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Inferring characteristics of bacterial swimming in biofilm matrix from time-lapse confocal laser scanning microscopy

hal.structure.identifierPleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorRAVEL, Guillaume
hal.structure.identifierModeling Enablers for Multi-PHysics and InteractionS [MEMPHIS]
dc.contributor.authorBERGMANN, Michel
hal.structure.identifierMathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] [MaIAGE]
dc.contributor.authorTRUBUIL, Alain
hal.structure.identifierMICrobiologie de l'ALImentation au Service de la Santé [MICALIS]
dc.contributor.authorDESCHAMPS, Julien
hal.structure.identifierMICrobiologie de l'ALImentation au Service de la Santé [MICALIS]
dc.contributor.authorBRIANDET, Romain
hal.structure.identifierPleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
hal.structure.identifierMathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] [MaIAGE]
dc.contributor.authorLABARTHE, Simon
dc.description.abstractEnBiofilms are spatially organized microorganism colonies embedded in a self-produced matrix, conferring to the microbial community resistance to environmental stresses. Motile bacteria have been observed swimming in the matrix of pathogenic exogeneous host biofilms. This observation opened new promising routes for deleterious biofilms biocontrol: these bacterial swimmers enhance biofilm vascularization for chemical treatment or could deliver biocontrol agent by microbial hitchhiking or local synthesis. %\cite{muok2021microbial,yu2020hitchhiking,samad2017swimming}. Hence, characterizing swimmer trajectories in the biofilm matrix is of particular interest to understand and optimize its biocontrol.In this study, a new methodology is developed to analyze time-lapse confocal laser scanning images to describe and compare the swimming trajectories of bacterial swimmers populations and their adaptations to the biofilm structure. The method is based on the inference of a kinetic model of swimmer population including mechanistic interactions with the host biofilm. After validation on synthetic data, the methodology is implemented on images of three different motile {Bacillus species swimming in a Staphylococcus aureus biofilm. The fitted model allows to stratify the swimmer populations by their swimming behavior and provides insights into the mechanisms deployed by the micro-swimmers to adapt their swimming traits to the biofilm matrix.
dc.description.sponsorshipSensibilisation de biofilms industriels à l'action de désinfectants par l'infiltration de bactéries hyper-motiles
dc.language.isoen
dc.subject.enbiofilm
dc.subject.enmicroswinner : image processing
dc.subject.eninferrence
dc.subject.ensystem dynamics
dc.subject.enbiofilm
dc.subject.enbiofilm
dc.title.enInferring characteristics of bacterial swimming in biofilm matrix from time-lapse confocal laser scanning microscopy
dc.typeDocument de travail - Pré-publication
dc.subject.halInformatique [cs]/Modélisation et simulation
dc.subject.halSciences du Vivant [q-bio]/Bio-Informatique, Biologie Systémique [q-bio.QM]
dc.identifier.arxiv2201.04371
hal.identifierhal-03479903
hal.version1
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-03479903v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.au=RAVEL,%20Guillaume&BERGMANN,%20Michel&TRUBUIL,%20Alain&DESCHAMPS,%20Julien&BRIANDET,%20Romain&rft.genre=preprint


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