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Dutilloy E, Arias AA, Richet N, Guise JF, Duban M, Leclere V, Selim S, Jacques P, Jacquard C, Clément C, Ait Barka E, Esmaeel Q. Bacillus velezensis BE2 controls wheat and barley diseases by direct antagonism and induced systemic resistance. Appl Microbiol Biotechnol 2024; 108:64. [PMID: 38189957 DOI: 10.1007/s00253-023-12864-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 10/19/2023] [Accepted: 11/05/2023] [Indexed: 01/09/2024]
Abstract
Wheat and barley rank among the main crops cultivated on a global scale, providing the essential nutritional foundation for both humans and animals. Nevertheless, these crops are vulnerable to several fungal diseases, such as Septoria tritici blotch and net blotch, which significantly reduce yields by adversely affecting leaves and grain quality. To mitigate the effect of these diseases, chemical fungicides have proven to be genuinely effective; however, they impose a serious environmental burden. Currently, biocontrol agents have attracted attention as a sustainable alternative to fungicides, offering an eco-friendly option. The study aimed to assess the efficacy of Bacillus velezensis BE2 in reducing disease symptoms caused by Zymoseptoria tritici and Pyrenophora teres. This bacterium exhibited significant antagonistic effects in vitro by suppressing fungal development when pathogens and the beneficial strain were in direct confrontation. These findings were subsequently confirmed through microscopic analysis, which illustrated the strain's capacity to inhibit spore germination and mycelial growth in both pathogens. Additionally, the study analysed the cell-free supernatant of the bacterium using UPLC-MS (ultra-performance liquid chromatography-mass spectrometry). The results revealed that strain BE2 produces, among other metabolites, different families of cyclic lipopeptides that may be involved in biocontrol. Furthermore, the beneficial effects of strain BE2 in planta were assessed by quantifying the fungal DNA content directly at the leaf level after bacterization, using two different application methods (foliar and drenching). The results indicated that applying the beneficial bacterium at the root level significantly reduced pathogens pressure. Finally, gene expression analysis of different markers showed that BE2 application induced a priming effect within the first hours after infection. KEY POINTS: • BE2 managed Z. tritici and P. teres by direct antagonism and induced systemic resistance. • Strain BE2 produced seven metabolite families, including three cyclic lipopeptides. • Application of strain BE2 at the root level triggered plant defense mechanisms.
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Affiliation(s)
- Emma Dutilloy
- Université de Reims Champagne Ardenne, INRAE, RIBP USC 1488, 51100, Reims, France
| | - Anthony Arguëlles Arias
- Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Nicolas Richet
- Université de Reims Champagne Ardenne, Plateau Technique Mobile de Cytométrie Environnementale MOBICYTE, URCA/INERIS, UFR Sciences Exactes Et Naturelles, Reims, France
| | - Jean-François Guise
- Université de Reims Champagne Ardenne, INRAE, RIBP USC 1488, 51100, Reims, France
| | - Matthieu Duban
- Université de Lille, Université de Liège, UMRT, 1158 BioEcoAgro, Institut Charles Viollette, 59000, Lille, France
| | - Valérie Leclere
- Université de Lille, Université de Liège, UMRT, 1158 BioEcoAgro, Institut Charles Viollette, 59000, Lille, France
| | - Sameh Selim
- AGHYLE UP 2018.C101, SFR Condorcet FR CNRS 3417, Institut Polytechnique UniLaSalle, 19 Rue Pierre Waguet, BP 30313, F-60026, Beauvais Cedex, France
| | - Philippe Jacques
- Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Cédric Jacquard
- Université de Reims Champagne Ardenne, INRAE, RIBP USC 1488, 51100, Reims, France
| | - Christophe Clément
- Université de Reims Champagne Ardenne, INRAE, RIBP USC 1488, 51100, Reims, France
| | - Essaïd Ait Barka
- Université de Reims Champagne Ardenne, INRAE, RIBP USC 1488, 51100, Reims, France
| | - Qassim Esmaeel
- Université de Reims Champagne Ardenne, INRAE, RIBP USC 1488, 51100, Reims, France.
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El Arbi A, Arnauld S, Chataigné G, Lecouturier D, Bricout A, Gharsallah N, Jacques P, Siah A, Rochex A. Lipopeptide culture filtrates from Bacillus spp. provide effective protection to wheat against the foliar pathogen Zymoseptoria tritici. J Appl Microbiol 2024; 135:lxad306. [PMID: 38115638 DOI: 10.1093/jambio/lxad306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 11/23/2023] [Accepted: 12/18/2023] [Indexed: 12/21/2023]
Abstract
AIMS Biocontrol products based on microorganisms and natural substances are promising alternatives to chemical pesticides that could contribute to develop a more sustainable agriculture. Here, we investigated the potential of cell-free culture filtrates (CFCFs) from two strains of the Bacillus subtilis group to inhibit Zymoseptoria tritici, a major fungal pathogen of wheat. METHODS AND RESULTS Foliar application of CFCFs from Bacillus velezensis GA1 and Bacillus sp. III1 on wheat seedlings in a greenhouse strongly reduced Z. tritici disease severity (>90%). In vitro bioassays showed that CFCFs completely inhibited the spore germination and fungal growth (100%). In planta cytological investigations revealed a significant impact of the treatments on both spore germination (∼40% inhibition) and fungal growth of Z. tritici (>80% inhibition). High Performance Liquid Chromatography (HPLC) analysis showed that the Bacillus strains displayed different lipopeptide profiles. The CFCF obtained from Bacillus GA1 contained 90 mg l-1 of iturin A + surfactins + fengycins and the CFCF obtained from Bacillus sp. III1 contained 25 mg l-1 of mojavensin A (iturin family) + surfactins + fengycins. CONCLUSIONS Strains of the B. subtilis group producing different iturins could provide several CFCF-based solutions for the biocontrol of Z. tritici.
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Affiliation(s)
- Amel El Arbi
- Université de Lille, UMRT BioEcoAgro 1158, 42 rue Paul Duez, F-59000 Lille, France
- Faculté des Sciences de Sfax, Laboratoire de Biotechnologie Microbienne,B.P. 802, 3018 Sfax, Tunisia
| | - Ségolène Arnauld
- Université de Lille, UMRT BioEcoAgro 1158, 42 rue Paul Duez, F-59000 Lille, France
| | - Gabrielle Chataigné
- Université de Lille, UMRT BioEcoAgro 1158, 42 rue Paul Duez, F-59000 Lille, France
| | - Didier Lecouturier
- Université de Lille, UMRT BioEcoAgro 1158, 42 rue Paul Duez, F-59000 Lille, France
| | - Alexandre Bricout
- Université de Lille, UMRT BioEcoAgro 1158, 42 rue Paul Duez, F-59000 Lille, France
| | - Néji Gharsallah
- Faculté des Sciences de Sfax, Laboratoire de Biotechnologie Microbienne,B.P. 802, 3018 Sfax, Tunisia
| | - Philippe Jacques
- Université de Liège, UMRT BioEcoAgro 1158, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, Av. de la Faculté d'Agronomie 41/13, B-5030 Gembloux, Belgium
| | - Ali Siah
- JUNIA, UMRT BioEcoAgro, 2 rue Norbert Ségard, BP 41290, F-59014 Lille, France
| | - Alice Rochex
- Université de Lille, UMRT BioEcoAgro 1158, 42 rue Paul Duez, F-59000 Lille, France
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Platel R, Lucau-Danila A, Baltenweck R, Maia-Grondard A, Trapet P, Magnin-Robert M, Randoux B, Duret M, Halama P, Hilbert JL, Coutte F, Jacques P, Hugueney P, Reignault P, Siah A. Deciphering immune responses primed by a bacterial lipopeptide in wheat towards Zymoseptoria tritici. Front Plant Sci 2023; 13:1074447. [PMID: 36777540 PMCID: PMC9909289 DOI: 10.3389/fpls.2022.1074447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/27/2022] [Indexed: 06/18/2023]
Abstract
Plant immunity induction with natural biocontrol compounds is a valuable and promising ecofriendly tool that fits with sustainable agriculture and healthy food. Despite the agroeconomic significance of wheat, the mechanisms underlying its induced defense responses remain obscure. We reveal here, using combined transcriptomic, metabolomic and cytologic approach, that the lipopeptide mycosubtilin from the beneficial bacterium Bacillus subtilis, protects wheat against Zymoseptoria tritici through a dual mode of action (direct and indirect) and that the indirect one relies mainly on the priming rather than on the elicitation of plant defense-related mechanisms. Indeed, the molecule primes the expression of 80 genes associated with sixteen functional groups during the early stages of infection, as well as the accumulation of several flavonoids during the period preceding the fungal switch to the necrotrophic phase. Moreover, genes involved in abscisic acid (ABA) biosynthesis and ABA-associated signaling pathways are regulated, suggesting a role of this phytohormone in the indirect activity of mycosubtilin. The priming-based bioactivity of mycosubtilin against a biotic stress could result from an interaction of the molecule with leaf cell plasma membranes that may mimic an abiotic stress stimulus in wheat leaves. This study provides new insights into induced immunity in wheat and opens new perspectives for the use of mycosubtilin as a biocontrol compound against Z. tritici.
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Affiliation(s)
- Rémi Platel
- Joint Research Unit 1158 BioEcoAgro, Junia, Université de Lille, Université de Liège, UPJV, Université d’Artois, ULCO, INRAE, Lille, France
| | - Anca Lucau-Danila
- Joint Research Unit 1158 BioEcoAgro, Junia, Université de Lille, Université de Liège, UPJV, Université d’Artois, ULCO, INRAE, Lille, France
| | | | | | - Pauline Trapet
- Joint Research Unit 1158 BioEcoAgro, Junia, Université de Lille, Université de Liège, UPJV, Université d’Artois, ULCO, INRAE, Lille, France
| | - Maryline Magnin-Robert
- Unité de Chimie Environnementale et Interactions sur le Vivant, Université du Littoral Côte d’Opale, Calais Cedex, France
| | - Béatrice Randoux
- Unité de Chimie Environnementale et Interactions sur le Vivant, Université du Littoral Côte d’Opale, Calais Cedex, France
| | - Morgane Duret
- Joint Research Unit 1158 BioEcoAgro, Junia, Université de Lille, Université de Liège, UPJV, Université d’Artois, ULCO, INRAE, Lille, France
| | - Patrice Halama
- Joint Research Unit 1158 BioEcoAgro, Junia, Université de Lille, Université de Liège, UPJV, Université d’Artois, ULCO, INRAE, Lille, France
| | - Jean-Louis Hilbert
- Joint Research Unit 1158 BioEcoAgro, Junia, Université de Lille, Université de Liège, UPJV, Université d’Artois, ULCO, INRAE, Lille, France
| | - François Coutte
- Joint Research Unit 1158 BioEcoAgro, Junia, Université de Lille, Université de Liège, UPJV, Université d’Artois, ULCO, INRAE, Lille, France
| | - Philippe Jacques
- Joint Research Unit 1158 BioEcoAgro, TERRA Teaching and Research Centre, MiPI, Gembloux Agro-Bio Tech, Université de Liège, Gembloux, Belgium
| | | | - Philippe Reignault
- Unité de Chimie Environnementale et Interactions sur le Vivant, Université du Littoral Côte d’Opale, Calais Cedex, France
| | - Ali Siah
- Joint Research Unit 1158 BioEcoAgro, Junia, Université de Lille, Université de Liège, UPJV, Université d’Artois, ULCO, INRAE, Lille, France
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Flissi A, Duban M, Jacques P, Leclère V, Pupin M. Norine: Bioinformatics Methods and Tools for the Characterization of Newly Discovered Nonribosomal Peptides. Methods Mol Biol 2023; 2670:303-318. [PMID: 37184712 DOI: 10.1007/978-1-0716-3214-7_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
In this chapter, we present Norine ( https://norine.univ-lille.fr/norine ), the unique resource dedicated to nonribosomal peptides. First, the content of the knowledgebase and the related tools are described. Then, a study case shows how to query Norine by annotations or structure and how to interpret the obtained results.
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Affiliation(s)
- Areski Flissi
- Université de Lille, CNRS, Centrale Lille, UMR 9189 CRIStAL, Lille, France.
| | - Matthieu Duban
- Université de Lille, UMRt BioEcoAgro 1158-INRAe, Métabolites secondaires d'origine microbienne, Charles Viollette Institute, Lille, France
| | - Philippe Jacques
- Université de Liège, UMRt BioEcoAgro 1158-INRAe, Métabolites secondaires d'origine microbienne, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, Gembloux, Belgium
| | - Valérie Leclère
- Université de Lille, UMRt BioEcoAgro 1158-INRAe, Métabolites secondaires d'origine microbienne, Charles Viollette Institute, Lille, France
| | - Maude Pupin
- Université de Lille, CNRS, Centrale Lille, UMR 9189 CRIStAL, Lille, France
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Bricout A, Morris CE, Chandeysson C, Duban M, Boistel C, Chataigné G, Lecouturier D, Jacques P, Leclère V, Rochex A. The Diversity of Lipopeptides in the Pseudomonas syringae Complex Parallels Phylogeny and Sheds Light on Structural Diversification during Evolutionary History. Microbiol Spectr 2022; 10:e0145622. [PMID: 36287007 PMCID: PMC9769872 DOI: 10.1128/spectrum.01456-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/12/2022] [Indexed: 01/05/2023] Open
Abstract
Pseudomonas spp. colonize diverse aquatic and terrestrial habitats and produce a wide variety of secondary metabolites, including lipopeptides. However, previous studies have often examined a limited number of lipopeptide-producing strains. In this study, we performed a systematic analysis of lipopeptide production across a wide data set of strains of the Pseudomonas syringae complex (724) by using a combined bioinformatics, mass spectrometry, and phylogenetics approach. The large P. syringae complex, which is composed of 13 phylogroups, is known to produce factins (including syringafactin-like lipopeptides), mycins (including syringomycin-like lipopeptides), and peptins (such as syringopeptins). We found that 80.8% of P. syringae strains produced lipopeptides and that factins were the most frequently produced (by 96% of the producing strains). P. syringae strains were either factin monoproducers or factin, mycin, and peptin coproducers or lipopeptide nonproducers in relation to their phylogenetic group. Our analyses led to the discovery of 42 new lipopeptides, bringing the number of lipopeptides identified in the P. syringae complex to 75. We also highlighted that factins have high structural resemblance and are widely distributed among the P. syringae complex, while mycins and peptins are highly structurally diverse and patchily distributed. IMPORTANCE This study provides an insight into the P. syringae metabolome that emphasizes the high diversity of lipopeptides produced within the P. syringae complex. The production profiles of strains are closely related to their phylogenetic classification, indicating that structural diversification of lipopeptides parallels the phylogeny of this bacterial complex, thereby further illustrating the inherent importance of lipopeptides in the ecology of this group of bacteria throughout its evolutionary history. Furthermore, this overview of P. syringae lipopeptides led us to propose a refined classification that could be extended to the lipopeptides produced by other bacterial groups.
