YSMR: a video tracking and analysis program for bacterial motility

Julian Schwanbeck,Andreas E Zautner,Jerôme Dretzke,Ines Oehmig,Uwe Groß,Wolfgang Bohne

doi:10.1186/s12859-020-3495-9

Julian Schwanbeck, Andreas E Zautner + Show 4 more

Open Access

https://doi.org/10.1186/s12859-020-3495-9

Copy DOI

Abstract

BackgroundMotility in bacteria forms the basis for taxis and is in some pathogenic bacteria important for virulence. Video tracking of motile bacteria allows the monitoring of bacterial swimming behaviour and taxis on the level of individual cells, which is a prerequisite to study the underlying molecular mechanisms.ResultsThe open-source python program YSMR (Your Software for Motility Recognition) was designed to simultaneously track a large number of bacterial cells on standard computers from video files in various formats. In order to cope with the high number of tracked objects, we use a simple detection and tracking approach based on grey-value and position, followed by stringent selection against suspicious data points. The generated data can be used for statistical analyses either directly with YSMR or with external programs.ConclusionIn contrast to existing video tracking software, which either requires expensive computer hardware or only tracks a limited number of bacteria for a few seconds, YSMR is an open-source program which allows the 2-D tracking of several hundred objects over at least 5 minutes on standard computer hardware.The code is freely available at https://github.com/schwanbeck/YSMR

Highlights

Motility in bacteria forms the basis for taxis and is in some pathogenic bacteria important for virulence
The molecular processes that regulate motility in bacteria are an active area in research, as they form the basis for dispersion, tactile processes, and virulence in some pathogenic bacteria [1]
The best studied example is the “run and tumble” motility type of Escherichia coli, in which counter clockwise rotation of flagella leads to a run phase, while clockwise rotation leads to a tumbling phase with a random cell rotation [3]

Summary

Introduction

Motility in bacteria forms the basis for taxis and is in some pathogenic bacteria important for virulence. Video tracking of motile bacteria allows the monitoring of bacterial swimming behaviour and taxis on the level of individual cells, which is a prerequisite to study the underlying molecular mechanisms. Bacteria developed different types of motility, most of them driven by flagella or pili. The molecular processes that regulate motility in bacteria are an active area in research, as they form the basis for dispersion, tactile processes, and virulence in some pathogenic bacteria [1]. The best studied example is the “run and tumble” motility type of Escherichia coli, in which counter clockwise rotation of flagella leads to a run phase, while clockwise rotation leads to a tumbling phase with a random cell rotation [3]. In recent years additional motility types were discovered, as the “forward-revers-flick” motility type in Vibrio alginolyticus [4] or the “stop-and-coil” type in Rhodobacter sphaeroides [5].

Results

Discussion

Conclusion