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Biofilms are spatially organized microorganism colonies embedded in aself-produced matrix, conferring to the microbial community resistance toenvironmental stresses. Motile bacteria have been observed swimming in thematrix of pathogenic exogeneous host biofilms. This observation opened newpromising routes for deleterious biofilms biocontrol: these bacterial swimmersenhance biofilm vascularization for chemical treatment or could deliverbiocontrol agent by microbial hitchhiking or local synthesis.%\cite{muok2021microbial,yu2020hitchhiking,samad2017swimming}. Hence,characterizing swimmer trajectories in the biofilm matrix is of particularinterest to understand and optimize its biocontrol.In this study, a newmethodology is developed to analyze time-lapse confocal laser scanning imagesto describe and compare the swimming trajectories of bacterial swimmerspopulations and their adaptations to the biofilm structure. The method is basedon the inference of a kinetic model of swimmer population including mechanisticinteractions with the host biofilm. After validation on synthetic data, themethodology is implemented on images of three different motile {Bacillusspecies swimming in a Staphylococcus aureus biofilm. The fitted model allows tostratify the swimmer populations by their swimming behavior and providesinsights into the mechanisms deployed by the micro-swimmers to adapt theirswimming traits to the biofilm matrix.

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