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Affiliation(s)
- Alexandre Bricout
- Université de Lille, Université de Liège, UMRt BioEcoAgro 1158-INRAE, Métabolites Secondaires d’Origine Microbienne, Charles Viollette Institute, Lille, France
- Agence de la transition écologique (ADEME), Angers, France
| | | | | | - Matthieu Duban
- Université de Lille, Université de Liège, UMRt BioEcoAgro 1158-INRAE, Métabolites Secondaires d’Origine Microbienne, Charles Viollette Institute, Lille, France
| | - Corinne Boistel
- Université de Lille, Université de Liège, UMRt BioEcoAgro 1158-INRAE, Métabolites Secondaires d’Origine Microbienne, Charles Viollette Institute, Lille, France
| | - Gabrielle Chataigné
- Université de Lille, Université de Liège, UMRt BioEcoAgro 1158-INRAE, Métabolites Secondaires d’Origine Microbienne, Charles Viollette Institute, Lille, France
| | - Didier Lecouturier
- Université de Lille, Université de Liège, UMRt BioEcoAgro 1158-INRAE, Métabolites Secondaires d’Origine Microbienne, Charles Viollette Institute, Lille, France
| | - Philippe Jacques
- Université de Liège, Université de Lille, UMRt BioEcoAgro 1158-INRAE, Métabolites Secondaires d’Origine Microbienne, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, Gembloux, Belgium
| | - Valérie Leclère
- Université de Lille, Université de Liège, UMRt BioEcoAgro 1158-INRAE, Métabolites Secondaires d’Origine Microbienne, Charles Viollette Institute, Lille, France
| | - Alice Rochex
- Université de Lille, Université de Liège, UMRt BioEcoAgro 1158-INRAE, Métabolites Secondaires d’Origine Microbienne, Charles Viollette Institute, Lille, France
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Raouani NEH, Claverie E, Randoux B, Chaveriat L, Yaseen Y, Yada B, Martin P, Cabrera JC, Jacques P, Reignault P, Magnin-Robert M, Lounès-Hadj Sahraoui A. Bio-Inspired Rhamnolipids, Cyclic Lipopeptides and a Chito-Oligosaccharide Confer Protection against Wheat Powdery Mildew and Inhibit Conidia Germination. Molecules 2022; 27:molecules27196672. [PMID: 36235207 PMCID: PMC9571057 DOI: 10.3390/molecules27196672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022] Open
Abstract
Plant protection is mainly based on the application of synthetic pesticides to limit yield losses resulting from diseases. However, the use of more eco-friendly strategies for sustainable plant protection has become a necessity that could contribute to controlling pathogens through a direct antimicrobial effect and/or an induction of plant resistance. Three different families of natural or bioinspired compounds originated from bacterial or fungal strains have been evaluated to protect wheat against powdery mildew, caused by the biotrophic Blumeria graminis f.sp. tritici (Bgt). Thus, three bio-inspired mono-rhamnolipids (smRLs), three cyclic lipopeptides (CLPs, mycosubtilin (M), fengycin (F), surfactin (S)) applied individually and in mixtures (M + F and M + F + S), as well as a chitosan oligosaccharide (COS) BioA187 were tested against Bgt, in planta and in vitro. Only the three smRLs (Rh-Eth-C12, Rh-Est-C12 and Rh-Succ-C12), the two CLP mixtures and the BioA187 led to a partial protection of wheat against Bgt. The higher inhibitor effects on the germination of Bgt spores in vitro were observed from smRLs Rh-Eth-C12 and Rh-Succ-C12, mycosubtilin and the two CLP mixtures. Taking together, these results revealed that such molecules could constitute promising tools for a more eco-friendly agriculture.
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Affiliation(s)
- Nour El Houda Raouani
- Unité de Chimie Environnementale et Interactions sur le Vivant (EA 4492), Université Littoral Côte d’Opale, CEDEX CS 80699, 62228 Calais, France
| | - Elodie Claverie
- Materia Nova ASBL, Avenue du Champ de Mars 6, 7000 Mons, Belgium
| | - Béatrice Randoux
- Unité de Chimie Environnementale et Interactions sur le Vivant (EA 4492), Université Littoral Côte d’Opale, CEDEX CS 80699, 62228 Calais, France
| | - Ludovic Chaveriat
- ULR 7519—Unité Transformations & Agroressources, Université d’Artois, UnilaSalle, CEDEX CS 20819, 62408 Béthune, France
| | - Yazen Yaseen
- Lipofabrik, Parc d’Activités du Mélantois, 917 Rue des Saules, 59810 Lesquin, France
| | - Bopha Yada
- Materia Nova ASBL, Avenue du Champ de Mars 6, 7000 Mons, Belgium
| | - Patrick Martin
- ULR 7519—Unité Transformations & Agroressources, Université d’Artois, UnilaSalle, CEDEX CS 20819, 62408 Béthune, France
| | | | - Philippe Jacques
- JUNIA, Joint Research Unit UMRt 1158-INRAE, BioEcoAgro, Équipe Métabolites Spécialisés d’Origine Végétale, University Lille, INRAE, University Liège, UPJV, University Artois, ULCO, 48, Boulevard Vauban, CEDEX BP 41290, 59014 Lille, France
- Joint Research Unit 1158 BioEcoAgro, Équipe Métabolites Spécialisés d’Origine Végétale, Microbial Processes and Interactions, TERRA Research Centre, Gembloux Agro-Bio Tech, Université de Liège, 5030 Gembloux, Belgium
| | - Philippe Reignault
- Unité de Chimie Environnementale et Interactions sur le Vivant (EA 4492), Université Littoral Côte d’Opale, CEDEX CS 80699, 62228 Calais, France
| | - Maryline Magnin-Robert
- Unité de Chimie Environnementale et Interactions sur le Vivant (EA 4492), Université Littoral Côte d’Opale, CEDEX CS 80699, 62228 Calais, France
- Correspondence: (M.M.-R.); (A.L.-H.S.)
| | - Anissa Lounès-Hadj Sahraoui
- Unité de Chimie Environnementale et Interactions sur le Vivant (EA 4492), Université Littoral Côte d’Opale, CEDEX CS 80699, 62228 Calais, France
- Correspondence: (M.M.-R.); (A.L.-H.S.)
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Van Hoovels L, Vander Cruyssen B, Sieghart D, Bonroy C, Nagy E, Pullerits R, Čučnik S, Dahle C, Heijnen I, Bernasconi L, Benkhadra F, Bogaert L, Van Den Bremt S, Vanliedekerke A, Vanheule G, Robbrecht J, Studholme L, Claudine W, Müller R, Kyburz D, Sjowall C, Kastbom A, Jese R, Jovancevic B, Kiss EV, Jacques P, Steiner G, Verschueren P, Bossuyt X. POS0536 REFINING THE SEROLOGICAL SCORES OF THE ACR/EULAR 2010 RHEUMATOID ARTHRITIS CLASSIFICATION CRITERIA: AN INTERNATIONAL STUDY. Ann Rheum Dis 2022. [DOI: 10.1136/annrheumdis-2022-eular.2174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BackgroundRheumatoid factor (RF) and anti-cyclic citrullinated protein/peptide antibodies (ACPA) are included in the ACR/EULAR 2010 classification criteria for rheumatoid arthritis (RA)(1). Both markers are given the same weight in the criteria.ObjectivesAs the performance characteristics differ significantly between RF and ACPA(2), we set out to refine the serological scores for RA classification.MethodsDiagnostic samples from 398 RA patients and from 1073 diseased controls were evaluated with five RF assays (two RF IgM isotype-specific assays and three total RF assays) and five ACPA IgG assays from five different manufacturers.ResultsFirstly, we harmonized thresholds between manufacturers based on predefined specificity for low positive (at 92.5% specificity for RF and at 97.5% specificity ACPA) and high positive results (at 97.5% specificity RF and at 99.0% specificity for ACPA). Next, we determined likelihood ratios (LRs) for RF, ACPA, and combinations of both, for negative, low positive, and high positive results. The LR was higher for ACPA than for RF, for high positive results than for low positive results and for double positivity than for single positivity. Based on these data we refined the weights of serological scores for classification (Table 1).Table 1.Refined weights of serological scores for RA classificationRF negativeRF low positiveRF high positiveACPA negative011ACPA low positive233ACPA high positive344Application of such refined serological weights significantly increased the area under the curve of receiver operating characteristics analysis to distinguish RA from controls, significantly reduced the serological scores in the controls as well as the number of RA misclassifications without affecting the diagnostic sensitivity.Besides, we showed that combining predefined specificity thresholds with the refined serological scoring, reduced manufacturer-dependent variability in RA classification impacting RA classification for controls from 18.0-29.0% by ACR/EULAR to 11.0-13.0% (significantly increasing specificity) and for RA patients from 67.8-74.0% to 67.6-71.5% (without significantly affecting sensitivity).ConclusionSerological weight factors for RA classification can be improved by taking into account the antibody type (RF versus ACPA), the antibody level, and single or combined positivity.References[1]Aletaha D, Neogi T, Silman AJ, Funovits J, Felson DT, Bingham COr, et al. 2010 rheumatoid arthritis classification criteria: an American College of Rheumatology/European League Against Rheumatism collaborative initiative. Ann Rheum Dis 2010; 69: 1580-8.[2]Bossuyt X. Anticitrullinated protein antibodies: taking into account antibody levels improves interpretation. Ann Rheum Dis 2017; 76: e33.AcknowledgementsWe thank all participating diagnostic companies for the in-kind support of assays, their technical training and the constructive discussions. Furthermore, we are very thankful to the laboratory technicians of all participating laboratories for their most appreciated assistance in the performance of the RF/ACPA analyses.Disclosure of InterestsLieve Van Hoovels Speakers bureau: Thermo Fisher, Consultant of: Thermo Fisher, Grant/research support from: Thermo Fisher, Bert Vander Cruyssen: None declared, Daniela Sieghart Speakers bureau: Thermo Fisher, Consultant of: Thermo Fisher, Carolien Bonroy: None declared, Eszter Nagy: None declared, Rille Pullerits: None declared, Saša Čučnik: None declared, Charlotte Dahle: None declared, Ingmar Heijnen Speakers bureau: Thermo Fisher, Luca Bernasconi Speakers bureau: Thermo Fisher, Farid Benkhadra: None declared, Laura Bogaert: None declared, Stefanie Van Den Bremt: None declared, Ann Vanliedekerke: None declared, Geert Vanheule: None declared, Johan Robbrecht: None declared, Lucy Studholme: None declared, Wirth Claudine: None declared, Rüdiger Müller: None declared, Diego Kyburz: None declared, Christopher Sjowall: None declared, Alf Kastbom: None declared, Rok Jese: None declared, Boja Jovancevic: None declared, Emese Virag Kiss: None declared, Peggy Jacques: None declared, Günter Steiner Speakers bureau: Thermo Fisher, Consultant of: Thermo Fisher, Patrick Verschueren: None declared, Xavier Bossuyt Speakers bureau: Thermo Fisher, Consultant of: Thermo Fisher.
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Lara YJ, McCann A, Malherbe C, François C, Demoulin CF, Sforna MC, Eppe G, De Pauw E, Wilmotte A, Jacques P, Javaux EJ. Characterization of the Halochromic Gloeocapsin Pigment, a Cyanobacterial Biosignature for Paleobiology and Astrobiology. Astrobiology 2022; 22:735-754. [PMID: 35333546 DOI: 10.1089/ast.2021.0061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Ultraviolet (UV)-screening compounds represent a substantial asset for the survival of cyanobacteria in extreme environments exposed to high doses of UV radiations on modern and early Earth. Among these molecules, the halochromic pigment gloeocapsin remains poorly characterized and studied. In this study, we identified a gloeocapsin-producing cultivable cyanobacteria: the strain Phormidesmis nigrescens ULC007. We succeeded to extract, to partially purify, and to compare the dark blue pigment from both the ULC007 culture and an environmental Gloeocapsa alpina dominated sample. FT-IR and Raman spectra of G. alpina and P. nigrescens ULC007 pigment extracts strongly suggested a common backbone structure. The high-pressure liquid chromatography-UV-MS/MS analysis of the ULC007 pigment extract allowed to narrow down the molecular formula of gloeocapsin to potentially five candidates within three classes of halochromic molecules: anthraquinone derivatives, coumarin derivatives, and flavonoids. With the discovery of gloeocapsin in P. nigrescens, the production of this pigment is now established for three lineages of cyanobacteria (including G. alpina, P. nigrescens, and Solentia paulocellulare) that belong to three distinct orders (Chroococcales, Pleurocapsales, Synechoccocales), inhabiting very diverse environments. This suggests that gloeocapsin production was a trait of their common ancestor or was acquired by lateral gene transfer. This work represents an important step toward the elucidation of the structure of this enigmatic pigment and its biosynthesis, and it potentially provides a new biosignature for ancient cyanobacteria. It also gives a glimpse on the evolution of UV protection strategies, which are relevant for early phototrophic life on Earth and possibly beyond.
