  Biofilms 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.
