, low temperatures lead to the success of particular organisms featuring adaptations to molecular and cellular disturbances such as rigidity of membranes, reduction of enzyme-catalyzed reactions, and solute transport. Our results underline the importance of functional categories of genes involved in the production of key molecules for the survival of polar P. priestleyi (e.g. exopolysaccharides, chaperone proteins, fatty acids and phospholipids). The study of Antarctic cyanobacteria is promising to find new analog biosignatures for Life in rocky habitable planets. This project is supported by the mini-ARC PUMA (ULiège, Belgium). [less ▲]

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See detailAstin C production by the endophytic fungus Cyanodermella asteris in planktonic and immobilized culture conditions
Vassaux, Antoine ULiege; Tarayre, Cédric; Arguelles Arias, Anthony ULiege et al

in Biotechnology Journal (2019)

The fungal endophyte Cyanodermella asteris was recently isolated from the medicinal plant Aster tataricus. This fungus produces astin C, a cyclic pentapeptide with anticancer and anti-inflammatory ... [more ▼]

The fungal endophyte Cyanodermella asteris was recently isolated from the medicinal plant Aster tataricus. This fungus produces astin C, a cyclic pentapeptide with anticancer and anti-inflammatory properties. The production of this secondary metabolite was compared in immobilized and planktonic conditions. For immobilized cultures, a stainless steel packing immersed in the culture broth was used as a support. In these conditions, the fungus exclusively grew on the packing, which provides a considerable advantage for astin C recovery and purification. C. asteris metabolism was different according to the culture conditions in terms of substrate consumption rate, cell-growth, and astin C production. Immobilized-cell cultures yielded a 30% increase of astin C production associate to a 39% increase in biomass. The inoculum type as spores rather than hyphae, and a pre-inoculation washing procedure with sodium hydroxide, turned out to be beneficial both for astin C production and fungus development onto the support. Finally, influence of culture parameters such as pH and medium composition, on astin C production was evaluated. With optimized culture conditions, astin C yield was further improved reaching a five times higher final specific yield compared to the value reported with astin C extraction from Aster tataricus (0.89 and 0.16 mg/g respectively). [less ▲]

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See detailOptimization of scalable biofilm bioreactors with genetically improved bacteria for microbial biosurfactant production
Brück, Hannah ULiege; Coutte, François; Delvigne, Frank ULiege et al

Poster (2019, May)

The Gram-positive soil bacterium Bacillus subtilis is a potential producer of a very powerful biosurfactant called surfactin. It offers many environmental advantages because surfactin is biodegradable and ... [more ▼]

The Gram-positive soil bacterium Bacillus subtilis is a potential producer of a very powerful biosurfactant called surfactin. It offers many environmental advantages because surfactin is biodegradable and less toxic than chemical compounds. In the phytosanitary field, surfactin represents a very promising biocontrol agent as it is able to induce systemic resistance in plants. Furthermore, due to its exceptional foaming and emulsifying properties, surfactin has many applications in different industrial sectors. Industrial surfactin production in conventional stirred tank reactors necessitates the control of excessive foam formation. Biofilm bioreactors are more efficient alternative bubbleless systems for biosurfactant production since foam formation can be avoided while a high air/liquid mass transfer can be obtained. This is a very important parameter because a high aeration rate is necessary for a good surfactin productivity. However, the control of the cell colonization on the reactor support is challenging as biofilm formation is a heterogeneous phenomenon. The laboratory strain B. subtilis 168 is very easy to cultivate and manipulate genetically. Yet, this strain has very low cell adhesion capacities making it difficult to fix the cells by natural cell immobilization through biofilm formation on the bioreactor support. Here, genetically modified B. subtilis 168 mutants have been tested for improved colonization capacities on the bioreactor support to achieve a more robust and stable process. The cell adhesion capacities of the selected B. subtilis 168 mutants have been improved through the restoration of the biofilm matrix production and the induction of cell filamentation by genetic engineering. Through the additional change of cell shape, the aim was to promote the initial cell adhesion step followed by the support colonization and to reduce the cell detachment under stress conditions. The biofilm adhesion capacities were analyzed by means of a drip flow biofilm reactor. The mutants with the best performance were then selected for the cultivation in a lab-scale trickle-bed biofilm bioreactor. This device contains a structured metal packing providing a very high specific surface area for cell immobilization. For the mutant with functional biofilm matrix production the cell attachment capacities were significantly improved compared to the control strain resultant in an improved surfactin productivity. Cell filamentation seemed to decrease cell detachment under stress conditions, leading to a more stable colonization and process. [less ▲]

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See detailNatural products: what is the biosynthetic potential of unicellular eukaryotes?
Meunier, Loïc ULiege; Jacques, Philippe ULiege; Baurain, Denis ULiege

Poster (2019, March 14)

Microbial organisms are a precious source of natural products for medical and agricultural fields. These natural products are produced by different enzymes classes from the secondary metabolism, resulting ... [more ▼]

Microbial organisms are a precious source of natural products for medical and agricultural fields. These natural products are produced by different enzymes classes from the secondary metabolism, resulting in a large diversity of molecular structures and bioactivities. Currently, the main known microbial producers of bioactive compounds are bacteria and fungi, which have already been extensively exploited for the pharmaceutical and phytosanitary drugs. However, other unicellular eukaryotes seem to also have potential for the production of bioactive compounds, which present somehow a new continent for the discovery of natural products. A preliminary large-scale in silico analysis through unicellular eukaryotic lineages, for which genomic data are available, indicates that a part of these organisms might possess diverse classes of secondary metabolism pathways and thus be potential candidates for the discovery of novel compounds. [less ▲]

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