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Affiliation(s)
- Yannick J Lara
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, Liège, Belgium
| | - Andréa McCann
- MolSys Research Unit, Mass Spectrometry Laboratory, University of Liège, Liège, Belgium
| | - Cédric Malherbe
- MolSys Research Unit, Mass Spectrometry Laboratory, University of Liège, Liège, Belgium
| | - Camille François
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, Liège, Belgium
| | - Catherine F Demoulin
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, Liège, Belgium
| | - Marie Catherine Sforna
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, Liège, Belgium
| | - Gauthier Eppe
- MolSys Research Unit, Mass Spectrometry Laboratory, University of Liège, Liège, Belgium
| | - Edwin De Pauw
- MolSys Research Unit, Mass Spectrometry Laboratory, University of Liège, Liège, Belgium
| | - Annick Wilmotte
- BCCM/ULC Cyanobacteria Collection, InBios-CIP, Institut de Chimie B6a, University of Liège, Liège, Belgium
| | - Philippe Jacques
- Microbial Processes and Interactions, Gembloux Agro-Bio Tech, TERRA Teaching and Research Centre, Joint Research Unit BioEcoAgro UMRt 1158, University of Liège, Gembloux, Belgium
| | - Emmanuelle J Javaux
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, Liège, Belgium
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9
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Fifani B, Steels S, Helmus C, Delacuvellerie A, Deracinois B, Phalip V, Delvigne F, Jacques P. Coculture of Trichoderma harzianum and Bacillus velezensis Based on Metabolic Cross-Feeding Modulates Lipopeptide Production. Microorganisms 2022; 10:microorganisms10051059. [PMID: 35630500 PMCID: PMC9148127 DOI: 10.3390/microorganisms10051059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/18/2022] [Accepted: 05/18/2022] [Indexed: 01/27/2023] Open
Abstract
Cocultures have been widely explored for their use in deciphering microbial interaction and its impact on the metabolisms of the interacting microorganisms. In this work, we investigate, in different liquid coculture conditions, the compatibility of two microorganisms with the potential for the biocontrol of plant diseases: the fungus Trichoderma harzianum IHEM5437 and the bacterium Bacillus velezensis GA1 (a strong antifungal lipopeptide producing strain). While the Bacillus overgrew the Trichoderma in a rich medium due to its antifungal lipopeptide production, a drastically different trend was observed in a medium in which a nitrogen nutritional dependency was imposed. Indeed, in this minimum medium containing nitrate as the sole nitrogen source, cooperation between the bacterium and the fungus was established. This is reflected by the growth of both species as well as the inhibition of the expression of Bacillus genes encoding lipopeptide synthetases. Interestingly, the growth of the bacterium in the minimum medium was enabled by the amendment of the culture by the fungal supernatant, which, in this case, ensures a high production yield of lipopeptides. These results highlight, for the first time, that Trichoderma harzianum and Bacillus velezensis are able, in specific environmental conditions, to adapt their metabolisms in order to grow together.
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Affiliation(s)
- Barbara Fifani
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, TERRA—Teaching and Research Centre, Gembloux Agro-Bio Tech, University Liège, 5030 Gembloux, Belgium; (B.F.); (S.S.); (C.H.); (F.D.)
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, ICV—Charles Viollette Institute, 59000 Lille, France; (B.D.); (V.P.)
| | - Sebastien Steels
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, TERRA—Teaching and Research Centre, Gembloux Agro-Bio Tech, University Liège, 5030 Gembloux, Belgium; (B.F.); (S.S.); (C.H.); (F.D.)
| | - Catherine Helmus
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, TERRA—Teaching and Research Centre, Gembloux Agro-Bio Tech, University Liège, 5030 Gembloux, Belgium; (B.F.); (S.S.); (C.H.); (F.D.)
| | | | - Barbara Deracinois
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, ICV—Charles Viollette Institute, 59000 Lille, France; (B.D.); (V.P.)
| | - Vincent Phalip
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, ICV—Charles Viollette Institute, 59000 Lille, France; (B.D.); (V.P.)
| | - Frank Delvigne
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, TERRA—Teaching and Research Centre, Gembloux Agro-Bio Tech, University Liège, 5030 Gembloux, Belgium; (B.F.); (S.S.); (C.H.); (F.D.)
| | - Philippe Jacques
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, TERRA—Teaching and Research Centre, Gembloux Agro-Bio Tech, University Liège, 5030 Gembloux, Belgium; (B.F.); (S.S.); (C.H.); (F.D.)
- Correspondence:
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10
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Valdés-Velasco LM, Favela-Torres E, Théatre A, Arguelles-Arias A, Saucedo-Castañeda JG, Jacques P. Relationship between lipopeptide biosurfactant and primary metabolite production by Bacillus strains in solid-state and submerged fermentation. Bioresour Technol 2022; 345:126556. [PMID: 34923080 DOI: 10.1016/j.biortech.2021.126556] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
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.
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Affiliation(s)
- Luisa Marcela Valdés-Velasco
- Department of Biotechnology, Universidad Autonoma Metropolitana, Unidad Iztapalapa, Avenida San Rafael Atlixco 186, Colonia Vicentina, 09340, Mexico City, Mexico
| | - Ernesto Favela-Torres
- Department of Biotechnology, Universidad Autonoma Metropolitana, Unidad Iztapalapa, Avenida San Rafael Atlixco 186, Colonia Vicentina, 09340, Mexico City, Mexico.
| | - Ariane Théatre
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Joint Research Unit BioEcoAgro, UMRt 1158, Gembloux Agro-Bio Tech, University of Liège, Avenue de la Faculté d́ Agronomie, 2B, B-5030 Gembloux, Belgium
| | - Anthony Arguelles-Arias
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Joint Research Unit BioEcoAgro, UMRt 1158, Gembloux Agro-Bio Tech, University of Liège, Avenue de la Faculté d́ Agronomie, 2B, B-5030 Gembloux, Belgium
| | - Jesús Gerardo Saucedo-Castañeda
- Department of Biotechnology, Universidad Autonoma Metropolitana, Unidad Iztapalapa, Avenida San Rafael Atlixco 186, Colonia Vicentina, 09340, Mexico City, Mexico
| | - Philippe Jacques
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Joint Research Unit BioEcoAgro, UMRt 1158, Gembloux Agro-Bio Tech, University of Liège, Avenue de la Faculté d́ Agronomie, 2B, B-5030 Gembloux, Belgium
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11
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Guez JS, Coucheney F, Guy J, Béchet M, Fontanille P, Chihib NE, Niehren J, Coutte F, Jacques P. Bioinformatics Modelling and Metabolic Engineering of the Branched Chain Amino Acid Pathway for Specific Production of Mycosubtilin Isoforms in Bacillus subtilis. Metabolites 2022; 12:metabo12020107. [PMID: 35208182 PMCID: PMC8877110 DOI: 10.3390/metabo12020107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/11/2022] [Accepted: 01/19/2022] [Indexed: 02/05/2023] Open
Abstract
Mycosubtilin belongs to the family of lipopeptides. Different isoforms with various antifungal activities can be obtained according to the length and the isomery of the fatty acid. In this work, the activities of the mycosubtilin isoforms were first studied against the pathogen Aspergillus niger, revealing the high activity of the anteiso-C17 isoform. Modification of the mycosubtilin isoform patterns during cultures of the natural strain Bacillus subtilis ATCC 6633 was then investigated through amino acid feeding experiments. In parallel, single-gene knockouts and single-gene overexpression, leading to the overproduction of the anteiso-C15 fatty acid chains, were predicted using informatics tools which provide logical reasoning with formal models of reaction networks. In this way, it was in silico predicted that the single overexpression of the ilvA gene as well as the single knockout of the codY gene may lead to the overproduction of anteiso-C15 fatty acid chains. For the first time, it has been demonstrated that overexpression of ilvA helps to enhance the furniture of odd anteiso fatty acids leading to a favored mycosubtilin anteiso-C17 production pattern (+41%). Alternatively, a knock-out codY mutant led to a higher furniture of even iso fatty acids, leading to a favored mycosubtilin iso-C16 production pattern (+180%). These results showed that increased selective synthesis of particular isoforms of mycosubtilin through metabolic engineering is feasible, disclosing the interest of these approaches for future development of lipopeptide-producing strains.
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Affiliation(s)
- Jean-Sébastien Guez
- Institut Pascal, Clermont Auvergne INP, CNRS, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France; (J.-S.G.); (P.F.)
| | - Françoise Coucheney
- Équipe Métabolites Secondaires d’Origine Microbienne, Institut Charles Viollette, UMRt BioEcoAgro 1158-INRAE, Université de Lille, F-59000 Lille, France; (F.C.); (J.G.); (M.B.)
| | - Joany Guy
- Équipe Métabolites Secondaires d’Origine Microbienne, Institut Charles Viollette, UMRt BioEcoAgro 1158-INRAE, Université de Lille, F-59000 Lille, France; (F.C.); (J.G.); (M.B.)
| | - Max Béchet
- Équipe Métabolites Secondaires d’Origine Microbienne, Institut Charles Viollette, UMRt BioEcoAgro 1158-INRAE, Université de Lille, F-59000 Lille, France; (F.C.); (J.G.); (M.B.)
| | - Pierre Fontanille
- Institut Pascal, Clermont Auvergne INP, CNRS, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France; (J.-S.G.); (P.F.)
| | - Nour-Eddine Chihib
- UMR 8207–UMET–Unité Matériaux et Transformations, Centrale Lille, INRAE, CNRS, Université de Lille, F-59000 Lille, France;
| | - Joachim Niehren
- Biocomputing Team, Centre de Recherche en Informatique, Signal et Automatique de Lille CRIStAL, UMR CNRS 9189, Université de Lille, F-59000 Lille, France;
- INRIA, Université de Lille, F-59000 Lille, France
| | - François Coutte
- Équipe Métabolites Secondaires d’Origine Microbienne, Institut Charles Viollette, UMRt BioEcoAgro 1158-INRAE, Université de Lille, F-59000 Lille, France; (F.C.); (J.G.); (M.B.)
- Correspondence: ; Tel.: +33-(0)-328767497
| | - Philippe Jacques
- Équipe Métabolites Spécialisés d’Origine Microbienne, UMRt BioEcoAgro 1158-INRAE, TERRA Teaching and Research Centre, MiPI, Gembloux Agro-Bio Tech, Université de Liège, B-5030 Gembloux, Belgium;
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12
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Vassaux A, Rannou M, Peers S, Daboudet T, Jacques P, Coutte F. Impact of the Purification Process on the Spray-Drying Performances of the Three Families of Lipopeptide Biosurfactant Produced by Bacillus subtilis. Front Bioeng Biotechnol 2022; 9:815337. [PMID: 35004661 PMCID: PMC8727909 DOI: 10.3389/fbioe.2021.815337] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 11/23/2021] [Indexed: 12/30/2022] Open
Abstract
Lipopeptides produced by Bacillus subtilis display many activities (surfactant, antimicrobial, and antitumoral), which make them interesting compounds with a wide range of applications. During the past years, several processes have been developed to enable their production and purification with suitable yield and purity. The already implemented processes mainly end with a critical drying step, which is currently achieved by freeze-drying. In this study, the possibility to replace this freeze-drying step with a spray-drying one, more suited to industrial applications, was analyzed. After evaluating their thermal resistance, we have developed a spray-drying methodology applicable for the three lipopeptides families produced by B. subtilis, i.e., surfactin, mycosubtilin (iturin family), and plipastatin (fengycin family). For each lipopeptide, the spray-drying procedure was applied at three steps of the purification process by ultrafiltration (supernatant, diafiltered solution, and pre-purified fraction). The analysis of the activities of each spray-dried lipopeptide showed that this drying method is not decreasing its antimicrobial and biosurfactant properties. The methodology developed in this study enabled for the first time the spray-drying of surfactin, without adjuvants’ addition and regardless of the purification step considered. In the case of fengycin and mycosubtilin, only diafiltered solution and purified fraction could be successfully spray-dried without the addition of adjuvant. Maltodextrin addition was also investigated as the solution for the direct drying of supernatant. As expected, the performances of the spray-drying step and the purity of the powder obtained are highly related to the purification step at which the product was dried. Interestingly, the impact of mycosubtilin concentration on spray-drying yield was also evidenced.
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Affiliation(s)
- Antoine Vassaux
- Université de Lille, UMRt BioEcoAgro 1158-INRAE, Équipe Métabolites Secondaires d'Origine Microbienne, Institut Charles Viollette, Lille, France
| | - Marie Rannou
- Université de Lille, UMRt BioEcoAgro 1158-INRAE, Équipe Métabolites Secondaires d'Origine Microbienne, Institut Charles Viollette, Lille, France
| | | | - Théo Daboudet
- Université de Lille, UMRt BioEcoAgro 1158-INRAE, Équipe Métabolites Secondaires d'Origine Microbienne, Institut Charles Viollette, Lille, France
| | - Philippe Jacques
- LIPOFABRIK, Villeneuve d'Ascq, France.,TERRA Teaching and Research Centre, Université de Liège, UMRt BioEcoAgro 1158-INRAE, Équipe Métabolites Secondaires D'origine Microbienne, MiPI, Gembloux Agro-Bio Tech, Gembloux, Belgium
| | - François Coutte
- Université de Lille, UMRt BioEcoAgro 1158-INRAE, Équipe Métabolites Secondaires d'Origine Microbienne, Institut Charles Viollette, Lille, France.,LIPOFABRIK, Villeneuve d'Ascq, France
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13
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Jahn L, Storm-Johannsen L, Seidler D, Noack J, Gao W, Schafhauser T, Wohlleben W, van Berkel WJH, Jacques P, Kar T, Piechulla B, Ludwig-Müller J. The Endophytic Fungus Cyanodermella asteris Influences Growth of the Nonnatural Host Plant Arabidopsis thaliana. Mol Plant Microbe Interact 2022; 35:49-63. [PMID: 34615362 DOI: 10.1094/mpmi-03-21-0072-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Cyanodermella asteris is a fungal endophyte from Aster tataricus, a perennial plant from the northern part of Asia. Here, we demonstrated an interaction of C. asteris with Arabidopsis thaliana, Chinese cabbage, rapeseed, tomato, maize, or sunflower resulting in different phenotypes such as shorter main roots, massive lateral root growth, higher leaf and root biomass, and increased anthocyanin levels. In a variety of cocultivation assays, it was shown that these altered phenotypes are caused by fungal CO2, volatile organic compounds, and soluble compounds, notably astins. Astins A, C, and G induced plant growth when they were individually included in the medium. In return, A. thaliana stimulates the fungal astin C production during cocultivation. Taken together, our results indicate a bilateral interaction between the fungus and the plant. A stress response in plants is induced by fungal metabolites while plant stress hormones induced astin C production of the fungus. Interestingly, our results not only show unidirectional influence of the fungus on the plant but also vice versa. The plant is able to influence growth and secondary metabolite production in the endophyte, even when both organisms do not live in close contact, suggesting the involvement of volatile compounds.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Linda Jahn
- Plant Physiology, Faculty of Biology, Technische Universität Dresden, 01062 Dresden, Germany
| | - Lisa Storm-Johannsen
- Plant Physiology, Faculty of Biology, Technische Universität Dresden, 01062 Dresden, Germany
| | - Diana Seidler
- Plant Physiology, Faculty of Biology, Technische Universität Dresden, 01062 Dresden, Germany
| | - Jasmin Noack
- Plant Physiology, Faculty of Biology, Technische Universität Dresden, 01062 Dresden, Germany
| | - Wei Gao
- Biopsychology, Faculty of Psychology, Technische Universität Dresden, 01062 Dresden, Germany
| | - Thomas Schafhauser
- Plant Physiology, Faculty of Biology, Technische Universität Dresden, 01062 Dresden, Germany
- Interfaculty Institute of Microbiology and Infection Medicine, Microbiology and Biotechnology, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Wolfgang Wohlleben
- Interfaculty Institute of Microbiology and Infection Medicine, Microbiology and Biotechnology, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Willem J H van Berkel
- Laboratory of Biochemistry, Wageningen University Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Philippe Jacques
- MiPI, TERRA Teaching and Research Centre, Joint Research Unit BioEcoAgro, UMRt 1158, Gembloux, Belgium
| | - Tambi Kar
- Lipofabrik, Cité Scientifique, Bât. Polytech-Lille, Avenue Langevin 59 655, Villeneuve d'Ascq, France
| | - Birgit Piechulla
- Institute for Biological Science, Biochemistry, University of Rostock, 18059 Rostock, Germany
| | - Jutta Ludwig-Müller
- Plant Physiology, Faculty of Biology, Technische Universität Dresden, 01062 Dresden, Germany
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14
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Guez JS, Vassaux A, Larroche C, Jacques P, Coutte F. New Continuous Process for the Production of Lipopeptide Biosurfactants in Foam Overflowing Bioreactor. Front Bioeng Biotechnol 2021; 9:678469. [PMID: 34124025 PMCID: PMC8194703 DOI: 10.3389/fbioe.2021.678469] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 04/12/2021] [Indexed: 11/13/2022] Open
Abstract
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.
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Affiliation(s)
- Jean-Sébastien Guez
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, Institut Pascal, Clermont-Ferrand, France
| | - Antoine Vassaux
- Université de Lille, UMRt BioEcoAgro 1158-INRAE, équipe Métabolites Secondaires d'origine Microbienne, Institut Charles Viollette, Lille, France
| | - Christian Larroche
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, Institut Pascal, Clermont-Ferrand, France
| | - Philippe Jacques
- Université de Liège, UMRt BioEcoAgro 1158-INRAE, équipe Métabolites Secondaires d'origine Microbienne, TERRA Teaching and Research Centre, MiPI, Gembloux Agro-Bio Tech, Gembloux, Belgium.,Lipofabrik, Polytech-Lille, Cité Scientifique, Villeneuve d'Ascq, France
| | - François Coutte
- Université de Lille, UMRt BioEcoAgro 1158-INRAE, équipe Métabolites Secondaires d'origine Microbienne, Institut Charles Viollette, Lille, France.,Lipofabrik, Polytech-Lille, Cité Scientifique, Villeneuve d'Ascq, France
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15
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Théatre A, Cano-Prieto C, Bartolini M, Laurin Y, Deleu M, Niehren J, Fida T, Gerbinet S, Alanjary M, Medema MH, Léonard A, Lins L, Arabolaza A, Gramajo H, Gross H, Jacques P. The Surfactin-Like Lipopeptides From Bacillus spp.: Natural Biodiversity and Synthetic Biology for a Broader Application Range. Front Bioeng Biotechnol 2021; 9:623701. [PMID: 33738277 PMCID: PMC7960918 DOI: 10.3389/fbioe.2021.623701] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/02/2021] [Indexed: 11/21/2022] Open
Abstract
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.
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Affiliation(s)
- Ariane Théatre
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Joint Research Unit BioEcoAgro, UMRt 1158, Gembloux Agro-Bio Tech, University of Liège, Avenue de la Faculté, Gembloux, Belgium
| | - Carolina Cano-Prieto
- Department of Pharmaceutical Biology, Pharmaceutical Institute, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Marco Bartolini
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias, Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Yoann Laurin
- Laboratoire de Biophysique Moléculaire aux Interfaces, TERRA Teaching and Research Centre, Joint Research Unit BioEcoAgro, UMRt 1158, Gembloux Agro-Bio Tech, Université de Liège, Gembloux, Belgium.,Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, Amiens, France
| | - Magali Deleu
- Laboratoire de Biophysique Moléculaire aux Interfaces, TERRA Teaching and Research Centre, Joint Research Unit BioEcoAgro, UMRt 1158, Gembloux Agro-Bio Tech, Université de Liège, Gembloux, Belgium
| | - Joachim Niehren
- Inria Lille, and BioComputing Team of CRISTAL Lab (CNRS UMR 9189), Lille, France
| | - Tarik Fida
- Department of Pharmaceutical Biology, Pharmaceutical Institute, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Saïcha Gerbinet
- Chemical Engineering, Products, Environment, and Processes, University of Liège, Liège, Belgium
| | - Mohammad Alanjary
- Bioinformatics Group, Wageningen University, Wageningen, Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, Netherlands
| | - Angélique Léonard
- Chemical Engineering, Products, Environment, and Processes, University of Liège, Liège, Belgium
| | - Laurence Lins
- Laboratoire de Biophysique Moléculaire aux Interfaces, TERRA Teaching and Research Centre, Joint Research Unit BioEcoAgro, UMRt 1158, Gembloux Agro-Bio Tech, Université de Liège, Gembloux, Belgium
| | - Ana Arabolaza
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias, Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Hugo Gramajo
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias, Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Harald Gross
- Department of Pharmaceutical Biology, Pharmaceutical Institute, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Philippe Jacques
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Joint Research Unit BioEcoAgro, UMRt 1158, Gembloux Agro-Bio Tech, University of Liège, Avenue de la Faculté, Gembloux, Belgium
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16
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Meunier L, Tocquin P, Cornet L, Sirjacobs D, Leclère V, Pupin M, Jacques P, Baurain D. Palantir: a springboard for the analysis of secondary metabolite gene clusters in large-scale genome mining projects. Bioinformatics 2021; 36:4345-4347. [PMID: 32415965 DOI: 10.1093/bioinformatics/btaa517] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/07/2020] [Accepted: 05/12/2020] [Indexed: 12/17/2022] Open
Abstract
SUMMARY To support small and large-scale genome mining projects, we present Post-processing Analysis tooLbox for ANTIsmash Reports (Palantir), 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 and domain). Moreover, it can parse user-provided antiSMASH reports and reformat them for direct use or storage in a relational database. AVAILABILITY AND IMPLEMENTATION 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.
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Affiliation(s)
- Loïc Meunier
- InBioS-PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, B-4000 Liège, Belgium.,Microbial Processes and Interactions, TERRA Teaching and Research Centre, Joint Research Unit BioEcoAgro UMRT 1158, Gembloux Agro-Bio Tech, University of Liège, B-5030 Gembloux, Belgium
| | - Pierre Tocquin
- InBioS-PhytoSYSTEMS, Plant Physiology, University of Liège, B-4000 Liège, Belgium.,Hedera-22 SCRL, B-4130 Tilff, Belgium
| | - Luc Cornet
- GIGA institute, Medical Genomics-Unit of Animal Genomics, University of Liège, B-4000 Liège, Belgium
| | - Damien Sirjacobs
- InBioS-PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, B-4000 Liège, Belgium
| | - Valérie Leclère
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV-Institut Charles Viollette, Joint Research Unit BioEcoAgro UMRT 1158, F-59000 Lille, France
| | - Maude Pupin
- UMR 9189- CRIStAL- Centre de Recherche en Informatique Signal et Automatique de Lille, University of Lille, CNRS, Centrale Lille, F-59000 Lille, France.,Bonsai Team, Inria-Lille Nord Europe, F-59655 Villeneuve d'Ascq Cedex, France
| | - Philippe Jacques
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Joint Research Unit BioEcoAgro UMRT 1158, Gembloux Agro-Bio Tech, University of Liège, B-5030 Gembloux, Belgium
| | - Denis Baurain
- InBioS-PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, B-4000 Liège, Belgium.,Hedera-22 SCRL, B-4130 Tilff, Belgium
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Théatre A, Hoste ACR, Rigolet A, Benneceur I, Bechet M, Ongena M, Deleu M, Jacques P. Bacillus sp.: A Remarkable Source of Bioactive Lipopeptides. Biosurfactants for the Biobased Economy 2021; 181:123-179. [DOI: 10.1007/10_2021_182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Abdallah DB, Krier F, Jacques P, Tounsi S, Frikha-Gargouri O. Agrobacterium tumefaciens C58 presence affects Bacillus velezensis 32a ecological fitness in the tomato rhizosphere. Environ Sci Pollut Res Int 2020; 27:28429-28437. [PMID: 32415456 DOI: 10.1007/s11356-020-09124-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 04/29/2020] [Indexed: 06/11/2023]
Abstract
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.
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Affiliation(s)
- Dorra Ben Abdallah
- Biopesticides Laboratory, Centre of Biotechnology of Sfax, Sfax University, P.O. Box 1177, 3018, Sfax, Tunisia
| | - François Krier
- Université de Lille, INRA, Université d'Artois, Université du Littoral-Côte d'Opale, EA 7394 - ICV-Institut Charles Viollette, F-59000, Lille, France
| | - Philippe Jacques
- Microbial Processes and Interactions (MiPI), TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech University of Liege, B-5030, Gembloux, Belgium
| | - Slim Tounsi
- Biopesticides Laboratory, Centre of Biotechnology of Sfax, Sfax University, P.O. Box 1177, 3018, Sfax, Tunisia
| | - Olfa Frikha-Gargouri
- Biopesticides Laboratory, Centre of Biotechnology of Sfax, Sfax University, P.O. Box 1177, 3018, Sfax, Tunisia.
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19
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Flissi A, Ricart E, Campart C, Chevalier M, Dufresne Y, Michalik J, Jacques P, Flahaut C, Lisacek F, Leclère V, Pupin M. Norine: update of the nonribosomal peptide resource. Nucleic Acids Res 2020; 48:D465-D469. [PMID: 31691799 PMCID: PMC7145658 DOI: 10.1093/nar/gkz1000] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/15/2019] [Accepted: 10/22/2019] [Indexed: 12/21/2022] Open
Abstract
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/
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Affiliation(s)
- Areski Flissi
- Univ. Lille, CNRS, Centrale Lille, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, F-59000 Lille, France
| | - Emma Ricart
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, CMU, Rue Michel-Servet 1, 1211 Geneva, Switzerland.,Computer Science Department, University of Geneva, CUI, 7 route de Drize, 1227 Carouge, Switzerland
| | - Clémentine Campart
- Univ. Lille, CNRS, Centrale Lille, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, F-59000 Lille, France
| | - Mickael Chevalier
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV- Institut Charles Viollette, F-59000 Lille, France
| | - Yoann Dufresne
- Univ. Lille, CNRS, Centrale Lille, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, F-59000 Lille, France
| | - Juraj Michalik
- Univ. Lille, CNRS, Centrale Lille, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, F-59000 Lille, France.,bilille, CNRS, cité scientifique, F-59650 Villeneuve d'Ascq, France
| | - Philippe Jacques
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liège, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium
| | - Christophe Flahaut
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV- Institut Charles Viollette, F-59000 Lille, France
| | - Frédérique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, CMU, Rue Michel-Servet 1, 1211 Geneva, Switzerland.,Computer Science Department, University of Geneva, CUI, 7 route de Drize, 1227 Carouge, Switzerland.,Section of Biology, University of Geneva, Sciences III, 30 quai Ernest-Ansermet, 1211 Geneva, Switzerland
| | - Valérie Leclère
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV- Institut Charles Viollette, F-59000 Lille, France
| | - Maude Pupin
- Univ. Lille, CNRS, Centrale Lille, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, F-59000 Lille, France
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Brück HL, Coutte F, Dhulster P, Gofflot S, Jacques P, Delvigne F. Growth Dynamics of Bacterial Populations in a Two-Compartment Biofilm Bioreactor Designed for Continuous Surfactin Biosynthesis. Microorganisms 2020; 8:microorganisms8050679. [PMID: 32392736 PMCID: PMC7285194 DOI: 10.3390/microorganisms8050679] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 04/28/2020] [Accepted: 05/01/2020] [Indexed: 11/16/2022] Open
Abstract
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.
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Affiliation(s)
- Hannah Luise Brück
- MiPI, TERRA Teaching and Research Centre, Joint Research Unit BioEcoAgro N° 1158, Gembloux Agro-Bio Tech, University Liège, University Lille, INRAE, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, B-5030 Gembloux, Belgium; (H.L.B.); (P.J.)
- ICV—Institut Charles Viollette, Joint Research Unit BioEcoAgro N° 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, F-59000 Lille, France; (F.C.); (P.D.)
| | - François Coutte
- ICV—Institut Charles Viollette, Joint Research Unit BioEcoAgro N° 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, F-59000 Lille, France; (F.C.); (P.D.)
| | - Pascal Dhulster
- ICV—Institut Charles Viollette, Joint Research Unit BioEcoAgro N° 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, F-59000 Lille, France; (F.C.); (P.D.)
| | - Sébastien Gofflot
- Walloon Agricultural Research Center (CRA-W), Agricultural Product Technology Unit, Chaussée de Namur, 24, B-5030 Gembloux, Belgium;
| | - Philippe Jacques
- MiPI, TERRA Teaching and Research Centre, Joint Research Unit BioEcoAgro N° 1158, Gembloux Agro-Bio Tech, University Liège, University Lille, INRAE, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, B-5030 Gembloux, Belgium; (H.L.B.); (P.J.)
| | - Frank Delvigne
- MiPI, TERRA Teaching and Research Centre, Joint Research Unit BioEcoAgro N° 1158, Gembloux Agro-Bio Tech, University Liège, University Lille, INRAE, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, B-5030 Gembloux, Belgium; (H.L.B.); (P.J.)
- Correspondence:
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Patel AK, Barghout V, Yenikomshian MA, Germain G, Jacques P, Laliberté F, Duh MS. Real-World Adherence in Patients with Metastatic Colorectal Cancer Treated with Trifluridine plus Tipiracil or Regorafenib. Oncologist 2020; 25:e75-e84. [PMID: 31591140 PMCID: PMC6964129 DOI: 10.1634/theoncologist.2019-0240] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/31/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Trifluridine and tipiracil (FTD + TPI) and regorafenib (REG) are approved treatments for the treatment of refractory metastatic colorectal cancer (mCRC). This study assesses adherence and duration of therapy with FTD + TPI versus REG and explores the effect of sequencing on adherence. MATERIALS AND METHODS Adults diagnosed with mCRC were identified in the IQVIA Real-World Data Adjudicated Claims: U.S. database (October 2014-July 2017). The observation period spanned from the index date (first dispensing of FTD + TPI or REG) to the earliest of a switch to another mCRC agent, the end of continuous enrollment, or the end of data availability. Medication possession ratio (MPR), proportion of days covered (PDC), and persistence and time to discontinuation (gap ≥45 days) were compared between FTD + TPI and REG users and among switchers (FTD + TPI-to-REG vs. REG-to-FTD + TPI). RESULTS A total of 469 FTD + TPI and 311 REG users were identified. FTD + TPI users had higher compliance with an MPR ≥80% (odds ratio [OR], 2.47; p < .001) and PDC ≥80% (OR, 2.77; p < .001). FTD + TPI users had better persistence (82.8% vs. 68.0%; p < .001) and lower risk of discontinuation (hazard ratio [HR], 0.76; p = .006). Among switchers (96 FTD + TPI-to-REG; 83 REG-to-FTD + TPI), those switching from FTD + TPI to REG were more likely to have an MPR ≥80% (OR, 2.91; p < .001) and PDC ≥80% (OR, 4.60; p < .001) compared with REG-to-FTD + TPI switchers while treated with these drugs. Additionally, FTD + TPI-to-REG switchers had a lower risk of first treatment discontinuation (HR, 0.66; p = .009). CONCLUSION FTD + TPI users had significantly higher adherence and persistence, and patients who were treated with FTD + TPI before switching to REG also had higher adherence and persistence outcomes. IMPLICATIONS FOR PRACTICE Trifluridine plus tipiracil (FTD + TPI) and regorafenib (REG) prolong survival in refractory metastatic colorectal cancer (mCRC) but have different tolerability profiles. This study assessed real-world adherence to treatment with FTD + TPI versus REG and compared outcomes among patients who switched from FTD + TPI to REG and vice versa. FTD + TPI was associated with significantly higher medication adherence and longer time to discontinuation than REG. Patients treated with FTD + TPI prior to switching to REG also showed higher adherence outcomes. Findings could help inform decision making regarding the choice and sequencing of treatment with FTD + TPI versus REG in patients with mCRC.
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Affiliation(s)
| | | | | | | | | | | | - Mei S. Duh
- Analysis Group, Inc.BostonMassachusettsUSA
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22
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Brück HL, Delvigne F, Dhulster P, Jacques P, Coutte F. Molecular strategies for adapting Bacillus subtilis 168 biosurfactant production to biofilm cultivation mode. Bioresour Technol 2019; 293:122090. [PMID: 31499329 DOI: 10.1016/j.biortech.2019.122090] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/28/2019] [Accepted: 08/29/2019] [Indexed: 06/10/2023]
Abstract
Biofilm bioreactors have already been proven to be efficient systems for microbial lipopeptide production since they avoid foam formation. However, the cell adhesion capacities of the laboratory strain B.subtilis 168 to the biofilm bioreactor support are limited. In this work, we present a novel approach for increasing cell adhesion through the generation of filamentous and/or exopolysaccharide producing B.subtilis 168 mutants by genetic engineering. The single cell growth behavior was analyzed using time-lapse microscopy and the colonization capacities were investigated under continuous flow conditions in a drip-flow reactor. Cell adhesion could be increased three times through filamentous growth in lipopeptide producing B. subtilis 168 derivatives strains. Further restored exopolysaccharide production increased up to 50 times the cell adhesion capacities. Enhanced cell immobilization resulted in 10 times increased surfactin production. These findings will be of particular interest regarding the design of more efficient microbial cell factories for biofilm cultivation.
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Affiliation(s)
- Hannah Luise Brück
- MiPI, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Avenue de la Faculté, 2B, B-5030 Gembloux, Belgium; Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394 ICV - Institut Charles Viollette, F-59000 Lille, France
| | - Frank Delvigne
- MiPI, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Avenue de la Faculté, 2B, B-5030 Gembloux, Belgium
| | - Pascal Dhulster
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394 ICV - Institut Charles Viollette, F-59000 Lille, France
| | - Philippe Jacques
- MiPI, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Avenue de la Faculté, 2B, B-5030 Gembloux, Belgium
| | - François Coutte
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394 ICV - Institut Charles Viollette, F-59000 Lille, France.
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23
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Chevalier M, Ricart E, Hanozin E, Pupin M, Jacques P, Smargiasso N, De Pauw E, Lisacek F, Leclère V, Flahaut C. Kendrick Mass Defect Approach Combined to NORINE Database for Molecular Formula Assignment of Nonribosomal Peptides. J Am Soc Mass Spectrom 2019; 30:2608-2616. [PMID: 31659720 DOI: 10.1007/s13361-019-02314-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 07/03/2019] [Accepted: 08/10/2019] [Indexed: 06/10/2023]
Abstract
The identification of known (dereplication) or unknown nonribosomal peptides (NRPs) produced by microorganisms is a time consuming, expensive, and challenging task where mass spectrometry and nuclear magnetic resonance play a key role. The first step of the identification process always involves the establishment of a molecular formula. Unfortunately, the number of potential molecular formulae increases significantly with higher molecular masses and the lower precision of their measurements. In the present article, we demonstrate that molecular formula assignment can be achieved by a combined approach using the regular Kendrick mass defect (RKMD) and NORINE, the reference curated database of NRPs. We observed that irrespective of the molecular formula, the addition and subtraction of a given atom or atom group always leads to the same RKMD variation and nominal Kendrick mass (NKM). Graphically, these variations translated into a vector mesh can be used to connect an unknown molecule to a known NRP of the NORINE database and establish its molecular formula. We explain and illustrate this concept through the high-resolution mass spectrometry analysis of a commercially available mixture composed of four surfactins. The Kendrick approach enriched with the NORINE database content is a fast, useful, and easy-to-use tool for molecular mass assignment of known and unknown NRP structures.
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Affiliation(s)
- Mickaël Chevalier
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-Institut Charles Viollette (ICV), F-59000, Lille, France
| | - Emma Ricart
- Proteome informatics Group, SIB Swiss Institute of Bioinformatics (SIB), and Computer Science Department, University of Geneva, Geneva, Switzerland
| | - Emeline Hanozin
- Mass Spectrometry Laboratory, Molecular Systems - MolSys Research Unit, University of Liège, Liège, Belgium
| | - Maude Pupin
- Univ. Lille, CNRS, Centrale Lille, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, F-59000, Lille, France
- Inria-Lille Nord Europe, Bonsai team, F-59655, Villeneuve d'Ascq Cedex, France
| | - Philippe Jacques
- TERRA Research Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech University of Liège, B-5030, Gembloux, Belgium
| | - Nicolas Smargiasso
- Mass Spectrometry Laboratory, Molecular Systems - MolSys Research Unit, University of Liège, Liège, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, Molecular Systems - MolSys Research Unit, University of Liège, Liège, Belgium
| | - Frédérique Lisacek
- Proteome informatics Group, SIB Swiss Institute of Bioinformatics (SIB), and Computer Science Department, University of Geneva, Geneva, Switzerland
| | - Valérie Leclère
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-Institut Charles Viollette (ICV), F-59000, Lille, France
| | - Christophe Flahaut
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-Institut Charles Viollette (ICV), F-59000, Lille, France.
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Desmyttere H, Deweer C, Muchembled J, Sahmer K, Jacquin J, Coutte F, Jacques P. Antifungal Activities of Bacillus subtilis Lipopeptides to Two Venturia inaequalis Strains Possessing Different Tebuconazole Sensitivity. Front Microbiol 2019; 10:2327. [PMID: 31695685 PMCID: PMC6817503 DOI: 10.3389/fmicb.2019.02327] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 09/24/2019] [Indexed: 01/27/2023] Open
Abstract
Within the framework of biocontrol development, three natural substances produced by Bacillus subtilis, called lipopeptides, have been studied: fengycin (F), surfactin (S), and mycosubtilin (M). Their antifungal properties were tested in vitro, in liquid medium, on two strains of Venturia inaequalis, ascomycete fungi causing apple scab. These two strains were, respectively sensitive and less sensitive to tebuconazole, an active substance of the triazole family. These three molecules were tested on their own, in binary (FS, FM, SM) and ternary mixtures (FSM). The antifungal activities of lipopeptides were estimated by calculating an IC50, compared to tebuconazole chemical substance. In tests involving the sensitive strain, all lipopeptide modalities exhibited antifungal activity. However, modalities involving fengycin and its mixtures exhibited the best antifungal activities; the activity of fengycin alone being very similar to that of tebuconazole. Interestingly, regarding the strain with reduced sensitivity to tebuconazole, surfactin and fengycin alone were not efficient while mycosubtilin and the different mixtures showed interesting antifungal activities. Specifically, the antifungal activity of FS and FSM mixture were equivalent to that of tebuconazole. For both fungal strains, microscopic observations revealed important morphological modifications in the presence of fengycin and in a less important proportion in the presence of surfactin but not in the presence of mycosubtilin. Overall, this study highlights the diversity in mode of action of lipopeptides on apple scab strains.
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Affiliation(s)
- Hélène Desmyttere
- Univ. Lille, INRA, ISA-Yncréa, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394 - ICV - Institut Charles Viollette, Lille, France
| | - Caroline Deweer
- Univ. Lille, INRA, ISA-Yncréa, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394 - ICV - Institut Charles Viollette, Lille, France
| | - Jérôme Muchembled
- Univ. Lille, INRA, ISA-Yncréa, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394 - ICV - Institut Charles Viollette, Lille, France
| | - Karin Sahmer
- Civil and Geo-Environmental Engineering Laboratory (LGCgE), ISA - Yncréa, Lille, France
| | - Justine Jacquin
- Univ. Lille, INRA, ISA-Yncréa, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394 - ICV - Institut Charles Viollette, Lille, France
| | - François Coutte
- Univ. Lille, INRA, ISA-Yncréa, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394 - ICV - Institut Charles Viollette, Lille, France
| | - Philippe Jacques
- MiPI, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
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Vassaux A, Meunier L, Vandenbol M, Baurain D, Fickers P, Jacques P, Leclère V. Nonribosomal peptides in fungal cell factories: from genome mining to optimized heterologous production. Biotechnol Adv 2019; 37:107449. [PMID: 31518630 DOI: 10.1016/j.biotechadv.2019.107449] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 12/15/2022]
Abstract
Fungi are notoriously prolific producers of secondary metabolites including nonribosomal peptides (NRPs). The structural complexity of NRPs grants them interesting activities such as antibiotic, anti-cancer, and anti-inflammatory properties. The discovery of these compounds with attractive activities can be achieved by using two approaches: either by screening samples originating from various environments for their biological activities, or by identifying the related clusters in genomic sequences thanks to bioinformatics tools. This genome mining approach has grown tremendously due to recent advances in genome sequencing, which have provided an incredible amount of genomic data from hundreds of microbial species. Regarding fungal organisms, the genomic data have revealed the presence of an unexpected number of putative NRP-related gene clusters. This highlights fungi as a goldmine for the discovery of putative novel bioactive compounds. Recent development of NRP dedicated bioinformatics tools have increased the capacity to identify these gene clusters and to deduce NRPs structures, speeding-up the screening process for novel metabolites discovery. Unfortunately, the newly identified compound is frequently not or poorly produced by native producers due to a lack of expression of the related genes cluster. A frequently employed strategy to increase production rates consists in transferring the related biosynthetic pathway in heterologous hosts. This review aims to provide a comprehensive overview about the topic of NRPs discovery, from gene cluster identification by genome mining to the heterologous production in fungal hosts. The main computational tools and methods for genome mining are herein presented with an emphasis on the particularities of the fungal systems. The different steps of the reconstitution of NRP biosynthetic pathway in heterologous fungal cell factories will be discussed, as well as the key factors to consider for maximizing productivity. Several examples will be developed to illustrate the potential of heterologous production to both discover uncharacterized novel compounds predicted in silico by genome mining, and to enhance the productivity of interesting bio-active natural products.
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Affiliation(s)
- Antoine Vassaux
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium; Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV-Institut Charles Viollette, F-59000 Lille, France
| | - Loïc Meunier
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium; InBioS-PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liege, Boulevard du Rectorat 27, B-4000 Liège, Belgium
| | - Micheline Vandenbol
- TERRA Teaching and Research Centre, Microbiologie et Génomique, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium
| | - Denis Baurain
- InBioS-PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liege, Boulevard du Rectorat 27, B-4000 Liège, Belgium
| | - Patrick Fickers
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium
| | - Philippe Jacques
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium
| | - Valérie Leclère
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV-Institut Charles Viollette, F-59000 Lille, France.
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Vassaux A, Tarayre C, Arguëlles‐Arias A, Compère P, Delvigne F, Fickers P, Jahn L, Lang A, Leclère V, Ludwig‐Müller J, Ongena M, Schafhauser T, Telek S, Théatre A, Berkel WJH, Vandenbol M, Pée K, Willems L, Wohlleben W, Jacques P. Astin C Production by the Endophytic Fungus
Cyanodermella asteris
in Planktonic and Immobilized Culture Conditions. Biotechnol J 2019; 14:e1800624. [DOI: 10.1002/biot.201800624] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 05/13/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Antoine Vassaux
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro‐Bio TechUniversity of LiegeAvenue de la Faculté d’ Agronomie B‐5030 Gembloux Belgium
- EA 7394‐ICV‐Institut Charles ViolletteUniversity Lille, INRA, ISA, University Artois, University Littoral Côte d'Opale F‐59000 Lille France
| | - Cédric Tarayre
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro‐Bio TechUniversity of LiegeAvenue de la Faculté d’ Agronomie B‐5030 Gembloux Belgium
| | - Anthony Arguëlles‐Arias
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro‐Bio TechUniversity of LiegeAvenue de la Faculté d’ Agronomie B‐5030 Gembloux Belgium
| | - Philippe Compère
- Département de Biologie, Ecologie et Evolution et Cellule d'Appui à la Recherche et à l'Enseignement en MicroscopieUniversité de LiègeAllée du Six Ao û t 15 B‐4000 Liege Belgium
| | - Frank Delvigne
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro‐Bio TechUniversity of LiegeAvenue de la Faculté d’ Agronomie B‐5030 Gembloux Belgium
| | - Patrick Fickers
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro‐Bio TechUniversity of LiegeAvenue de la Faculté d’ Agronomie B‐5030 Gembloux Belgium
| | - Linda Jahn
- Institut für BotanikTechnische Universität Dresden 01062 Dresden Germany
| | - Alexander Lang
- Allgemeine BiochemieTechnische Universität Dresden 01069 Dresden Germany
| | - Valérie Leclère
- EA 7394‐ICV‐Institut Charles ViolletteUniversity Lille, INRA, ISA, University Artois, University Littoral Côte d'Opale F‐59000 Lille France
| | | | - Marc Ongena
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro‐Bio TechUniversity of LiegeAvenue de la Faculté d’ Agronomie B‐5030 Gembloux Belgium
| | - Thomas Schafhauser
- Mikrobiologie Biotechnologie, Interfakultäres Institut für Mikrobiologie und InfektionsmedizinEberhard Karls Universität TübingenAuf der Morgenstelle 28 72076 Tübingen Germany
| | - Samuel Telek
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro‐Bio TechUniversity of LiegeAvenue de la Faculté d’ Agronomie B‐5030 Gembloux Belgium
| | - Ariane Théatre
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro‐Bio TechUniversity of LiegeAvenue de la Faculté d’ Agronomie B‐5030 Gembloux Belgium
| | - Willem J. H. Berkel
- Laboratory of BiochemistryWageningen University & ResearchStippeneng 4 6708 WE Wageningen The Netherlands
| | - Micheline Vandenbol
- TERRA Teaching and Research Centre, Microbiologie et Génomique, Gembloux Agro‐Bio TechUniversity of LiegeAvenue de la Faculté d'Agronomie B‐5030 Gembloux Belgium
| | - Karl‐Heinz Pée
- Allgemeine BiochemieTechnische Universität Dresden 01069 Dresden Germany
| | - Luc Willems
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro‐Bio TechUniversity of LiegeAvenue de la Faculté d’ Agronomie B‐5030 Gembloux Belgium
- GIGA Research, Cellular and Molecular EpigeneticsUniversity of LiegeAllée de l'Hôpital 1 B‐4000 Liege Belgium
| | - Wolfgang Wohlleben
- Mikrobiologie Biotechnologie, Interfakultäres Institut für Mikrobiologie und InfektionsmedizinEberhard Karls Universität TübingenAuf der Morgenstelle 28 72076 Tübingen Germany
| | - Philippe Jacques
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro‐Bio TechUniversity of LiegeAvenue de la Faculté d’ Agronomie B‐5030 Gembloux Belgium
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Verhaegen C, Lepropre S, Octave M, Kautbally S, Bertrand L, Beauloye C, Jacques P, Horman S, Kefer J. Fe-based alloy for stent application inhibits platelet activation. Archives of Cardiovascular Diseases Supplements 2019. [DOI: 10.1016/j.acvdsp.2019.02.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Pilon D, Sheehan JJ, Szukis H, Singer D, Jacques P, Lejeune D, Lefebvre P, Greenberg PE. Medicaid spending burden among beneficiaries with treatment-resistant depression. J Comp Eff Res 2019; 8:381-392. [DOI: 10.2217/cer-2018-0140] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Aim: To evaluate Medicaid spending and healthcare resource utilization (HRU) in treatment-resistant depression (TRD). Materials & methods: TRD beneficiaries were identified from Medicaid claims databases (January 2010–March 2017) and matched 1:1 with major depressive disorder (MDD) beneficiaries without TRD (non-TRD-MDD) and randomly selected patients without MDD (non-MDD). Differences in HRU and per-patient-per-year costs were reported in incidence rate ratios (IRRs) and cost differences (CDs), respectively. Results: TRD beneficiaries had higher HRU than 1:1 matched non-TRD-MDD (e.g., inpatient visits: IRR = 1.41) and non-MDD beneficiaries (N = 14,710 per cohort; e.g., inpatient visits: IRR = 3.42, p < 0.01). TRD beneficiaries incurred greater costs versus non-TRD-MDD (CD = US$4382) and non-MDD beneficiaries (CD = US$8294; p < 0.05). Conclusion: TRD is associated with higher HRU and costs versus non-TRD-MDD and non-MDD. TRD poses a significant burden to Medicaid.
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Affiliation(s)
| | - John J Sheehan
- Janssen Scientific Affairs, LLC, Titusville, NJ, 08560, USA
| | - Holly Szukis
- Janssen Scientific Affairs, LLC, Titusville, NJ, 08560, USA
| | - David Singer
- Thomas Jefferson University, Philadelphia, PA, 19107, USA
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Cohen AA, Dufour F, Jacques P. BROAD-SCALE, MULTI-SYSTEM DYSREGULATION OF GENE EXPRESSION: TOWARD CLINICAL QUANTIFICATION OF AGING. Innov Aging 2018. [DOI: 10.1093/geroni/igy023.232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- A A Cohen
- Universite de Sherbrooke, St-Denis-de-Brompton, Quebec, Canada
| | - F Dufour
- Department of Biology, University of Sherbrooke, Sherbrooke, QC, Canada
| | - P Jacques
- National Institute on Aging, Baltimore, Maryland, United States
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Patel AK, Barghout V, Yenikomshian MA, Germain G, Jacques P, Laliberté F, Duh MS. Real-world adherence in patients with metastatic colorectal cancer (mCRC) treated with trifluridine/tipiracil (FTD/TPI) or regorafenib (REG). J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.30_suppl.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
11 Background: Adherence to oral chemotherapies is a critical but difficult to measure factor in the care of patients with advanced cancer. FTD/TPI and REG have both demonstrated prolonged survival in patients with refractory mCRC, but with notably different side effect profiles. This study utilizes real-world data to assess adherence and discontinuation of patients treated with FTD/TPI or REG and explore the effect of sequencing on adherence. Methods: Adults diagnosed with mCRC were identified using the nationally representative IQVIA Real-World Data Adjudicated Claims – US database (10/2014–07/2017). The first dispensing date of FTD/TPI or REG (if after FTD/TPI approval [10/2015]) was defined as the index date and the 3 months before as the baseline period. The observation period spanned from the index to the earliest date of a switch to another mCRC agent, end of continuous enrollment, or end of data availability. Medication possession ratio (MPR), proportion of days covered (PDC) at 3 months, and discontinuation (i.e., allowable gap≥45 days) were compared. Logistic (odds ratio [OR]) and Cox proportional hazards (hazard ratio [HR]) regressions, adjusting for baseline characteristics, were used to compare adherence and discontinuation, respectively. A subgroup analysis was conducted among switchers (FTD/TPI to REG vs REG to FTD/TPI). Results: A total of 469 FTD/TPI and 311 REG users were identified. FTD/TPI users had higher compliance with an MPR ≥ 80% (OR = 2.47; p < 0.001) and PDC ≥ 80% (OR = 2.77; p < 0.001). FTD/TPI users had lower risk of discontinuation (HR = 0.76; p = 0.006). Among switchers (96 FTD/TPI to REG; 83 REG to FTD/TPI), those switching from FTD/TPI to REG were more likely to have an MPR ≥ 80% (OR = 2.91; p < 0.001) and PDC ≥ 80% (OR = 4.60; p < 0.001) compared to REG to FTD/TPI switchers. Additionally, FTD/TPI to REG switchers had a lower risk of first treatment discontinuation (HR = 0.66; p = 0.009). Conclusions: In this study, FTD/TPI users had significantly higher compliance, lower discontinuation rate, and switchers treated first with FTD/TPI had better compliance, demonstrating that claims data can provide insight into oral chemotherapy adherence patterns in mCRC.
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Subramanian J, Laliberté F, Fernandes A, Pavilack M, Jacques P, Duh M. P2.15-26 Rates and Economic Burden of Adverse Events in Patients With Metastatic NSCLC Treated with EGFR-TKIs. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.1468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Esmaeel Q, Pupin M, Jacques P, Leclère V. Nonribosomal peptides and polyketides of Burkholderia: new compounds potentially implicated in biocontrol and pharmaceuticals. Environ Sci Pollut Res Int 2018; 25:29794-29807. [PMID: 28547376 DOI: 10.1007/s11356-017-9166-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 05/01/2017] [Indexed: 06/07/2023]
Abstract
Bacteria belonging to the genus Burkholderia live in various ecological niches and present a significant role in the environments through the excretion of a wide variety of secondary metabolites including modular nonribosomal peptides (NRPs) and polyketides (PKs). These metabolites represent a widely distributed biomedically and biocontrol important class of natural products including antibiotics, siderophores, and anticancers as well as biopesticides that are considered as a novel source that can be used to defend ecological niche from competitors and to promote plant growth. The aim of this review is to present all NRPs produced or potentially produced by strains of Burkholderia, as NRPs represent a major source of active compounds implicated in biocontrol. The review is a compilation of results from a large screening we have performed on 48 complete sequenced genomes available in NCBI to identify NRPS gene clusters, and data found in the literature mainly because some interesting compounds are produced by strains not yet sequenced. In addition to NRPs, hybrids NRPs/PKs are also included. Specific features about biosynthetic gene clusters and structures of the modular enzymes responsible for the synthesis, the biological activities, and the potential uses in agriculture and pharmaceutical of NRPs and hybrids NRPs/PKs will also be discussed.
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Affiliation(s)
- Qassim Esmaeel
- University Lille, INRA, ISA, University Artois, University Littoral Côte d'Opale, EA 7394-ICV- Institut Charles Viollette, F-59000, Lille, France
- Laboratoire de Stress, Défenses et Reproduction des Plantes URVVC-EA 4707, UFR Sciences Exactes et Naturelles, University of Reims-Champagne-Ardenne, Reims, France
| | - Maude Pupin
- University Lille, CNRS, Centrale Lille, UMR 9189- CRIStAL- Centre de Recherche en Informatique Signal et Automatique de Lille, F-59000, Lille, France
- Inria-Lille Nord Europe, Bonsai team, F-59655, Villeneuve d'Ascq Cedex, France
| | - Philippe Jacques
- University Lille, INRA, ISA, University Artois, University Littoral Côte d'Opale, EA 7394-ICV- Institut Charles Viollette, F-59000, Lille, France
- TERRA Research Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech University of Liege, B-5030, Gembloux, Belgium
| | - Valérie Leclère
- University Lille, INRA, ISA, University Artois, University Littoral Côte d'Opale, EA 7394-ICV- Institut Charles Viollette, F-59000, Lille, France.
- University Lille, CNRS, Centrale Lille, UMR 9189- CRIStAL- Centre de Recherche en Informatique Signal et Automatique de Lille, F-59000, Lille, France.
- Inria-Lille Nord Europe, Bonsai team, F-59655, Villeneuve d'Ascq Cedex, France.
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Al-Ali A, Deravel J, Krier F, Béchet M, Ongena M, Jacques P. Biofilm formation is determinant in tomato rhizosphere colonization by Bacillus velezensis FZB42. Environ Sci Pollut Res Int 2018; 25:29910-29920. [PMID: 29063401 DOI: 10.1007/s11356-017-0469-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 10/10/2017] [Indexed: 06/07/2023]
Abstract
In this work, the behavior in tomato rhizosphere of Bacillus velezensis FZB42 was analyzed taking into account the surfactin production, the use of tomato roots exudate as substrates, and the biofilm formation. B. velezensis FZB42 and B. amyloliquefaciens S499 have a similar capability to colonize tomato rhizosphere. Little difference in this colonization was observed with surfactin non producing B. velezensis FZB42 mutant strains. B. velezensis is able to grow in the presence of root exudate and used preferentially sucrose, maltose, glutamic, and malic acids as carbon sources. A mutant enable to produce exopolysaccharide (EPS-) was constructed to demonstrate the main importance of biofilm formation on rhizosphere colonization. This mutant had completely lost its ability to form biofilm whatever the substrate present in the culture medium and was unable to efficiently colonize tomato rhizosphere.
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Affiliation(s)
- Ameen Al-Ali
- Université Lille, INRA, ISA, Université Artois, Université Littoral Côte d'Opale, EA 7394-ICV Institut Charles Viollette, F-59000, Lille, France
- College of Agriculture-Soil, Water and Environmental Research Department, Al-Qasim Green University, Babylon, Iraq
| | - Jovana Deravel
- Université Lille, INRA, ISA, Université Artois, Université Littoral Côte d'Opale, EA 7394-ICV Institut Charles Viollette, F-59000, Lille, France
| | - François Krier
- Université Lille, INRA, ISA, Université Artois, Université Littoral Côte d'Opale, EA 7394-ICV Institut Charles Viollette, F-59000, Lille, France.
| | - Max Béchet
- Université Lille, INRA, ISA, Université Artois, Université Littoral Côte d'Opale, EA 7394-ICV Institut Charles Viollette, F-59000, Lille, France
| | - Marc Ongena
- Terra Teaching and Research Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liege, B 5030, Gembloux, Belgium
| | - Philippe Jacques
- Université Lille, INRA, ISA, Université Artois, Université Littoral Côte d'Opale, EA 7394-ICV Institut Charles Viollette, F-59000, Lille, France
- Terra Teaching and Research Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liege, B 5030, Gembloux, Belgium
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Abdellaziz L, Chollet M, Abderrahmani A, Béchet M, Yaici L, Chataigné G, Arias AA, Leclère V, Jacques P. Lipopeptide biodiversity in antifungal Bacillus strains isolated from Algeria. Arch Microbiol 2018; 200:1205-1216. [PMID: 29947835 DOI: 10.1007/s00203-018-1537-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 05/18/2018] [Accepted: 05/29/2018] [Indexed: 10/14/2022]
Abstract
Several Bacillus strains have been well studied for their ability to control soil-borne plant diseases. This property is linked to the production of several families of lipopeptides. Depending of their structure, these compounds show antifungal and/or plant systemic resistance inducing activities. In this work, the biodiversity of lipopeptides produced by different antifungal Bacillus strains isolated from seeds, rhizospheric, and non-rhizospheric soils in Algeria was analyzed. Sixteen active strains were characterized by PCR for their content in genes involved in lipopeptide biosynthesis and by MALDI-ToF for their lipopeptide production, revealing a high biodiversity of products. The difficulty to detect kurstakin genes led us to design two new sets of specific primers. An interesting potential of antifungal activity and the synthesis of two forms of fengycins differing in the eighth amino acid (Gln/Glu) were found from the strain 8. Investigation of its genome led to the finding of an adenylation domain of the fengycin synthetase predicted to activate the glutamate residue instead of the glutamine one. According to the comparison of both the results of MALDI-ToF-MS and genome analysis, it was concluded that this adenylation domain could activate both residues at the same time. This study highlighted that the richness of the Algerian ecosystems in Bacillus strains is able to produce: surfactin, pumilacidin, lichenysin, kurstakin, and different types of fengycins.
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Affiliation(s)
- Lamia Abdellaziz
- Microbiological Team, Cellular and Molecular Biological Laboratory, Faculty of Biological Sciences, University of Sciences and Technology Houari Boumediene, Algiers, Algeria.,Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV-Institut Charles Viollette, 59000, Lille, France
| | - Marlène Chollet
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV-Institut Charles Viollette, 59000, Lille, France
| | - Ahmed Abderrahmani
- Microbiological Team, Cellular and Molecular Biological Laboratory, Faculty of Biological Sciences, University of Sciences and Technology Houari Boumediene, Algiers, Algeria.,Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV-Institut Charles Viollette, 59000, Lille, France
| | - Max Béchet
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV-Institut Charles Viollette, 59000, Lille, France
| | - Lamia Yaici
- Microbiological Team, Cellular and Molecular Biological Laboratory, Faculty of Biological Sciences, University of Sciences and Technology Houari Boumediene, Algiers, Algeria.,Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV-Institut Charles Viollette, 59000, Lille, France
| | - Gabrielle Chataigné
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV-Institut Charles Viollette, 59000, Lille, France
| | - Anthony Arguelles Arias
- Microbial Processes and Interactions, Gembloux Agro-Bio Tech, TERRA Teaching and Research Centre, University of Liege, Gembloux, Belgium
| | - Valérie Leclère
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV-Institut Charles Viollette, 59000, Lille, France
| | - Philippe Jacques
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV-Institut Charles Viollette, 59000, Lille, France. .,Microbial Processes and Interactions, Gembloux Agro-Bio Tech, TERRA Teaching and Research Centre, University of Liege, Gembloux, Belgium.
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Yaseen Y, Diop A, Gancel F, Béchet M, Jacques P, Drider D. Polynucleotide phosphorylase is involved in the control of lipopeptide fengycin production in Bacillus subtilis. Arch Microbiol 2018; 200:783-791. [PMID: 29423562 DOI: 10.1007/s00203-018-1483-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 01/18/2018] [Accepted: 01/23/2018] [Indexed: 10/18/2022]
Abstract
Bacillus subtilis is a wealth source of lipopeptide molecules such as iturins, surfactins and fengycins or plipastatins endowed with a range of biological activities. These molecules, designated secondary metabolites, are synthesized via non-ribosomal peptides synthesis (NRPS) machinery and are most often subjected to a complex regulation with involvement of several regulatory factors. To gain novel insights on mechanism regulating fengycin production, we investigated the effect of the fascinating polynucleotide phosphorylase (PNPase), as well as the effect of lipopeptide surfactin. Compared to the wild type, the production of fengycin in the mutant strains B. subtilis BBG235 and BBG236 altered for PNPase has not only decreased to about 70 and 40%, respectively, but also hampered its antifungal activity towards the plant pathogen Botrytis cinerea. On the other hand, mutant strains BBG231 (srfAA-) and BBG232 (srfAC-) displayed different levels of fengycin production. BBG231 had registered an important decrease in fengycin production, comparable to that observed for BBG235 or BBG236. This study permitted to establish that the products of pnpA gene (PNPase), and srfAA- (surfactin synthetase) are involved in fengycin production.
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Affiliation(s)
- Yazen Yaseen
- Université de Lille, INRA, Université d'Artois, Université du Littoral-Côte d'Opale, EA 7394 - ICV-Institut Charles Viollette, F-59000, Lille, France
| | - Awa Diop
- Université de Lille, INRA, Université d'Artois, Université du Littoral-Côte d'Opale, EA 7394 - ICV-Institut Charles Viollette, F-59000, Lille, France
| | - Frédérique Gancel
- Université de Lille, INRA, Université d'Artois, Université du Littoral-Côte d'Opale, EA 7394 - ICV-Institut Charles Viollette, F-59000, Lille, France
| | - Max Béchet
- Université de Lille, INRA, Université d'Artois, Université du Littoral-Côte d'Opale, EA 7394 - ICV-Institut Charles Viollette, F-59000, Lille, France
| | - Philippe Jacques
- Université de Lille, INRA, Université d'Artois, Université du Littoral-Côte d'Opale, EA 7394 - ICV-Institut Charles Viollette, F-59000, Lille, France
| | - Djamel Drider
- Université de Lille, INRA, Université d'Artois, Université du Littoral-Côte d'Opale, EA 7394 - ICV-Institut Charles Viollette, F-59000, Lille, France.
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36
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Ceugniez A, Taminiau B, Coucheney F, Jacques P, Delcenserie V, Daube G, Drider D. Fungal diversity of “Tomme d'Orchies” cheese during the ripening process as revealed by a metagenomic study. Int J Food Microbiol 2017; 258:89-93. [DOI: 10.1016/j.ijfoodmicro.2017.07.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 07/21/2017] [Accepted: 07/24/2017] [Indexed: 12/16/2022]
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Ceugniez A, Tourret M, Dussert E, Coucheney F, Deracinois B, Jacques P, Flahaut C, Heuson E, Drider D, Behra-Miellet J. Interactions between Kluyveromyces marxianus from cheese origin and the intestinal symbiont Bacteroides thetaiotaomicron: Impressive antioxidative effects. Lebensm Wiss Technol 2017. [DOI: 10.1016/j.lwt.2017.03.056] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Yaseen Y, Gancel F, Béchet M, Drider D, Jacques P. Study of the correlation between fengycin promoter expression and its production by Bacillus subtilis under different culture conditions and the impact on surfactin production. Arch Microbiol 2017; 199:1371-1382. [PMID: 28735377 DOI: 10.1007/s00203-017-1406-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 06/01/2017] [Accepted: 06/26/2017] [Indexed: 11/28/2022]
Abstract
This work aimed to rely expression of the fengycin promoter to fengycin production under different culture conditions. To this end, Bacillus subtilis BBG208, derived from BBG21, which is a fengycin overproducing strain carrying the green fluorescent protein (GFP) under the control of fengycin promoter, was used to assess the effects of different carbon and nitrogen sources on surfactin and fengycin production and the fengycin promoter expression. The data showed that some carbon sources oriented synthesis of one family of lipopeptides, while most of the nitrogen sources allowed high co-production of fengycin and surfactin. High expressions of promoter Pfen and fengycin synthesis were obtained with urea or urea + ammonium mixture as nitrogen source and mannitol as carbon source. Moreover, temperature, pH and oxygenation influenced their biosynthesis based on the nutrition conditions. Optimization of the production medium increased the fengycin production to 768 mg L-1, which is the highest level reported for this strain. This study defines the suitable nutrient conditions allowing as well the highest expression of the fengycin promoter and portrays the conditions relying on the fengycin and surfactin production.
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Affiliation(s)
- Yazen Yaseen
- Charles Viollette Institute, University Lille 1, Sciences and Technologies, Cité Scientifique, 59655, Villeneuve d'Ascq, France.,Terra Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Gembloux, B-5030, Liège, Belgium
| | - Frédérique Gancel
- Charles Viollette Institute, University Lille 1, Sciences and Technologies, Cité Scientifique, 59655, Villeneuve d'Ascq, France.,Terra Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Gembloux, B-5030, Liège, Belgium
| | - Max Béchet
- Charles Viollette Institute, University Lille 1, Sciences and Technologies, Cité Scientifique, 59655, Villeneuve d'Ascq, France.,Terra Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Gembloux, B-5030, Liège, Belgium
| | - Djamel Drider
- Charles Viollette Institute, University Lille 1, Sciences and Technologies, Cité Scientifique, 59655, Villeneuve d'Ascq, France.,Terra Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Gembloux, B-5030, Liège, Belgium
| | - Philippe Jacques
- Charles Viollette Institute, University Lille 1, Sciences and Technologies, Cité Scientifique, 59655, Villeneuve d'Ascq, France. .,Terra Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Gembloux, B-5030, Liège, Belgium.
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Coutte F, Lecouturier D, Dimitrov K, Guez JS, Delvigne F, Dhulster P, Jacques P. Microbial lipopeptide production and purification bioprocesses, current progress and future challenges. Biotechnol J 2017. [DOI: 10.1002/biot.201600566] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- François Coutte
- Institut Charles Viollette, Université Lille, INRA, ISA, Université d'Artois; Université Littoral Côte d'Opale; EA 7394-ICV Lille France
| | - Didier Lecouturier
- Institut Charles Viollette, Université Lille, INRA, ISA, Université d'Artois; Université Littoral Côte d'Opale; EA 7394-ICV Lille France
| | - Krasimir Dimitrov
- Institut Charles Viollette, Université Lille, INRA, ISA, Université d'Artois; Université Littoral Côte d'Opale; EA 7394-ICV Lille France
| | - Jean-Sébastien Guez
- Institut Charles Viollette, Université Lille, INRA, ISA, Université d'Artois; Université Littoral Côte d'Opale; EA 7394-ICV Lille France
- Axe GePEB, Institut Pascal, UMR 6602; Université Clermont Auvergne, CNRS, SIGMA; Clermont-Ferrand France
| | - Frank Delvigne
- Microbial Processes and Interactions, TERRA Teaching and Research Centre; Gembloux Agro-Bio Tech University of Liege; Gembloux Belgium
| | - Pascal Dhulster
- Institut Charles Viollette, Université Lille, INRA, ISA, Université d'Artois; Université Littoral Côte d'Opale; EA 7394-ICV Lille France
| | - Philippe Jacques
- Institut Charles Viollette, Université Lille, INRA, ISA, Université d'Artois; Université Littoral Côte d'Opale; EA 7394-ICV Lille France
- Microbial Processes and Interactions, TERRA Teaching and Research Centre; Gembloux Agro-Bio Tech University of Liege; Gembloux Belgium
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40
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Burget D, Jacques P. Interprétation des effets de solvants sur la
fluorescence de la thioxanthone en fonction des
paramètres solvatochromiques π*, α et β. ACTA ACUST UNITED AC 2017. [DOI: 10.1051/jcp/1991880675] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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41
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Eyman J, Jacques P, Kessaissia Z. The thermodynamic characteristics of gas-solid adsorption as determined by use of a computer program. ACTA ACUST UNITED AC 2017. [DOI: 10.1051/jcp/1980770861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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42
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Lougnot D, Floret-David D, Jacques P, Fouassier J. Effets électrostatiques sur le comportement des états excités de benzophénones chargées en solution micellaire. ACTA ACUST UNITED AC 2017. [DOI: 10.1051/jcp/1985820505] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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43
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Dhali D, Coutte F, Arias AA, Auger S, Bidnenko V, Chataigné G, Lalk M, Niehren J, de Sousa J, Versari C, Jacques P. Genetic engineering of the branched fatty acid metabolic pathway ofBacillus subtilisfor the overproduction of surfactin C14isoform. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201600574] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/13/2017] [Accepted: 03/31/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Debarun Dhali
- University Lille, INRA, ISA, University Artois, University Littoral Côte d'Opale; EA 7394 - ICV - Institut Charles Viollette; Lille France
| | - François Coutte
- University Lille, INRA, ISA, University Artois, University Littoral Côte d'Opale; EA 7394 - ICV - Institut Charles Viollette; Lille France
| | - Anthony Argüelles Arias
- MiPI, TERRA Research Centre, Gembloux Agro-Bio Tech; University of Liege; Passage des Déportés; Gembloux Belgium
| | - Sandrine Auger
- Micalis Institute, INRA, AgroParisTech; University Paris-Saclay; Jouy-en-Josas France
| | - Vladimir Bidnenko
- Micalis Institute, INRA, AgroParisTech; University Paris-Saclay; Jouy-en-Josas France
| | - Gabrielle Chataigné
- University Lille, INRA, ISA, University Artois, University Littoral Côte d'Opale; EA 7394 - ICV - Institut Charles Viollette; Lille France
| | - Michael Lalk
- Ernst-Moritz-Arndt-University Greifswald; Institute of Biochemistry; Greifswald Germany
| | - Joachim Niehren
- University Lille; BioComputing Team, CRIStAL Lab (CNRS UMR9189); Villeneuve d'Ascq France
- Inria Lille; Villeneuve d'Ascq France
| | - Joana de Sousa
- Ernst-Moritz-Arndt-University Greifswald; Institute of Biochemistry; Greifswald Germany
| | - Cristian Versari
- University Lille; BioComputing Team, CRIStAL Lab (CNRS UMR9189); Villeneuve d'Ascq France
| | - Philippe Jacques
- University Lille, INRA, ISA, University Artois, University Littoral Côte d'Opale; EA 7394 - ICV - Institut Charles Viollette; Lille France
- MiPI, TERRA Research Centre, Gembloux Agro-Bio Tech; University of Liege; Passage des Déportés; Gembloux Belgium
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Ceugniez A, Coucheney F, Jacques P, Daube G, Delcenserie V, Drider D. Anti-Salmonella activity and probiotic trends of Kluyveromyces marxianus S-2-05 and Kluyveromyces lactis S-3-05 isolated from a French cheese, Tomme d'Orchies. Res Microbiol 2017; 168:575-582. [PMID: 28366839 DOI: 10.1016/j.resmic.2017.03.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/17/2017] [Accepted: 03/22/2017] [Indexed: 12/14/2022]
Abstract
Kluyveromyces marxianus S-2-05 and Kluyveromyces lactis S-3-05 were recently isolated from a traditional French cheese, Tomme d'Orchies, and characterized here for their advantages using a different application perspective. First, we established their anti-Salmonella activity and downregulation of the virulence sopD gene of Salmonella enterica subsp. enterica serovar Typhimurium, mainly in the presence of K. marxianus S-2-05. In addition to their antagonism, these non-Saccharomyces yeasts were able to survive under conditions mimicking the gastrointestinal environment and to form biofilms on an abiotic device such as polystyrene. These strains also displayed highly hydrophilic cell wall surfaces properties and capacity for adhesion to intestinal Caco-2 cells, thus enhancing their potential as probiotic strains.
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Affiliation(s)
- Alexandre Ceugniez
- Université Lille, INRA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394 - ICV - Institut Charles Viollette, F-59000 Lille, France
| | - Françoise Coucheney
- Université Lille, INRA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394 - ICV - Institut Charles Viollette, F-59000 Lille, France.
| | - Philippe Jacques
- Université Lille, INRA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394 - ICV - Institut Charles Viollette, F-59000 Lille, France
| | - Georges Daube
- Fundamental and Applied Research for Animal & Health (FARAH), Food Science Department, Faculty of Veterinary Medicine, University of Liège, Liège, B-4000, Belgium
| | - Véronique Delcenserie
- Fundamental and Applied Research for Animal & Health (FARAH), Food Science Department, Faculty of Veterinary Medicine, University of Liège, Liège, B-4000, Belgium
| | - Djamel Drider
- Université Lille, INRA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394 - ICV - Institut Charles Viollette, F-59000 Lille, France.
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Ben Ayed H, Hmidet N, Béchet M, Jacques P, Nasri M. Identification and natural functions of cyclic lipopeptides from Bacillus amyloliquefaciens An6. Eng Life Sci 2016; 17:536-544. [PMID: 32624798 DOI: 10.1002/elsc.201600050] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 08/11/2016] [Accepted: 11/10/2016] [Indexed: 11/09/2022] Open
Abstract
Lipopeptides constitute a structurally diverse group of metabolites produced by various bacterial and fungal genera. In the past decades, research on lipopeptides has been fueled by their surfactant activities. However, natural functions of lipopeptides compounds have received considerably less attention. The aim of this study was to isolate and identify the lipopeptides from Bacillus amyloliquefaciens An6, and further evaluate their biological activities. An6 lipopeptides were detected by PCR using degenerated primers and MALDI-TOF-MS. An6 strain was found to produce surfactin, fengycin, and bacillomycin. Following their purification, the in vitro antioxidant activity of An6 lipopeptides was studied through different assays. The scavenging effect on 1,1-diphenyl-2-picrylhydrazyl radicals at a dosage of 0.75 mg/mL was 81%. Its reducing power was concentration-dependant and reached a maximum of 1.07 at 2.5 mg/mL. Moreover, they showed a strong inhibition of β-carotene bleaching. An6 lipopeptides mixture was also found to display significant antimicrobial activity against several Gram-positive, Gram-negative bacteria, and fungal strains. An6 lipopeptides were insensitive to proteolytic enzymes, stable between pH 4.0 and 12.0, and resistant to high temperature. Our results provided enough evidence proving that An6 lipopeptides could be used as functional-food components.
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Affiliation(s)
- Hanen Ben Ayed
- Laboratoire de Génie Enzymatique et de Microbiologie Ecole Nationale d'Ingénieurs de Sfax Université de Sfax Sfax Tunisia
| | - Noomen Hmidet
- Laboratoire de Génie Enzymatique et de Microbiologie Ecole Nationale d'Ingénieurs de Sfax Université de Sfax Sfax Tunisia
| | - Max Béchet
- ProBioGEM- EA1026, Polytech'Lille/IUTA Université Lille-Nord de France Villeneuve d'Asq France
| | - Philippe Jacques
- ProBioGEM- EA1026, Polytech'Lille/IUTA Université Lille-Nord de France Villeneuve d'Asq France
| | - Moncef Nasri
- Laboratoire de Génie Enzymatique et de Microbiologie Ecole Nationale d'Ingénieurs de Sfax Université de Sfax Sfax Tunisia
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Ceugniez A, Taminiau B, Coucheney F, Jacques P, Delcenserie V, Daube G, Drider D. Use of a metagenetic approach to monitor the bacterial microbiota of "Tomme d'Orchies" cheese during the ripening process. Int J Food Microbiol 2016; 247:65-69. [PMID: 27817942 DOI: 10.1016/j.ijfoodmicro.2016.10.034] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 10/10/2016] [Accepted: 10/27/2016] [Indexed: 12/17/2022]
Abstract
The study of microbial ecosystems in artisanal foodstuffs is important to complete in order to unveil its diversity. The number of studies performed on dairy products has increased during the last decade, particularly those performed on milk and cheese derivative products. In this work, we investigated the bacterial content of "Tomme d'Orchies" cheese, an artisanal pressed and uncooked French cheese. To this end, a metagenetic analysis, using Illumina technology, was utilized on samples taken from the surface and core of the cheese at 0, 1, 3, 14 and 21days of ripening process. In addition to the classical microbiota found in cheese, various strains likely from environmental origin were identified. A large difference between the surface and the core content was observed within samples withdrawn during the ripening process. The main species encountered in the core of the cheese were Lactococcus spp. and Streptococcus spp., with an inversion of this ratio during the ripening process. Less than 2.5% of the whole population was composed of strains issued from environmental origin, as Lactobacillales, Corynebacterium and Brevibacterium. In the core, about 85% of the microbiota was attributed to the starters used for the cheese making. In turn, the microbiota of the surface contained less than 30% of these starters and interestingly displayed more diversity. The predominant genus was Corynebacterium sp., likely originating from the environment. The less abundant microbiota of the surface was composed of Bifidobacteria, Brevibacterium and Micrococcales. To summarize, the "Tomme d'Orchies" cheese displayed a high diversity of bacterial species, especially on the surface, and this diversity is assumed to arise from the production environment and subsequent ripening process.
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Affiliation(s)
- Alexandre Ceugniez
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394 - ICV - Institut Charles Viollette, F-59000 Lille, France
| | - Bernard Taminiau
- Fundamental and Applied Research for Animal & Health (FARAH), Food Science Department, Faculty of Veterinary Medicine, University of Liège, Liège B-4000, Belgium
| | - Françoise Coucheney
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394 - ICV - Institut Charles Viollette, F-59000 Lille, France.
| | - Philippe Jacques
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394 - ICV - Institut Charles Viollette, F-59000 Lille, France
| | - Véronique Delcenserie
- Fundamental and Applied Research for Animal & Health (FARAH), Food Science Department, Faculty of Veterinary Medicine, University of Liège, Liège B-4000, Belgium
| | - Georges Daube
- Fundamental and Applied Research for Animal & Health (FARAH), Food Science Department, Faculty of Veterinary Medicine, University of Liège, Liège B-4000, Belgium
| | - Djamel Drider
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394 - ICV - Institut Charles Viollette, F-59000 Lille, France
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Abstract
This chapter helps in the use of bioinformatics tools relevant to the discovery of new nonribosomal peptides (NRPs) produced by microorganisms. The strategy described can be applied to draft or fully assembled genome sequences. It relies on the identification of the synthetase genes and the deciphering of the domain architecture of the nonribosomal peptide synthetases (NRPSs). In the next step, candidate peptides synthesized by these NRPSs are predicted in silico, considering the specificity of incorporated monomers together with their isomery. To assess their novelty, the two-dimensional structure of the peptides can be compared with the structural patterns of all known NRPs. The presented workflow leads to an efficient and rapid screening of genomic data generated by high throughput technologies. The exploration of such sequenced genomes may lead to the discovery of new drugs (i.e., antibiotics against multi-resistant pathogens or anti-tumors).
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Affiliation(s)
- Valérie Leclère
- ProBioGEM, Institut Charles Viollette, Polytech'Lille, University of Lille 1, 59650, Villeneuve d'Ascq, France.,CRIStAL, UMR 9189, Univ Lille, 59650, Villeneuve d'Ascq, France.,Inria Lille Nord-Europe, 59650, Villeneuve d'Ascq, France
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970, Hørsholm, Denmark
| | - Philippe Jacques
- ProBioGEM, Institut Charles Viollette, Polytech'Lille, University of Lille 1, 59650, Villeneuve d'Ascq, France
| | - Maude Pupin
- CRIStAL, UMR 9189, Univ Lille, 59650, Villeneuve d'Ascq, France. .,Inria Lille Nord-Europe, 59650, Villeneuve d'Ascq, France.
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Motta Dos Santos LF, Coutte F, Ravallec R, Dhulster P, Tournier-Couturier L, Jacques P. An improvement of surfactin production by B. subtilis BBG131 using design of experiments in microbioreactors and continuous process in bubbleless membrane bioreactor. Bioresour Technol 2016; 218:944-52. [PMID: 27447921 DOI: 10.1016/j.biortech.2016.07.053] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 07/11/2016] [Accepted: 07/12/2016] [Indexed: 05/12/2023]
Abstract
Culture medium elements were analysed by a screening DoE to identify their influence in surfactin specific production by a surfactin constitutive overproducing Bacillus subtilis strain. Statistics pointed the major enhancement caused by high glutamic acid concentrations, as well as a minor positive influence of tryptophan and glucose. Successively, a central composite design was performed in microplate bioreactors using a BioLector®, in which variations of these impressive parameters, glucose, glutamic acid and tryptophan concentrations were selected for optimization of product-biomass yield (YP/X). Results were exploited in combination with a RSM. In absolute terms, experiments attained an YP/X 3.28-fold higher than those obtained in Landy medium, a usual culture medium used for lipopeptide production by B. subtilis. Therefore, two medium compositions for enhancing biomass and surfactin specific production were proposed and tested in continuous regime in a bubbleless membrane bioreactor. An YP/X increase of 2.26-fold was observed in bioreactor scale.
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Affiliation(s)
- Luiz Fernando Motta Dos Santos
- Univ-Lille, EA 7394, Research Institute for Food and Biotechnology - Charles Viollette - Team ProBioGEM, F-59000 Lille, France; L'Oréal Research & Innovation, Advanced Research, Aulnay-sous-Bois, France
| | - François Coutte
- Univ-Lille, EA 7394, Research Institute for Food and Biotechnology - Charles Viollette - Team ProBioGEM, F-59000 Lille, France.
| | - Rozenn Ravallec
- Univ-Lille, EA 7394, Research Institute for Food and Biotechnology - Charles Viollette - Team ProBioGEM, F-59000 Lille, France
| | - Pascal Dhulster
- Univ-Lille, EA 7394, Research Institute for Food and Biotechnology - Charles Viollette - Team ProBioGEM, F-59000 Lille, France
| | | | - Philippe Jacques
- Univ-Lille, EA 7394, Research Institute for Food and Biotechnology - Charles Viollette - Team ProBioGEM, F-59000 Lille, France
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Etchegaray A, Coutte F, Chataigné G, Béchet M, Dos Santos RHZ, Leclère V, Jacques P. Production of Bacillus amyloliquefaciens OG and its metabolites in renewable media: valorisation for biodiesel production and p-xylene decontamination. Can J Microbiol 2016; 63:46-60. [PMID: 27912317 DOI: 10.1139/cjm-2016-0288] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Biosurfactants are important in many areas; however, costs impede large-scale production. This work aimed to develop a global sustainable strategy for the production of biosurfactants by a novel strain of Bacillus amyloliquefaciens. Initially, Bacillus sp. strain 0G was renamed B. amyloliquefaciens subsp. plantarum (syn. Bacillus velezensis) after analysis of the gyrA and gyrB DNA sequences. Growth in modified Landy's medium produced 3 main recoverable metabolites: surfactin, fengycin, and acetoin, which promote plant growth. Cultivation was studied in the presence of renewable carbon (as glycerol) and nitrogen (as arginine) sources. While diverse kinetics of acetoin production were observed in different media, similar yields (6-8 g·L-1) were obtained after 72 h of growth. Glycerol increased surfactin-specific production, while arginine increased the yields of surfactin and fengycin and increased biomass significantly. The specific production of fengycin increased ∼10 times, possibly due to a connecting pathway involving arginine and ornithine. Adding value to crude extracts and biomass, both were shown to be useful, respectively, for the removal of p-xylene from contaminated water and for biodiesel production, yielding ∼70 mg·g-1 cells and glycerol, which could be recycled in novel media. This is the first study considering circular bioeconomy to lower the production costs of biosurfactants by valorisation of both microbial cells and their primary and secondary metabolites.
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Affiliation(s)
- Augusto Etchegaray
- a Pontifical Catholic University of Campinas, Rodovia Dom Pedro I, km 136, Campinas, SP, 13086-900, Brazil
| | - François Coutte
- b ICV-Université Lille, EA 7394-ICV Institut Charles Viollette, F-59000 Lille, France
| | - Gabrielle Chataigné
- b ICV-Université Lille, EA 7394-ICV Institut Charles Viollette, F-59000 Lille, France
| | - Max Béchet
- b ICV-Université Lille, EA 7394-ICV Institut Charles Viollette, F-59000 Lille, France
| | - Ramon H Z Dos Santos
- a Pontifical Catholic University of Campinas, Rodovia Dom Pedro I, km 136, Campinas, SP, 13086-900, Brazil
| | - Valérie Leclère
- b ICV-Université Lille, EA 7394-ICV Institut Charles Viollette, F-59000 Lille, France
| | - Philippe Jacques
- b ICV-Université Lille, EA 7394-ICV Institut Charles Viollette, F-59000 Lille, France
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Ovando CA, Carvalho JCD, Vinícius de Melo Pereira G, Jacques P, Soccol VT, Soccol CR. Functional properties and health benefits of bioactive peptides derived fromSpirulina: A review. Food Reviews International 2016. [DOI: 10.1080/87559129.2016.1210632] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Claudia Anahite Ovando
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Julio Cesar de Carvalho
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná (UFPR), Curitiba, Brazil
| | | | - Philippe Jacques
- ICV—Institut Charles Viollette, University of Lille, Lille, France
- Terra Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Gembloux, Belgium
| | - Vanete Thomaz Soccol
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Carlos Ricardo Soccol
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná (UFPR), Curitiba, Brazil
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